ChimearaXでSMILESを扱う

# ChimearaXでSMILESを扱う

[#souyakuAC2024](https://adventar.org/calendars/10715)にて以下のような記事

https://zenn.dev/keetane/articles/9b4d52da17191f

が投稿されていたのでChimeraX過激派の私としては対抗せずにはいられなかったので書いてみることにしました。

:::note warn
あくまでchimeraxでの方法です。xのないUCSF chimeraに関してはご自身でお調べください。また、ChimearaXのインストール方法や細かいコマンドの仕様に関してもご自身でお調べください。

以下に参考リンクを貼っておきます。

**UCSF ChimeraX 公式HP**
[UCSF ChimeraX Home Page](https://www.cgl.ucsf.edu/chimerax/)

**ChimeraXノート**
[https://obsidian-gallimimus-08c.notion.site/ChimeraX-256372918a0d4cf2822503134c9b3fcb](https://www.notion.so/256372918a0d4cf2822503134c9b3fcb?pvs=21)
:::



</aside>

## 私の使用環境

OS: Mac OS (Mac Book Pro, M2)

ChimeraX-1.8

## **ChimeraXでSMILESを扱うには**

というわけで本題です。どうやらPyMOLくんはSMIELS形式に対応していないようですが、ChimeraXではデフォルトでSMILESを扱うことができます。

## GUIで開く方法

GUIのTool SMILES文字列から構造を作成する手順を説明します。

1. まず「Build Structure」ツールを開きます
    - これはTools メニューの「Structure Editing」セクションから開けます
        
        ![スクリーンショット 2024-12-08 15.02.50.png](https://qiita-image-store.s3.ap-northeast-1.amazonaws.com/0/3676860/8c372a3c-ec00-5bea-4edc-81f2f32dfa79.png)
    
2. 「Start Structure」セクションに移動します
    
    ![スクリーンショット 2024-12-08 15.05.29.png](https://qiita-image-store.s3.ap-northeast-1.amazonaws.com/0/3676860/8ef68eb5-b892-7002-8385-bd23bfd3e700.png)

    
3. 左の選択ボタンからSMILES stringを選択してSMILES文字列を入力フィールドに入力します
元記事に合わせて[ハリコンドリンのSMILES](https://pubchem.ncbi.nlm.nih.gov/compound/5488895#section=SMILES&fullscreen=true)を入力してみましょう。
    
    ![スクリーンショット 2024-12-08 15.05.44.png](https://qiita-image-store.s3.ap-northeast-1.amazonaws.com/0/3676860/245e0ef3-36b6-beff-a7de-1aba1635592f.png)

    
4. Applyをクリックすると、3D構造が生成されます
    
    ![スクリーンショット 2024-12-08 15.06.06.png](https://qiita-image-store.s3.ap-northeast-1.amazonaws.com/0/3676860/6017607d-c76e-3e28-a2d0-acdcebcf2620.png)


以上！！とっても簡単ですね！
    
:::note warn
注意点：

- 水素原子は自動的に含まれます
- ただし、望む正確なプロトン化状態にするために、水素原子の追加や削除が必要になる場合があります
- 構造は National Cancer Institute CADDグループのSMILES変換ツールを使って生成されます
- web serviceを介して行うため、インターネット環境が必要です
    ![スクリーンショット 2024-12-08 15.32.24.png](https://qiita-image-store.s3.ap-northeast-1.amazonaws.com/0/3676860/c63a42c4-9fff-0a7f-4299-b8b0fdbff57a.png)
    ネットなしだとこうなります。
:::


## Command lineからSMILESを開く

Command lineからもSMILESを開くことができます！

使うコマンドは`open` になります。

https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html

```bash
open smiles:"開きたいSMILES"
# 例:エタノール
open smiles:CCO
```

元記事に合わせて[ハリコンドリンのSMILES](https://pubchem.ncbi.nlm.nih.gov/compound/5488895#section=SMILES&fullscreen=true)を入力すると

![スクリーンショット 2024-12-08 15.25.06.png](https://qiita-image-store.s3.ap-northeast-1.amazonaws.com/0/3676860/c7b67439-7eff-a8d0-4698-1b9af0de52ab.png)

開けましたね！


`resName`オプションを使うと名前をつけることができます

```bash
open smiles:"開きたいSMILES" resName "つけたい名前"
```

ハンコドリンに**Halichondrin**という名前をつけてselectしてみましょう

```bash
open smiles:C[C@@...（省略） resName Halichondrin
```

![スクリーンショット 2024-12-08 15.37.22.png](https://qiita-image-store.s3.ap-northeast-1.amazonaws.com/0/3676860/e4794a4e-96d0-f31b-5143-cabbae2da65e.png)

きちんと名前が付けられていますね！！

### IUPAC名で開く

Build Structureのウィンドウで開いたときに気付いたかもしれませんがSMILES以外にも化合物を開くことができます。

詳しい文法や開けるファイル様式・idなどはchimeraXのopenコマンドのページをご覧ください

https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html

(pubchem CIDはなんかうまくいかない…ヴァージョンの問題だろうか…）

今回はIUPACで開いてみましょう。開き方は`smiles:` を`iupac:`にかえるだけ。（`smiles:`の部分は`[source]:`になっている）

```bash
open iupac:"開きたいIUPAC" resName "つけたい名前"
```

ハンコドリンはiupacがなかったので[Eribulin](https://pubchem.ncbi.nlm.nih.gov/compound/11354606)でやってみましょう。

https://pubchem.ncbi.nlm.nih.gov/compound/11354606#section=IUPAC-Name&fullscreen=true

![スクリーンショット 2024-12-08 16.03.03.png](https://qiita-image-store.s3.ap-northeast-1.amazonaws.com/0/3676860/70d95952-d13d-8271-de3b-56b716c6fab2.png)


開けましたね！！

IUPACの場合IUPAC → SMILES → 3D translatorとしているので少し時間がかかりますね。

## 開いた化合物を任意のファイル形式に保存する

もちろんですが、開いた化合物は対応している任意のファイル形式に保存することができます。

使うのは`save`コマンドになります。こちらもいろんな形式や構文があるのでユーザーガイドを要チェック！！

https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html

今回はPDB・mmCID(ChemComp形式は未対応)・mol2で保存してみましょうか。

### 基本の文法

```
save filename [ format [format-name]] [ models [model-spec]] other-options
```

formatに関しては拡張子で勝手に判別してくれるのでなくてもOK

ハリコンドリンをSMILESで読み込んで、resNameをわかりやすいようにHLCDNと名付けておきましょう。

```bash
open smiles:C[C@@...（省略） resName HLCDN
```

### PDB

```bash
save HalichondrinB.pdb
```

<details>
<summary>ファイルの中身</summary> 

```
HETATM    1  C1  ****    1       1.489   7.573  -1.504  1.00  0.00           C
HETATM    2  C2  ****    1       1.973   6.233  -0.944  1.00  0.00           C
HETATM    3  H1  ****    1       1.822   6.212   0.135  1.00  0.00           H
HETATM    4  C3  ****    1       3.460   6.054  -1.257  1.00  0.00           C
HETATM    5  C4  ****    1       3.855   4.587  -1.076  1.00  0.00           C
HETATM    6  H2  ****    1       3.629   4.267  -0.063  1.00  0.00           H
HETATM    7  C5  ****    1       5.360   4.450  -1.332  1.00  0.00           C
HETATM    8  C6  ****    1       5.950   3.404  -0.385  1.00  0.00           C
HETATM    9  C7  ****    1       7.165   2.752  -1.054  1.00  0.00           C
HETATM   10  H3  ****    1       7.107   2.911  -2.134  1.00  0.00           H
HETATM   11  C8  ****    1       8.435   3.367  -0.522  1.00  0.00           C
HETATM   12  C9  ****    1       8.730   4.642  -0.462  1.00  0.00           C
HETATM   13  C10 ****    1       9.299   2.207  -0.071  1.00  0.00           C
HETATM   14  C11 ****    1       8.321   1.024   0.005  1.00  0.00           C
HETATM   15  H4  ****    1       8.026   0.864   1.044  1.00  0.00           H
HETATM   16  O1  ****    1       7.181   1.359  -0.778  1.00  0.00           O
HETATM   17  C12 ****    1       8.990  -0.236  -0.547  1.00  0.00           C
HETATM   18  C13 ****    1       7.932  -1.308  -0.821  1.00  0.00           C
HETATM   19  C14 ****    1       8.196  -2.523   0.071  1.00  0.00           C
HETATM   20  C15 ****    1       9.698  -2.630   0.436  1.00  0.00           C
HETATM   21  C16 ****    1       9.775  -4.128   0.830  1.00  0.00           C
HETATM   22  H5  ****    1      10.776  -4.544   0.771  1.00  0.00           H
HETATM   23  C17 ****    1       8.764  -4.800  -0.153  1.00  0.00           C
HETATM   24  H6  ****    1       9.252  -5.336  -0.973  1.00  0.00           H
HETATM   25  O2  ****    1       7.903  -3.744  -0.607  1.00  0.00           O
HETATM   26  C18 ****    1       7.974  -5.713   0.812  1.00  0.00           C
HETATM   27  H7  ****    1       8.595  -6.574   1.103  1.00  0.00           H
HETATM   28  C19 ****    1       7.843  -4.746   2.010  1.00  0.00           C
HETATM   29  H8  ****    1       7.532  -5.276   2.908  1.00  0.00           H
HETATM   30  O3  ****    1       9.184  -4.230   2.144  1.00  0.00           O
HETATM   31  C20 ****    1       6.885  -3.626   1.678  1.00  0.00           C
HETATM   32  H9  ****    1       6.458  -3.375   2.661  1.00  0.00           H
HETATM   33  O4  ****    1       7.474  -2.413   1.291  1.00  0.00           O
HETATM   34  C21 ****    1       5.677  -4.012   0.869  1.00  0.00           C
HETATM   35  H10 ****    1       4.889  -4.355   1.551  1.00  0.00           H
HETATM   36  C22 ****    1       5.942  -5.117  -0.153  1.00  0.00           C
HETATM   37  H11 ****    1       6.368  -4.689  -1.067  1.00  0.00           H
HETATM   38  O5  ****    1       6.735  -6.159   0.341  1.00  0.00           O
HETATM   39  C23 ****    1       4.533  -5.610  -0.548  1.00  0.00           C
HETATM   40  C24 ****    1       3.811  -4.414  -1.154  1.00  0.00           C
HETATM   41  C25 ****    1       3.840  -3.155  -0.304  1.00  0.00           C
HETATM   42  H12 ****    1       3.160  -3.233   0.539  1.00  0.00           H
HETATM   43  O6  ****    1       5.167  -2.905   0.125  1.00  0.00           O
HETATM   44  C26 ****    1       3.416  -1.998  -1.220  1.00  0.00           C
HETATM   45  C27 ****    1       2.721  -0.897  -0.473  1.00  0.00           C
HETATM   46  O7  ****    1       3.063  -0.591   0.645  1.00  0.00           O
HETATM   47  O8  ****    1       1.712  -0.266  -1.083  1.00  0.00           O
HETATM   48  C28 ****    1       1.247   1.056  -0.710  1.00  0.00           C
HETATM   49  H13 ****    1       2.100   1.694  -0.515  1.00  0.00           H
HETATM   50  C29 ****    1       0.363   0.958   0.537  1.00  0.00           C
HETATM   51  H14 ****    1      -0.417   0.214   0.372  1.00  0.00           H
HETATM   52  C30 ****    1      -0.284   2.323   0.818  1.00  0.00           C
HETATM   53  H15 ****    1       0.495   3.028   1.138  1.00  0.00           H
HETATM   54  C31 ****    1      -0.946   2.829  -0.459  1.00  0.00           C
HETATM   55  H16 ****    1      -0.375   3.684  -0.845  1.00  0.00           H
HETATM   56  C32 ****    1      -2.388   3.253  -0.274  1.00  0.00           C
HETATM   57  C33 ****    1      -2.744   3.846   1.063  1.00  0.00           C
HETATM   58  H17 ****    1      -2.722   4.934   0.984  1.00  0.00           H
HETATM   59  C34 ****    1      -1.795   3.433   2.193  1.00  0.00           C
HETATM   60  H18 ****    1      -1.044   4.183   2.420  1.00  0.00           H
HETATM   61  O9  ****    1      -1.226   2.159   1.870  1.00  0.00           O
HETATM   62  C35 ****    1      -2.778   3.171   3.382  1.00  0.00           C
HETATM   63  C36 ****    1      -3.997   2.652   2.607  1.00  0.00           C
HETATM   64  O10 ****    1      -4.077   3.465   1.430  1.00  0.00           O
HETATM   65  C37 ****    1      -3.761   1.177   2.217  1.00  0.00           C
HETATM   66  C38 ****    1      -5.224   0.650   2.071  1.00  0.00           C
HETATM   67  H19 ****    1      -5.302  -0.404   2.357  1.00  0.00           H
HETATM   68  C39 ****    1      -5.995   1.550   3.028  1.00  0.00           C
HETATM   69  H20 ****    1      -6.059   0.991   3.972  1.00  0.00           H
HETATM   70  O11 ****    1      -5.216   2.707   3.337  1.00  0.00           O
HETATM   71  C40 ****    1      -7.417   1.858   2.649  1.00  0.00           C
HETATM   72  H21 ****    1      -8.066   1.106   3.098  1.00  0.00           H
HETATM   73  C41 ****    1      -7.666   1.881   1.154  1.00  0.00           C
HETATM   74  C42 ****    1      -6.942   0.711   0.481  1.00  0.00           C
HETATM   75  O12 ****    1      -5.549   0.857   0.699  1.00  0.00           O
HETATM   76  C43 ****    1      -7.230   0.768  -1.026  1.00  0.00           C
HETATM   77  C44 ****    1      -6.463  -0.346  -1.728  1.00  0.00           C
HETATM   78  H22 ****    1      -5.406  -0.080  -1.760  1.00  0.00           H
HETATM   79  C45 ****    1      -6.610  -1.671  -1.031  1.00  0.00           C
HETATM   80  H23 ****    1      -5.758  -2.288  -1.318  1.00  0.00           H
HETATM   81  C46 ****    1      -6.621  -1.596   0.496  1.00  0.00           C
HETATM   82  H24 ****    1      -5.608  -1.560   0.897  1.00  0.00           H
HETATM   83  O13 ****    1      -7.423  -0.527   0.988  1.00  0.00           O
HETATM   84  C47 ****    1      -7.337  -2.918   0.890  1.00  0.00           C
HETATM   85  C48 ****    1      -8.046  -3.369  -0.399  1.00  0.00           C
HETATM   86  H25 ****    1      -7.655  -4.335  -0.717  1.00  0.00           H
HETATM   87  O14 ****    1      -7.790  -2.384  -1.411  1.00  0.00           O
HETATM   88  C49 ****    1      -9.552  -3.476  -0.150  1.00  0.00           C
HETATM   89  H26 ****    1      -9.745  -4.268   0.574  1.00  0.00           H
HETATM   90  C50 ****    1     -10.264  -3.803  -1.465  1.00  0.00           C
HETATM   91  C51 ****    1     -11.752  -4.033  -1.195  1.00  0.00           C
HETATM   92  H27 ****    1     -11.868  -4.806  -0.435  1.00  0.00           H
HETATM   93  C52 ****    1     -12.441  -4.481  -2.486  1.00  0.00           C
HETATM   94  O15 ****    1     -13.804  -4.808  -2.210  1.00  0.00           O
HETATM   95  O16 ****    1     -12.347  -2.818  -0.735  1.00  0.00           O
HETATM   96  O17 ****    1     -10.040  -2.234   0.361  1.00  0.00           O
HETATM   97  C53 ****    1      -6.983  -0.477  -3.161  1.00  0.00           C
HETATM   98  C54 ****    1      -7.789   3.226   3.224  1.00  0.00           C
HETATM   99  O18 ****    1      -0.924   1.784  -1.441  1.00  0.00           O
HETATM  100  C55 ****    1       0.414   1.596  -1.879  1.00  0.00           C
HETATM  101  H28 ****    1       0.399   0.793  -2.648  1.00  0.00           H
HETATM  102  C56 ****    1       0.994   2.833  -2.522  1.00  0.00           C
HETATM  103  C57 ****    1       1.791   3.715  -1.574  1.00  0.00           C
HETATM  104  H29 ****    1       1.759   3.338  -0.557  1.00  0.00           H
HETATM  105  C58 ****    1       1.199   5.109  -1.586  1.00  0.00           C
HETATM  106  C59 ****    1       0.037   5.333  -2.147  1.00  0.00           C
HETATM  107  O19 ****    1       3.149   3.781  -2.018  1.00  0.00           O
HETATM  108  C60 ****    1       1.217   0.544   1.736  1.00  0.00           C
HETATM  109  H30 ****    1       1.642   7.592  -2.583  1.00  0.00           H
HETATM  110  H31 ****    1       0.429   7.696  -1.284  1.00  0.00           H
HETATM  111  H32 ****    1       2.053   8.384  -1.042  1.00  0.00           H
HETATM  112  H33 ****    1       3.653   6.358  -2.286  1.00  0.00           H
HETATM  113  H34 ****    1       4.049   6.674  -0.581  1.00  0.00           H
HETATM  114  H35 ****    1       5.527   4.141  -2.363  1.00  0.00           H
HETATM  115  H36 ****    1       5.846   5.411  -1.159  1.00  0.00           H
HETATM  116  H37 ****    1       6.260   3.885   0.543  1.00  0.00           H
HETATM  117  H38 ****    1       5.201   2.643  -0.170  1.00  0.00           H
HETATM  118  H39 ****    1       8.024   5.377  -0.819  1.00  0.00           H
HETATM  119  H40 ****    1       9.680   4.957  -0.056  1.00  0.00           H
HETATM  120  H41 ****    1      10.084   2.008  -0.800  1.00  0.00           H
HETATM  121  H42 ****    1       9.730   2.410   0.910  1.00  0.00           H
HETATM  122  H43 ****    1       9.508   0.006  -1.475  1.00  0.00           H
HETATM  123  H44 ****    1       9.708  -0.614   0.181  1.00  0.00           H
HETATM  124  H45 ****    1       6.942  -0.905  -0.604  1.00  0.00           H
HETATM  125  H46 ****    1       7.981  -1.608  -1.868  1.00  0.00           H
HETATM  126  H47 ****    1      10.330  -2.414  -0.425  1.00  0.00           H
HETATM  127  H48 ****    1       9.948  -1.985   1.278  1.00  0.00           H
HETATM  128  H49 ****    1       4.610  -6.412  -1.284  1.00  0.00           H
HETATM  129  H50 ****    1       3.998  -5.962   0.334  1.00  0.00           H
HETATM  130  H51 ****    1       4.267  -4.189  -2.118  1.00  0.00           H
HETATM  131  H52 ****    1       2.771  -4.690  -1.325  1.00  0.00           H
HETATM  132  H53 ****    1       4.303  -1.590  -1.706  1.00  0.00           H
HETATM  133  H54 ****    1       2.743  -2.383  -1.986  1.00  0.00           H
HETATM  134  H55 ****    1      -2.627   3.986  -1.044  1.00  0.00           H
HETATM  135  H56 ****    1      -3.021   2.380  -0.436  1.00  0.00           H
HETATM  136  H57 ****    1      -2.387   2.412   4.059  1.00  0.00           H
HETATM  137  H58 ****    1      -3.011   4.093   3.914  1.00  0.00           H
HETATM  138  H59 ****    1      -3.224   1.105   1.271  1.00  0.00           H
HETATM  139  H60 ****    1      -3.231   0.645   3.006  1.00  0.00           H
HETATM  140  H61 ****    1      -8.736   1.800   0.965  1.00  0.00           H
HETATM  141  H62 ****    1      -7.297   2.819   0.740  1.00  0.00           H
HETATM  142  H63 ****    1      -8.299   0.639  -1.197  1.00  0.00           H
HETATM  143  H64 ****    1      -6.913   1.734  -1.420  1.00  0.00           H
HETATM  144  H65 ****    1      -6.609  -3.666   1.206  1.00  0.00           H
HETATM  145  H66 ****    1      -8.064  -2.737   1.682  1.00  0.00           H
HETATM  146  H67 ****    1     -10.145  -2.971  -2.159  1.00  0.00           H
HETATM  147  H68 ****    1      -9.829  -4.703  -1.899  1.00  0.00           H
HETATM  148  H69 ****    1     -12.402  -3.674  -3.217  1.00  0.00           H
HETATM  149  H70 ****    1     -11.930  -5.358  -2.885  1.00  0.00           H
HETATM  150  H71 ****    1     -14.200  -5.085  -3.047  1.00  0.00           H
HETATM  151  H72 ****    1     -12.222  -2.163  -1.435  1.00  0.00           H
HETATM  152  H73 ****    1      -9.850  -1.563  -0.309  1.00  0.00           H
HETATM  153  H74 ****    1      -6.833   0.464  -3.690  1.00  0.00           H
HETATM  154  H75 ****    1      -6.440  -1.272  -3.673  1.00  0.00           H
HETATM  155  H76 ****    1      -8.046  -0.718  -3.141  1.00  0.00           H
HETATM  156  H77 ****    1      -7.123   3.986   2.815  1.00  0.00           H
HETATM  157  H78 ****    1      -8.819   3.465   2.958  1.00  0.00           H
HETATM  158  H79 ****    1      -7.690   3.203   4.309  1.00  0.00           H
HETATM  159  H80 ****    1       1.647   2.524  -3.339  1.00  0.00           H
HETATM  160  H81 ****    1       0.178   3.422  -2.939  1.00  0.00           H
HETATM  161  H82 ****    1      -0.570   4.505  -2.483  1.00  0.00           H
HETATM  162  H83 ****    1      -0.315   6.347  -2.273  1.00  0.00           H
HETATM  163  H84 ****    1       2.145   1.117   1.736  1.00  0.00           H
HETATM  164  H85 ****    1       0.669   0.741   2.658  1.00  0.00           H
HETATM  165  H86 ****    1       1.446  -0.519   1.670  1.00  0.00           H
CONECT    1    2  109  110  111
CONECT    2    1    3    4  105
CONECT    3    2
CONECT    4    2    5  112  113
CONECT    5    4    6    7  107
CONECT    6    5
CONECT    7    5    8  114  115
CONECT    8    7    9  116  117
CONECT    9    8   10   11   16
CONECT   10    9
CONECT   11    9   12   13
CONECT   12   11  118  119
CONECT   13   11   14  120  121
CONECT   14   13   15   16   17
CONECT   15   14
CONECT   16   14    9
CONECT   17   14   18  122  123
CONECT   18   17   19  124  125
CONECT   19   18   20   25   33
CONECT   20   19   21  126  127
CONECT   21   20   22   23   30
CONECT   22   21
CONECT   23   21   24   25   26
CONECT   24   23
CONECT   25   23   19
CONECT   26   23   27   28   38
CONECT   27   26
CONECT   28   26   29   30   31
CONECT   29   28
CONECT   30   28   21
CONECT   31   28   32   33   34
CONECT   32   31
CONECT   33   31   19
CONECT   34   31   35   36   43
CONECT   35   34
CONECT   36   34   37   38   39
CONECT   37   36
CONECT   38   36   26
CONECT   39   36   40  128  129
CONECT   40   39   41  130  131
CONECT   41   40   42   43   44
CONECT   42   41
CONECT   43   41   34
CONECT   44   41   45  132  133
CONECT   45   44   46   47
CONECT   46   45
CONECT   47   45   48
CONECT   48   47   49   50  100
CONECT   49   48
CONECT   50   48   51   52  108
CONECT   51   50
CONECT   52   50   53   54   61
CONECT   53   52
CONECT   54   52   55   56   99
CONECT   55   54
CONECT   56   54   57  134  135
CONECT   57   56   58   59   64
CONECT   58   57
CONECT   59   57   60   61   62
CONECT   60   59
CONECT   61   59   52
CONECT   62   59   63  136  137
CONECT   63   62   64   65   70
CONECT   64   63   57
CONECT   65   63   66  138  139
CONECT   66   65   67   68   75
CONECT   67   66
CONECT   68   66   69   70   71
CONECT   69   68
CONECT   70   68   63
CONECT   71   68   72   73   98
CONECT   72   71
CONECT   73   71   74  140  141
CONECT   74   73   75   76   83
CONECT   75   74   66
CONECT   76   74   77  142  143
CONECT   77   76   78   79   97
CONECT   78   77
CONECT   79   77   80   81   87
CONECT   80   79
CONECT   81   79   82   83   84
CONECT   82   81
CONECT   83   81   74
CONECT   84   81   85  144  145
CONECT   85   84   86   87   88
CONECT   86   85
CONECT   87   85   79
CONECT   88   85   89   90   96
CONECT   89   88
CONECT   90   88   91  146  147
CONECT   91   90   92   93   95
CONECT   92   91
CONECT   93   91   94  148  149
CONECT   94   93  150
CONECT   95   91  151
CONECT   96   88  152
CONECT   97   77  153  154  155
CONECT   98   71  156  157  158
CONECT   99   54  100
CONECT  100   99  101   48  102
CONECT  101  100
CONECT  102  100  103  159  160
CONECT  103  102  104  105  107
CONECT  104  103
CONECT  105  103    2  106
CONECT  106  105  161  162
CONECT  107  103    5
CONECT  108   50  163  164  165
CONECT  109    1
CONECT  110    1
CONECT  111    1
CONECT  112    4
CONECT  113    4
CONECT  114    7
CONECT  115    7
CONECT  116    8
CONECT  117    8
CONECT  118   12
CONECT  119   12
CONECT  120   13
CONECT  121   13
CONECT  122   17
CONECT  123   17
CONECT  124   18
CONECT  125   18
CONECT  126   20
CONECT  127   20
CONECT  128   39
CONECT  129   39
CONECT  130   40
CONECT  131   40
CONECT  132   44
CONECT  133   44
CONECT  134   56
CONECT  135   56
CONECT  136   62
CONECT  137   62
CONECT  138   65
CONECT  139   65
CONECT  140   73
CONECT  141   73
CONECT  142   76
CONECT  143   76
CONECT  144   84
CONECT  145   84
CONECT  146   90
CONECT  147   90
CONECT  148   93
CONECT  149   93
CONECT  150   94
CONECT  151   95
CONECT  152   96
CONECT  153   97
CONECT  154   97
CONECT  155   97
CONECT  156   98
CONECT  157   98
CONECT  158   98
CONECT  159  102
CONECT  160  102
CONECT  161  106
CONECT  162  106
CONECT  163  108
CONECT  164  108
CONECT  165  108
END

```
</details>




PDBは5文字の残基にに対応していないので****となっている

### mmCIF

```bash
save HalichondrinB.cif
```
<details>
<summary>ファイルの中身</summary> 

```
#\#CIF_1.1
# mmCIF
data_smiles:C[C@@H]1C[C@@H]2CC[C@H]3C(=C)C[C@@H](O3)CC[C@]45C[C@@H]6[C@H](O4)[C@H]7[C@@H](O6)[C@@H](O5)[C@@H]8[C@@H](O7)CC[C@@H](O8)CC(=O)O[C@@H]9[C@H]([C@H]3[C@H](C[C@@H]4[C@H](O3)C[C@@]3(O4)C[C@H]4[C@@H](O3)[C@H](C[C@]3(O4)C[C@@H]([C@H]4[C@@H](O3)C[C@H](O4)[C@H](C[C@H](CO)O)O)C)C)O[C@H]9C[C@H](C1=C)O2)C
#
_audit_conform.dict_name mmcif_pdbx.dic
_audit_conform.dict_version 4.007
_audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
#
_audit_syntax.case_sensitive_flag Y
_audit_syntax.fixed_width "atom_site atom_site_anisotrop"
#
_citation.id chimerax
_citation.title 
;UCSF ChimeraX: Structure visualization for researchers, educators, and developers
;

_citation.journal_abbrev "Protein Sci."
_citation.journal_volume 30
_citation.page_first 70
_citation.page_last 82
_citation.journal_issue 1
_citation.year 2021
_citation.pdbx_database_id_PubMed 28710774
_citation.pdbx_database_id_DOI 10.1002/pro.3943
#
loop_
_citation_author.citation_id
_citation_author.name
_citation_author.ordinal
chimerax "Pettersen EF" 1 
chimerax "Goddard TD"   2 
chimerax "Huang CC"     3 
chimerax "Meng EC"      4 
chimerax "Couch GS"     5 
chimerax "Croll TI"     6 
chimerax "Morris JH"    7 
chimerax "Ferrin TE"    8 
#
_software.name "UCSF ChimeraX"
_software.version 1.8/v10
_software.location https://www.rbvi.ucsf.edu/chimerax/
_software.classification "model building"
_software.os macOS
_software.type package
_software.citation_id chimerax
_software.pdbx_ordinal 1
#
_chem_comp.id HLCDN
_chem_comp.type non-polymer
#
_entity.id 1
_entity.type non-polymer
_entity.pdbx_description ?
#
_struct_asym.id .
_struct_asym.entity_id 1
#
loop_
_atom_type.symbol
H 
C 
O 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.auth_asym_id
_atom_site.auth_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_PDB_model_num
HETATM 1   C C1  . HLCDN . 1 . 1.489   7.573  -1.504 . 1 ? 1.00 0.00 1 
HETATM 2   C C2  . HLCDN . 1 . 1.973   6.233  -0.944 . 1 ? 1.00 0.00 1 
HETATM 3   H H1  . HLCDN . 1 . 1.822   6.212  0.135  . 1 ? 1.00 0.00 1 
HETATM 4   C C3  . HLCDN . 1 . 3.460   6.054  -1.257 . 1 ? 1.00 0.00 1 
HETATM 5   C C4  . HLCDN . 1 . 3.855   4.587  -1.076 . 1 ? 1.00 0.00 1 
HETATM 6   H H2  . HLCDN . 1 . 3.629   4.267  -0.063 . 1 ? 1.00 0.00 1 
HETATM 7   C C5  . HLCDN . 1 . 5.360   4.450  -1.331 . 1 ? 1.00 0.00 1 
HETATM 8   C C6  . HLCDN . 1 . 5.950   3.404  -0.385 . 1 ? 1.00 0.00 1 
HETATM 9   C C7  . HLCDN . 1 . 7.165   2.752  -1.054 . 1 ? 1.00 0.00 1 
HETATM 10  H H3  . HLCDN . 1 . 7.107   2.911  -2.134 . 1 ? 1.00 0.00 1 
HETATM 11  C C8  . HLCDN . 1 . 8.435   3.367  -0.522 . 1 ? 1.00 0.00 1 
HETATM 12  C C9  . HLCDN . 1 . 8.730   4.642  -0.462 . 1 ? 1.00 0.00 1 
HETATM 13  C C10 . HLCDN . 1 . 9.299   2.207  -0.070 . 1 ? 1.00 0.00 1 
HETATM 14  C C11 . HLCDN . 1 . 8.321   1.024  0.005  . 1 ? 1.00 0.00 1 
HETATM 15  H H4  . HLCDN . 1 . 8.026   0.864  1.044  . 1 ? 1.00 0.00 1 
HETATM 16  O O1  . HLCDN . 1 . 7.181   1.359  -0.778 . 1 ? 1.00 0.00 1 
HETATM 17  C C12 . HLCDN . 1 . 8.989   -0.236 -0.547 . 1 ? 1.00 0.00 1 
HETATM 18  C C13 . HLCDN . 1 . 7.932   -1.308 -0.821 . 1 ? 1.00 0.00 1 
HETATM 19  C C14 . HLCDN . 1 . 8.196   -2.522 0.071  . 1 ? 1.00 0.00 1 
HETATM 20  C C15 . HLCDN . 1 . 9.698   -2.630 0.435  . 1 ? 1.00 0.00 1 
HETATM 21  C C16 . HLCDN . 1 . 9.775   -4.128 0.830  . 1 ? 1.00 0.00 1 
HETATM 22  H H5  . HLCDN . 1 . 10.776  -4.544 0.771  . 1 ? 1.00 0.00 1 
HETATM 23  C C17 . HLCDN . 1 . 8.764   -4.800 -0.153 . 1 ? 1.00 0.00 1 
HETATM 24  H H6  . HLCDN . 1 . 9.252   -5.336 -0.973 . 1 ? 1.00 0.00 1 
HETATM 25  O O2  . HLCDN . 1 . 7.903   -3.744 -0.607 . 1 ? 1.00 0.00 1 
HETATM 26  C C18 . HLCDN . 1 . 7.974   -5.713 0.812  . 1 ? 1.00 0.00 1 
HETATM 27  H H7  . HLCDN . 1 . 8.595   -6.574 1.103  . 1 ? 1.00 0.00 1 
HETATM 28  C C19 . HLCDN . 1 . 7.843   -4.746 2.010  . 1 ? 1.00 0.00 1 
HETATM 29  H H8  . HLCDN . 1 . 7.532   -5.276 2.908  . 1 ? 1.00 0.00 1 
HETATM 30  O O3  . HLCDN . 1 . 9.184   -4.229 2.143  . 1 ? 1.00 0.00 1 
HETATM 31  C C20 . HLCDN . 1 . 6.885   -3.626 1.678  . 1 ? 1.00 0.00 1 
HETATM 32  H H9  . HLCDN . 1 . 6.458   -3.375 2.661  . 1 ? 1.00 0.00 1 
HETATM 33  O O4  . HLCDN . 1 . 7.474   -2.413 1.291  . 1 ? 1.00 0.00 1 
HETATM 34  C C21 . HLCDN . 1 . 5.677   -4.012 0.869  . 1 ? 1.00 0.00 1 
HETATM 35  H H10 . HLCDN . 1 . 4.888   -4.355 1.551  . 1 ? 1.00 0.00 1 
HETATM 36  C C22 . HLCDN . 1 . 5.942   -5.117 -0.153 . 1 ? 1.00 0.00 1 
HETATM 37  H H11 . HLCDN . 1 . 6.368   -4.689 -1.067 . 1 ? 1.00 0.00 1 
HETATM 38  O O5  . HLCDN . 1 . 6.735   -6.159 0.341  . 1 ? 1.00 0.00 1 
HETATM 39  C C23 . HLCDN . 1 . 4.533   -5.610 -0.548 . 1 ? 1.00 0.00 1 
HETATM 40  C C24 . HLCDN . 1 . 3.811   -4.414 -1.154 . 1 ? 1.00 0.00 1 
HETATM 41  C C25 . HLCDN . 1 . 3.840   -3.155 -0.304 . 1 ? 1.00 0.00 1 
HETATM 42  H H12 . HLCDN . 1 . 3.159   -3.233 0.539  . 1 ? 1.00 0.00 1 
HETATM 43  O O6  . HLCDN . 1 . 5.167   -2.905 0.124  . 1 ? 1.00 0.00 1 
HETATM 44  C C26 . HLCDN . 1 . 3.416   -1.998 -1.220 . 1 ? 1.00 0.00 1 
HETATM 45  C C27 . HLCDN . 1 . 2.721   -0.897 -0.473 . 1 ? 1.00 0.00 1 
HETATM 46  O O7  . HLCDN . 1 . 3.063   -0.591 0.645  . 1 ? 1.00 0.00 1 
HETATM 47  O O8  . HLCDN . 1 . 1.712   -0.266 -1.083 . 1 ? 1.00 0.00 1 
HETATM 48  C C28 . HLCDN . 1 . 1.247   1.056  -0.710 . 1 ? 1.00 0.00 1 
HETATM 49  H H13 . HLCDN . 1 . 2.100   1.694  -0.515 . 1 ? 1.00 0.00 1 
HETATM 50  C C29 . HLCDN . 1 . 0.363   0.958  0.536  . 1 ? 1.00 0.00 1 
HETATM 51  H H14 . HLCDN . 1 . -0.417  0.214  0.372  . 1 ? 1.00 0.00 1 
HETATM 52  C C30 . HLCDN . 1 . -0.283  2.323  0.818  . 1 ? 1.00 0.00 1 
HETATM 53  H H15 . HLCDN . 1 . 0.495   3.028  1.138  . 1 ? 1.00 0.00 1 
HETATM 54  C C31 . HLCDN . 1 . -0.946  2.829  -0.459 . 1 ? 1.00 0.00 1 
HETATM 55  H H16 . HLCDN . 1 . -0.375  3.684  -0.845 . 1 ? 1.00 0.00 1 
HETATM 56  C C32 . HLCDN . 1 . -2.388  3.253  -0.274 . 1 ? 1.00 0.00 1 
HETATM 57  C C33 . HLCDN . 1 . -2.744  3.846  1.063  . 1 ? 1.00 0.00 1 
HETATM 58  H H17 . HLCDN . 1 . -2.722  4.934  0.984  . 1 ? 1.00 0.00 1 
HETATM 59  C C34 . HLCDN . 1 . -1.795  3.433  2.193  . 1 ? 1.00 0.00 1 
HETATM 60  H H18 . HLCDN . 1 . -1.044  4.183  2.420  . 1 ? 1.00 0.00 1 
HETATM 61  O O9  . HLCDN . 1 . -1.226  2.159  1.870  . 1 ? 1.00 0.00 1 
HETATM 62  C C35 . HLCDN . 1 . -2.778  3.171  3.381  . 1 ? 1.00 0.00 1 
HETATM 63  C C36 . HLCDN . 1 . -3.997  2.652  2.607  . 1 ? 1.00 0.00 1 
HETATM 64  O O10 . HLCDN . 1 . -4.077  3.465  1.430  . 1 ? 1.00 0.00 1 
HETATM 65  C C37 . HLCDN . 1 . -3.761  1.177  2.217  . 1 ? 1.00 0.00 1 
HETATM 66  C C38 . HLCDN . 1 . -5.224  0.650  2.071  . 1 ? 1.00 0.00 1 
HETATM 67  H H19 . HLCDN . 1 . -5.302  -0.404 2.357  . 1 ? 1.00 0.00 1 
HETATM 68  C C39 . HLCDN . 1 . -5.995  1.550  3.028  . 1 ? 1.00 0.00 1 
HETATM 69  H H20 . HLCDN . 1 . -6.059  0.991  3.972  . 1 ? 1.00 0.00 1 
HETATM 70  O O11 . HLCDN . 1 . -5.215  2.707  3.337  . 1 ? 1.00 0.00 1 
HETATM 71  C C40 . HLCDN . 1 . -7.417  1.858  2.649  . 1 ? 1.00 0.00 1 
HETATM 72  H H21 . HLCDN . 1 . -8.066  1.106  3.098  . 1 ? 1.00 0.00 1 
HETATM 73  C C41 . HLCDN . 1 . -7.666  1.881  1.154  . 1 ? 1.00 0.00 1 
HETATM 74  C C42 . HLCDN . 1 . -6.942  0.711  0.481  . 1 ? 1.00 0.00 1 
HETATM 75  O O12 . HLCDN . 1 . -5.549  0.857  0.699  . 1 ? 1.00 0.00 1 
HETATM 76  C C43 . HLCDN . 1 . -7.230  0.768  -1.026 . 1 ? 1.00 0.00 1 
HETATM 77  C C44 . HLCDN . 1 . -6.463  -0.346 -1.728 . 1 ? 1.00 0.00 1 
HETATM 78  H H22 . HLCDN . 1 . -5.406  -0.080 -1.760 . 1 ? 1.00 0.00 1 
HETATM 79  C C45 . HLCDN . 1 . -6.610  -1.671 -1.031 . 1 ? 1.00 0.00 1 
HETATM 80  H H23 . HLCDN . 1 . -5.758  -2.288 -1.318 . 1 ? 1.00 0.00 1 
HETATM 81  C C46 . HLCDN . 1 . -6.620  -1.596 0.496  . 1 ? 1.00 0.00 1 
HETATM 82  H H24 . HLCDN . 1 . -5.607  -1.560 0.896  . 1 ? 1.00 0.00 1 
HETATM 83  O O13 . HLCDN . 1 . -7.423  -0.526 0.988  . 1 ? 1.00 0.00 1 
HETATM 84  C C47 . HLCDN . 1 . -7.337  -2.918 0.890  . 1 ? 1.00 0.00 1 
HETATM 85  C C48 . HLCDN . 1 . -8.046  -3.369 -0.399 . 1 ? 1.00 0.00 1 
HETATM 86  H H25 . HLCDN . 1 . -7.655  -4.335 -0.717 . 1 ? 1.00 0.00 1 
HETATM 87  O O14 . HLCDN . 1 . -7.790  -2.384 -1.411 . 1 ? 1.00 0.00 1 
HETATM 88  C C49 . HLCDN . 1 . -9.552  -3.476 -0.150 . 1 ? 1.00 0.00 1 
HETATM 89  H H26 . HLCDN . 1 . -9.745  -4.268 0.574  . 1 ? 1.00 0.00 1 
HETATM 90  C C50 . HLCDN . 1 . -10.264 -3.803 -1.465 . 1 ? 1.00 0.00 1 
HETATM 91  C C51 . HLCDN . 1 . -11.752 -4.033 -1.195 . 1 ? 1.00 0.00 1 
HETATM 92  H H27 . HLCDN . 1 . -11.868 -4.806 -0.435 . 1 ? 1.00 0.00 1 
HETATM 93  C C52 . HLCDN . 1 . -12.441 -4.481 -2.486 . 1 ? 1.00 0.00 1 
HETATM 94  O O15 . HLCDN . 1 . -13.804 -4.808 -2.210 . 1 ? 1.00 0.00 1 
HETATM 95  O O16 . HLCDN . 1 . -12.347 -2.818 -0.735 . 1 ? 1.00 0.00 1 
HETATM 96  O O17 . HLCDN . 1 . -10.040 -2.234 0.360  . 1 ? 1.00 0.00 1 
HETATM 97  C C53 . HLCDN . 1 . -6.983  -0.477 -3.161 . 1 ? 1.00 0.00 1 
HETATM 98  C C54 . HLCDN . 1 . -7.789  3.226  3.224  . 1 ? 1.00 0.00 1 
HETATM 99  O O18 . HLCDN . 1 . -0.924  1.784  -1.441 . 1 ? 1.00 0.00 1 
HETATM 100 C C55 . HLCDN . 1 . 0.414   1.596  -1.879 . 1 ? 1.00 0.00 1 
HETATM 101 H H28 . HLCDN . 1 . 0.399   0.793  -2.648 . 1 ? 1.00 0.00 1 
HETATM 102 C C56 . HLCDN . 1 . 0.994   2.833  -2.522 . 1 ? 1.00 0.00 1 
HETATM 103 C C57 . HLCDN . 1 . 1.791   3.715  -1.573 . 1 ? 1.00 0.00 1 
HETATM 104 H H29 . HLCDN . 1 . 1.759   3.338  -0.557 . 1 ? 1.00 0.00 1 
HETATM 105 C C58 . HLCDN . 1 . 1.199   5.109  -1.586 . 1 ? 1.00 0.00 1 
HETATM 106 C C59 . HLCDN . 1 . 0.037   5.333  -2.147 . 1 ? 1.00 0.00 1 
HETATM 107 O O19 . HLCDN . 1 . 3.148   3.781  -2.018 . 1 ? 1.00 0.00 1 
HETATM 108 C C60 . HLCDN . 1 . 1.217   0.544  1.736  . 1 ? 1.00 0.00 1 
HETATM 109 H H30 . HLCDN . 1 . 1.642   7.592  -2.583 . 1 ? 1.00 0.00 1 
HETATM 110 H H31 . HLCDN . 1 . 0.429   7.696  -1.284 . 1 ? 1.00 0.00 1 
HETATM 111 H H32 . HLCDN . 1 . 2.053   8.384  -1.042 . 1 ? 1.00 0.00 1 
HETATM 112 H H33 . HLCDN . 1 . 3.653   6.358  -2.286 . 1 ? 1.00 0.00 1 
HETATM 113 H H34 . HLCDN . 1 . 4.049   6.674  -0.581 . 1 ? 1.00 0.00 1 
HETATM 114 H H35 . HLCDN . 1 . 5.527   4.141  -2.363 . 1 ? 1.00 0.00 1 
HETATM 115 H H36 . HLCDN . 1 . 5.846   5.411  -1.159 . 1 ? 1.00 0.00 1 
HETATM 116 H H37 . HLCDN . 1 . 6.260   3.885  0.543  . 1 ? 1.00 0.00 1 
HETATM 117 H H38 . HLCDN . 1 . 5.200   2.643  -0.170 . 1 ? 1.00 0.00 1 
HETATM 118 H H39 . HLCDN . 1 . 8.024   5.377  -0.819 . 1 ? 1.00 0.00 1 
HETATM 119 H H40 . HLCDN . 1 . 9.680   4.957  -0.056 . 1 ? 1.00 0.00 1 
HETATM 120 H H41 . HLCDN . 1 . 10.084  2.008  -0.800 . 1 ? 1.00 0.00 1 
HETATM 121 H H42 . HLCDN . 1 . 9.730   2.410  0.910  . 1 ? 1.00 0.00 1 
HETATM 122 H H43 . HLCDN . 1 . 9.508   0.006  -1.474 . 1 ? 1.00 0.00 1 
HETATM 123 H H44 . HLCDN . 1 . 9.708   -0.614 0.181  . 1 ? 1.00 0.00 1 
HETATM 124 H H45 . HLCDN . 1 . 6.942   -0.905 -0.604 . 1 ? 1.00 0.00 1 
HETATM 125 H H46 . HLCDN . 1 . 7.981   -1.608 -1.868 . 1 ? 1.00 0.00 1 
HETATM 126 H H47 . HLCDN . 1 . 10.330  -2.414 -0.425 . 1 ? 1.00 0.00 1 
HETATM 127 H H48 . HLCDN . 1 . 9.948   -1.985 1.278  . 1 ? 1.00 0.00 1 
HETATM 128 H H49 . HLCDN . 1 . 4.609   -6.412 -1.284 . 1 ? 1.00 0.00 1 
HETATM 129 H H50 . HLCDN . 1 . 3.998   -5.962 0.334  . 1 ? 1.00 0.00 1 
HETATM 130 H H51 . HLCDN . 1 . 4.267   -4.189 -2.118 . 1 ? 1.00 0.00 1 
HETATM 131 H H52 . HLCDN . 1 . 2.771   -4.690 -1.325 . 1 ? 1.00 0.00 1 
HETATM 132 H H53 . HLCDN . 1 . 4.303   -1.590 -1.706 . 1 ? 1.00 0.00 1 
HETATM 133 H H54 . HLCDN . 1 . 2.743   -2.383 -1.986 . 1 ? 1.00 0.00 1 
HETATM 134 H H55 . HLCDN . 1 . -2.627  3.986  -1.044 . 1 ? 1.00 0.00 1 
HETATM 135 H H56 . HLCDN . 1 . -3.021  2.380  -0.436 . 1 ? 1.00 0.00 1 
HETATM 136 H H57 . HLCDN . 1 . -2.387  2.412  4.059  . 1 ? 1.00 0.00 1 
HETATM 137 H H58 . HLCDN . 1 . -3.011  4.093  3.914  . 1 ? 1.00 0.00 1 
HETATM 138 H H59 . HLCDN . 1 . -3.224  1.105  1.271  . 1 ? 1.00 0.00 1 
HETATM 139 H H60 . HLCDN . 1 . -3.231  0.645  3.006  . 1 ? 1.00 0.00 1 
HETATM 140 H H61 . HLCDN . 1 . -8.736  1.800  0.965  . 1 ? 1.00 0.00 1 
HETATM 141 H H62 . HLCDN . 1 . -7.297  2.819  0.740  . 1 ? 1.00 0.00 1 
HETATM 142 H H63 . HLCDN . 1 . -8.299  0.638  -1.197 . 1 ? 1.00 0.00 1 
HETATM 143 H H64 . HLCDN . 1 . -6.913  1.734  -1.420 . 1 ? 1.00 0.00 1 
HETATM 144 H H65 . HLCDN . 1 . -6.609  -3.666 1.206  . 1 ? 1.00 0.00 1 
HETATM 145 H H66 . HLCDN . 1 . -8.064  -2.737 1.682  . 1 ? 1.00 0.00 1 
HETATM 146 H H67 . HLCDN . 1 . -10.145 -2.971 -2.159 . 1 ? 1.00 0.00 1 
HETATM 147 H H68 . HLCDN . 1 . -9.829  -4.703 -1.899 . 1 ? 1.00 0.00 1 
HETATM 148 H H69 . HLCDN . 1 . -12.402 -3.674 -3.217 . 1 ? 1.00 0.00 1 
HETATM 149 H H70 . HLCDN . 1 . -11.930 -5.358 -2.885 . 1 ? 1.00 0.00 1 
HETATM 150 H H71 . HLCDN . 1 . -14.200 -5.085 -3.047 . 1 ? 1.00 0.00 1 
HETATM 151 H H72 . HLCDN . 1 . -12.222 -2.163 -1.435 . 1 ? 1.00 0.00 1 
HETATM 152 H H73 . HLCDN . 1 . -9.850  -1.563 -0.309 . 1 ? 1.00 0.00 1 
HETATM 153 H H74 . HLCDN . 1 . -6.833  0.464  -3.690 . 1 ? 1.00 0.00 1 
HETATM 154 H H75 . HLCDN . 1 . -6.440  -1.272 -3.673 . 1 ? 1.00 0.00 1 
HETATM 155 H H76 . HLCDN . 1 . -8.046  -0.718 -3.141 . 1 ? 1.00 0.00 1 
HETATM 156 H H77 . HLCDN . 1 . -7.122  3.986  2.815  . 1 ? 1.00 0.00 1 
HETATM 157 H H78 . HLCDN . 1 . -8.819  3.465  2.958  . 1 ? 1.00 0.00 1 
HETATM 158 H H79 . HLCDN . 1 . -7.690  3.203  4.309  . 1 ? 1.00 0.00 1 
HETATM 159 H H80 . HLCDN . 1 . 1.647   2.524  -3.339 . 1 ? 1.00 0.00 1 
HETATM 160 H H81 . HLCDN . 1 . 0.178   3.422  -2.939 . 1 ? 1.00 0.00 1 
HETATM 161 H H82 . HLCDN . 1 . -0.570  4.505  -2.483 . 1 ? 1.00 0.00 1 
HETATM 162 H H83 . HLCDN . 1 . -0.315  6.347  -2.273 . 1 ? 1.00 0.00 1 
HETATM 163 H H84 . HLCDN . 1 . 2.145   1.117  1.736  . 1 ? 1.00 0.00 1 
HETATM 164 H H85 . HLCDN . 1 . 0.669   0.741  2.658  . 1 ? 1.00 0.00 1 
HETATM 165 H H86 . HLCDN . 1 . 1.446   -0.519 1.670  . 1 ? 1.00 0.00 1 
#

```
</details>
cifなら5文字の残基もOK！！

### mol2

```bash
save HalichondrinB.mol2
```

<details>
<summary>ファイルの中身</summary> 
    
```
@<TRIPOS>MOLECULE
smiles:C[C@@H]1C[C@@H]2CC[C@H]3C(=C)C[C@@H](O3)CC[C@]45C[C@@H]6[C@H](O4)[C@H]7[C@@H](O6)[C@@H](O5)[C@@H]8[C@@H](O7)CC[C@@H](O8)CC(=O)O[C@@H]9[C@H]([C@H]3[C@H](C[C@@H]4[C@H](O3)C[C@@]3(O4)C[C@H]4[C@@H](O3)[C@H](C[C@]3(O4)C[C@@H]([C@H]4[C@@H](O3)C[C@H](O4)[C@H](C[C@H](CO)O)O)C)C)O[C@H]9C[C@H](C1=C)O2)C
165 179 1 0 0
SMALL
NO_CHARGES

@<TRIPOS>ATOM
      1 C1          1.4894    7.5727   -1.5036 C.3       1 HLCDN    0.0000
      2 C2          1.9732    6.2332   -0.9444 C.3       1 HLCDN    0.0000
      3 H1          1.8216    6.2118    0.1348 H         1 HLCDN    0.0000
      4 C3          3.4597    6.0543   -1.2567 C.3       1 HLCDN    0.0000
      5 C4          3.8553    4.5867   -1.0763 C.3       1 HLCDN    0.0000
      6 H2          3.6292    4.2673   -0.0634 H         1 HLCDN    0.0000
      7 C5          5.3603    4.4503   -1.3315 C.3       1 HLCDN    0.0000
      8 C6          5.9504    3.4037   -0.3849 C.3       1 HLCDN    0.0000
      9 C7          7.1652    2.7517   -1.0542 C.3       1 HLCDN    0.0000
     10 H3          7.1069    2.9114   -2.1342 H         1 HLCDN    0.0000
     11 C8          8.4347    3.3667   -0.5219 C.2       1 HLCDN    0.0000
     12 C9          8.7300    4.6416   -0.4619 C.2       1 HLCDN    0.0000
     13 C10         9.2987    2.2069   -0.0705 C.3       1 HLCDN    0.0000
     14 C11         8.3206    1.0241    0.0053 C.3       1 HLCDN    0.0000
     15 H4          8.0259    0.8637    1.0435 H         1 HLCDN    0.0000
     16 O1          7.1810    1.3589   -0.7784 O.3       1 HLCDN    0.0000
     17 C12         8.9895   -0.2359   -0.5471 C.3       1 HLCDN    0.0000
     18 C13         7.9316   -1.3075   -0.8209 C.3       1 HLCDN    0.0000
     19 C14         8.1957   -2.5225    0.0713 C.3       1 HLCDN    0.0000
     20 C15         9.6976   -2.6299    0.4355 C.3       1 HLCDN    0.0000
     21 C16         9.7746   -4.1282    0.8301 C.3       1 HLCDN    0.0000
     22 H5         10.7763   -4.5444    0.7712 H         1 HLCDN    0.0000
     23 C17         8.7644   -4.7995   -0.1532 C.3       1 HLCDN    0.0000
     24 H6          9.2516   -5.3362   -0.9727 H         1 HLCDN    0.0000
     25 O2          7.9028   -3.7439   -0.6071 O.3       1 HLCDN    0.0000
     26 C18         7.9743   -5.7127    0.8121 C.3       1 HLCDN    0.0000
     27 H7          8.5951   -6.5739    1.1028 H         1 HLCDN    0.0000
     28 C19         7.8430   -4.7462    2.0097 C.3       1 HLCDN    0.0000
     29 H8          7.5322   -5.2759    2.9081 H         1 HLCDN    0.0000
     30 O3          9.1840   -4.2295    2.1435 O.3       1 HLCDN    0.0000
     31 C20         6.8854   -3.6259    1.6784 C.3       1 HLCDN    0.0000
     32 H9          6.4576   -3.3752    2.6608 H         1 HLCDN    0.0000
     33 O4          7.4738   -2.4134    1.2910 O.3       1 HLCDN    0.0000
     34 C21         5.6773   -4.0120    0.8687 C.3       1 HLCDN    0.0000
     35 H10         4.8885   -4.3554    1.5512 H         1 HLCDN    0.0000
     36 C22         5.9418   -5.1173   -0.1531 C.3       1 HLCDN    0.0000
     37 H11         6.3684   -4.6895   -1.0670 H         1 HLCDN    0.0000
     38 O5          6.7354   -6.1592    0.3411 O.3       1 HLCDN    0.0000
     39 C23         4.5326   -5.6104   -0.5484 C.3       1 HLCDN    0.0000
     40 C24         3.8112   -4.4138   -1.1536 C.3       1 HLCDN    0.0000
     41 C25         3.8399   -3.1548   -0.3041 C.3       1 HLCDN    0.0000
     42 H12         3.1595   -3.2334    0.5393 H         1 HLCDN    0.0000
     43 O6          5.1667   -2.9045    0.1245 O.3       1 HLCDN    0.0000
     44 C26         3.4162   -1.9981   -1.2203 C.3       1 HLCDN    0.0000
     45 C27         2.7212   -0.8974   -0.4727 C.2       1 HLCDN    0.0000
     46 O7          3.0630   -0.5911    0.6450 O.2       1 HLCDN    0.0000
     47 O8          1.7118   -0.2657   -1.0830 O.3       1 HLCDN    0.0000
     48 C28         1.2468    1.0562   -0.7104 C.3       1 HLCDN    0.0000
     49 H13         2.1004    1.6938   -0.5147 H         1 HLCDN    0.0000
     50 C29         0.3627    0.9578    0.5365 C.3       1 HLCDN    0.0000
     51 H14        -0.4166    0.2138    0.3717 H         1 HLCDN    0.0000
     52 C30        -0.2835    2.3227    0.8177 C.3       1 HLCDN    0.0000
     53 H15         0.4947    3.0279    1.1380 H         1 HLCDN    0.0000
     54 C31        -0.9459    2.8286   -0.4593 C.3       1 HLCDN    0.0000
     55 H16        -0.3749    3.6839   -0.8445 H         1 HLCDN    0.0000
     56 C32        -2.3877    3.2526   -0.2738 C.3       1 HLCDN    0.0000
     57 C33        -2.7435    3.8458    1.0630 C.3       1 HLCDN    0.0000
     58 H17        -2.7223    4.9344    0.9843 H         1 HLCDN    0.0000
     59 C34        -1.7952    3.4326    2.1931 C.3       1 HLCDN    0.0000
     60 H18        -1.0437    4.1833    2.4198 H         1 HLCDN    0.0000
     61 O9         -1.2255    2.1589    1.8699 O.3       1 HLCDN    0.0000
     62 C35        -2.7782    3.1706    3.3815 C.3       1 HLCDN    0.0000
     63 C36        -3.9974    2.6516    2.6069 C.3       1 HLCDN    0.0000
     64 O10        -4.0767    3.4654    1.4296 O.3       1 HLCDN    0.0000
     65 C37        -3.7613    1.1774    2.2166 C.3       1 HLCDN    0.0000
     66 C38        -5.2239    0.6499    2.0711 C.3       1 HLCDN    0.0000
     67 H19        -5.3021   -0.4038    2.3571 H         1 HLCDN    0.0000
     68 C39        -5.9952    1.5505    3.0279 C.3       1 HLCDN    0.0000
     69 H20        -6.0591    0.9914    3.9722 H         1 HLCDN    0.0000
     70 O11        -5.2155    2.7066    3.3365 O.3       1 HLCDN    0.0000
     71 C40        -7.4167    1.8581    2.6489 C.3       1 HLCDN    0.0000
     72 H21        -8.0658    1.1061    3.0975 H         1 HLCDN    0.0000
     73 C41        -7.6658    1.8805    1.1537 C.3       1 HLCDN    0.0000
     74 C42        -6.9421    0.7110    0.4810 C.3       1 HLCDN    0.0000
     75 O12        -5.5490    0.8567    0.6992 O.3       1 HLCDN    0.0000
     76 C43        -7.2299    0.7684   -1.0257 C.3       1 HLCDN    0.0000
     77 C44        -6.4626   -0.3456   -1.7283 C.3       1 HLCDN    0.0000
     78 H22        -5.4059   -0.0800   -1.7604 H         1 HLCDN    0.0000
     79 C45        -6.6104   -1.6714   -1.0311 C.3       1 HLCDN    0.0000
     80 H23        -5.7580   -2.2877   -1.3176 H         1 HLCDN    0.0000
     81 C46        -6.6205   -1.5957    0.4963 C.3       1 HLCDN    0.0000
     82 H24        -5.6075   -1.5597    0.8965 H         1 HLCDN    0.0000
     83 O13        -7.4226   -0.5265    0.9878 O.3       1 HLCDN    0.0000
     84 C47        -7.3366   -2.9182    0.8900 C.3       1 HLCDN    0.0000
     85 C48        -8.0460   -3.3685   -0.3986 C.3       1 HLCDN    0.0000
     86 H25        -7.6546   -4.3348   -0.7167 H         1 HLCDN    0.0000
     87 O14        -7.7900   -2.3836   -1.4107 O.3       1 HLCDN    0.0000
     88 C49        -9.5518   -3.4763   -0.1501 C.3       1 HLCDN    0.0000
     89 H26        -9.7449   -4.2679    0.5739 H         1 HLCDN    0.0000
     90 C50       -10.2635   -3.8027   -1.4646 C.3       1 HLCDN    0.0000
     91 C51       -11.7518   -4.0333   -1.1951 C.3       1 HLCDN    0.0000
     92 H27       -11.8680   -4.8055   -0.4346 H         1 HLCDN    0.0000
     93 C52       -12.4405   -4.4811   -2.4859 C.3       1 HLCDN    0.0000
     94 O15       -13.8038   -4.8083   -2.2097 O.3       1 HLCDN    0.0000
     95 O16       -12.3465   -2.8182   -0.7349 O.3       1 HLCDN    0.0000
     96 O17       -10.0404   -2.2343    0.3605 O.3       1 HLCDN    0.0000
     97 C53        -6.9827   -0.4774   -3.1611 C.3       1 HLCDN    0.0000
     98 C54        -7.7887    3.2263    3.2240 C.3       1 HLCDN    0.0000
     99 O18        -0.9245    1.7838   -1.4414 O.3       1 HLCDN    0.0000
    100 C55         0.4136    1.5956   -1.8786 C.3       1 HLCDN    0.0000
    101 H28         0.3990    0.7934   -2.6479 H         1 HLCDN    0.0000
    102 C56         0.9944    2.8326   -2.5219 C.3       1 HLCDN    0.0000
    103 C57         1.7910    3.7151   -1.5735 C.3       1 HLCDN    0.0000
    104 H29         1.7587    3.3376   -0.5570 H         1 HLCDN    0.0000
    105 C58         1.1991    5.1085   -1.5860 C.2       1 HLCDN    0.0000
    106 C59         0.0368    5.3333   -2.1468 C.2       1 HLCDN    0.0000
    107 O19         3.1485    3.7810   -2.0182 O.3       1 HLCDN    0.0000
    108 C60         1.2172    0.5444    1.7364 C.3       1 HLCDN    0.0000
    109 H30         1.6418    7.5923   -2.5827 H         1 HLCDN    0.0000
    110 H31         0.4289    7.6963   -1.2840 H         1 HLCDN    0.0000
    111 H32         2.0529    8.3837   -1.0423 H         1 HLCDN    0.0000
    112 H33         3.6527    6.3576   -2.2858 H         1 HLCDN    0.0000
    113 H34         4.0490    6.6741   -0.5809 H         1 HLCDN    0.0000
    114 H35         5.5266    4.1410   -2.3633 H         1 HLCDN    0.0000
    115 H36         5.8460    5.4107   -1.1585 H         1 HLCDN    0.0000
    116 H37         6.2599    3.8846    0.5430 H         1 HLCDN    0.0000
    117 H38         5.2005    2.6425   -0.1699 H         1 HLCDN    0.0000
    118 H39         8.0239    5.3767   -0.8188 H         1 HLCDN    0.0000
    119 H40         9.6795    4.9574   -0.0556 H         1 HLCDN    0.0000
    120 H41        10.0838    2.0080   -0.8001 H         1 HLCDN    0.0000
    121 H42         9.7302    2.4100    0.9096 H         1 HLCDN    0.0000
    122 H43         9.5084    0.0062   -1.4745 H         1 HLCDN    0.0000
    123 H44         9.7078   -0.6135    0.1807 H         1 HLCDN    0.0000
    124 H45         6.9421   -0.9052   -0.6037 H         1 HLCDN    0.0000
    125 H46         7.9806   -1.6076   -1.8676 H         1 HLCDN    0.0000
    126 H47        10.3303   -2.4141   -0.4254 H         1 HLCDN    0.0000
    127 H48         9.9479   -1.9852    1.2780 H         1 HLCDN    0.0000
    128 H49         4.6095   -6.4115   -1.2835 H         1 HLCDN    0.0000
    129 H50         3.9983   -5.9617    0.3344 H         1 HLCDN    0.0000
    130 H51         4.2668   -4.1888   -2.1179 H         1 HLCDN    0.0000
    131 H52         2.7707   -4.6898   -1.3250 H         1 HLCDN    0.0000
    132 H53         4.3027   -1.5897   -1.7055 H         1 HLCDN    0.0000
    133 H54         2.7433   -2.3834   -1.9864 H         1 HLCDN    0.0000
    134 H55        -2.6265    3.9862   -1.0439 H         1 HLCDN    0.0000
    135 H56        -3.0206    2.3802   -0.4361 H         1 HLCDN    0.0000
    136 H57        -2.3870    2.4117    4.0590 H         1 HLCDN    0.0000
    137 H58        -3.0106    4.0930    3.9138 H         1 HLCDN    0.0000
    138 H59        -3.2241    1.1049    1.2710 H         1 HLCDN    0.0000
    139 H60        -3.2307    0.6446    3.0057 H         1 HLCDN    0.0000
    140 H61        -8.7362    1.7995    0.9646 H         1 HLCDN    0.0000
    141 H62        -7.2971    2.8192    0.7402 H         1 HLCDN    0.0000
    142 H63        -8.2985    0.6385   -1.1972 H         1 HLCDN    0.0000
    143 H64        -6.9129    1.7337   -1.4203 H         1 HLCDN    0.0000
    144 H65        -6.6091   -3.6660    1.2056 H         1 HLCDN    0.0000
    145 H66        -8.0636   -2.7368    1.6816 H         1 HLCDN    0.0000
    146 H67       -10.1446   -2.9706   -2.1585 H         1 HLCDN    0.0000
    147 H68        -9.8292   -4.7031   -1.8991 H         1 HLCDN    0.0000
    148 H69       -12.4015   -3.6740   -3.2174 H         1 HLCDN    0.0000
    149 H70       -11.9300   -5.3578   -2.8847 H         1 HLCDN    0.0000
    150 H71       -14.2001   -5.0848   -3.0473 H         1 HLCDN    0.0000
    151 H72       -12.2219   -2.1632   -1.4353 H         1 HLCDN    0.0000
    152 H73        -9.8502   -1.5628   -0.3088 H         1 HLCDN    0.0000
    153 H74        -6.8331    0.4638   -3.6901 H         1 HLCDN    0.0000
    154 H75        -6.4401   -1.2722   -3.6730 H         1 HLCDN    0.0000
    155 H76        -8.0457   -0.7179   -3.1411 H         1 HLCDN    0.0000
    156 H77        -7.1225    3.9857    2.8149 H         1 HLCDN    0.0000
    157 H78        -8.8185    3.4646    2.9576 H         1 HLCDN    0.0000
    158 H79        -7.6903    3.2031    4.3093 H         1 HLCDN    0.0000
    159 H80         1.6472    2.5242   -3.3386 H         1 HLCDN    0.0000
    160 H81         0.1779    3.4217   -2.9395 H         1 HLCDN    0.0000
    161 H82        -0.5698    4.5054   -2.4829 H         1 HLCDN    0.0000
    162 H83        -0.3149    6.3467   -2.2730 H         1 HLCDN    0.0000
    163 H84         2.1450    1.1165    1.7361 H         1 HLCDN    0.0000
    164 H85         0.6692    0.7412    2.6578 H         1 HLCDN    0.0000
    165 H86         1.4463   -0.5192    1.6700 H         1 HLCDN    0.0000
@<TRIPOS>BOND
     1    1    2 1
     2    2    3 1
     3    2    4 1
     4    4    5 1
     5    5    6 1
     6    5    7 1
     7    7    8 1
     8    8    9 1
     9    9   10 1
    10    9   11 1
    11   11   12 2
    12   11   13 1
    13   13   14 1
    14   14   15 1
    15   14   16 1
    16    9   16 1
    17   14   17 1
    18   17   18 1
    19   18   19 1
    20   19   20 1
    21   20   21 1
    22   21   22 1
    23   21   23 1
    24   23   24 1
    25   23   25 1
    26   19   25 1
    27   23   26 1
    28   26   27 1
    29   26   28 1
    30   28   29 1
    31   28   30 1
    32   21   30 1
    33   28   31 1
    34   31   32 1
    35   31   33 1
    36   19   33 1
    37   31   34 1
    38   34   35 1
    39   34   36 1
    40   36   37 1
    41   36   38 1
    42   26   38 1
    43   36   39 1
    44   39   40 1
    45   40   41 1
    46   41   42 1
    47   41   43 1
    48   34   43 1
    49   41   44 1
    50   44   45 1
    51   45   46 2
    52   45   47 1
    53   47   48 1
    54   48   49 1
    55   48   50 1
    56   50   51 1
    57   50   52 1
    58   52   53 1
    59   52   54 1
    60   54   55 1
    61   54   56 1
    62   56   57 1
    63   57   58 1
    64   57   59 1
    65   59   60 1
    66   59   61 1
    67   52   61 1
    68   59   62 1
    69   62   63 1
    70   63   64 1
    71   57   64 1
    72   63   65 1
    73   65   66 1
    74   66   67 1
    75   66   68 1
    76   68   69 1
    77   68   70 1
    78   63   70 1
    79   68   71 1
    80   71   72 1
    81   71   73 1
    82   73   74 1
    83   74   75 1
    84   66   75 1
    85   74   76 1
    86   76   77 1
    87   77   78 1
    88   77   79 1
    89   79   80 1
    90   79   81 1
    91   81   82 1
    92   81   83 1
    93   74   83 1
    94   81   84 1
    95   84   85 1
    96   85   86 1
    97   85   87 1
    98   79   87 1
    99   85   88 1
   100   88   89 1
   101   88   90 1
   102   90   91 1
   103   91   92 1
   104   91   93 1
   105   93   94 1
   106   91   95 1
   107   88   96 1
   108   77   97 1
   109   71   98 1
   110   54   99 1
   111   99  100 1
   112  100  101 1
   113   48  100 1
   114  100  102 1
   115  102  103 1
   116  103  104 1
   117  103  105 1
   118    2  105 1
   119  105  106 2
   120  103  107 1
   121    5  107 1
   122   50  108 1
   123    1  109 1
   124    1  110 1
   125    1  111 1
   126    4  112 1
   127    4  113 1
   128    7  114 1
   129    7  115 1
   130    8  116 1
   131    8  117 1
   132   12  118 1
   133   12  119 1
   134   13  120 1
   135   13  121 1
   136   17  122 1
   137   17  123 1
   138   18  124 1
   139   18  125 1
   140   20  126 1
   141   20  127 1
   142   39  128 1
   143   39  129 1
   144   40  130 1
   145   40  131 1
   146   44  132 1
   147   44  133 1
   148   56  134 1
   149   56  135 1
   150   62  136 1
   151   62  137 1
   152   65  138 1
   153   65  139 1
   154   73  140 1
   155   73  141 1
   156   76  142 1
   157   76  143 1
   158   84  144 1
   159   84  145 1
   160   90  146 1
   161   90  147 1
   162   93  148 1
   163   93  149 1
   164   94  150 1
   165   95  151 1
   166   96  152 1
   167   97  153 1
   168   97  154 1
   169   97  155 1
   170   98  156 1
   171   98  157 1
   172   98  158 1
   173  102  159 1
   174  102  160 1
   175  106  161 1
   176  106  162 1
   177  108  163 1
   178  108  164 1
   179  108  165 1
@<TRIPOS>SUBSTRUCTURE
     1 HLCDN     1 RESIDUE           4 A     HLCDN     0 ROOT
@<TRIPOS>MOLECULE
smiles:C[C@@H]1C[C@@H]2CC[C@H]3C(=C)C[C@@H](O3)CC[C@]45C[C@@H]6[C@H](O4)[C@H]7[C@@H](O6)[C@@H](O5)[C@@H]8[C@@H](O7)CC[C@@H](O8)CC(=O)O[C@@H]9[C@H]([C@H]3[C@H](C[C@@H]4[C@H](O3)C[C@@]3(O4)C[C@H]4[C@@H](O3)[C@H](C[C@]3(O4)C[C@@H]([C@H]4[C@@H](O3)C[C@H](O4)[C@H](C[C@H](CO)O)O)C)C)O[C@H]9C[C@H](C1=C)O2)C
165 179 1 0 0
SMALL
NO_CHARGES

@<TRIPOS>ATOM
      1 C1          1.4894    7.5727   -1.5036 C.3       1 HLCDN    0.0000
      2 C2          1.9732    6.2332   -0.9444 C.3       1 HLCDN    0.0000
      3 H1          1.8216    6.2118    0.1348 H         1 HLCDN    0.0000
      4 C3          3.4597    6.0543   -1.2567 C.3       1 HLCDN    0.0000
      5 C4          3.8553    4.5867   -1.0763 C.3       1 HLCDN    0.0000
      6 H2          3.6292    4.2673   -0.0634 H         1 HLCDN    0.0000
      7 C5          5.3603    4.4503   -1.3315 C.3       1 HLCDN    0.0000
      8 C6          5.9504    3.4037   -0.3849 C.3       1 HLCDN    0.0000
      9 C7          7.1652    2.7517   -1.0542 C.3       1 HLCDN    0.0000
     10 H3          7.1069    2.9114   -2.1342 H         1 HLCDN    0.0000
     11 C8          8.4347    3.3667   -0.5219 C.2       1 HLCDN    0.0000
     12 C9          8.7300    4.6416   -0.4619 C.2       1 HLCDN    0.0000
     13 C10         9.2987    2.2069   -0.0705 C.3       1 HLCDN    0.0000
     14 C11         8.3206    1.0241    0.0053 C.3       1 HLCDN    0.0000
     15 H4          8.0259    0.8637    1.0435 H         1 HLCDN    0.0000
     16 O1          7.1810    1.3589   -0.7784 O.3       1 HLCDN    0.0000
     17 C12         8.9895   -0.2359   -0.5471 C.3       1 HLCDN    0.0000
     18 C13         7.9316   -1.3075   -0.8209 C.3       1 HLCDN    0.0000
     19 C14         8.1957   -2.5225    0.0713 C.3       1 HLCDN    0.0000
     20 C15         9.6976   -2.6299    0.4355 C.3       1 HLCDN    0.0000
     21 C16         9.7746   -4.1282    0.8301 C.3       1 HLCDN    0.0000
     22 H5         10.7763   -4.5444    0.7712 H         1 HLCDN    0.0000
     23 C17         8.7644   -4.7995   -0.1532 C.3       1 HLCDN    0.0000
     24 H6          9.2516   -5.3362   -0.9727 H         1 HLCDN    0.0000
     25 O2          7.9028   -3.7439   -0.6071 O.3       1 HLCDN    0.0000
     26 C18         7.9743   -5.7127    0.8121 C.3       1 HLCDN    0.0000
     27 H7          8.5951   -6.5739    1.1028 H         1 HLCDN    0.0000
     28 C19         7.8430   -4.7462    2.0097 C.3       1 HLCDN    0.0000
     29 H8          7.5322   -5.2759    2.9081 H         1 HLCDN    0.0000
     30 O3          9.1840   -4.2295    2.1435 O.3       1 HLCDN    0.0000
     31 C20         6.8854   -3.6259    1.6784 C.3       1 HLCDN    0.0000
     32 H9          6.4576   -3.3752    2.6608 H         1 HLCDN    0.0000
     33 O4          7.4738   -2.4134    1.2910 O.3       1 HLCDN    0.0000
     34 C21         5.6773   -4.0120    0.8687 C.3       1 HLCDN    0.0000
     35 H10         4.8885   -4.3554    1.5512 H         1 HLCDN    0.0000
     36 C22         5.9418   -5.1173   -0.1531 C.3       1 HLCDN    0.0000
     37 H11         6.3684   -4.6895   -1.0670 H         1 HLCDN    0.0000
     38 O5          6.7354   -6.1592    0.3411 O.3       1 HLCDN    0.0000
     39 C23         4.5326   -5.6104   -0.5484 C.3       1 HLCDN    0.0000
     40 C24         3.8112   -4.4138   -1.1536 C.3       1 HLCDN    0.0000
     41 C25         3.8399   -3.1548   -0.3041 C.3       1 HLCDN    0.0000
     42 H12         3.1595   -3.2334    0.5393 H         1 HLCDN    0.0000
     43 O6          5.1667   -2.9045    0.1245 O.3       1 HLCDN    0.0000
     44 C26         3.4162   -1.9981   -1.2203 C.3       1 HLCDN    0.0000
     45 C27         2.7212   -0.8974   -0.4727 C.2       1 HLCDN    0.0000
     46 O7          3.0630   -0.5911    0.6450 O.2       1 HLCDN    0.0000
     47 O8          1.7118   -0.2657   -1.0830 O.3       1 HLCDN    0.0000
     48 C28         1.2468    1.0562   -0.7104 C.3       1 HLCDN    0.0000
     49 H13         2.1004    1.6938   -0.5147 H         1 HLCDN    0.0000
     50 C29         0.3627    0.9578    0.5365 C.3       1 HLCDN    0.0000
     51 H14        -0.4166    0.2138    0.3717 H         1 HLCDN    0.0000
     52 C30        -0.2835    2.3227    0.8177 C.3       1 HLCDN    0.0000
     53 H15         0.4947    3.0279    1.1380 H         1 HLCDN    0.0000
     54 C31        -0.9459    2.8286   -0.4593 C.3       1 HLCDN    0.0000
     55 H16        -0.3749    3.6839   -0.8445 H         1 HLCDN    0.0000
     56 C32        -2.3877    3.2526   -0.2738 C.3       1 HLCDN    0.0000
     57 C33        -2.7435    3.8458    1.0630 C.3       1 HLCDN    0.0000
     58 H17        -2.7223    4.9344    0.9843 H         1 HLCDN    0.0000
     59 C34        -1.7952    3.4326    2.1931 C.3       1 HLCDN    0.0000
     60 H18        -1.0437    4.1833    2.4198 H         1 HLCDN    0.0000
     61 O9         -1.2255    2.1589    1.8699 O.3       1 HLCDN    0.0000
     62 C35        -2.7782    3.1706    3.3815 C.3       1 HLCDN    0.0000
     63 C36        -3.9974    2.6516    2.6069 C.3       1 HLCDN    0.0000
     64 O10        -4.0767    3.4654    1.4296 O.3       1 HLCDN    0.0000
     65 C37        -3.7613    1.1774    2.2166 C.3       1 HLCDN    0.0000
     66 C38        -5.2239    0.6499    2.0711 C.3       1 HLCDN    0.0000
     67 H19        -5.3021   -0.4038    2.3571 H         1 HLCDN    0.0000
     68 C39        -5.9952    1.5505    3.0279 C.3       1 HLCDN    0.0000
     69 H20        -6.0591    0.9914    3.9722 H         1 HLCDN    0.0000
     70 O11        -5.2155    2.7066    3.3365 O.3       1 HLCDN    0.0000
     71 C40        -7.4167    1.8581    2.6489 C.3       1 HLCDN    0.0000
     72 H21        -8.0658    1.1061    3.0975 H         1 HLCDN    0.0000
     73 C41        -7.6658    1.8805    1.1537 C.3       1 HLCDN    0.0000
     74 C42        -6.9421    0.7110    0.4810 C.3       1 HLCDN    0.0000
     75 O12        -5.5490    0.8567    0.6992 O.3       1 HLCDN    0.0000
     76 C43        -7.2299    0.7684   -1.0257 C.3       1 HLCDN    0.0000
     77 C44        -6.4626   -0.3456   -1.7283 C.3       1 HLCDN    0.0000
     78 H22        -5.4059   -0.0800   -1.7604 H         1 HLCDN    0.0000
     79 C45        -6.6104   -1.6714   -1.0311 C.3       1 HLCDN    0.0000
     80 H23        -5.7580   -2.2877   -1.3176 H         1 HLCDN    0.0000
     81 C46        -6.6205   -1.5957    0.4963 C.3       1 HLCDN    0.0000
     82 H24        -5.6075   -1.5597    0.8965 H         1 HLCDN    0.0000
     83 O13        -7.4226   -0.5265    0.9878 O.3       1 HLCDN    0.0000
     84 C47        -7.3366   -2.9182    0.8900 C.3       1 HLCDN    0.0000
     85 C48        -8.0460   -3.3685   -0.3986 C.3       1 HLCDN    0.0000
     86 H25        -7.6546   -4.3348   -0.7167 H         1 HLCDN    0.0000
     87 O14        -7.7900   -2.3836   -1.4107 O.3       1 HLCDN    0.0000
     88 C49        -9.5518   -3.4763   -0.1501 C.3       1 HLCDN    0.0000
     89 H26        -9.7449   -4.2679    0.5739 H         1 HLCDN    0.0000
     90 C50       -10.2635   -3.8027   -1.4646 C.3       1 HLCDN    0.0000
     91 C51       -11.7518   -4.0333   -1.1951 C.3       1 HLCDN    0.0000
     92 H27       -11.8680   -4.8055   -0.4346 H         1 HLCDN    0.0000
     93 C52       -12.4405   -4.4811   -2.4859 C.3       1 HLCDN    0.0000
     94 O15       -13.8038   -4.8083   -2.2097 O.3       1 HLCDN    0.0000
     95 O16       -12.3465   -2.8182   -0.7349 O.3       1 HLCDN    0.0000
     96 O17       -10.0404   -2.2343    0.3605 O.3       1 HLCDN    0.0000
     97 C53        -6.9827   -0.4774   -3.1611 C.3       1 HLCDN    0.0000
     98 C54        -7.7887    3.2263    3.2240 C.3       1 HLCDN    0.0000
     99 O18        -0.9245    1.7838   -1.4414 O.3       1 HLCDN    0.0000
    100 C55         0.4136    1.5956   -1.8786 C.3       1 HLCDN    0.0000
    101 H28         0.3990    0.7934   -2.6479 H         1 HLCDN    0.0000
    102 C56         0.9944    2.8326   -2.5219 C.3       1 HLCDN    0.0000
    103 C57         1.7910    3.7151   -1.5735 C.3       1 HLCDN    0.0000
    104 H29         1.7587    3.3376   -0.5570 H         1 HLCDN    0.0000
    105 C58         1.1991    5.1085   -1.5860 C.2       1 HLCDN    0.0000
    106 C59         0.0368    5.3333   -2.1468 C.2       1 HLCDN    0.0000
    107 O19         3.1485    3.7810   -2.0182 O.3       1 HLCDN    0.0000
    108 C60         1.2172    0.5444    1.7364 C.3       1 HLCDN    0.0000
    109 H30         1.6418    7.5923   -2.5827 H         1 HLCDN    0.0000
    110 H31         0.4289    7.6963   -1.2840 H         1 HLCDN    0.0000
    111 H32         2.0529    8.3837   -1.0423 H         1 HLCDN    0.0000
    112 H33         3.6527    6.3576   -2.2858 H         1 HLCDN    0.0000
    113 H34         4.0490    6.6741   -0.5809 H         1 HLCDN    0.0000
    114 H35         5.5266    4.1410   -2.3633 H         1 HLCDN    0.0000
    115 H36         5.8460    5.4107   -1.1585 H         1 HLCDN    0.0000
    116 H37         6.2599    3.8846    0.5430 H         1 HLCDN    0.0000
    117 H38         5.2005    2.6425   -0.1699 H         1 HLCDN    0.0000
    118 H39         8.0239    5.3767   -0.8188 H         1 HLCDN    0.0000
    119 H40         9.6795    4.9574   -0.0556 H         1 HLCDN    0.0000
    120 H41        10.0838    2.0080   -0.8001 H         1 HLCDN    0.0000
    121 H42         9.7302    2.4100    0.9096 H         1 HLCDN    0.0000
    122 H43         9.5084    0.0062   -1.4745 H         1 HLCDN    0.0000
    123 H44         9.7078   -0.6135    0.1807 H         1 HLCDN    0.0000
    124 H45         6.9421   -0.9052   -0.6037 H         1 HLCDN    0.0000
    125 H46         7.9806   -1.6076   -1.8676 H         1 HLCDN    0.0000
    126 H47        10.3303   -2.4141   -0.4254 H         1 HLCDN    0.0000
    127 H48         9.9479   -1.9852    1.2780 H         1 HLCDN    0.0000
    128 H49         4.6095   -6.4115   -1.2835 H         1 HLCDN    0.0000
    129 H50         3.9983   -5.9617    0.3344 H         1 HLCDN    0.0000
    130 H51         4.2668   -4.1888   -2.1179 H         1 HLCDN    0.0000
    131 H52         2.7707   -4.6898   -1.3250 H         1 HLCDN    0.0000
    132 H53         4.3027   -1.5897   -1.7055 H         1 HLCDN    0.0000
    133 H54         2.7433   -2.3834   -1.9864 H         1 HLCDN    0.0000
    134 H55        -2.6265    3.9862   -1.0439 H         1 HLCDN    0.0000
    135 H56        -3.0206    2.3802   -0.4361 H         1 HLCDN    0.0000
    136 H57        -2.3870    2.4117    4.0590 H         1 HLCDN    0.0000
    137 H58        -3.0106    4.0930    3.9138 H         1 HLCDN    0.0000
    138 H59        -3.2241    1.1049    1.2710 H         1 HLCDN    0.0000
    139 H60        -3.2307    0.6446    3.0057 H         1 HLCDN    0.0000
    140 H61        -8.7362    1.7995    0.9646 H         1 HLCDN    0.0000
    141 H62        -7.2971    2.8192    0.7402 H         1 HLCDN    0.0000
    142 H63        -8.2985    0.6385   -1.1972 H         1 HLCDN    0.0000
    143 H64        -6.9129    1.7337   -1.4203 H         1 HLCDN    0.0000
    144 H65        -6.6091   -3.6660    1.2056 H         1 HLCDN    0.0000
    145 H66        -8.0636   -2.7368    1.6816 H         1 HLCDN    0.0000
    146 H67       -10.1446   -2.9706   -2.1585 H         1 HLCDN    0.0000
    147 H68        -9.8292   -4.7031   -1.8991 H         1 HLCDN    0.0000
    148 H69       -12.4015   -3.6740   -3.2174 H         1 HLCDN    0.0000
    149 H70       -11.9300   -5.3578   -2.8847 H         1 HLCDN    0.0000
    150 H71       -14.2001   -5.0848   -3.0473 H         1 HLCDN    0.0000
    151 H72       -12.2219   -2.1632   -1.4353 H         1 HLCDN    0.0000
    152 H73        -9.8502   -1.5628   -0.3088 H         1 HLCDN    0.0000
    153 H74        -6.8331    0.4638   -3.6901 H         1 HLCDN    0.0000
    154 H75        -6.4401   -1.2722   -3.6730 H         1 HLCDN    0.0000
    155 H76        -8.0457   -0.7179   -3.1411 H         1 HLCDN    0.0000
    156 H77        -7.1225    3.9857    2.8149 H         1 HLCDN    0.0000
    157 H78        -8.8185    3.4646    2.9576 H         1 HLCDN    0.0000
    158 H79        -7.6903    3.2031    4.3093 H         1 HLCDN    0.0000
    159 H80         1.6472    2.5242   -3.3386 H         1 HLCDN    0.0000
    160 H81         0.1779    3.4217   -2.9395 H         1 HLCDN    0.0000
    161 H82        -0.5698    4.5054   -2.4829 H         1 HLCDN    0.0000
    162 H83        -0.3149    6.3467   -2.2730 H         1 HLCDN    0.0000
    163 H84         2.1450    1.1165    1.7361 H         1 HLCDN    0.0000
    164 H85         0.6692    0.7412    2.6578 H         1 HLCDN    0.0000
    165 H86         1.4463   -0.5192    1.6700 H         1 HLCDN    0.0000
@<TRIPOS>BOND
     1    1    2 1
     2    2    3 1
     3    2    4 1
     4    4    5 1
     5    5    6 1
     6    5    7 1
     7    7    8 1
     8    8    9 1
     9    9   10 1
    10    9   11 1
    11   11   12 2
    12   11   13 1
    13   13   14 1
    14   14   15 1
    15   14   16 1
    16    9   16 1
    17   14   17 1
    18   17   18 1
    19   18   19 1
    20   19   20 1
    21   20   21 1
    22   21   22 1
    23   21   23 1
    24   23   24 1
    25   23   25 1
    26   19   25 1
    27   23   26 1
    28   26   27 1
    29   26   28 1
    30   28   29 1
    31   28   30 1
    32   21   30 1
    33   28   31 1
    34   31   32 1
    35   31   33 1
    36   19   33 1
    37   31   34 1
    38   34   35 1
    39   34   36 1
    40   36   37 1
    41   36   38 1
    42   26   38 1
    43   36   39 1
    44   39   40 1
    45   40   41 1
    46   41   42 1
    47   41   43 1
    48   34   43 1
    49   41   44 1
    50   44   45 1
    51   45   46 2
    52   45   47 1
    53   47   48 1
    54   48   49 1
    55   48   50 1
    56   50   51 1
    57   50   52 1
    58   52   53 1
    59   52   54 1
    60   54   55 1
    61   54   56 1
    62   56   57 1
    63   57   58 1
    64   57   59 1
    65   59   60 1
    66   59   61 1
    67   52   61 1
    68   59   62 1
    69   62   63 1
    70   63   64 1
    71   57   64 1
    72   63   65 1
    73   65   66 1
    74   66   67 1
    75   66   68 1
    76   68   69 1
    77   68   70 1
    78   63   70 1
    79   68   71 1
    80   71   72 1
    81   71   73 1
    82   73   74 1
    83   74   75 1
    84   66   75 1
    85   74   76 1
    86   76   77 1
    87   77   78 1
    88   77   79 1
    89   79   80 1
    90   79   81 1
    91   81   82 1
    92   81   83 1
    93   74   83 1
    94   81   84 1
    95   84   85 1
    96   85   86 1
    97   85   87 1
    98   79   87 1
    99   85   88 1
   100   88   89 1
   101   88   90 1
   102   90   91 1
   103   91   92 1
   104   91   93 1
   105   93   94 1
   106   91   95 1
   107   88   96 1
   108   77   97 1
   109   71   98 1
   110   54   99 1
   111   99  100 1
   112  100  101 1
   113   48  100 1
   114  100  102 1
   115  102  103 1
   116  103  104 1
   117  103  105 1
   118    2  105 1
   119  105  106 2
   120  103  107 1
   121    5  107 1
   122   50  108 1
   123    1  109 1
   124    1  110 1
   125    1  111 1
   126    4  112 1
   127    4  113 1
   128    7  114 1
   129    7  115 1
   130    8  116 1
   131    8  117 1
   132   12  118 1
   133   12  119 1
   134   13  120 1
   135   13  121 1
   136   17  122 1
   137   17  123 1
   138   18  124 1
   139   18  125 1
   140   20  126 1
   141   20  127 1
   142   39  128 1
   143   39  129 1
   144   40  130 1
   145   40  131 1
   146   44  132 1
   147   44  133 1
   148   56  134 1
   149   56  135 1
   150   62  136 1
   151   62  137 1
   152   65  138 1
   153   65  139 1
   154   73  140 1
   155   73  141 1
   156   76  142 1
   157   76  143 1
   158   84  144 1
   159   84  145 1
   160   90  146 1
   161   90  147 1
   162   93  148 1
   163   93  149 1
   164   94  150 1
   165   95  151 1
   166   96  152 1
   167   97  153 1
   168   97  154 1
   169   97  155 1
   170   98  156 1
   171   98  157 1
   172   98  158 1
   173  102  159 1
   174  102  160 1
   175  106  161 1
   176  106  162 1
   177  108  163 1
   178  108  164 1
   179  108  165 1
@<TRIPOS>SUBSTRUCTURE
     1 HLCDN     1 RESIDUE           4 A     HLCDN     0 ROOT

```
</details>


resNum trueとすることで残機番号を入れられる。

## 終わりに

いかがでしょうか、chimeraxはpymolよりも遥かに高機能で素晴らしいViewerです（思想強）

ただ、高機能すぎて全部を把握するのは少し難しいところはありますので、色々いじくりながら感覚で身につけていきましょう！！

わからない時はUser guideをChat-GPTに投げて訊いたりするのもありです！！