東京大学 生産技術研究所
北條 博彦

化学生命工学専攻

有機機能材料学特論II

分子構造の表現法
原子位置のデータ・デカルト座標系
・分率座標系
・内部座標系

分子構造の描画・wireframe（線画）・ball&stick（豆細工模型, boll&stickとも）
・CPK（Corey-Pauling-Kultun）
・ORTEP・helix, sheet, ribbon

http://wiki.jmol.org/index.php/Main_Page

Jmol version 13.0.10
74 77 0 0 0 00.166240.190311.150730.85579-0.94451 -0.51277-0.25988
0.93999
0.71619 -0.49904
1.67797
0.08506
0.42335
1.81508
2.123071.57098-0.66651
1.09068-0.00207
2.65385
1.14206
2.27163-0.16902
0.38735-1.69556
0.31440-1.18052
1.82397-2.60598
1.32680-2.53141 -0.62780-3.42921
0.11439-1.80410 -1.17990-3.30201 -1.70732-2.30864 -2.57695-3.97765 -1.23107-1.83380 -3.31760-1.22325 -1.80479-2.85689 -3.14439-0.64113 -2.34629
2.79031
1.90191-2.04699
1.95231-3.09639
2.01700-3.38612
0.82406-4.07655
0.83430-2.79841
0.69891-4.30522 -0.81860-3.65933 -1.39028-5.13978 -1.77630-4.93644 -0.18755-4.10899 -2.56685

2012-12-08 14:54 EXTRACT: ({0:73})
1 V2000-0.18677 C
0 0 0 0 0 00.77290 C
0 0 0 0 0 00.55997 C
0 0 0 0 0 0-0.86836 H
0 0 0 0 0 0-0.83499 H
0 0 0 0 0 01.35514 H
0 0 0 0 0 01.70870 C
0 0 0 0 0 00.01874 O
0 0 0 0 0 02.49679 C
0 0 0 0 0 01.13814 H
0 0 0 0 0 02.40334 H
0 0 0 0 0 03.18376 H
0 0 0 0 0 01.61658 C0 0 0 0 0 03.12643 H
0 0 0 0 0 00.87993 C
0 0 0 0 0 02.56237 C
0 0 0 0 0 03.58436 C
0 0 0 0 0 03.17458 H
0 0 0 0 0 01.75629 C
0 0 0 0 0 00.96903 C
0 0 0 0 0 01.03965 H
0 0 0 0 0 01.62879 H
0 0 0 0 0 00.29921 C
0 0 0 0 0 00.20453 H
0 0 0 0 0 0-0.44051 H
0 0 0 0 0 00.64986 H
0 0 0 0 0 00.18054 H
0 0 0 0 0 01.57865 H
0 0 0 0 0 00.30237 H
0 0 0 0 0 03.08368 H
0 0 0 0 0 04.26780 H
0 0 0 0 0 04.44020 C
0 0 0 0 0 05.12324 H
0 0 0 0 0 03.57388 C
0 0 0 0 0 05.07210 H
0 0 0 0 0 02.73260 C
0 0 0 0 0 0-4.19756 -4.64357-7.88084 -2.19029-6.90912 -1.72471-7.86818 -3.94331-6.72357 -0.70906-6.05733 -2.05133-7.78173 -1.65081-7.15472 -4.48005-8.53214 -4.96055-8.66634 -3.59589-7.77455 -5.57975-9.48791 -4.35929-9.10247 -5.65866-9.04241 -3.49568-10.37138 -3.97718-9.95751 -5.34142-10.59882 -6.60639-8.83974 -5.69540-10.73051 -4.81554-11.41067 -6.35597-9.87040 -7.22784-11.02185 -7.21286-8.02323 -6.24164-8.42683 -4.79672-9.22345 -6.33253-3.37467 -2.99540
1 2 1 0 0 0
1 3 1 0 0 0
1 4 1 0 0 0
1 5 1 0 0 0
6 2 1 0 0 0
7 2 1 0 0 0
8 2 1 0 0 0
9 7 1 0 0 0
10 7 1 0 0 0
11 7 1 0 0 0
12 9 1 0 0 02.14685 H
4.43067 H
6.26315 C
5.68874 C
5.90584 H
6.87325 H
6.91869 H
6.32457 H
4.74667 C
6.36472 H
4.27165 H
3.70825 C
5.37947 H
3.21198 H
4.24009 H
2.61477 C
3.17382 C
1.63181 C
2.03455 H
3.86741 H
3.71008 H
2.37036 H
2.11983 H
1.16751 H
0.82520 H
3.44034 H

000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
0
00
000

http://www.ccdc.cam.ac.uk/pages/Home.aspx

O1 O 0.5320(3) -0.0258(2) 0.41626(13) 0.0611(7) Uani 1 1 d . . .
C1 C 0.5619(4) 0.0157(3) 0.3576(2) 0.0541(9) Uani 1 1 d . . .
H1 H 0.6038 -0.0310 0.3233 0.065 Uiso 1 1 calc R . .
C2 C 0.5387(3) 0.1282(3) 0.33712(17) 0.0405(7) Uani 1 1 d . . .
C3 C 0.4779(3) 0.2041(2) 0.38497(16) 0.0358(6) Uani 1 1 d . . .
O2 O 0.4365(2) 0.17240(19) 0.45170(11) 0.0428(5) Uani 1 1 d . . .
H2 H 0.457(3) 0.099(3) 0.4569(18) 0.037(9) Uiso 1 1 d . . .
C4 C 0.4594(3) 0.3129(2) 0.36492(15) 0.0339(6) Uani 1 1 d . . .
O3 O 0.4050(2) 0.38488(17) 0.41346(11) 0.0394(5) Uani 1 1 d . . .
H3 H 0.332(5) 0.430(4) 0.388(2) 0.075(13) Uiso 1 1 d . . .
C5 C 0.5003(3) 0.3522(2) 0.29604(15) 0.0326(6) Uani 1 1 d . . .
O4 O 0.4860(2) 0.45444(17) 0.27914(11) 0.0394(5) Uani 1 1 d . . .
C6 C 0.5578(3) 0.2736(2) 0.24724(15) 0.0353(6) Uani 1 1 d . . .
C7 C 0.6044(3) 0.3121(3) 0.17510(16) 0.0370(7) Uani 1 1 d . . .
H4 H 0.6640 0.2545 0.1543 0.044 Uiso 1 1 calc R . .
H5 H 0.6619 0.3793 0.1823 0.044 Uiso 1 1 calc R . .
N1 N 0.4847(3) 0.3372(2) 0.12138(13) 0.0367(6) Uani 1 1 d . . .
H6 H 0.429(5) 0.401(4) 0.137(2) 0.073(13) Uiso 1 1 d . . .
C8 C 0.5405(4) 0.3726(3) 0.05131(18) 0.0525(9) Uani 1 1 d . . .
H7 H 0.5953 0.3126 0.0312 0.079 Uiso 1 1 calc R . .
H8 H 0.6003 0.4375 0.0593 0.079 Uiso 1 1 calc R . .
H9 H 0.4630 0.3914 0.0170 0.079 Uiso 1 1 calc R . .
C9 C 0.3909(4) 0.2415(3) 0.1100(2) 0.0490(8) Uani 1 1 d . . .
H10 H 0.3173 0.2600 0.0734 0.073 Uiso 1 1 calc R . .
H11 H 0.3487 0.2227 0.1559 0.073 Uiso 1 1 calc R . .
H12 H 0.4445 0.1784 0.0931 0.073 Uiso 1 1 calc R . .
C10 C 0.5748(3) 0.1657(3) 0.26838(17) 0.0405(7) Uani 1 1 d . . .
H13 H 0.6122 0.1146 0.2352 0.049 Uiso 1 1 calc R . .
O5 O 0.5535(3) 0.9894(2) 0.10181(18) 0.0672(8) Uani 1 1 d . . .
C11 C 0.4397(4) 0.9455(3) 0.0863(2) 0.0548(9) Uani 1 1 d . . .
H14 H 0.3694 0.9906 0.0636 0.066 Uiso 1 1 calc R . .
C12 C 0.4049(3) 0.8332(3) 0.09946(18) 0.0411(7) Uani 1 1 d . . .
C13 C 0.5014(3) 0.7595(3) 0.13255(17) 0.0390(7) Uani 1 1 d . . .
O6 O 0.6325(2) 0.7938(2) 0.15250(14) 0.0499(6) Uani 1 1 d . . .
H15 H 0.640(4) 0.869(4) 0.139(2) 0.057(11) Uiso 1 1 d . . .
C14 C 0.4666(3) 0.6513(2) 0.14435(16) 0.0346(6) Uani 1 1 d . . .

http://www.rcsb.org/pdb/home/home.doATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOMATOMATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM

123456789101112131415161718192021222324252627282930313233343536373839404142N
TYR C
CA TYR C
C
TYR C
O
TYR C
CB TYR C
CG TYR C
CD1 TYR C
CD2 TYR C
CE1 TYR C
CE2 TYR CCZ TYR C
OH TYR CN
VAL C
CA VAL C
C
VAL C
O
VAL C
CB VAL C
CG1 VAL C
CG2 VAL CN
ALA C
CA ALA C
C
ALA C
O
ALA C
CB ALA C
NPRO CCA PRO C
CPRO C
OPRO CCB PRO CCG PRO C
CD PRO CN
THR C
CA THR C
C
THR C
O
THR C
CB THR C
OG1 THR C
CG2 THR CN
ASN C
CA ASN C
C
ASN C
O
ASN C

8888888888889999999101010
101011
111111111111
121212121212
12
13
13
13
13

28.28928.62330.12130.69427.79028.24827.84729.11128.29129.56029.14529.61030.73532.12232.20031.84633.06934.51932.88832.68932.74733.79434.74033.11333.62734.65336.00636.06034.08532.59932.33137.07538.43739.33140.49939.11139.29838.25538.80439.57038.63937.41816.43717.14917.46318.04518.43719.34819.13620.42419.96721.25821.03321.851
17.11417.47718.21517.68016.23516.65615.41919.45620.28019.68019.07021.72119.83019.39220.06621.26119.78419.79520.07119.30019.72919.881
20.25718.70517.46718.46419.571
19.69719.80819.67330.73629.47229.37430.29529.35128.23326.91528.49725.88927.48626.18925.19528.24627.97626.64825.59927.96627.78729.23926.68525.47924.56225.05925.82923.23122.28922.51122.86420.931
21.11622.56822.29922.61021.37321.49223.54322.84324.781
20.19518.94617.74817.8901.00 30.26
1.00 29.23
1.00 29.62
1.00 29.96
1.00 28.95
1.00 29.23
1.00 29.00
1.00 30.57
1.00 30.24
1.00 30.01
1.00 31.07
1.00 31.72
1.00 26.60
1.00 25.73
1.00 24.69
1.00 21.62
1.00 25.06
1.00 25.50
1.00 24.57
1.00 24.40
1.00 23.79
1.00 23.36
1.00 25.68
1.00 23.10
1.00 22.26
1.00 23.32
1.00 28.69
1.00 29.11
1.00 22.13
1.00 22.12
1.00 21.91
1.00 30.16
1.00 33.54
1.00 33.71
1.00 37.27
1.00 33.92
1.00 33.13
1.00 34.27
1.00 34.37
1.00 33.47
1.00 33.33
1.00 32.23

N
C
C
O
C
C
C
C
C
C
C
O
N
C
C
O
C
C
C
N
C
C
O
C
N
C
C
O
C
C
C
N
C
C
O
C
O
C
N
C
C
O

Gaussianの使い方%chk=default#N HF/6-311G**
comments
0 2H入力ファイル%chk=default

チェックポイントファイルの指定#N HF/6-311G**
comments

出力フォーマット（Normal, Print, Terse）
Hartree-Fock法,6-311G**基底関数
コメント

0 2H

電荷、スピン多重度
元素記号分子構造の情報
XYZ座標で指定
water molecule

内部参照座標（Zマトリクス）で指定

0 1
O -0.464 0.177 0.0
H -0.464 1.137 0.0
H 0.441 -0.143 0.0

0 1O
H 1 r2
H 1 r3water moleculer2 1.0r3 1.0
a3 104.5

2 a3