Shape sorting of two distinct amino acid residues at the multiple binding sites of a porous metal-macrocycle framework.
Tashiro, Shohei; Nakata, Kosuke; Hayashi, Ryunosuke; Shionoya, Mitsuhiko; Chemical science 16 (2025) 12303–12308; doi:10.1039/d5sc00795j

data_1574777
_publ_section_title
;
 Shape sorting of two distinct amino acid residues at the multiple binding
 sites of a porous metal-macrocycle framework.
;
_journal_issue                   27
_journal_name_full               'Chemical science'
_journal_page_first              12303
_journal_page_last               12308
_journal_paper_doi               10.1039/d5sc00795j
_journal_volume                  16
_journal_year                    2025
_chemical_absolute_configuration rmad
_chemical_formula_moiety
'4(C42 H42 Cl6 N6 Pd3), 2.25(O), 3(C2 H3 N), 0.931(C12 H10 N2 O), 0.554(C9 H6 N)'
_chemical_formula_sum            'C190.16 H189.64 Cl24 N29.41 O3.18 Pd12'
_chemical_formula_weight         5065.61
_space_group_crystal_system      monoclinic
_space_group_IT_number           4
_space_group_name_Hall           'P 2yb'
_space_group_name_H-M_alt        'P 1 21 1'
_atom_sites_solution_hydrogens   geom
_audit_creation_date             2022-11-18
_audit_creation_method
;
Olex2 1.5
(compiled 2022.04.07 svn.rca3783a0 for OlexSys, GUI svn.r6498)
;
_audit_update_record
;
2025-05-22 deposited with the CCDC.	2025-06-02 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 91.2660(10)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   14.31918(16)
_cell_length_b                   51.9317(8)
_cell_length_c                   19.4811(2)
_cell_measurement_reflns_used    49702
_cell_measurement_temperature    93
_cell_measurement_theta_max      27.3060
_cell_measurement_theta_min      1.8340
_cell_volume                     14483.0(3)
_computing_cell_refinement       'CrysAlisPro 1.171.39.9g (Rigaku Oxford, 2015)'
_computing_data_collection       'CrysAlisPro 1.171.39.9g (Rigaku Oxford, 2015)'
_computing_data_reduction        'CrysAlisPro 1.171.39.9g (Rigaku Oxford, 2015)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXS Version 2013/1 (Sheldrick, 2008)'
_diffrn_ambient_temperature      93
_diffrn_measured_fraction_theta_full 0.998
_diffrn_measured_fraction_theta_max 0.943
_diffrn_measurement_device_type  'XtaLAB AFC12 (RINC): Kappa single'
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71075
_diffrn_reflns_av_R_equivalents  0.0277
_diffrn_reflns_av_unetI/netI     0.0406
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.943
_diffrn_reflns_limit_h_max       18
_diffrn_reflns_limit_h_min       -18
_diffrn_reflns_limit_k_max       65
_diffrn_reflns_limit_k_min       -67
_diffrn_reflns_limit_l_max       25
_diffrn_reflns_limit_l_min       -24
_diffrn_reflns_number            98802
_diffrn_reflns_point_group_measured_fraction_full 0.839
_diffrn_reflns_point_group_measured_fraction_max 0.764
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         27.617
_diffrn_reflns_theta_min         1.846
_exptl_absorpt_coefficient_mu    0.988
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.66393
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.39.9g (Rigaku Oxford Diffraction, 2015)

Empirical absorption correction using spherical harmonics,

 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            yellow
_exptl_crystal_colour_primary    yellow
_exptl_crystal_density_diffrn    1.162
_exptl_crystal_description       plate
_exptl_crystal_F_000             5044
_exptl_crystal_size_max          0.433
_exptl_crystal_size_mid          0.227
_exptl_crystal_size_min          0.108
_refine_diff_density_max         3.776
_refine_diff_density_min         -2.661
_refine_diff_density_rms         0.195
_refine_ls_abs_structure_details
;
 Refined as an inversion twin.
;
_refine_ls_abs_structure_Flack   0.16(4)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.229
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     2297
_refine_ls_number_reflns         51423
_refine_ls_number_restraints     1312
_refine_ls_restrained_S_all      1.236
_refine_ls_R_factor_all          0.1058
_refine_ls_R_factor_gt           0.0959
_refine_ls_shift/su_max          0.004
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.2000P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2813
_refine_ls_wR_factor_ref         0.2901
_reflns_Friedel_coverage         0.603
_reflns_Friedel_fraction_full    0.676
_reflns_Friedel_fraction_max     0.581
_reflns_number_gt                42897
_reflns_number_total             51423
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5sc00795j2.cif
_cod_data_source_block           Z-Trp@MMF
_cod_depositor_comments
'Adding full bibliography for 1574776--1574779.cif.'
_cod_database_code               1574777
_shelx_shelxl_version_number     2018/3
_olex2_refinement_description
;
1. Twinned data refinement
 Scales: 0.84(4)
 0.16(4)
2. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All N(H) groups
 At 1.5 times of:
  All C(H,H,H) groups
3. Restrained distances
 N11-C71 = N12-C76 = N21-C141 = N22-C146 = N23-C155 = N24-C160
 1.5 with sigma of 0.02
 C67-C70
 1.5 with sigma of 0.02
 N10-C62 = N9-C57
 1.5 with sigma of 0.02
 C9A-C10A
 1.5 with sigma of 0.02
 C10A-C11A
 1.5 with sigma of 0.02
 C2A-C9A
 1.5 with sigma of 0.02
 C77-N12
 1.5 with sigma of 0.02
 C10A-N2A
 1.5 with sigma of 0.02
 C12A-O1A
 1.5 with sigma of 0.02
 C154-N23
 1.5 with sigma of 0.02
 N22-C147
 1.5 with sigma of 0.02
 C154-C151
 1.5 with sigma of 0.02
 C147-C148
 1.5 with sigma of 0.02
 C7S-C8S
 1.45 with sigma of 0.02
 N4S-C7S
 1.15 with sigma of 0.02
 C70-N11
 1.5 with sigma of 0.02
4. Uiso/Uaniso restraints and constraints
C99 \\sim C100 \\sim C101 \\sim C102 \\sim C103 \\sim C104: within 1.7A with
sigma of 0.01 and sigma for terminal atoms of 0.02 within 1.7A
Cl23 \\sim Pd12 \\sim Cl24: within 1.7A with sigma of 0.02 and sigma for
terminal atoms of 0.04 within 1.7A
C77 \\sim C78: within 1.7A with sigma of 0.02 and sigma for terminal atoms of
0.04 within 1.7A
C62 \\sim C57 \\sim C58 \\sim C59 \\sim C60 \\sim C61: within 1.7A with sigma
of 0.01 and sigma for terminal atoms of 0.02 within 1.7A
C73 \\sim C74 \\sim C75 \\sim C76 \\sim C72 \\sim C71 \\sim N12 \\sim N11 \\sim
Pd6 \\sim Cl11 \\sim Cl12 \\sim C70 \\sim C77: within 1.7A with sigma of 0.005
and sigma for terminal atoms of 0.01 within 1.7A
C160 \\sim C155 \\sim C156 \\sim C157 \\sim C158 \\sim C159 \\sim N23 \\sim N24
\\sim C154 \\sim C153 \\sim C148 \\sim C149 \\sim C150 \\sim C151 \\sim C152:
within 1.7A with sigma of 0.01 and sigma for terminal atoms of 0.02 within 1.7A
C9B \\sim C2B \\sim C1B \\sim N1B \\sim C8B \\sim C3B \\sim C4B \\sim C5B \\sim
C6B \\sim C7B: within 1.7A with sigma of 0.02 and sigma for terminal atoms of
0.04 within 1.7A
C6S \\sim C5S \\sim N3S: within 1.7A with sigma of 0.02 and sigma for terminal
atoms of 0.04 within 1.7A
N4S \\sim C7S \\sim C8S: within 1.7A with sigma of 0.02 and sigma for terminal
atoms of 0.04 within 1.7A
C162 \\sim C167 \\sim C166 \\sim C165 \\sim C164 \\sim C163: within 1.7A with
sigma of 0.02 and sigma for terminal atoms of 0.04 within 1.7A
Uanis(C15) \\sim Ueq, Uanis(C20) \\sim Ueq: with sigma of 0.01 and sigma for
terminal atoms of 0.02
Uanis(Cl23) \\sim Ueq: with sigma of 0.02 and sigma for terminal atoms of 0.04
Uanis(C62) \\sim Ueq: with sigma of 0.005 and sigma for terminal atoms of 0.01
Uanis(C9A) \\sim Ueq, Uanis(C10A) \\sim Ueq, Uanis(N2A) \\sim Ueq, Uanis(C11A)
\\sim Ueq, Uanis(C12A) \\sim Ueq, Uanis(O1A) \\sim Ueq: with sigma of 0.01 and
sigma for terminal atoms of 0.02
Uanis(N23) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C146) \\sim Ueq: with sigma of 0.005 and sigma for terminal atoms of 0.01
Uanis(Cl11) \\sim Ueq: with sigma of 0.02 and sigma for terminal atoms of 0.04
Uanis(C8) \\sim Ueq: with sigma of 0.005 and sigma for terminal atoms of 0.01
Uanis(C104) \\sim Ueq: with sigma of 0.005 and sigma for terminal atoms of 0.01
Uanis(C35) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C84) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C89) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C165) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
5. Rigid body (RIGU) restrains
 C67, C66, C65, C64, C69, C68, C63
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 N9, N10, C57, C62, C61, C60, C59, C58, C63
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 N16, C104, C103, C102, C101, C100, C99, N15
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 C82, C81, C80, C84
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 C83, C78, C79
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 C77, C78
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 Pd12, Cl23, Cl24
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 C5A, C6A, C7A, C8A, C3A, C4A, C2A, C1A, N1A
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 C73, C74, C75, C76, C71, C72, N11, N12, Pd6, Cl11, Cl12, C70, C77
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 C160, C155, C156, C157, C158, C159, N23, N24, C154, C153, C148, C149, C150,
 C151, C152
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 C9A, C10A, C11A, N2A, O1A, C12A
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 C146, C141, C142, C143, C144, C145, N22, N21, C147, C140
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 C9A, C2A
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 C164, C165, C166
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 C163, C162, C167, C161
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 C9B, C2B, C1B, N1B, C8B, C3B, C4B, C5B, C6B, C7B
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 N4S, C7S, C8S
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 C6S, C5S, N3S
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 C81, C82, C83, C78, C79, C80
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C128, C127, C132, C131, C130, C129
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 C107, C108, C109, C110, C111, C106
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
6. Others
 Sof(C1A)=Sof(H1A)=Sof(C2A)=Sof(C3A)=Sof(C8A)=Sof(C7A)=Sof(H7AA)=Sof(C6A)=
 Sof(H6A)=Sof(C5A)=Sof(H5AA)=Sof(C4A)=Sof(H4AA)=Sof(C9A)=Sof(H9AA)=Sof(H9AB)=
 Sof(C10A)=Sof(H10D)=Sof(O1A)=Sof(N1A)=Sof(H1AA)=Sof(N2A)=Sof(H2AA)=Sof(C12A)=
 Sof(C11A)=FVAR(1)
 Sof(C1B)=Sof(H1B)=Sof(C2B)=Sof(C3B)=Sof(C4B)=Sof(H4B)=Sof(C5B)=Sof(H5B)=
 Sof(C6B)=Sof(H6B)=Sof(C7B)=Sof(H7BA)=Sof(C8B)=Sof(C9B)=Sof(N1B)=Sof(H1BA)=
 FVAR(2)
 Fixed Sof: O1W(0.75) O3W(0.5) C8S(0.5) H8SA(0.5) H8SB(0.5) H8SC(0.5) C7S(0.5)
 N4S(0.5) N3S(0.5) O4W(0.5) C6S(0.5) H6SA(0.5) H6SB(0.5) H6SC(0.5) C5S(0.5)
 O2W(0.5)
7.a Ternary CH refined with riding coordinates:
 N2(H2), N1(H1), N6(H6), N5(H5), N4(H4), N3(H3), N7(H7), N8(H8), N9(H9A),
 N10(H10A), N11(H11), N12(H12A), N14(H14), N13(H13A), N18(H18A), N17(H17A),
 N16(H16A), N15(H15), N19(H19A), N20(H20), N21(H21), N22(H22), N23(H23A),
 N24(H24A), C10A(H10D)
7.b Secondary CH2 refined with riding coordinates:
 C42(H42A,H42B), C35(H35A,H35B), C28(H28A,H28B), C21(H21A,H21B), C14(H14A,
 H14B), C7(H7A,H7B), C49(H49A,H49B), C56(H56A,H56B), C63(H63A,H63B), C70(H70A,
 H70B), C77(H77A,H77B), C84(H84A,H84B), C126(H12B,H12C), C119(H11A,H11B),
 C112(H11C,H11D), C105(H10B,H10C), C98(H98A,H98B), C91(H91A,H91B), C133(H13B,
 H13C), C140(H14C,H14D), C147(H14E,H14F), C154(H15A,H15B), C161(H16B,H16C),
 C168(H16D,H16E), C9A(H9AA,H9AB)
7.c Aromatic/amide H refined with riding coordinates:
 C5(H5A), C4(H4A), C3(H3A), C2(H2A), C38(H38), C40(H40), C41(H41), C37(H37),
 C33(H33), C32(H32), C31(H31), C30(H30), C23(H23), C24(H24), C26(H26), C27(H27),
  C16(H16), C17(H17), C18(H18), C19(H19), C10(H10), C12(H12), C13(H13), C9(H9),
 C44(H44), C45(H45), C46(H46), C47(H47), C51(H51), C55(H55), C54(H54), C52(H52),
  C61(H61), C60(H60), C59(H59), C58(H58), C66(H66), C65(H65), C69(H69),
 C68(H68), C75(H75), C74(H74), C73(H73), C72(H72), C79(H79), C80(H80), C82(H82),
  C83(H83), C89(H89), C88(H88), C87(H87), C86(H86), C124(H124), C122(H122),
 C121(H121), C125(H125), C117(H117), C116(H116), C115(H115), C114(H114),
 C110(H110), C108(H108), C107(H107), C111(H111), C103(H103), C102(H102),
 C101(H101), C100(H100), C96(H96), C94(H94), C93(H93), C97(H97), C128(H128),
 C129(H129), C130(H130), C131(H131), C139(H139), C135(H135), C136(H136),
 C138(H138), C145(H145), C144(H144), C143(H143), C142(H142), C150(H150),
 C149(H149), C153(H153), C152(H152), C159(H159), C158(H158), C157(H157),
 C156(H156), C166(H166), C167(H167), C163(H163), C164(H164), C1A(H1A),
 C7A(H7AA), C6A(H6A), C5A(H5AA), C4A(H4AA), N1A(H1AA), N2A(H2AA), C1B(H1B),
 C4B(H4B), C5B(H5B), C6B(H6B), C7B(H7BA), N1B(H1BA)
7.d Fitted hexagon refined as free rotating group:
 C15(C16,C17,C18,C19,C20), C62(C61,C60,C59,C58,C57), C67(C66,C65,C64,C69,C68),
 C76(C75,C74,C73,C72,C71), C79(C80,C81,C82,C83,C78), C146(C145,C144,C143,C142,
 C141), C151(C150,C149,C148,C153,C152), C160(C159,C158,C157,C156,C155),
 C165(C166,C167,C162,C163,C164), C3A(C8A,C7A,C6A,C5A,C4A), C3B(C4B,C5B,C6B,C7B,
 C8B)
7.e Idealised Me refined as rotating group:
 C8S(H8SA,H8SB,H8SC), C4S(H4SA,H4SB,H4SC), C2S(H2SA,H2SB,H2SC), C6S(H6SA,H6SB,
 H6SC)
;
_shelx_res_checksum              20996
_olex2_submission_special_instructions 'No special instructions were received'