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_1574779
_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
'1.122(C11 H11 N O5), 0.374(C8 H6 N), 0.504(C13 H10 N2 O4), 4(C42 H42 Cl6 N6 Pd3), 5.126(C2 H3 N), 2.998(O)'
_chemical_formula_sum            'C200.14 H203.01 Cl24 N31.63 O10.62 Pd12'
_chemical_formula_weight         5349.03
_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             2022-11-21
_audit_creation_method
;
Olex2 1.5
(compiled 2022.04.07 svn.rca3783a0 for OlexSys, GUI svn.r6498)
;
_audit_update_record
;
2025-04-01 deposited with the CCDC.	2025-06-02 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 91.2340(10)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   14.3191(3)
_cell_length_b                   52.5328(10)
_cell_length_c                   19.6294(4)
_cell_measurement_reflns_used    95028
_cell_measurement_temperature    93(2)
_cell_measurement_theta_max      27.53
_cell_measurement_theta_min      3.05
_cell_volume                     14762.3(5)
_computing_cell_refinement       'RAPID AUTO'
_computing_data_collection       'RAPID AUTO'
_computing_data_reduction        'RAPID AUTO'
_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 2013/1 (Sheldrick, 2008)'
_diffrn_ambient_temperature      93.15
_diffrn_measured_fraction_theta_full 0.997
_diffrn_measured_fraction_theta_max 0.998
_diffrn_measurement_device_type  RAPID
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71075
_diffrn_reflns_av_R_equivalents  0.0455
_diffrn_reflns_av_unetI/netI     0.0634
_diffrn_reflns_Laue_measured_fraction_full 0.997
_diffrn_reflns_Laue_measured_fraction_max 0.998
_diffrn_reflns_limit_h_max       17
_diffrn_reflns_limit_h_min       -18
_diffrn_reflns_limit_k_max       68
_diffrn_reflns_limit_k_min       -66
_diffrn_reflns_limit_l_max       25
_diffrn_reflns_limit_l_min       -25
_diffrn_reflns_number            143503
_diffrn_reflns_point_group_measured_fraction_full 0.992
_diffrn_reflns_point_group_measured_fraction_max 0.988
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         27.486
_diffrn_reflns_theta_min         3.050
_exptl_absorpt_coefficient_mu    0.975
_exptl_absorpt_correction_T_max  1.0000
_exptl_absorpt_correction_T_min  0.5801
_exptl_absorpt_correction_type   multi-scan
_exptl_crystal_colour            yellow
_exptl_crystal_colour_primary    yellow
_exptl_crystal_density_diffrn    1.203
_exptl_crystal_description       plate
_exptl_crystal_F_000             5341
_exptl_crystal_size_max          0.42
_exptl_crystal_size_mid          0.24
_exptl_crystal_size_min          0.06
_refine_diff_density_max         2.683
_refine_diff_density_min         -2.667
_refine_diff_density_rms         0.145
_refine_ls_abs_structure_details
;
 Refined as an inversion twin.
;
_refine_ls_abs_structure_Flack   0.17(4)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.031
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     2490
_refine_ls_number_reflns         66960
_refine_ls_number_restraints     1779
_refine_ls_restrained_S_all      1.033
_refine_ls_R_factor_all          0.0964
_refine_ls_R_factor_gt           0.0702
_refine_ls_shift/su_max          0.003
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.1340P)^2^+16.5433P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2014
_refine_ls_wR_factor_ref         0.2229
_reflns_Friedel_coverage         0.959
_reflns_Friedel_fraction_full    0.987
_reflns_Friedel_fraction_max     0.979
_reflns_number_gt                48504
_reflns_number_total             66960
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5sc00795j2.cif
_cod_data_source_block           Z-Trp-Z-Ser@MMF
_cod_depositor_comments
'Adding full bibliography for 1574776--1574779.cif.'
_cod_database_code               1574779
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.944
_shelx_estimated_absorpt_t_min   0.685
_olex2_refinement_description
;
1. Twinned data refinement
 Scales: 0.83(4)
 0.17(4)
2. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, {H2SA,H2SB,H2SC} of C2S, {H6SA,H6SB,H6SC} of C6S, {H12D,
  H12E,H12F} of C12S, All C(H,H) groups, All N(H) groups
 At 1.5 times of:
  {H4SA,H4SB,H4SC} of C4S, {H10G,H10H,H10I} of C10S, {H8SA,H8SB,H8SC} of C8S
3. Restrained distances
 C7S-C8S
 1.45 with sigma of 0.02
 C9S-C10S
 1.45 with sigma of 0.02
 N5S-C9S
 1.15 with sigma of 0.02
 C7S-N4S
 1.15 with sigma of 0.02
 C9A-C10A
 1.5 with sigma of 0.02
 C10A-C11A
 1.5 with sigma of 0.02
 C11A-O2A
 1.5 with sigma of 0.02
 C2B-N1B
 2.35 with sigma of 0.02
 C1B-C3B
 2.4 with sigma of 0.02
 C71-N11 = C76-N12 = C70-N11 = C77-N12
 1.5 with sigma of 0.01
 C154-N23 = C161-N24 = C155-N23 = C160-N24
 1.5 with sigma of 0.01
 N23-N24
 2.8 with sigma of 0.02
 N23-Pd12 = N24-Pd12
 2 with sigma of 0.02
 C141-N21 = C146-N22 = C140-N21 = C147-N22
 1.5 with sigma of 0.01
 N21-N22
 2.8 with sigma of 0.01
 N21-Pd11 = N22-Pd11
 2 with sigma of 0.01
 C43-N7 = C48-N8 = C84-N7 = C49-N8
 1.5 with sigma of 0.01
 N7-N8
 2.8 with sigma of 0.01
 N7-Pd4 = N8-Pd4
 2 with sigma of 0.01
 N11-N12
 2.8 with sigma of 0.01
 N11-Pd6 = N12-Pd6
 2 with sigma of 0.01
 C2C-N1C
 1.47 with sigma of 0.01
 C1C-C2C
 1.53 with sigma of 0.01
 C2C-C3C
 1.53 with sigma of 0.01
 C2D-C3D
 1.53 with sigma of 0.02
 N1B-C1B \\sim C1B-C2B \\sim C2B-C3B \\sim C3B-C8B \\sim C8B-N1B
 with sigma of 0.01
4. Restrained planarity
 N1B, C1B, C2B, C3B, C4B, C5B, C6B, C7B, C8B
 with sigma of 0.1
 N1A, C1A, C2A, C3A, C4A, C5A, C6A, C7A, C8A
 with sigma of 0.1
 C10A, C11A, O1A, O2A
 with sigma of 0.1
5. Uiso/Uaniso restraints and constraints
N2S \\sim C3S \\sim C4S: within 1.7A with sigma of 0.01 and sigma for terminal
atoms of 0.02 within 1.7A
C9A \\sim C10A \\sim N2A \\sim C12A \\sim O4A \\sim C13A \\sim C11A \\sim O3A
\\sim O2A \\sim O1A: within 1.7A with sigma of 0.01 and sigma for terminal
atoms of 0.02 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
C6B \\sim C5B \\sim C4B \\sim C3B \\sim C8B \\sim C7B \\sim N1B \\sim C1B \\sim
C2B: within 1.7A with sigma of 0.01 and sigma for terminal atoms of 0.02 within
1.7A
C2A \\sim C1A \\sim N1A \\sim C8A \\sim C3A \\sim C4A \\sim C5A \\sim C6A \\sim
C7A: within 1.7A with sigma of 0.01 and sigma for terminal atoms of 0.02 within
1.7A
C99 \\sim C100 \\sim C101 \\sim C102 \\sim C103 \\sim C104 \\sim N15 \\sim N16:
within 1.7A with sigma of 0.01 and sigma for terminal atoms of 0.02 within 1.7A
N3 \\sim C15 \\sim C16 \\sim C17 \\sim C18 \\sim C19 \\sim C20 \\sim N4: within
1.7A with sigma of 0.01 and sigma for terminal atoms of 0.02 within 1.7A
C9C \\sim C8C \\sim C7C \\sim C6C \\sim C11C \\sim C10C: within 1.7A with sigma
of 0.01 and sigma for terminal atoms of 0.02 within 1.7A
C5D \\sim O5D \\sim C4D \\sim O4D \\sim N1D \\sim C2D \\sim C3D \\sim O3D \\sim
O2D \\sim C1D \\sim O1D: within 1.7A with sigma of 0.01 and sigma for terminal
atoms of 0.02 within 1.7A
C5C \\sim O5C \\sim C4C \\sim O4C \\sim N1C \\sim O1C \\sim C1C \\sim C2C \\sim
C3C \\sim O2C \\sim O3C: within 1.7A with sigma of 0.01 and sigma for terminal
atoms of 0.02 within 1.7A
C9D \\sim C8D \\sim C7D \\sim C6D \\sim C11D \\sim C10D: within 1.7A with sigma
of 0.01 and sigma for terminal atoms of 0.02 within 1.7A
C146 \\sim C141 \\sim C142 \\sim C143 \\sim C144 \\sim C145 \\sim N22 \\sim
N21: within 1.7A with sigma of 0.02 and sigma for terminal atoms of 0.04 within
1.7A
C14 \\sim C11 \\sim C12 \\sim C13 \\sim C8 \\sim C9 \\sim C10: within 1.7A with
sigma of 0.01 and sigma for terminal atoms of 0.02 within 1.7A
C70 \\sim N11 \\sim C71 \\sim C72 \\sim C73 \\sim C74 \\sim C75 \\sim C76 \\sim
N12: within 1.7A with sigma of 0.01 and sigma for terminal atoms of 0.02 within
1.7A
Uanis(C9A) \\sim Ueq, Uanis(C11A) \\sim Ueq, Uanis(O1A) \\sim Ueq, Uanis(O2A)
\\sim Ueq, Uanis(C10A) \\sim Ueq, Uanis(N2A) \\sim Ueq, Uanis(C12A) \\sim Ueq,
Uanis(O4A) \\sim Ueq, Uanis(C13A) \\sim Ueq, Uanis(O3A) \\sim Ueq: with sigma
of 0.02 and sigma for terminal atoms of 0.04
Uanis(C146) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(O4W) \\sim Ueq, Uanis(N2S) \\sim Ueq, Uanis(C3S) \\sim Ueq, Uanis(C4S)
\\sim Ueq, Uanis(O5W) \\sim Ueq: with sigma of 0.01 and sigma for terminal
atoms of 0.02
6. Rigid body (RIGU) restrains
 C4S, C3S, N2S
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 N5S, C9S, C10S
 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
 C9A, C10A, C11A, O2A, O1A, N2A, C12A, O3A, O4A, C13A
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 C9A, C2A
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 C6A, C5A, C4A, C3A, C8A, C7A, N1A, C1A, C2A
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 N10, C62, C61, C60, C59, C58, C57, N9
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 C1B, C2B, N1B, C8B, C3B, C4B, C5B, C6B, C7B
 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
 N3, C15, C16, C17, C18, C19, C20, N4
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 N12, C76, C75, C74, C73, C72, C71, N11, C77, C70
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 O1D, C1D, C2D, C3D, O3D, O2D, N1D, O4D, C4D, O5D, C5D
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 N24, C160, C159, C158, C157, C156, C155, N23, C154
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 C6C, C11C, C10C, C9C, C8C, C7C
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 C6D, C7D, C8D, C9D, C10D, C11D
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 C5C, O5C, C4C, O4C, N1C, C2C, C1C, O1C, C3C, O3C, O2C
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 C92, C93, C94, C95, C96, C97
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 C7, C8, C13, C12, C11, C10, C9, C14
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 C168, N19, C127, C128, C129, C130, C131, C132, N20
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 N22, C146, C145, C144, C143, C142, C141, N21
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 C67, C66, C65, C64, C69, C68
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
7. Others
 Sof(N1A)=Sof(H1A)=Sof(C1A)=Sof(H1AA)=Sof(C2A)=Sof(C3A)=Sof(C4A)=Sof(H4AA)=
 Sof(C5A)=Sof(H5AA)=Sof(C6A)=Sof(H6A)=Sof(C7A)=Sof(H7AA)=Sof(C8A)=Sof(C9A)=
 Sof(H9AA)=Sof(H9AB)=Sof(C10A)=Sof(H10D)=Sof(C12A)=Sof(C13A)=Sof(C11A)=Sof(O2A)=
 Sof(O3A)=Sof(O4A)=Sof(O1A)=Sof(N2A)=Sof(H2AA)=1-FVAR(1)
 Sof(C1C)=Sof(H1CA)=Sof(H1CB)=Sof(C2C)=Sof(H2C)=Sof(C3C)=Sof(C4C)=Sof(C5C)=
 Sof(H5CA)=Sof(H5CB)=Sof(C6C)=Sof(C11C)=Sof(H11E)=Sof(C10C)=Sof(H10E)=Sof(C9C)=
 Sof(H9C)=Sof(C8C)=Sof(H8C)=Sof(C7C)=Sof(H7C)=Sof(O1C)=Sof(O3C)=Sof(O2C)=
 Sof(O4C)=Sof(O5C)=Sof(N1C)=Sof(H1C)=FVAR(1)
 Sof(N1B)=Sof(H1B)=Sof(C1B)=Sof(H1BA)=Sof(C2B)=Sof(C3B)=Sof(C4B)=Sof(H4B)=
 Sof(C5B)=Sof(H5B)=Sof(C6B)=Sof(H6B)=Sof(C7B)=Sof(H7BA)=Sof(C8B)=Sof(O5W)=
 Sof(O4W)=1-FVAR(2)
 Sof(C1D)=Sof(H1DA)=Sof(H1DB)=Sof(C2D)=Sof(H2D)=Sof(C3D)=Sof(C4D)=Sof(C5D)=
 Sof(H5DA)=Sof(H5DB)=Sof(C6D)=Sof(C7D)=Sof(H7D)=Sof(C8D)=Sof(H8D)=Sof(C9D)=
 Sof(H9D)=Sof(C10D)=Sof(H10F)=Sof(C11D)=Sof(H11F)=Sof(O1D)=Sof(O2D)=Sof(O3D)=
 Sof(O4D)=Sof(O5D)=Sof(N1D)=Sof(H1D)=Sof(C4S)=Sof(H4SA)=Sof(H4SB)=Sof(H4SC)=
 Sof(C3S)=Sof(N2S)=FVAR(2)
 Fixed Sof: O3W(0.5) O2W(0.75) C8S(0.5) H8SA(0.5) H8SB(0.5) H8SC(0.5) C7S(0.5)
 N4S(0.5)
8.a Ternary CH refined with riding coordinates:
 C2C(H2C), C2D(H2D), C10A(H10D), N14(H14), N13(H13), N18(H18), N17(H17),
 N16(H16), N15(H15), N19(H19), N20(H20), N21(H21), N22(H22), N23(H23), N24(H24),
  N2(H2), N1(H1), N6(H6), N5(H5), N4(H4), N3(H3), N7(H7), N8(H8), N9(H9A),
 N10(H10C), N11(H11), N12(H12C)
8.b Secondary CH2 refined with riding coordinates:
 C1C(H1CA,H1CB), C5C(H5CA,H5CB), C1D(H1DA,H1DB), C5D(H5DA,H5DB), C9A(H9AA,
 H9AB), C126(H12A,H12B), C119(H11A,H11B), C112(H11C,H11D), C105(H10A,H10B),
 C98(H98A,H98B), C91(H91A,H91B), C133(H13A,H13B), C140(H14A,H14B), C147(H14C,
 H14D), C154(H15A,H15B), C161(H16A,H16B), C168(H16C,H16D), C42(H42A,H42B),
 C35(H35A,H35B), C28(H28A,H28B), C21(H21A,H21B), C14(H14E,H14F), C7(H7A,H7B),
 C49(H49A,H49B), C56(H56A,H56B), C63(H63A,H63B), C70(H70A,H70B), C77(H77A,H77B),
  C84(H84A,H84B)
8.c Me refined as rotating group:
 C10S(H10G,H10H,H10I)
8.d Aromatic/amide H refined with riding coordinates:
 C11C(H11E), C10C(H10E), C9C(H9C), C8C(H8C), C7C(H7C), N1C(H1C), C7D(H7D),
 C8D(H8D), C9D(H9D), C10D(H10F), C11D(H11F), N1D(H1D), N1B(H1B), C1B(H1BA),
 C4B(H4B), C5B(H5B), C6B(H6B), C7B(H7BA), N1A(H1A), C1A(H1AA), C4A(H4AA),
 C5A(H5AA), C6A(H6A), C7A(H7AA), N2A(H2AA), C89(H89), C88(H88), C87(H87),
 C86(H86), C122(H122), C124(H124), C125(H125), C121(H121), C117(H117),
 C116(H116), C115(H115), C114(H114), C107(H107), C108(H108), C110(H110),
 C111(H111), C103(H103), C102(H102), C101(H101), C100(H100), C94(H94), C96(H96),
  C97(H97), C93(H93), C128(H128), C129(H129), C130(H130), C131(H131),
 C135(H135), C139(H139), C138(H138), C136(H136), C142(H142), C143(H143),
 C144(H144), C145(H145), C149(H149), C153(H153), C152(H152), C150(H150),
 C156(H156), C157(H157), C158(H158), C159(H159), C167(H167), C163(H163),
 C164(H164), C166(H166), C5(H5A), C4(H4A), C3(H3A), C2(H2A), C40(H40), C38(H38),
  C37(H37), C41(H41), C33(H33), C32(H32), C31(H31), C30(H30), C26(H26),
 C24(H24A), C23(H23A), C27(H27), C19(H19A), C18(H18A), C17(H17A), C16(H16E),
 C12(H12), C10(H10), C9(H9), C13(H13C), C44(H44), C45(H45), C46(H46), C47(H47),
 C55(H55), C51(H51), C52(H52), C54(H54), C58(H58), C59(H59), C60(H60), C61(H61),
  C69(H69), C65(H65), C66(H66), C68(H68), C72(H72), C73(H73), C74(H74),
 C75(H75), C83(H83), C79(H79), C80(H80), C82(H82)
8.e Fitted hexagon refined as free rotating group:
 C6C(C11C,C10C,C9C,C8C,C7C), C6D(C7D,C8D,C9D,C10D,C11D), C3B(C4B,C5B,C6B,C7B,
 C8B), C3A(C4A,C5A,C6A,C7A,C8A), C90(C89,C88,C87,C86,C85), C122(C123,C124,C125,
 C120,C121), C118(C117,C116,C115,C114,C113), C107(C108,C109,C110,C111,C106),
 C104(C103,C102,C101,C100,C99), C94(C95,C96,C97,C92,C93), C127(C128,C129,C130,
 C131,C132), C135(C134,C139,C138,C137,C136), C141(C142,C143,C144,C145,C146),
 C149(C148,C153,C152,C151,C150), C155(C156,C157,C158,C159,C160), C167(C162,C163,
 C164,C165,C166), C6(C5,C4,C3,C2,C1), C40(C39,C38,C37,C36,C41), C34(C33,C32,C31,
 C30,C29), C26(C25,C24,C23,C22,C27), C20(C19,C18,C17,C16,C15), C12(C11,C10,C9,
 C8,C13), C43(C44,C45,C46,C47,C48), C55(C50,C51,C52,C53,C54), C57(C58,C59,C60,
 C61,C62), C69(C64,C65,C66,C67,C68), C71(C72,C73,C74,C75,C76), C83(C78,C79,C80,
 C81,C82)
8.f Idealised Me refined with riding coordinates:
 C8S(H8SA,H8SB,H8SC)
8.g Idealised Me refined as rotating group:
 C4S(H4SA,H4SB,H4SC), C2S(H2SA,H2SB,H2SC), C6S(H6SA,H6SB,H6SC), C12S(H12D,H12E,
 H12F)
;
_shelx_res_checksum              90346
_olex2_submission_special_instructions 'No special instructions were received'