# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 03:26:26 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: (2~{R},3~{R},4~{S})-3-(2-methylpropanoylamino)-4-(4-phenyl-1,2,3-triazol-1-yl)-2-[(1~{R},2~{R})-1,2,3-tris(oxidanyl)propyl]-3,4-dihydro-2~{H}-pyran-6-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C(=O)N[C@H]1[C@@H](OC(=C[C@@H]1n2cc(nn2)c3ccccc3)C(O)=O)[C@H](O)[C@H](O)CO
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 I57  I57  '(2~{R},3~{R},4~{S})-3-(2-methylpropanoylamino)-4-(4-phenyl-1,2,3-triazol-1-yl)-2-[(1~{R},2~{R})-1,2,3-tris(oxidanyl)propyl]-3,4-dihydro-2~{H}-pyran-6-carboxylic acid'  D-saccharide  57  32  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_I57
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 I57  O1A  O  O      0  -0.585  -1.0667  -4.7058  -0.9952
 I57  O1B  O  OC    -1  -0.587  -2.9302  -4.1608   0.1107
 I57  C01  C  C      0   0.382  -1.8836  -3.9076  -0.5039
 I57  C02  C  C      0   0.179  -1.5506  -2.4250  -0.6722
 I57  C03  C  C1     0  -0.372  -0.4500  -1.9921  -1.2903
 I57  C04  C  CH1    0  -0.077  -0.1238  -0.5396  -1.3961
 I57  N04  N  NR5    0  -0.275   1.2920  -0.2905  -1.1820
 I57  C05  C  CH1    0  -0.116  -0.9466   0.2566  -0.3756
 I57  N05  N  NH1    0  -0.651  -0.8209   1.6680  -0.6025
 I57  C06  C  CH1    0   0.031  -2.3960  -0.2207  -0.4635
 I57  O06  O  O2     0  -0.478  -2.4726  -1.5997  -0.1355
 I57  C07  C  CH1    0  -0.032  -3.3160   0.5145   0.5076
 I57  O07  O  OH1    0  -0.658  -2.8381   0.4305   1.8279
 I57  C08  C  CH1    0  -0.019  -4.7771   0.0406   0.3991
 I57  O08  O  OH1    0  -0.661  -5.2226   0.0678  -0.9378
 I57  C09  C  CH2    0  -0.160  -5.6758   0.8623   1.3102
 I57  O09  O  OH1    0  -0.671  -6.9827   0.3413   1.2448
 I57  C41  C  CR15   0  -0.075   2.0999  -0.8127  -0.2472
 I57  C42  C  CR5    0   0.163   3.2861  -0.1359  -0.4110
 I57  N42  N  N      0  -0.322   3.1125   0.7464  -1.4225
 I57  N41  N  N      0  -0.084   1.9135   0.6488  -1.8748
 I57  C43  C  CR6    0   0.063   4.5483  -0.2730   0.3108
 I57  C44  C  CR16   0  -0.337   4.7243  -1.2852   1.2554
 I57  C45  C  CR16   0  -0.235   5.9229  -1.4126   1.9402
 I57  C46  C  CR16   0  -0.267   6.9681  -0.5321   1.6921
 I57  C47  C  CR16   0  -0.239   6.8023   0.4770   0.7523
 I57  C48  C  CR16   0  -0.290   5.6037   0.6074   0.0675
 I57  C54  C  CH3    0  -0.647  -0.8058   4.7676   0.5549
 I57  C52  C  CH1    0  -0.383   0.0796   3.9014  -0.3426
 I57  C53  C  CH3    0  -0.648   1.5264   4.3809  -0.3294
 I57  C51  C  C      0   0.586  -0.0003   2.4603   0.1246
 I57  O52  O  O      0  -0.486   0.6064   2.0629   1.1053
 I57  H2   H  H      0   0.268   0.2178  -2.7149  -1.7363
 I57  H3   H  HCH1   0   0.295  -0.3274  -0.1603  -2.4025
 I57  H4   H  HCH1   0   0.283  -0.5682   0.0490   0.6266
 I57  H5   H  HNH1   0   0.400  -1.2162   2.0467  -1.4496
 I57  H6   H  HCH1   0   0.249  -2.7583  -0.0737  -1.4897
 I57  H7   H  HCH1   0   0.247  -3.2817   1.5773   0.2423
 I57  H8   H  HOH1   0   0.446  -2.8387  -0.4953   2.0970
 I57  H9   H  HCH1   0   0.238  -4.8352  -1.0088   0.7087
 I57  H10  H  HOH1   0   0.445  -5.2882   0.9858  -1.2241
 I57  H11  H  HCH2   0   0.209  -5.2802   0.8308   2.3303
 I57  H12  H  HCH2   0   0.188  -5.6428   1.9152   0.9883
 I57  H13  H  HOH1   0   0.455  -7.5200   0.8069   1.8912
 I57  H14  H  HCR5   0   0.312   1.7821  -1.5869   0.4304
 I57  H15  H  HCR6   0   0.248   3.9243  -1.9865   1.4583
 I57  H16  H  HCR6   0   0.259   6.0402  -2.2047   2.6681
 I57  H17  H  HCR6   0   0.257   7.9041  -0.6323   2.2261
 I57  H18  H  HCR6   0   0.257   7.6106   1.1679   0.5500
 I57  H19  H  HCR6   0   0.254   5.4846   1.3984  -0.6609
 I57  H20  H  HCH3   0   0.238  -0.7709   5.8073   0.2287
 I57  H21  H  HCH3   0   0.234  -1.8476   4.4454   0.5263
 I57  H22  H  HCH3   0   0.228  -0.4668   4.7294   1.5908
 I57  H23  H  HCH1   0   0.249  -0.2996   3.9700  -1.3668
 I57  H24  H  HCH3   0   0.224   1.9320   4.3731   0.6822
 I57  H25  H  HCH3   0   0.235   2.1640   3.7537  -0.9535
 I57  H26  H  HCH3   0   0.231   1.5860   5.4021  -0.7067

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 I57  O08  C08  single    1.409  0.020  1.409
 I57  C09  O09  single    1.408  0.020  1.408
 I57  C09  C08  single    1.521  0.020  1.521
 I57  C08  C07  single    1.540  0.020  1.540
 I57  O1A  C01  deloc     1.243  0.020  1.243
 I57  C07  C06  single    1.526  0.020  1.526
 I57  C07  O07  single    1.407  0.020  1.407
 I57  C01  O1B  deloc     1.240  0.020  1.240
 I57  C01  C02  single    1.529  0.020  1.529
 I57  O06  C06  single    1.420  0.020  1.420
 I57  O06  C02  single    1.349  0.020  1.349
 I57  C06  C05  single    1.529  0.020  1.529
 I57  C02  C03  double    1.334  0.020  1.334
 I57  C03  C04  single    1.492  0.020  1.492
 I57  C05  N05  single    1.435  0.020  1.435
 I57  C05  C04  single    1.534  0.020  1.534
 I57  N05  C51  single    1.353  0.020  1.353
 I57  C04  N04  single    1.453  0.020  1.453
 I57  C54  C52  single    1.530  0.020  1.530
 I57  C51  C52  single    1.517  0.020  1.517
 I57  C51  O52  double    1.220  0.020  1.220
 I57  C52  C53  single    1.524  0.020  1.524
 I57  N04  N41  aromatic  1.322  0.020  1.322
 I57  N04  C41  aromatic  1.341  0.020  1.341
 I57  N41  N42  aromatic  1.285  0.020  1.285
 I57  C41  C42  aromatic  1.375  0.020  1.375
 I57  N42  C42  aromatic  1.353  0.020  1.353
 I57  C42  C43  single    1.460  0.020  1.460
 I57  C43  C48  aromatic  1.396  0.020  1.396
 I57  C43  C44  aromatic  1.396  0.020  1.396
 I57  C48  C47  aromatic  1.387  0.020  1.387
 I57  C44  C45  aromatic  1.386  0.020  1.386
 I57  C47  C46  aromatic  1.389  0.020  1.389
 I57  C45  C46  aromatic  1.389  0.020  1.389
 I57  C03  H2   single    0.930  0.020  1.080
 I57  C04  H3   single    0.970  0.020  1.090
 I57  C05  H4   single    0.970  0.020  1.090
 I57  N05  H5   single    0.860  0.020  1.020
 I57  C06  H6   single    0.970  0.020  1.090
 I57  C07  H7   single    0.970  0.020  1.090
 I57  O07  H8   single    0.850  0.020  0.980
 I57  C08  H9   single    0.970  0.020  1.090
 I57  O08  H10  single    0.850  0.020  0.980
 I57  C09  H11  single    0.970  0.020  1.090
 I57  C09  H12  single    0.970  0.020  1.090
 I57  O09  H13  single    0.850  0.020  0.980
 I57  C41  H14  single    0.930  0.020  1.080
 I57  C44  H15  single    0.930  0.020  1.080
 I57  C45  H16  single    0.930  0.020  1.080
 I57  C46  H17  single    0.930  0.020  1.080
 I57  C47  H18  single    0.930  0.020  1.080
 I57  C48  H19  single    0.930  0.020  1.080
 I57  C54  H20  single    0.970  0.020  1.090
 I57  C54  H21  single    0.970  0.020  1.090
 I57  C54  H22  single    0.970  0.020  1.090
 I57  C52  H23  single    0.970  0.020  1.090
 I57  C53  H24  single    0.970  0.020  1.090
 I57  C53  H25  single    0.970  0.020  1.090
 I57  C53  H26  single    0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 I57  C02  C01  O1B  115.88  3.000
 I57  C02  C01  O1A  115.85  3.000
 I57  O1B  C01  O1A  128.27  3.000
 I57  O06  C02  C03  123.34  3.000
 I57  C03  C02  C01  123.04  3.000
 I57  O06  C02  C01  113.62  3.000
 I57  H2   C03  C04  119.13  3.000
 I57  H2   C03  C02  118.95  3.000
 I57  C04  C03  C02  121.92  3.000
 I57  H3   C04  C05  109.40  3.000
 I57  H3   C04  N04  104.91  3.000
 I57  C05  C04  N04  109.61  3.000
 I57  H3   C04  C03  111.21  3.000
 I57  N04  C04  C03  111.67  3.000
 I57  C05  C04  C03  109.93  3.000
 I57  N41  N04  C41  111.01  3.000
 I57  C41  N04  C04  128.51  3.000
 I57  N41  N04  C04  120.16  3.000
 I57  H4   C05  C06  108.80  3.000
 I57  H4   C05  N05  107.58  3.000
 I57  C06  C05  N05  112.40  3.000
 I57  H4   C05  C04  109.05  3.000
 I57  N05  C05  C04  111.00  3.000
 I57  C06  C05  C04  107.96  3.000
 I57  H5   N05  C51  117.99  3.000
 I57  H5   N05  C05  117.89  3.000
 I57  C51  N05  C05  122.97  3.000
 I57  H6   C06  C07  109.34  3.000
 I57  H6   C06  O06  109.16  3.000
 I57  C07  C06  O06  106.76  3.000
 I57  H6   C06  C05  108.95  3.000
 I57  O06  C06  C05  109.95  3.000
 I57  C07  C06  C05  112.61  3.000
 I57  C06  O06  C02  117.74  3.000
 I57  H7   C07  C08  108.12  3.000
 I57  H7   C07  O07  105.93  3.000
 I57  C08  C07  O07  111.72  3.000
 I57  H7   C07  C06  107.11  3.000
 I57  O07  C07  C06  111.32  3.000
 I57  C08  C07  C06  112.26  3.000
 I57  H8   O07  C07  108.61  3.000
 I57  H9   C08  C09  108.47  3.000
 I57  H9   C08  O08  105.65  3.000
 I57  C09  C08  O08  111.78  3.000
 I57  H9   C08  C07  108.98  3.000
 I57  C09  C08  C07  110.63  3.000
 I57  O08  C08  C07  111.15  3.000
 I57  H10  O08  C08  108.76  3.000
 I57  H12  C09  H11  106.80  3.000
 I57  H12  C09  O09  111.58  3.000
 I57  H11  C09  O09  111.59  3.000
 I57  H12  C09  C08  108.88  3.000
 I57  H11  C09  C08  109.22  3.000
 I57  O09  C09  C08  108.70  3.000
 I57  H13  O09  C09  107.96  3.000
 I57  H14  C41  C42  133.09  3.000
 I57  H14  C41  N04  122.73  3.000
 I57  C42  C41  N04  104.17  3.000
 I57  C43  C42  N42  122.78  3.000
 I57  C43  C42  C41  129.81  3.000
 I57  N42  C42  C41  107.41  3.000
 I57  N41  N42  C42  109.45  3.000
 I57  N42  N41  N04  107.95  3.000
 I57  C48  C43  C44  118.69  3.000
 I57  C44  C43  C42  120.77  3.000
 I57  C48  C43  C42  120.54  3.000
 I57  H15  C44  C45  119.11  3.000
 I57  H15  C44  C43  120.22  3.000
 I57  C45  C44  C43  120.67  3.000
 I57  H16  C45  C46  120.17  3.000
 I57  H16  C45  C44  119.56  3.000
 I57  C46  C45  C44  120.27  3.000
 I57  H17  C46  C47  120.29  3.000
 I57  H17  C46  C45  120.27  3.000
 I57  C47  C46  C45  119.44  3.000
 I57  H18  C47  C48  119.55  3.000
 I57  H18  C47  C46  120.07  3.000
 I57  C48  C47  C46  120.37  3.000
 I57  H19  C48  C47  119.76  3.000
 I57  H19  C48  C43  119.70  3.000
 I57  C47  C48  C43  120.55  3.000
 I57  H22  C54  H21  108.14  3.000
 I57  H22  C54  H20  107.91  3.000
 I57  H21  C54  H20  107.72  3.000
 I57  H22  C54  C52  110.96  3.000
 I57  H21  C54  C52  111.73  3.000
 I57  H20  C54  C52  110.24  3.000
 I57  H23  C52  C51  109.24  3.000
 I57  H23  C52  C53  108.50  3.000
 I57  C51  C52  C53  110.26  3.000
 I57  H23  C52  C54  108.24  3.000
 I57  C53  C52  C54  111.48  3.000
 I57  C51  C52  C54  109.07  3.000
 I57  H26  C53  H25  107.98  3.000
 I57  H26  C53  H24  107.91  3.000
 I57  H25  C53  H24  108.03  3.000
 I57  H26  C53  C52  110.10  3.000
 I57  H25  C53  C52  111.65  3.000
 I57  H24  C53  C52  111.04  3.000
 I57  O52  C51  C52  122.07  3.000
 I57  O52  C51  N05  122.89  3.000
 I57  C52  C51  N05  115.01  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 I57  CONST_01  C42  N42  N41  N04    0.00   0.0  0
 I57  CONST_02  N42  C42  C41  N04    0.00   0.0  0
 I57  CONST_03  C43  C42  C41  N04  180.00   0.0  0
 I57  CONST_04  N42  N41  N04  C41    0.00   0.0  0
 I57  CONST_05  N41  N42  C42  C41    0.00   0.0  0
 I57  CONST_06  C48  C43  C42  C41  180.00   0.0  0
 I57  CONST_07  C44  C43  C42  C41    0.00   0.0  0
 I57  CONST_08  N41  N04  C41  C42    0.00   0.0  0
 I57  CONST_09  C47  C48  C43  C42  180.00   0.0  0
 I57  CONST_10  C45  C44  C43  C42  180.00   0.0  0
 I57  CONST_11  C48  C43  C42  N42    0.00   0.0  0
 I57  CONST_12  C44  C43  C42  N42  180.00   0.0  0
 I57  CONST_13  C43  C42  N42  N41  180.00   0.0  0
 I57  CONST_14  C46  C47  C48  C43    0.00   0.0  0
 I57  CONST_15  C46  C45  C44  C43    0.00   0.0  0
 I57  CONST_16  C47  C48  C43  C44    0.00   0.0  0
 I57  CONST_17  C47  C46  C45  C44    0.00   0.0  0
 I57  CONST_18  C48  C43  C44  C45    0.00   0.0  0
 I57  CONST_19  C48  C47  C46  C45    0.00   0.0  0
 I57  CONST_20  N42  N41  N04  C04  180.00   0.0  0
 I57  CONST_21  C42  C41  N04  C04  180.00   0.0  0
 I57  CONST_22  H14  C41  N04  C04    0.00   0.0  0
 I57  CONST_23  H19  C48  C43  C42    0.00   0.0  0
 I57  CONST_24  H15  C44  C43  C42    0.00   0.0  0
 I57  CONST_25  H18  C47  C48  C43  180.00   0.0  0
 I57  CONST_26  H16  C45  C44  C43  180.00   0.0  0
 I57  CONST_27  H17  C46  C45  C44  180.00   0.0  0
 I57  CONST_28  C52  C51  N05  C05  180.00   0.0  0
 I57  CONST_29  O52  C51  N05  C05    0.00   0.0  0
 I57  CONST_30  H5   N05  C51  C52    0.00   0.0  0
 I57  Var_01    O06  C02  C03  C04    2.22  30.0  1
 I57  Var_02    C54  C52  C51  N05  100.62  30.0  3
 I57  Var_03    H24  C53  C52  C54   58.28  30.0  3
 I57  Var_04    H20  C54  C52  C53   58.63  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 I57  chir_01  C04  C03  C05  N04  negativ
 I57  chir_02  C05  N05  C06  C04  negativ
 I57  chir_03  C06  O06  C07  C05  negativ
 I57  chir_04  C07  O07  C06  C08  negativ
 I57  chir_05  C08  O08  C07  C09  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 I57  plan-1  C04  0.020
 I57  plan-1  N04  0.020
 I57  plan-1  C41  0.020
 I57  plan-1  C42  0.020
 I57  plan-1  N42  0.020
 I57  plan-1  N41  0.020
 I57  plan-1  C43  0.020
 I57  plan-1  H14  0.020
 I57  plan-2  C42  0.020
 I57  plan-2  C43  0.020
 I57  plan-2  C44  0.020
 I57  plan-2  C45  0.020
 I57  plan-2  C46  0.020
 I57  plan-2  C47  0.020
 I57  plan-2  C48  0.020
 I57  plan-2  H15  0.020
 I57  plan-2  H16  0.020
 I57  plan-2  H17  0.020
 I57  plan-2  H18  0.020
 I57  plan-2  H19  0.020
 I57  plan-3  C05  0.020
 I57  plan-3  N05  0.020
 I57  plan-3  C52  0.020
 I57  plan-3  C51  0.020
 I57  plan-3  O52  0.020
 I57  plan-3  H5   0.020
 I57  plan-4  O1A  0.020
 I57  plan-4  O1B  0.020
 I57  plan-4  C01  0.020
 I57  plan-4  C02  0.020

