# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 12:57:05 2022
#   Inital geometry file: a 169 line input string
#   Ligand name: methyl {(1R,4Z,8S,13E)-8-{[4,6-dideoxy-4-(hydroxyamino)-beta-D-glucopyranosyl]oxy}-1-hydroxy-13-[2-(methyltrisulfanyl)ethylidene]-11-oxobicyclo[7.3.1]trideca-4,9-diene-2,6-diyn-10-yl}carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)NC1=C\2[C@@H](O[C@@H]3O[C@H](C)[C@@H](NO)[C@H](O)[C@H]3O)C#C\C=C/C#C[C@](O)(CC1=O)C\2=C/CSSSC
#
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
 C0T  C0T  'methyl {(1R,4Z,8S,13E)-8-{[4,6-dideoxy-4-(hydroxyamino)-beta-D-glucopyranosyl]oxy}-1-hydroxy-13-[2-(methyltrisulfanyl)ethylidene]-11-oxobicyclo[7.3.1]trideca-4,9-diene-2,6-diyn-10-yl}carbamate'  ligand  66  38  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_C0T
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
 C0T  C1    C  C     0   0.351   3.8338  -1.5570  -0.5871
 C0T  N1    N  NH1   0  -0.735   3.4778   0.6344  -1.6333
 C0T  O1    O  O     0  -0.506   4.8917  -1.6905  -1.1604
 C0T  S1    S  S2    0  -0.048  -1.1578  -3.7366  -1.8451
 C0T  C2    C  C     0   0.176   2.9286  -0.4275  -0.9086
 C0T  N2    N  NH1   0  -0.423  -4.5540   4.1248   0.8038
 C0T  O2    O  O     0  -0.268   5.0035   1.1496  -0.0305
 C0T  S2    S  S2    0  -0.043  -2.2423  -4.7846  -0.4423
 C0T  C3    C  C     0   0.033   1.6533  -0.4198  -0.4845
 C0T  O3    O  O2    0  -0.570   4.8955   2.2988  -1.9653
 C0T  S3    S  S2    0  -0.068  -4.1317  -3.9784  -0.4972
 C0T  C4    C  C     0   0.051   1.1662  -1.5561   0.3210
 C0T  O4    O  OH1   0  -0.662   1.6842  -3.0397   2.1259
 C0T  C5    C  CT    0   0.067   2.2129  -2.0204   1.3346
 C0T  O5    O  O2    0  -0.543  -0.5181   0.6181  -0.4293
 C0T  C6    C  CH2   0  -0.552   3.3831  -2.5283   0.4726
 C0T  O6    O  OH1   0  -0.600  -5.0921   4.2228   2.1013
 C0T  C7    C  C     0   0.692   4.5095   1.3467  -1.1157
 C0T  O7    O  O2    0  -0.488  -1.4739   2.0976   0.9671
 C0T  C8    C  CH3   0  -0.438   5.9456   3.1563  -1.5267
 C0T  O8    O  OH1   0  -0.642  -2.6570   1.0558  -2.3039
 C0T  C9    C  CSP   0   0.018   2.6335  -0.8758   2.1603
 C0T  O9    O  OH1   0  -0.676  -4.9972   2.1252  -1.1046
 C0T  C10   C  CSP   0   0.028   2.9544   0.1362   2.7319
 C0T  C11   C  C1    0  -0.294   3.2015   1.4447   3.2171
 C0T  C12   C  C1    0  -0.317   2.7315   2.5025   2.5246
 C0T  C13   C  CSP   0   0.223   1.9976   2.2482   1.3413
 C0T  C14   C  CSP   0  -0.134   1.4167   1.7473   0.4123
 C0T  C15   C  CH1   0  -0.081   0.8512   0.8761  -0.6216
 C0T  C16   C  C1    0  -0.167   0.0534  -2.2619   0.1255
 C0T  C17   C  CH2   0  -0.666  -0.9104  -2.1343  -1.0003
 C0T  C18   C  CH3   0  -0.758  -4.8265  -4.7437  -1.9815
 C0T  C19   C  CH1   0   0.311  -1.3504   1.7254  -0.3684
 C0T  C20   C  CH1   0  -0.025  -2.7139   1.3331  -0.9288
 C0T  C21   C  CH1   0  -0.025  -3.6884   2.4897  -0.7420
 C0T  C22   C  CH1   0  -0.062  -3.7064   2.9482   0.7158
 C0T  C23   C  CH1   0   0.076  -2.2689   3.2548   1.1573
 C0T  C24   C  CH3   0  -0.669  -2.1144   3.6577   2.6084
 C0T  HN1   H  HNH1  0   0.427   3.0797   0.8943  -2.5246
 C0T  HO4   H  HOH1  0   0.453   2.3963  -3.4416   2.6377
 C0T  H6    H  HCH2  0   0.338   3.0458  -3.4318  -0.0410
 C0T  H6A   H  HCH2  0   0.301   4.2441  -2.7969   1.0899
 C0T  H8    H  HCH3  0   0.267   6.0851   3.8843  -2.3209
 C0T  H8A   H  HCH3  0   0.180   5.6822   3.6749  -0.6052
 C0T  H8B   H  HCH3  0   0.250   6.8750   2.6075  -1.3761
 C0T  HO8   H  HOH1  0   0.480  -2.1523   0.2501  -2.4442
 C0T  HO9   H  HOH1  0   0.461  -5.0295   2.0076  -2.0587
 C0T  H11   H  H     0   0.305   3.7620   1.5883   4.1320
 C0T  H12   H  H     0   0.293   2.9084   3.5140   2.8654
 C0T  H15   H  HCH1  0   0.272   1.0046   1.3142  -1.6143
 C0T  H16   H  H     0   0.296  -0.1581  -3.0696   0.8163
 C0T  H17   H  HCH2  0   0.326  -0.5613  -1.4712  -1.7916
 C0T  H17A  H  HCH2  0   0.329  -1.8944  -1.7944  -0.6708
 C0T  H18   H  HCH3  0   0.264  -4.2466  -4.4665  -2.8593
 C0T  H18A  H  HCH3  0   0.294  -4.8715  -5.8249  -1.8802
 C0T  H18B  H  HCH3  0   0.283  -5.8368  -4.3511  -2.0895
 C0T  H19   H  HCH1  0   0.212  -0.9402   2.5609  -0.9676
 C0T  H20   H  HCH1  0   0.234  -3.0828   0.4704  -0.3512
 C0T  H21   H  HCH1  0   0.227  -3.3391   3.3332  -1.3607
 C0T  H22   H  HCH1  0   0.243  -4.0967   2.1242   1.3338
 C0T  H23   H  HCH1  0   0.138  -1.8904   4.0746   0.5254
 C0T  H24   H  HCH3  0   0.236  -2.5832   2.9396   3.2816
 C0T  H24A  H  HCH3  0   0.247  -1.0546   3.7225   2.8543
 C0T  H24B  H  HCH3  0   0.241  -2.5481   4.6371   2.7944
 C0T  H27   H  HNH1  0   0.381  -5.3609   3.9704   0.2101
 C0T  H28   H  HOH1  0   0.456  -4.8461   5.1044   2.3910

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
 C0T  C1   C6    single  1.507  0.020  1.507
 C0T  N1   C2    single  1.398  0.020  1.398
 C0T  N1   HN1   single  0.860  0.020  1.020
 C0T  O1   C1    double  1.211  0.020  1.211
 C0T  S1   S2    single  2.060  0.020  2.060
 C0T  C2   C1    single  1.483  0.020  1.483
 C0T  N2   O6    single  1.408  0.020  1.408
 C0T  N2   C22   single  1.453  0.020  1.453
 C0T  O2   C7    double  1.208  0.020  1.208
 C0T  C3   C2    double  1.344  0.020  1.344
 C0T  C3   C4    single  1.476  0.020  1.476
 C0T  O3   C7    single  1.333  0.020  1.333
 C0T  S3   S2    single  2.055  0.020  2.055
 C0T  C4   C5    single  1.529  0.020  1.529
 C0T  O4   HO4   single  0.850  0.020  0.980
 C0T  C5   O4    single  1.395  0.020  1.395
 C0T  C5   C9    single  1.473  0.020  1.473
 C0T  O5   C15   single  1.407  0.020  1.407
 C0T  C6   C5    single  1.540  0.020  1.540
 C0T  C6   H6    single  0.970  0.020  1.090
 C0T  C6   H6A   single  0.970  0.020  1.090
 C0T  C7   N1    single  1.356  0.020  1.356
 C0T  C8   O3    single  1.425  0.020  1.425
 C0T  C8   H8    single  0.970  0.020  1.090
 C0T  C8   H8A   single  0.970  0.020  1.090
 C0T  C8   H8B   single  0.970  0.020  1.090
 C0T  O8   C20   single  1.404  0.020  1.404
 C0T  O8   HO8   single  0.850  0.020  0.980
 C0T  C9   C10   triple  1.206  0.020  1.206
 C0T  O9   C21   single  1.406  0.020  1.406
 C0T  O9   HO9   single  0.850  0.020  0.980
 C0T  C11  C10   single  1.417  0.020  1.417
 C0T  C11  H11   single  0.930  0.020  1.080
 C0T  C12  C11   double  1.349  0.020  1.349
 C0T  C12  H12   single  0.930  0.020  1.080
 C0T  C13  C12   single  1.415  0.020  1.415
 C0T  C14  C13   triple  1.205  0.020  1.205
 C0T  C15  C3    single  1.530  0.020  1.530
 C0T  C15  C14   single  1.466  0.020  1.466
 C0T  C15  H15   single  0.970  0.020  1.090
 C0T  C16  C4    double  1.332  0.020  1.332
 C0T  C16  H16   single  0.930  0.020  1.080
 C0T  C17  S1    single  1.828  0.020  1.828
 C0T  C17  C16   single  1.488  0.020  1.488
 C0T  C17  H17   single  0.970  0.020  1.090
 C0T  C17  H17A  single  0.970  0.020  1.090
 C0T  C18  S3    single  1.809  0.020  1.809
 C0T  C18  H18   single  0.970  0.020  1.090
 C0T  C18  H18A  single  0.970  0.020  1.090
 C0T  C18  H18B  single  0.970  0.020  1.090
 C0T  C19  O5    single  1.387  0.020  1.387
 C0T  C19  O7    single  1.392  0.020  1.392
 C0T  C19  H19   single  0.970  0.020  1.090
 C0T  C20  C19   single  1.526  0.020  1.526
 C0T  C20  H20   single  0.970  0.020  1.090
 C0T  C21  C20   single  1.524  0.020  1.524
 C0T  C21  C22   single  1.528  0.020  1.528
 C0T  C21  H21   single  0.970  0.020  1.090
 C0T  C22  C23   single  1.535  0.020  1.535
 C0T  C22  H22   single  0.970  0.020  1.090
 C0T  C23  O7    single  1.417  0.020  1.417
 C0T  C23  C24   single  1.514  0.020  1.514
 C0T  C23  H23   single  0.970  0.020  1.090
 C0T  C24  H24   single  0.970  0.020  1.090
 C0T  C24  H24A  single  0.970  0.020  1.090
 C0T  C24  H24B  single  0.970  0.020  1.090
 C0T  N2   H27   single  0.890  0.020  1.040
 C0T  O6   H28   single  0.850  0.020  0.980

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
 C0T  C6    C1   C2    117.45  3.000
 C0T  C2    C1   O1    120.99  3.000
 C0T  C6    C1   O1    121.56  3.000
 C0T  HN1   N1   C7    120.09  3.000
 C0T  C7    N1   C2    119.99  3.000
 C0T  HN1   N1   C2    119.87  3.000
 C0T  C17   S1   S2    101.68  3.000
 C0T  C3    C2   N1    122.14  3.000
 C0T  C3    C2   C1    121.02  3.000
 C0T  N1    C2   C1    116.82  3.000
 C0T  H27   N2   C22   107.80  3.000
 C0T  H27   N2   O6    104.24  3.000
 C0T  C22   N2   O6    109.58  3.000
 C0T  S3    S2   S1    105.44  3.000
 C0T  C15   C3   C4    121.87  3.000
 C0T  C15   C3   C2    118.29  3.000
 C0T  C4    C3   C2    118.76  3.000
 C0T  C8    O3   C7    116.55  3.000
 C0T  C18   S3   S2    102.07  3.000
 C0T  C16   C4   C5    120.55  3.000
 C0T  C16   C4   C3    127.13  3.000
 C0T  C5    C4   C3    111.69  3.000
 C0T  HO4   O4   C5    109.01  3.000
 C0T  C9    C5   C6    110.69  3.000
 C0T  C6    C5   O4    111.39  3.000
 C0T  C9    C5   O4    110.99  3.000
 C0T  C6    C5   C4    104.44  3.000
 C0T  C9    C5   C4    109.34  3.000
 C0T  O4    C5   C4    109.78  3.000
 C0T  C19   O5   C15   116.35  3.000
 C0T  H6A   C6   H6    107.79  3.000
 C0T  H6A   C6   C5    111.33  3.000
 C0T  H6    C6   C5    107.54  3.000
 C0T  H6A   C6   C1    108.67  3.000
 C0T  H6    C6   C1    107.15  3.000
 C0T  C5    C6   C1    114.11  3.000
 C0T  H28   O6   N2    104.13  3.000
 C0T  O3    C7   O2    124.78  3.000
 C0T  O3    C7   N1    110.62  3.000
 C0T  O2    C7   N1    124.60  3.000
 C0T  C23   O7   C19   113.40  3.000
 C0T  H8B   C8   H8A   109.20  3.000
 C0T  H8B   C8   H8    109.21  3.000
 C0T  H8A   C8   H8    109.29  3.000
 C0T  H8B   C8   O3    111.59  3.000
 C0T  H8A   C8   O3    111.62  3.000
 C0T  H8    C8   O3    105.84  3.000
 C0T  HO8   O8   C20   109.26  3.000
 C0T  C10   C9   C5    180.00  3.000
 C0T  HO9   O9   C21   108.59  3.000
 C0T  C11   C10  C9    180.00  3.000
 C0T  H11   C11  C12   120.68  3.000
 C0T  C12   C11  C10   119.18  3.000
 C0T  H11   C11  C10   120.14  3.000
 C0T  H12   C12  C13   121.06  3.000
 C0T  C13   C12  C11   117.97  3.000
 C0T  H12   C12  C11   120.97  3.000
 C0T  C14   C13  C12   180.00  3.000
 C0T  C15   C14  C13   180.00  3.000
 C0T  H15   C15  C14   110.33  3.000
 C0T  H15   C15  O5    109.48  3.000
 C0T  C14   C15  O5    112.85  3.000
 C0T  H15   C15  C3    110.26  3.000
 C0T  C14   C15  C3    103.77  3.000
 C0T  O5    C15  C3    110.04  3.000
 C0T  H16   C16  C17   114.83  3.000
 C0T  C17   C16  C4    127.37  3.000
 C0T  H16   C16  C4    117.67  3.000
 C0T  H17A  C17  H17   108.57  3.000
 C0T  H17A  C17  C16   112.47  3.000
 C0T  H17   C17  C16   113.21  3.000
 C0T  H17A  C17  S1    106.87  3.000
 C0T  H17   C17  S1    103.95  3.000
 C0T  C16   C17  S1    111.24  3.000
 C0T  H18B  C18  H18A  109.24  3.000
 C0T  H18B  C18  H18   108.82  3.000
 C0T  H18A  C18  H18   110.54  3.000
 C0T  H18B  C18  S3    106.56  3.000
 C0T  H18A  C18  S3    111.12  3.000
 C0T  H18   C18  S3    110.46  3.000
 C0T  H19   C19  C20   109.05  3.000
 C0T  C20   C19  O7    109.99  3.000
 C0T  H19   C19  O7    110.51  3.000
 C0T  C20   C19  O5    108.36  3.000
 C0T  H19   C19  O5    110.89  3.000
 C0T  O7    C19  O5    108.00  3.000
 C0T  H20   C20  C21   108.42  3.000
 C0T  C21   C20  C19   109.35  3.000
 C0T  H20   C20  C19   107.94  3.000
 C0T  C21   C20  O8    107.21  3.000
 C0T  H20   C20  O8    111.87  3.000
 C0T  C19   C20  O8    111.98  3.000
 C0T  H21   C21  C22   108.02  3.000
 C0T  H21   C21  C20   108.01  3.000
 C0T  C22   C21  C20   110.62  3.000
 C0T  H21   C21  O9    110.39  3.000
 C0T  C22   C21  O9    108.23  3.000
 C0T  C20   C21  O9    111.52  3.000
 C0T  H22   C22  C23   108.66  3.000
 C0T  H22   C22  C21   108.36  3.000
 C0T  C23   C22  C21   108.87  3.000
 C0T  H22   C22  N2    111.42  3.000
 C0T  C23   C22  N2    111.55  3.000
 C0T  C21   C22  N2    107.91  3.000
 C0T  H23   C23  C24   108.45  3.000
 C0T  H23   C23  C22   107.78  3.000
 C0T  C24   C23  C22   115.12  3.000
 C0T  H23   C23  O7    109.75  3.000
 C0T  C24   C23  O7    106.79  3.000
 C0T  C22   C23  O7    108.89  3.000
 C0T  H24B  C24  H24A  107.20  3.000
 C0T  H24B  C24  H24   108.44  3.000
 C0T  H24A  C24  H24   108.54  3.000
 C0T  H24B  C24  C23   111.28  3.000
 C0T  H24A  C24  C23   109.35  3.000
 C0T  H24   C24  C23   111.88  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
 C0T  Var_01  C5   C6   C1   C2   -15.03  30.0  1
 C0T  Var_02  C6   C1   C2   C3   -13.45  30.0  1
 C0T  Var_03  C7   N1   C2   C1   -61.19  30.0  1
 C0T  Var_04  C4   C16  C17  S1   125.04  30.0  3
 C0T  Var_05  O2   C7   N1   C2    -1.20  30.0  1
 C0T  Var_06  C16  C17  S1   S2    71.39  30.0  1
 C0T  Var_07  H18  C18  S3   S2   -61.18  30.0  3
 C0T  Var_08  H8   C8   O3   C7  -177.37  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
 C0T  chir_01  C5   C4  C9   C6   positiv
 C0T  chir_02  C15  O5  C14  C3   negativ
 C0T  chir_03  C19  O5  O7   C20  positiv
 C0T  chir_04  C20  O8  C19  C21  negativ
 C0T  chir_05  C21  O9  C20  C22  positiv
 C0T  chir_06  C22  N2  C23  C21  positiv
 C0T  chir_07  C23  O7  C22  C24  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
 C0T  plan-1  C1  0.020
 C0T  plan-1  O1  0.020
 C0T  plan-1  C2  0.020
 C0T  plan-1  C6  0.020
 C0T  plan-2  N1  0.020
 C0T  plan-2  O2  0.020
 C0T  plan-2  O3  0.020
 C0T  plan-2  C7  0.020

