# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jun 19 19:58:42 2020
#   Inital geometry file: a 167 line input string
#   Ligand name: (3R,4S,5S,7S,9E,11R,12R)-12-ethyl-3,5,7,11-tetramethyl-2,8-dioxooxacyclododec-9-en-4-yl 3,4,6-trideoxy-3-(dimethylamino)-beta-L-xylo-hexopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H]1OC(=O)[C@H](C)[C@@H](O[C@H]2O[C@@H](C)C[C@H]([C@@H]2O)N(C)C)[C@@H](C)C[C@H](C)C(=O)\C=C\[C@H]1C
#
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
 PXI  PXI  '(3R,4S,5S,7S,9E,11R,12R)-12-ethyl-3,5,7,11-tetramethyl-2,8-dioxooxacyclododec-9-en-4-yl 3,4,6-trideoxy-3-(dimethylamino)-beta-L-xylo-hexopyranoside'  ligand  75  32  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PXI
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
 PXI  C1    C  CH3   0  -0.654   4.1611   3.6772  -0.3230
 PXI  C2    C  CH2   0  -0.459   4.3367   2.4436   0.5517
 PXI  C3    C  CH1   0   0.041   3.1002   1.5754   0.7491
 PXI  O1    O  O2    0  -0.474   2.8014   0.7682  -0.4020
 PXI  C4    C  C     0   0.611   1.9576   1.1784  -1.3538
 PXI  O2    O  O     0  -0.425   1.6442   2.3243  -1.5297
 PXI  C5    C  CH1   0  -0.381   1.4827  -0.0077  -2.1690
 PXI  C6    C  CH3   0  -0.655   0.8250   0.4170  -3.4716
 PXI  C7    C  CH1   0   0.051   0.5923  -0.9329  -1.2934
 PXI  O3    O  O2    0  -0.511  -0.7763  -0.5925  -1.4503
 PXI  C8    C  CH1   0   0.290  -1.3932   0.0605  -0.4018
 PXI  O4    O  O2    0  -0.481  -0.9517   1.3862  -0.3711
 PXI  C9    C  CH1   0   0.037  -1.4900   2.1102   0.7238
 PXI  C10   C  CH3   0  -0.677  -0.8799   3.4958   0.7189
 PXI  C11   C  CH2   0  -0.458  -3.0097   2.1387   0.6282
 PXI  C12   C  CH1   0  -0.115  -3.5874   0.7195   0.5341
 PXI  N1    N  NT    0  -0.409  -5.0355   0.6319   0.4616
 PXI  C13   C  CH3   0  -0.522  -5.6807   0.9872   1.7053
 PXI  C14   C  CH3   0  -0.536  -5.6426   1.3069  -0.6644
 PXI  C15   C  CH1   0   0.007  -2.9061  -0.0137  -0.6190
 PXI  O5    O  OH1   0  -0.663  -3.3532  -1.3445  -0.6399
 PXI  C16   C  CH1   0  -0.231   0.7329  -2.4363  -1.5863
 PXI  C17   C  CH3   0  -0.712   2.1821  -2.8900  -1.7552
 PXI  C18   C  CH2   0  -0.437   0.0091  -3.2966  -0.5313
 PXI  C19   C  CH1   0  -0.362   0.7085  -3.5686   0.8216
 PXI  C20   C  CH3   0  -0.652  -0.0085  -4.7122   1.5394
 PXI  C21   C  C     0   0.380   0.7455  -2.3414   1.7182
 PXI  O6    O  O     0  -0.413  -0.2417  -1.9776   2.3284
 PXI  C22   C  C1    0  -0.352   2.0189  -1.5938   1.7713
 PXI  C23   C  C1    0  -0.139   2.0613  -0.2829   2.0216
 PXI  C24   C  CH1   0  -0.308   3.2785   0.5832   1.9221
 PXI  C25   C  CH3   0  -0.698   4.5799  -0.2073   1.8513
 PXI  H1C1  H  HCH3  0   0.227   4.0002   3.4247  -1.3686
 PXI  H1C2  H  HCH3  0   0.218   3.3204   4.2876   0.0077
 PXI  H1C3  H  HCH3  0   0.225   5.0590   4.2939  -0.2686
 PXI  H2C1  H  HCH2  0   0.238   5.1516   1.8313   0.1587
 PXI  H2C2  H  HCH2  0   0.235   4.6547   2.7637   1.5480
 PXI  H3    H  HCH1  0   0.254   2.2385   2.2181   0.9599
 PXI  H5    H  HCH1  0   0.278   2.3895  -0.5657  -2.4128
 PXI  H6C1  H  HCH3  0   0.232   1.5400   0.9397  -4.1068
 PXI  H6C2  H  HCH3  0   0.231   0.4730  -0.4534  -4.0265
 PXI  H6C3  H  HCH3  0   0.236  -0.0237   1.0760  -3.3040
 PXI  H7    H  HCH1  0   0.241   0.8877  -0.7814  -0.2558
 PXI  H8    H  HCH1  0   0.189  -1.1512  -0.4258   0.5600
 PXI  H9    H  HCH1  0   0.201  -1.2102   1.6029   1.6622
 PXI  H101  H  HCH3  0   0.224  -1.1251   4.0295  -0.2005
 PXI  H102  H  HCH3  0   0.228  -1.2649   4.0727   1.5596
 PXI  H103  H  HCH3  0   0.244   0.2054   3.4530   0.8086
 PXI  H111  H  HCH2  0   0.244  -3.4121   2.6495   1.5062
 PXI  H112  H  HCH2  0   0.228  -3.3003   2.7293  -0.2466
 PXI  H12   H  HCH1  0   0.230  -3.2996   0.1914   1.4540
 PXI  H131  H  HCH3  0   0.233  -6.7438   0.7469   1.6478
 PXI  H132  H  HCH3  0   0.230  -5.2542   0.4104   2.5279
 PXI  H133  H  HCH3  0   0.193  -5.6031   2.0524   1.9708
 PXI  H141  H  HCH3  0   0.237  -5.2305   0.9483  -1.6074
 PXI  H142  H  HCH3  0   0.235  -6.7112   1.0868  -0.6781
 PXI  H143  H  HCH3  0   0.198  -5.5373   2.4014  -0.6476
 PXI  H15   H  HCH1  0   0.210  -3.1285   0.4972  -1.5687
 PXI  HA    H  HOH1  0   0.450  -2.9180  -1.7926  -1.3723
 PXI  H16   H  HCH1  0   0.239   0.2177  -2.6325  -2.5341
 PXI  H171  H  HCH3  0   0.225   2.8342  -2.5047  -0.9686
 PXI  H172  H  HCH3  0   0.246   2.2455  -3.9789  -1.7284
 PXI  H173  H  HCH3  0   0.245   2.6015  -2.5721  -2.7095
 PXI  H181  H  HCH2  0   0.234  -0.9932  -2.9072  -0.3372
 PXI  H182  H  HCH2  0   0.245  -0.1470  -4.2796  -0.9848
 PXI  H19   H  HCH1  0   0.255   1.7376  -3.8815   0.6254
 PXI  H201  H  HCH3  0   0.235   0.0096  -5.6108   0.9224
 PXI  H202  H  HCH3  0   0.237   0.4708  -4.9520   2.4891
 PXI  H203  H  HCH3  0   0.228  -1.0505  -4.4632   1.7396
 PXI  H22   H  H     0   0.265   2.9143  -2.1329   1.4846
 PXI  H23   H  H     0   0.265   1.1310   0.2307   2.2562
 PXI  H24   H  HCH1  0   0.269   3.3002   1.2086   2.8225
 PXI  H251  H  HCH3  0   0.231   4.6710  -0.7648   0.9186
 PXI  H252  H  HCH3  0   0.254   5.4437   0.4500   1.9316
 PXI  H253  H  HCH3  0   0.245   4.6417  -0.9193   2.6747

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
 PXI  C1   C2    single  1.522  0.020  1.522
 PXI  C1   H1C1  single  0.970  0.020  1.090
 PXI  C1   H1C2  single  0.970  0.020  1.090
 PXI  C1   H1C3  single  0.970  0.020  1.090
 PXI  C2   C3    single  1.524  0.020  1.524
 PXI  C2   H2C1  single  0.970  0.020  1.090
 PXI  C2   H2C2  single  0.970  0.020  1.090
 PXI  C3   O1    single  1.437  0.020  1.437
 PXI  C3   C24   single  1.547  0.020  1.547
 PXI  C3   H3    single  0.970  0.020  1.090
 PXI  O1   C4    single  1.336  0.020  1.336
 PXI  C4   O2    double  1.201  0.020  1.201
 PXI  C4   C5    single  1.516  0.020  1.516
 PXI  C5   C6    single  1.520  0.020  1.520
 PXI  C5   C7    single  1.554  0.020  1.554
 PXI  C5   H5    single  0.970  0.020  1.090
 PXI  C6   H6C1  single  0.970  0.020  1.090
 PXI  C6   H6C2  single  0.970  0.020  1.090
 PXI  C6   H6C3  single  0.970  0.020  1.090
 PXI  C7   O3    single  1.419  0.020  1.419
 PXI  C7   C16   single  1.538  0.020  1.538
 PXI  C7   H7    single  0.970  0.020  1.090
 PXI  O3   C8    single  1.381  0.020  1.381
 PXI  C8   O4    single  1.398  0.020  1.398
 PXI  C8   C15   single  1.530  0.020  1.530
 PXI  C8   H8    single  0.970  0.020  1.090
 PXI  O4   C9    single  1.419  0.020  1.419
 PXI  C9   C10   single  1.514  0.020  1.514
 PXI  C9   C11   single  1.523  0.020  1.523
 PXI  C9   H9    single  0.970  0.020  1.090
 PXI  C10  H101  single  0.970  0.020  1.090
 PXI  C10  H102  single  0.970  0.020  1.090
 PXI  C10  H103  single  0.970  0.020  1.090
 PXI  C11  C12   single  1.535  0.020  1.535
 PXI  C11  H111  single  0.970  0.020  1.090
 PXI  C11  H112  single  0.970  0.020  1.090
 PXI  C12  N1    single  1.453  0.020  1.453
 PXI  C12  C15   single  1.527  0.020  1.527
 PXI  C12  H12   single  0.970  0.020  1.090
 PXI  N1   C13   single  1.445  0.020  1.445
 PXI  N1   C14   single  1.446  0.020  1.446
 PXI  C13  H131  single  0.970  0.020  1.090
 PXI  C13  H132  single  0.970  0.020  1.090
 PXI  C13  H133  single  0.970  0.020  1.090
 PXI  C14  H141  single  0.970  0.020  1.090
 PXI  C14  H142  single  0.970  0.020  1.090
 PXI  C14  H143  single  0.970  0.020  1.090
 PXI  C15  O5    single  1.404  0.020  1.404
 PXI  C15  H15   single  0.970  0.020  1.090
 PXI  O5   HA    single  0.850  0.020  0.980
 PXI  C16  C17   single  1.528  0.020  1.528
 PXI  C16  C18   single  1.542  0.020  1.542
 PXI  C16  H16   single  0.970  0.020  1.090
 PXI  C17  H171  single  0.970  0.020  1.090
 PXI  C17  H172  single  0.970  0.020  1.090
 PXI  C17  H173  single  0.970  0.020  1.090
 PXI  C18  C19   single  1.547  0.020  1.547
 PXI  C18  H181  single  0.970  0.020  1.090
 PXI  C18  H182  single  0.970  0.020  1.090
 PXI  C19  C20   single  1.529  0.020  1.529
 PXI  C19  C21   single  1.520  0.020  1.520
 PXI  C19  H19   single  0.970  0.020  1.090
 PXI  C20  H201  single  0.970  0.020  1.090
 PXI  C20  H202  single  0.970  0.020  1.090
 PXI  C20  H203  single  0.970  0.020  1.090
 PXI  C21  O6    double  1.216  0.020  1.216
 PXI  C21  C22   single  1.478  0.020  1.478
 PXI  C22  C23   double  1.335  0.020  1.335
 PXI  C22  H22   single  0.930  0.020  1.080
 PXI  C23  C24   single  1.497  0.020  1.497
 PXI  C23  H23   single  0.930  0.020  1.080
 PXI  C24  C25   single  1.524  0.020  1.524
 PXI  C24  H24   single  0.970  0.020  1.090
 PXI  C25  H251  single  0.970  0.020  1.090
 PXI  C25  H252  single  0.970  0.020  1.090
 PXI  C25  H253  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
 PXI  H1C3  C1   H1C2  107.64  3.000
 PXI  H1C3  C1   H1C1  107.52  3.000
 PXI  H1C2  C1   H1C1  107.90  3.000
 PXI  H1C3  C1   C2    109.55  3.000
 PXI  H1C2  C1   C2    111.61  3.000
 PXI  H1C1  C1   C2    112.42  3.000
 PXI  H2C2  C2   H2C1  105.96  3.000
 PXI  H2C2  C2   C3    106.54  3.000
 PXI  H2C1  C2   C3    109.43  3.000
 PXI  H2C2  C2   C1    108.65  3.000
 PXI  H2C1  C2   C1    109.48  3.000
 PXI  C3    C2   C1    116.26  3.000
 PXI  H3    C3   C24   108.73  3.000
 PXI  H3    C3   O1    108.67  3.000
 PXI  C24   C3   O1    105.73  3.000
 PXI  H3    C3   C2    109.21  3.000
 PXI  C24   C3   C2    111.72  3.000
 PXI  O1    C3   C2    112.64  3.000
 PXI  C4    O1   C3    121.95  3.000
 PXI  C5    C4   O2    125.89  3.000
 PXI  C5    C4   O1    109.92  3.000
 PXI  O2    C4   O1    124.19  3.000
 PXI  H5    C5   C7    107.30  3.000
 PXI  H5    C5   C6    108.10  3.000
 PXI  C7    C5   C6    113.66  3.000
 PXI  H5    C5   C4    105.05  3.000
 PXI  C7    C5   C4    110.02  3.000
 PXI  C6    C5   C4    112.20  3.000
 PXI  H6C3  C6   H6C2  108.07  3.000
 PXI  H6C3  C6   H6C1  108.13  3.000
 PXI  H6C2  C6   H6C1  107.33  3.000
 PXI  H6C3  C6   C5    112.02  3.000
 PXI  H6C2  C6   C5    110.66  3.000
 PXI  H6C1  C6   C5    110.47  3.000
 PXI  H7    C7   C16   107.01  3.000
 PXI  H7    C7   O3    109.48  3.000
 PXI  C16   C7   O3    107.55  3.000
 PXI  H7    C7   C5    107.36  3.000
 PXI  C16   C7   C5    114.97  3.000
 PXI  O3    C7   C5    110.33  3.000
 PXI  C8    O3   C7    117.41  3.000
 PXI  H8    C8   C15   108.59  3.000
 PXI  H8    C8   O4    109.23  3.000
 PXI  C15   C8   O4    111.19  3.000
 PXI  H8    C8   O3    110.80  3.000
 PXI  C15   C8   O3    108.12  3.000
 PXI  O4    C8   O3    108.92  3.000
 PXI  C9    O4   C8    112.40  3.000
 PXI  H9    C9   C11   108.38  3.000
 PXI  H9    C9   C10   108.75  3.000
 PXI  C11   C9   C10   112.63  3.000
 PXI  H9    C9   O4    109.01  3.000
 PXI  C11   C9   O4    109.86  3.000
 PXI  C10   C9   O4    108.16  3.000
 PXI  H103  C10  H102  108.00  3.000
 PXI  H103  C10  H101  108.21  3.000
 PXI  H102  C10  H101  108.16  3.000
 PXI  H103  C10  C9    111.41  3.000
 PXI  H102  C10  C9    109.85  3.000
 PXI  H101  C10  C9    111.09  3.000
 PXI  H112  C11  H111  106.98  3.000
 PXI  H112  C11  C12   110.48  3.000
 PXI  H111  C11  C12   110.05  3.000
 PXI  H112  C11  C9    108.97  3.000
 PXI  H111  C11  C9    109.02  3.000
 PXI  C12   C11  C9    111.23  3.000
 PXI  H12   C12  C15   106.53  3.000
 PXI  H12   C12  N1    105.89  3.000
 PXI  C15   C12  N1    112.22  3.000
 PXI  H12   C12  C11   107.12  3.000
 PXI  C15   C12  C11   108.80  3.000
 PXI  N1    C12  C11   115.72  3.000
 PXI  C14   N1   C13   111.57  3.000
 PXI  C14   N1   C12   115.42  3.000
 PXI  C13   N1   C12   112.78  3.000
 PXI  H133  C13  H132  107.58  3.000
 PXI  H133  C13  H131  107.13  3.000
 PXI  H132  C13  H131  107.69  3.000
 PXI  H133  C13  N1    114.46  3.000
 PXI  H132  C13  N1    110.13  3.000
 PXI  H131  C13  N1    109.60  3.000
 PXI  H143  C14  H142  107.14  3.000
 PXI  H143  C14  H141  107.72  3.000
 PXI  H142  C14  H141  107.05  3.000
 PXI  H143  C14  N1    114.36  3.000
 PXI  H142  C14  N1    109.07  3.000
 PXI  H141  C14  N1    111.18  3.000
 PXI  H15   C15  O5    111.26  3.000
 PXI  H15   C15  C12   109.78  3.000
 PXI  O5    C15  C12   108.92  3.000
 PXI  H15   C15  C8    107.44  3.000
 PXI  O5    C15  C8    111.28  3.000
 PXI  C12   C15  C8    108.10  3.000
 PXI  HA    O5   C15   107.97  3.000
 PXI  H16   C16  C18   105.73  3.000
 PXI  H16   C16  C17   107.28  3.000
 PXI  C18   C16  C17   110.81  3.000
 PXI  H16   C16  C7    107.25  3.000
 PXI  C18   C16  C7    111.85  3.000
 PXI  C17   C16  C7    113.45  3.000
 PXI  H173  C17  H172  106.87  3.000
 PXI  H173  C17  H171  107.34  3.000
 PXI  H172  C17  H171  107.44  3.000
 PXI  H173  C17  C16   112.03  3.000
 PXI  H172  C17  C16   110.41  3.000
 PXI  H171  C17  C16   112.46  3.000
 PXI  H182  C18  H181  105.25  3.000
 PXI  H182  C18  C19   105.61  3.000
 PXI  H181  C18  C19   108.78  3.000
 PXI  H182  C18  C16   106.55  3.000
 PXI  H181  C18  C16   110.69  3.000
 PXI  C19   C18  C16   118.96  3.000
 PXI  H19   C19  C21   108.30  3.000
 PXI  H19   C19  C20   108.16  3.000
 PXI  C21   C19  C20   109.78  3.000
 PXI  H19   C19  C18   108.60  3.000
 PXI  C21   C19  C18   112.63  3.000
 PXI  C20   C19  C18   109.27  3.000
 PXI  H203  C20  H202  108.09  3.000
 PXI  H203  C20  H201  107.95  3.000
 PXI  H202  C20  H201  107.72  3.000
 PXI  H203  C20  C19   111.33  3.000
 PXI  H202  C20  C19   111.55  3.000
 PXI  H201  C20  C19   110.07  3.000
 PXI  C22   C21  O6    122.02  3.000
 PXI  C22   C21  C19   116.78  3.000
 PXI  O6    C21  C19   121.17  3.000
 PXI  H22   C22  C23   120.77  3.000
 PXI  H22   C22  C21   116.80  3.000
 PXI  C23   C22  C21   122.06  3.000
 PXI  H23   C23  C24   115.87  3.000
 PXI  H23   C23  C22   118.46  3.000
 PXI  C24   C23  C22   125.55  3.000
 PXI  H24   C24  C25   108.48  3.000
 PXI  H24   C24  C23   106.95  3.000
 PXI  C25   C24  C23   113.40  3.000
 PXI  H24   C24  C3    105.02  3.000
 PXI  C25   C24  C3    113.33  3.000
 PXI  C23   C24  C3    109.13  3.000
 PXI  H253  C25  H252  107.08  3.000
 PXI  H253  C25  H251  107.90  3.000
 PXI  H252  C25  H251  107.78  3.000
 PXI  H253  C25  C24   110.61  3.000
 PXI  H252  C25  C24   111.16  3.000
 PXI  H251  C25  C24   112.10  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
 PXI  Var_01  C24   C23  C22  C21  -171.70   0.0  0
 PXI  Var_02  C5    C4   O1   C3   -161.19  30.0  1
 PXI  Var_03  C23   C22  C21  C19   151.46  30.0  1
 PXI  Var_04  H22   C22  C23  C24     1.15   0.0  0
 PXI  Var_05  H1C1  C1   C2   C3    -69.04  30.0  3
 PXI  Var_06  H131  C13  N1   C12  -170.66  30.0  3
 PXI  Var_07  H141  C14  N1   C12    56.16  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
 PXI  chir_01  C3   C2   O1   C24  negativ
 PXI  chir_02  C5   C7   C6   C4   negativ
 PXI  chir_03  C7   O3   C5   C16  positiv
 PXI  chir_04  C8   O3   O4   C15  negativ
 PXI  chir_05  C9   O4   C10  C11  negativ
 PXI  chir_06  C12  N1   C15  C11  negativ
 PXI  chir_07  C15  O5   C8   C12  positiv
 PXI  chir_08  C16  C7   C17  C18  negativ
 PXI  chir_09  C19  C21  C20  C18  negativ
 PXI  chir_10  C24  C3   C23  C25  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
 PXI  plan-1  C19  0.020
 PXI  plan-1  C21  0.020
 PXI  plan-1  O6   0.020
 PXI  plan-1  C22  0.020
 PXI  plan-2  O1   0.020
 PXI  plan-2  C4   0.020
 PXI  plan-2  O2   0.020
 PXI  plan-2  C5   0.020
 PXI  plan-3  C21  0.020
 PXI  plan-3  C22  0.020
 PXI  plan-3  C23  0.020
 PXI  plan-3  C24  0.020
 PXI  plan-3  H22  0.020
 PXI  plan-3  H23  0.020

