# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 15:07:14 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: (5R,12R,17R)-17-amino-12-carboxy-1,1,5-trihydroxy-4,4-dimethyl-6,10-dioxo-2-oxa-14,15-dithia-7,11-diaza-1-phosphaoctadecan-18-oic acid 1-oxide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(CO[P](O)(O)=O)[C@@H](O)C(=O)NCCC(=O)N[C@@H](CSSC[C@H](N)C(O)=O)C(O)=O
#
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
 9Z6  9Z6  '(5R,12R,17R)-17-amino-12-carboxy-1,1,5-trihydroxy-4,4-dimethyl-6,10-dioxo-2-oxa-14,15-dithia-7,11-diaza-1-phosphaoctadecan-18-oic acid 1-oxide (non-preferred name)'  ligand  60  32  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9Z6
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
 9Z6  C11  C  C     0   0.513   3.3594  -2.3265  -0.6749
 9Z6  O12  O  O     0  -0.494   3.5379  -2.5543   0.5165
 9Z6  C10  C  CH1   0  -0.033   4.4493  -1.6250  -1.4866
 9Z6  O32  O  OH1   0  -0.662   5.6996  -2.0711  -1.0372
 9Z6  C02  C  CT    0  -0.159   4.3256  -0.0741  -1.4578
 9Z6  C04  C  CH2   0  -0.153   4.5545   0.4286  -0.0333
 9Z6  C01  C  CH3   0  -0.653   5.3941   0.4923  -2.3970
 9Z6  C03  C  CH3   0  -0.675   2.9406   0.3508  -1.9515
 9Z6  P06  P  P     0   1.452   5.0060   2.6837   1.2105
 9Z6  O09  O  O     0  -0.711   4.5925   2.2349   2.5529
 9Z6  O05  O  O2    0  -0.589   4.4422   1.8593  -0.0305
 9Z6  O07  O  OH1   0  -0.732   4.5179   4.1204   0.7219
 9Z6  O08  O  OH1   0  -0.742   6.6018   2.6469   1.1052
 9Z6  N13  N  NH1   0  -0.624   2.2530  -2.6734  -1.3383
 9Z6  C14  C  CH2   0  -0.286   1.0852  -3.2380  -0.7004
 9Z6  C15  C  CH2   0  -0.596   0.1246  -2.1521  -0.2203
 9Z6  C16  C  C     0   0.579  -1.0866  -2.7400   0.4651
 9Z6  O17  O  O     0  -0.493  -1.0055  -3.6693   1.2545
 9Z6  N18  N  NH1   0  -0.633  -2.2580  -2.1482   0.1705
 9Z6  C19  C  CH1   0  -0.167  -3.4932  -2.5953   0.7422
 9Z6  C20  C  C     0   0.547  -3.9189  -3.9264   0.1275
 9Z6  O21  O  O     0  -0.423  -3.4685  -4.3814  -0.8890
 9Z6  C23  C  CH2   0  -0.615  -4.5990  -1.5600   0.5361
 9Z6  S24  S  S2    0   0.002  -4.3115   0.0103   1.4047
 9Z6  O22  O  OH1   0  -0.589  -4.8682  -4.5011   0.8502
 9Z6  N28  N  NH2   0  -0.759  -5.0843   3.1640   1.1387
 9Z6  C27  C  CH1   0  -0.187  -4.4314   3.4004  -0.1184
 9Z6  C29  C  C     0   0.521  -5.2289   4.2739  -1.0851
 9Z6  O31  O  O     0  -0.432  -6.3825   4.5838  -0.9330
 9Z6  C26  C  CH2   0  -0.584  -4.0954   2.0815  -0.8199
 9Z6  S25  S  S2    0  -0.026  -3.0137   1.0189   0.1732
 9Z6  O30  O  OH1   0  -0.592  -4.4958   4.6534  -2.1243
 9Z6  H11  H  HCH1  0   0.258   4.3561  -1.9213  -2.5383
 9Z6  H29  H  HOH1  0   0.447   5.6218  -2.2686  -0.0948
 9Z6  H7   H  HCH2  0   0.252   3.8106   0.0205   0.6534
 9Z6  H8   H  HCH2  0   0.241   5.5469   0.1311   0.3186
 9Z6  H1   H  HCH3  0   0.233   5.2322   0.1391  -3.4174
 9Z6  H2   H  HCH3  0   0.240   5.3567   1.5811  -2.4220
 9Z6  H3   H  HCH3  0   0.237   6.3983   0.1961  -2.0937
 9Z6  H4   H  HCH3  0   0.236   2.1542   0.1258  -1.2291
 9Z6  H5   H  HCH3  0   0.251   2.9090   1.4229  -2.1416
 9Z6  H6   H  HCH3  0   0.235   2.6872  -0.1469  -2.8900
 9Z6  H10  H  HOH1  0   0.494   6.9789   2.9854   0.2821
 9Z6  H9   H  HOH1  0   0.504   4.6465   4.8228   1.3734
 9Z6  H12  H  HNH1  0   0.407   2.1851  -2.4465  -2.3177
 9Z6  H14  H  HCH2  0   0.268   0.5920  -3.8866  -1.4239
 9Z6  H13  H  HCH2  0   0.259   1.4030  -3.8609   0.1328
 9Z6  H15  H  HCH2  0   0.283   0.6348  -1.5081   0.5029
 9Z6  H16  H  HCH2  0   0.262  -0.1671  -1.5173  -1.0592
 9Z6  H17  H  HNH1  0   0.405  -2.2890  -1.4524  -0.5578
 9Z6  H18  H  HCH1  0   0.301  -3.3640  -2.7486   1.8169
 9Z6  H20  H  HCH2  0   0.302  -4.7768  -1.3635  -0.5226
 9Z6  H21  H  HCH2  0   0.318  -5.5327  -1.9345   0.9585
 9Z6  H19  H  HOH1  0   0.487  -5.1597  -5.3262   0.4331
 9Z6  H26  H  HNH2  0   0.346  -5.9800   2.7130   1.0014
 9Z6  H24  H  HCH1  0   0.283  -3.4884   3.9210   0.0766
 9Z6  H22  H  HCH2  0   0.294  -4.9971   1.5252  -1.0824
 9Z6  H23  H  HCH2  0   0.306  -3.5430   2.2631  -1.7427
 9Z6  H28  H  HOH1  0   0.484  -5.0247   5.1928  -2.7317
 9Z6  H25  H  HNH2  0   0.359  -5.2667   4.0388   1.6126

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
 9Z6  O09  P06  double  1.475  0.020  1.475
 9Z6  O07  P06  single  1.594  0.020  1.594
 9Z6  P06  O08  single  1.600  0.020  1.600
 9Z6  P06  O05  single  1.593  0.020  1.593
 9Z6  C04  O05  single  1.435  0.020  1.435
 9Z6  C04  C02  single  1.528  0.020  1.528
 9Z6  C10  O32  single  1.402  0.020  1.402
 9Z6  C10  C02  single  1.556  0.020  1.556
 9Z6  C10  C11  single  1.529  0.020  1.529
 9Z6  O31  C29  double  1.204  0.020  1.204
 9Z6  N13  C11  single  1.336  0.020  1.336
 9Z6  N13  C14  single  1.446  0.020  1.446
 9Z6  C01  C02  single  1.531  0.020  1.531
 9Z6  S24  S25  single  2.054  0.020  2.054
 9Z6  S24  C23  single  1.817  0.020  1.817
 9Z6  S25  C26  single  1.813  0.020  1.813
 9Z6  C02  C03  single  1.531  0.020  1.531
 9Z6  C11  O12  double  1.226  0.020  1.226
 9Z6  C14  C15  single  1.527  0.020  1.527
 9Z6  C29  O30  single  1.327  0.020  1.327
 9Z6  C29  C27  single  1.528  0.020  1.528
 9Z6  C15  C16  single  1.511  0.020  1.511
 9Z6  C23  C19  single  1.529  0.020  1.529
 9Z6  C16  N18  single  1.345  0.020  1.345
 9Z6  C16  O17  double  1.222  0.020  1.222
 9Z6  C26  C27  single  1.531  0.020  1.531
 9Z6  N18  C19  single  1.433  0.020  1.433
 9Z6  C27  N28  single  1.436  0.020  1.436
 9Z6  C19  C20  single  1.527  0.020  1.527
 9Z6  C20  O21  double  1.201  0.020  1.201
 9Z6  C20  O22  single  1.324  0.020  1.324
 9Z6  C01  H1   single  0.970  0.020  1.090
 9Z6  C01  H2   single  0.970  0.020  1.090
 9Z6  C01  H3   single  0.970  0.020  1.090
 9Z6  C03  H4   single  0.970  0.020  1.090
 9Z6  C03  H5   single  0.970  0.020  1.090
 9Z6  C03  H6   single  0.970  0.020  1.090
 9Z6  C04  H7   single  0.970  0.020  1.090
 9Z6  C04  H8   single  0.970  0.020  1.090
 9Z6  O07  H9   single  0.850  0.020  0.980
 9Z6  O08  H10  single  0.850  0.020  0.980
 9Z6  C10  H11  single  0.970  0.020  1.090
 9Z6  N13  H12  single  0.860  0.020  1.020
 9Z6  C14  H13  single  0.970  0.020  1.090
 9Z6  C14  H14  single  0.970  0.020  1.090
 9Z6  C15  H15  single  0.970  0.020  1.090
 9Z6  C15  H16  single  0.970  0.020  1.090
 9Z6  N18  H17  single  0.860  0.020  1.020
 9Z6  C19  H18  single  0.970  0.020  1.090
 9Z6  O22  H19  single  0.850  0.020  0.980
 9Z6  C23  H20  single  0.970  0.020  1.090
 9Z6  C23  H21  single  0.970  0.020  1.090
 9Z6  C26  H22  single  0.970  0.020  1.090
 9Z6  C26  H23  single  0.970  0.020  1.090
 9Z6  C27  H24  single  0.970  0.020  1.090
 9Z6  N28  H25  single  0.890  0.020  1.040
 9Z6  N28  H26  single  0.890  0.020  1.040
 9Z6  O30  H28  single  0.850  0.020  0.980
 9Z6  O32  H29  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
 9Z6  N13  C11  C10  116.47  3.000
 9Z6  N13  C11  O12  123.71  3.000
 9Z6  C10  C11  O12  119.82  3.000
 9Z6  H11  C10  C02  106.28  3.000
 9Z6  H11  C10  O32  107.29  3.000
 9Z6  C02  C10  O32  112.47  3.000
 9Z6  H11  C10  C11  108.94  3.000
 9Z6  C02  C10  C11  113.00  3.000
 9Z6  O32  C10  C11  108.64  3.000
 9Z6  H29  O32  C10  107.82  3.000
 9Z6  C03  C02  C01  109.32  3.000
 9Z6  C03  C02  C04  110.18  3.000
 9Z6  C01  C02  C04  110.22  3.000
 9Z6  C03  C02  C10  110.04  3.000
 9Z6  C01  C02  C10  107.57  3.000
 9Z6  C04  C02  C10  109.47  3.000
 9Z6  H8   C04  H7   108.31  3.000
 9Z6  H8   C04  O05  109.96  3.000
 9Z6  H7   C04  O05  108.55  3.000
 9Z6  H8   C04  C02  110.26  3.000
 9Z6  H7   C04  C02  111.19  3.000
 9Z6  O05  C04  C02  108.55  3.000
 9Z6  H3   C01  H2   108.03  3.000
 9Z6  H3   C01  H1   107.98  3.000
 9Z6  H2   C01  H1   107.25  3.000
 9Z6  H3   C01  C02  111.82  3.000
 9Z6  H2   C01  C02  111.08  3.000
 9Z6  H1   C01  C02  110.49  3.000
 9Z6  H6   C03  H5   106.97  3.000
 9Z6  H6   C03  H4   107.91  3.000
 9Z6  H5   C03  H4   107.31  3.000
 9Z6  H6   C03  C02  111.14  3.000
 9Z6  H5   C03  C02  110.85  3.000
 9Z6  H4   C03  C02  112.42  3.000
 9Z6  O08  P06  O07  107.82  3.000
 9Z6  O08  P06  O05  106.85  3.000
 9Z6  O07  P06  O05   96.85  3.000
 9Z6  O05  P06  O09  116.90  3.000
 9Z6  O08  P06  O09  109.43  3.000
 9Z6  O07  P06  O09  117.87  3.000
 9Z6  P06  O05  C04  119.33  3.000
 9Z6  H9   O07  P06  114.06  3.000
 9Z6  H10  O08  P06  115.92  3.000
 9Z6  H12  N13  C14  117.54  3.000
 9Z6  H12  N13  C11  118.69  3.000
 9Z6  C14  N13  C11  123.46  3.000
 9Z6  H13  C14  H14  107.46  3.000
 9Z6  H14  C14  C15  110.32  3.000
 9Z6  H13  C14  C15  110.50  3.000
 9Z6  H14  C14  N13  107.76  3.000
 9Z6  H13  C14  N13  109.01  3.000
 9Z6  C15  C14  N13  111.66  3.000
 9Z6  H16  C15  H15  106.87  3.000
 9Z6  H16  C15  C16  111.14  3.000
 9Z6  H15  C15  C16  107.64  3.000
 9Z6  H16  C15  C14  109.87  3.000
 9Z6  H15  C15  C14  109.44  3.000
 9Z6  C16  C15  C14  111.72  3.000
 9Z6  N18  C16  O17  122.27  3.000
 9Z6  O17  C16  C15  122.40  3.000
 9Z6  N18  C16  C15  115.31  3.000
 9Z6  H17  N18  C19  118.51  3.000
 9Z6  H17  N18  C16  119.27  3.000
 9Z6  C19  N18  C16  121.75  3.000
 9Z6  H18  C19  C23  108.23  3.000
 9Z6  H18  C19  C20  107.85  3.000
 9Z6  C23  C19  C20  109.54  3.000
 9Z6  H18  C19  N18  109.51  3.000
 9Z6  C20  C19  N18  110.60  3.000
 9Z6  C23  C19  N18  111.01  3.000
 9Z6  O22  C20  O21  124.48  3.000
 9Z6  O22  C20  C19  111.01  3.000
 9Z6  O21  C20  C19  124.50  3.000
 9Z6  H21  C23  H20  107.33  3.000
 9Z6  H21  C23  S24  104.30  3.000
 9Z6  H20  C23  S24  109.50  3.000
 9Z6  H21  C23  C19  109.53  3.000
 9Z6  H20  C23  C19  111.74  3.000
 9Z6  S24  C23  C19  113.98  3.000
 9Z6  S25  S24  C23  103.75  3.000
 9Z6  H19  O22  C20  110.49  3.000
 9Z6  H26  N28  H25  106.82  3.000
 9Z6  H26  N28  C27  110.92  3.000
 9Z6  H25  N28  C27  110.47  3.000
 9Z6  H24  C27  C26  107.59  3.000
 9Z6  H24  C27  C29  106.89  3.000
 9Z6  C26  C27  C29  108.49  3.000
 9Z6  H24  C27  N28  108.30  3.000
 9Z6  C26  C27  N28  111.04  3.000
 9Z6  C29  C27  N28  114.25  3.000
 9Z6  O30  C29  O31  123.68  3.000
 9Z6  O30  C29  C27  111.76  3.000
 9Z6  O31  C29  C27  124.56  3.000
 9Z6  H23  C26  H22  107.44  3.000
 9Z6  H23  C26  S25  105.00  3.000
 9Z6  H22  C26  S25  109.02  3.000
 9Z6  H23  C26  C27  110.82  3.000
 9Z6  H22  C26  C27  111.58  3.000
 9Z6  S25  C26  C27  112.64  3.000
 9Z6  C26  S25  S24  103.85  3.000
 9Z6  H28  O30  C29  110.39  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
 9Z6  CONST_01  C14  N13  C11  O12     0.00   0.0  0
 9Z6  CONST_02  C14  N13  C11  C10   180.00   0.0  0
 9Z6  CONST_03  C19  N18  C16  C15   180.00   0.0  0
 9Z6  CONST_04  C19  N18  C16  O17     0.00   0.0  0
 9Z6  CONST_05  H12  N13  C11  O12   180.00   0.0  0
 9Z6  CONST_06  H17  N18  C16  C15     0.00   0.0  0
 9Z6  CONST_07  H19  O22  C20  C19   180.00   0.0  0
 9Z6  CONST_08  H28  O30  C29  C27   180.00   0.0  0
 9Z6  Var_01    C15  C14  N13  C11    88.28  30.0  3
 9Z6  Var_02    O05  C04  C02  C10   179.74  30.0  1
 9Z6  Var_03    O09  P06  O05  C04   -49.85  30.0  1
 9Z6  Var_04    C16  C15  C14  N13  -179.15  30.0  3
 9Z6  Var_05    N18  C16  C15  C14  -138.97  30.0  3
 9Z6  Var_06    C27  C26  S25  S24    84.72  30.0  3
 9Z6  Var_07    H1   C01  C02  C10    60.95  30.0  3
 9Z6  Var_08    H4   C03  C02  C10    72.11  30.0  3
 9Z6  Var_09    H20  C23  S24  S25   -45.08  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
 9Z6  chir_01  C10  O32  C02  C11  positiv
 9Z6  chir_02  C19  C23  N18  C20  positiv
 9Z6  chir_03  C27  N28  C29  C26  positiv

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
 9Z6  plan-1  C11  0.020
 9Z6  plan-1  O12  0.020
 9Z6  plan-1  C10  0.020
 9Z6  plan-1  N13  0.020
 9Z6  plan-1  C14  0.020
 9Z6  plan-1  H12  0.020
 9Z6  plan-2  C15  0.020
 9Z6  plan-2  C16  0.020
 9Z6  plan-2  O17  0.020
 9Z6  plan-2  N18  0.020
 9Z6  plan-2  C19  0.020
 9Z6  plan-2  H17  0.020
 9Z6  plan-3  C19  0.020
 9Z6  plan-3  C20  0.020
 9Z6  plan-3  O21  0.020
 9Z6  plan-3  O22  0.020
 9Z6  plan-3  H19  0.020
 9Z6  plan-4  C27  0.020
 9Z6  plan-4  C29  0.020
 9Z6  plan-4  O31  0.020
 9Z6  plan-4  O30  0.020
 9Z6  plan-4  H28  0.020

