# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 19:14:40 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (1R,2R,4S,5S,7s)-7-({[4-fluoro-2-(thiophen-2-yl)phenyl]carbamoyl}oxy)-9,9-dimethyl-3-oxa-9-azatricyclo[3.3.1.0~2,4~]nonan-9-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[N+]1(C)[C@H]2C[C@@H](C[C@@H]1[C@H]3O[C@@H]23)OC(=O)Nc4ccc(F)cc4c5sccc5
#
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
 9EC  9EC  (1R,2R,4S,5S,7s)-7-({[4-fluoro-2-(thiophen-2-yl)phenyl]carbamoyl}oxy)-9,9-dimethyl-3-oxa-9-azatricyclo[3.3.1.0~2,4~]nonan-9-ium  ligand  49  27  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_9EC
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
 9EC  C10  C  CR6   0   0.148  -3.3492  -0.2090  -0.1063
 9EC  C11  C  CR5   0  -0.227  -3.2995   1.2006   0.2878
 9EC  C12  C  CR15  0  -0.223  -4.2485   2.1517   0.0225
 9EC  C13  C  CR15  0  -0.179  -3.9608   3.4099   0.6077
 9EC  C14  C  CR15  0  -0.459  -2.7991   3.3996   1.3179
 9EC  C02  C  C     0   0.738   0.0626  -0.7919   0.4011
 9EC  C04  C  CR6   0   0.250  -2.2109  -0.9612  -0.4267
 9EC  C05  C  CR16  0  -0.241  -2.3350  -2.2934  -0.8025
 9EC  C06  C  CR16  0  -0.431  -3.5736  -2.9076  -0.8637
 9EC  C07  C  CR6   0   0.562  -4.6878  -2.1508  -0.5571
 9EC  C09  C  CR16  0  -0.505  -4.5995  -0.8281  -0.1843
 9EC  C17  C  CH1   0   0.001   2.3240  -0.3602   0.9784
 9EC  C18  C  CH2   0  -0.534   3.0534  -1.5553   0.3302
 9EC  C19  C  CR15  0  -0.148   4.0592  -1.1476  -0.7422
 9EC  C20  C  CR15  0   0.010   3.2869  -0.3494  -1.7732
 9EC  C21  C  CR15  0   0.009   3.3461   1.0428  -1.3679
 9EC  C26  C  CR15  0  -0.155   4.1523   1.0980  -0.0859
 9EC  C27  C  CH2   0  -0.514   3.1600   0.9297   1.0630
 9EC  F08  F  F     0  -0.312  -5.8990  -2.7229  -0.6126
 9EC  N03  N  NH1   0  -0.773  -0.9368  -0.3601  -0.4036
 9EC  N23  N  N     1  -0.407   5.0347  -0.1362  -0.1583
 9EC  O01  O  O     0  -0.489  -0.0098  -1.7272   1.1647
 9EC  O16  O  O2    0  -0.483   1.1449  -0.0270   0.2339
 9EC  O22  O  O2    0  -0.457   4.0150   0.5955  -2.5309
 9EC  S15  S  S2    0   0.219  -2.0400   1.8686   1.2669
 9EC  H37  H  HCR5  0   0.270  -5.1220   1.9585  -0.5849
 9EC  H38  H  HCR5  0   0.271  -4.5870   4.2832   0.4977
 9EC  H39  H  HCR5  0   0.300  -2.3408   4.2138   1.8578
 9EC  H34  H  HCR6  0   0.281  -1.4502  -2.8554  -1.0690
 9EC  H35  H  HCR6  0   0.288  -3.6681  -3.9459  -1.1517
 9EC  H36  H  HCR6  0   0.283  -5.4971  -0.2840   0.0778
 9EC  H28  H  HCH1  0   0.299   2.0336  -0.6428   1.9905
 9EC  H40  H  HCH2  0   0.302   3.5358  -2.1595   1.0970
 9EC  H41  H  HCH2  0   0.315   2.3348  -2.2300  -0.1369
 9EC  H29  H  HCR5  0   0.329   4.6206  -2.0008  -1.1218
 9EC  H30  H  HCR5  0   0.301   2.4337  -0.8190  -2.2501
 9EC  H31  H  HCR5  0   0.303   2.5442   1.7608  -1.4997
 9EC  H43  H  HCH3  0   0.291   6.7345  -0.9044  -1.1350
 9EC  H42  H  HCH3  0   0.317   6.0092   0.4748  -1.9784
 9EC  H44  H  HCH3  0   0.289   6.9273   0.7352  -0.4850
 9EC  H45  H  HCH3  0   0.306   6.1723   0.2908   1.5573
 9EC  H46  H  HCH3  0   0.298   4.8232  -0.7958   1.8876
 9EC  H47  H  HCH3  0   0.308   6.2366  -1.3993   1.0202
 9EC  H32  H  HCR5  0   0.330   4.7851   1.9758   0.0422
 9EC  H49  H  HCH2  0   0.314   2.4916   1.7922   1.0630
 9EC  H48  H  HCH2  0   0.302   3.6792   0.9733   2.0191
 9EC  H33  H  HNH1  0   0.413  -0.7793   0.4609  -0.9702
 9EC  C24  C  CH3   0  -0.553   6.2556   0.0636  -1.0128
 9EC  C25  C  CH3   0  -0.559   5.5891  -0.5399   1.1695

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
 9EC  C25  N23  single    1.494  0.020  1.494
 9EC  C24  N23  single    1.504  0.020  1.504
 9EC  N23  C19  single    1.522  0.020  1.522
 9EC  N23  C26  single    1.519  0.020  1.519
 9EC  C19  C18  single    1.526  0.020  1.526
 9EC  C19  C20  single    1.515  0.020  1.515
 9EC  C18  C17  single    1.543  0.020  1.543
 9EC  C20  O22  single    1.413  0.020  1.413
 9EC  C20  C21  single    1.451  0.020  1.451
 9EC  C26  C27  single    1.527  0.020  1.527
 9EC  C26  C21  single    1.515  0.020  1.515
 9EC  C17  C27  single    1.539  0.020  1.539
 9EC  C17  O16  single    1.434  0.020  1.434
 9EC  O22  C21  single    1.414  0.020  1.414
 9EC  O01  C02  double    1.210  0.020  1.210
 9EC  O16  C02  single    1.336  0.020  1.336
 9EC  C14  C13  aromatic  1.362  0.020  1.362
 9EC  C14  S15  aromatic  1.710  0.020  1.710
 9EC  C02  N03  single    1.354  0.020  1.354
 9EC  C13  C12  aromatic  1.417  0.020  1.417
 9EC  S15  C11  aromatic  1.729  0.020  1.729
 9EC  N03  C04  single    1.409  0.020  1.409
 9EC  C12  C11  aromatic  1.369  0.020  1.369
 9EC  C11  C10  single    1.465  0.020  1.465
 9EC  C04  C10  aromatic  1.402  0.020  1.402
 9EC  C04  C05  aromatic  1.390  0.020  1.390
 9EC  C10  C09  aromatic  1.397  0.020  1.397
 9EC  C05  C06  aromatic  1.384  0.020  1.384
 9EC  C09  C07  aromatic  1.377  0.020  1.377
 9EC  C06  C07  aromatic  1.381  0.020  1.381
 9EC  C07  F08  single    1.341  0.020  1.341
 9EC  C12  H37  single    0.930  0.020  1.080
 9EC  C13  H38  single    0.930  0.020  1.080
 9EC  C14  H39  single    0.930  0.020  1.080
 9EC  C05  H34  single    0.930  0.020  1.080
 9EC  C06  H35  single    0.930  0.020  1.080
 9EC  C09  H36  single    0.930  0.020  1.080
 9EC  C17  H28  single    0.970  0.020  1.090
 9EC  C18  H40  single    0.970  0.020  1.090
 9EC  C18  H41  single    0.970  0.020  1.090
 9EC  C19  H29  single    0.970  0.020  1.090
 9EC  C20  H30  single    0.970  0.020  1.090
 9EC  C21  H31  single    0.970  0.020  1.090
 9EC  C24  H43  single    0.970  0.020  1.090
 9EC  C24  H42  single    0.970  0.020  1.090
 9EC  C24  H44  single    0.970  0.020  1.090
 9EC  C25  H45  single    0.970  0.020  1.090
 9EC  C25  H46  single    0.970  0.020  1.090
 9EC  C25  H47  single    0.970  0.020  1.090
 9EC  C26  H32  single    0.970  0.020  1.090
 9EC  C27  H49  single    0.970  0.020  1.090
 9EC  C27  H48  single    0.970  0.020  1.090
 9EC  N03  H33  single    0.860  0.020  1.020

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
 9EC  C09  C10  C04  118.44  3.000
 9EC  C09  C10  C11  118.15  3.000
 9EC  C04  C10  C11  123.40  3.000
 9EC  S15  C11  C12  110.25  3.000
 9EC  C12  C11  C10  126.35  3.000
 9EC  S15  C11  C10  123.29  3.000
 9EC  H37  C12  C13  123.68  3.000
 9EC  H37  C12  C11  122.99  3.000
 9EC  C13  C12  C11  113.32  3.000
 9EC  H38  C13  C14  123.63  3.000
 9EC  H38  C13  C12  123.92  3.000
 9EC  C14  C13  C12  112.45  3.000
 9EC  H39  C14  S15  120.14  3.000
 9EC  H39  C14  C13  128.14  3.000
 9EC  S15  C14  C13  111.72  3.000
 9EC  O16  C02  O01  124.77  3.000
 9EC  O16  C02  N03  109.94  3.000
 9EC  O01  C02  N03  125.29  3.000
 9EC  N03  C04  C05  119.61  3.000
 9EC  C05  C04  C10  120.25  3.000
 9EC  N03  C04  C10  120.12  3.000
 9EC  H34  C05  C06  119.38  3.000
 9EC  H34  C05  C04  119.45  3.000
 9EC  C06  C05  C04  121.15  3.000
 9EC  H35  C06  C07  120.97  3.000
 9EC  H35  C06  C05  121.07  3.000
 9EC  C07  C06  C05  117.96  3.000
 9EC  F08  C07  C09  118.62  3.000
 9EC  F08  C07  C06  119.06  3.000
 9EC  C09  C07  C06  122.32  3.000
 9EC  H36  C09  C07  119.70  3.000
 9EC  H36  C09  C10  120.40  3.000
 9EC  C07  C09  C10  119.87  3.000
 9EC  H28  C17  O16  108.86  3.000
 9EC  H28  C17  C27  108.10  3.000
 9EC  O16  C17  C27  106.29  3.000
 9EC  H28  C17  C18  108.37  3.000
 9EC  O16  C17  C18  110.53  3.000
 9EC  C27  C17  C18  114.55  3.000
 9EC  H41  C18  H40  104.49  3.000
 9EC  H41  C18  C19  107.37  3.000
 9EC  H40  C18  C19  110.55  3.000
 9EC  H41  C18  C17  110.34  3.000
 9EC  H40  C18  C17  110.09  3.000
 9EC  C19  C18  C17  113.57  3.000
 9EC  H29  C19  N23  108.90  3.000
 9EC  H29  C19  C20  115.97  3.000
 9EC  N23  C19  C20  103.75  3.000
 9EC  H29  C19  C18  112.04  3.000
 9EC  C20  C19  C18  106.44  3.000
 9EC  N23  C19  C18  109.30  3.000
 9EC  H30  C20  O22  117.33  3.000
 9EC  H30  C20  C21  124.77  3.000
 9EC  O22  C20  C21   59.15  3.000
 9EC  H30  C20  C19  118.17  3.000
 9EC  C21  C20  C19  107.12  3.000
 9EC  O22  C20  C19  117.03  3.000
 9EC  H31  C21  O22  117.33  3.000
 9EC  H31  C21  C26  118.17  3.000
 9EC  O22  C21  C26  117.11  3.000
 9EC  H31  C21  C20  124.82  3.000
 9EC  O22  C21  C20   59.08  3.000
 9EC  C26  C21  C20  107.03  3.000
 9EC  H32  C26  N23  108.83  3.000
 9EC  H32  C26  C27  112.19  3.000
 9EC  N23  C26  C27  108.89  3.000
 9EC  H32  C26  C21  115.96  3.000
 9EC  C27  C26  C21  106.66  3.000
 9EC  N23  C26  C21  103.83  3.000
 9EC  H48  C27  H49  105.10  3.000
 9EC  H48  C27  C26  110.26  3.000
 9EC  H49  C27  C26  108.11  3.000
 9EC  H48  C27  C17  109.92  3.000
 9EC  H49  C27  C17  109.25  3.000
 9EC  C26  C27  C17  113.81  3.000
 9EC  H33  N03  C04  118.60  3.000
 9EC  H33  N03  C02  118.53  3.000
 9EC  C04  N03  C02  122.77  3.000
 9EC  C26  N23  C25  113.12  3.000
 9EC  C26  N23  C24  113.01  3.000
 9EC  C25  N23  C24  103.86  3.000
 9EC  C26  N23  C19  100.72  3.000
 9EC  C24  N23  C19  113.00  3.000
 9EC  C25  N23  C19  113.53  3.000
 9EC  C17  O16  C02  117.92  3.000
 9EC  C21  O22  C20   61.76  3.000
 9EC  C14  S15  C11   92.26  3.000
 9EC  H44  C24  H42  109.91  3.000
 9EC  H44  C24  H43  109.43  3.000
 9EC  H42  C24  H43  109.86  3.000
 9EC  H44  C24  N23  107.94  3.000
 9EC  H42  C24  N23  111.97  3.000
 9EC  H43  C24  N23  107.66  3.000
 9EC  H47  C25  H46  109.06  3.000
 9EC  H47  C25  H45  109.51  3.000
 9EC  H46  C25  H45  108.93  3.000
 9EC  H47  C25  N23  108.22  3.000
 9EC  H46  C25  N23  113.05  3.000
 9EC  H45  C25  N23  108.04  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
 9EC  CONST_01  C14  S15  C11  C10   180.00   0.0  0
 9EC  CONST_02  C13  C12  C11  C10   180.00   0.0  0
 9EC  CONST_03  C06  C05  C04  C10     0.00   0.0  0
 9EC  CONST_04  C06  C07  C09  C10     0.00   0.0  0
 9EC  CONST_05  C13  C14  S15  C11     0.00   0.0  0
 9EC  CONST_06  C14  C13  C12  C11     0.00   0.0  0
 9EC  CONST_07  C05  C04  C10  C11   180.00   0.0  0
 9EC  CONST_08  C07  C09  C10  C11   180.00   0.0  0
 9EC  CONST_09  S15  C14  C13  C12     0.00   0.0  0
 9EC  CONST_10  C14  S15  C11  C12     0.00   0.0  0
 9EC  CONST_13  S15  C11  C12  C13     0.00   0.0  0
 9EC  CONST_15  C07  C09  C10  C04     0.00   0.0  0
 9EC  CONST_16  C07  C06  C05  C04     0.00   0.0  0
 9EC  CONST_17  C09  C10  C04  C05     0.00   0.0  0
 9EC  CONST_18  C09  C07  C06  C05     0.00   0.0  0
 9EC  CONST_20  F08  C07  C09  C10   180.00   0.0  0
 9EC  CONST_21  N03  C04  C10  C11     0.00   0.0  0
 9EC  CONST_22  F08  C07  C06  C05   180.00   0.0  0
 9EC  CONST_23  N03  C04  C05  C06   180.00   0.0  0
 9EC  CONST_24  N03  C04  C10  C09   180.00   0.0  0
 9EC  CONST_25  H37  C12  C11  C10     0.00   0.0  0
 9EC  CONST_26  H34  C05  C04  C10   180.00   0.0  0
 9EC  CONST_27  H39  C14  S15  C11   180.00   0.0  0
 9EC  CONST_28  H38  C13  C12  C11   180.00   0.0  0
 9EC  CONST_29  H36  C09  C10  C11     0.00   0.0  0
 9EC  CONST_30  H35  C06  C05  C04   180.00   0.0  0
 9EC  CONST_34  O01  C02  N03  C04     0.00   0.0  0
 9EC  CONST_35  O16  C02  N03  C04   180.00   0.0  0
 9EC  Var_01    C26  C21  C20  C19    -0.13  30.0  1
 9EC  Var_02    H30  C20  O22  C21   116.04  30.0  1
 9EC  Var_03    H45  C25  N23  C19  -173.16  30.0  3
 9EC  Var_04    H43  C24  N23  C19   -57.51  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
 9EC  chir_01  C17  C18  C27  O16  negativ
 9EC  chir_02  C19  N23  C18  C20  negativ
 9EC  chir_05  C26  N23  C27  C21  positiv
 9EC  chir_06  C20  C19  O22  C21  both
 9EC  chir_07  C21  O22  C26  C20  both

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
 9EC  plan-1  C10  0.020
 9EC  plan-1  C11  0.020
 9EC  plan-1  C12  0.020
 9EC  plan-1  C13  0.020
 9EC  plan-1  C14  0.020
 9EC  plan-1  S15  0.020
 9EC  plan-1  H37  0.020
 9EC  plan-1  H38  0.020
 9EC  plan-1  H39  0.020
 9EC  plan-2  C10  0.020
 9EC  plan-2  C11  0.020
 9EC  plan-2  C04  0.020
 9EC  plan-2  C05  0.020
 9EC  plan-2  C06  0.020
 9EC  plan-2  C07  0.020
 9EC  plan-2  C09  0.020
 9EC  plan-2  F08  0.020
 9EC  plan-2  N03  0.020
 9EC  plan-2  H34  0.020
 9EC  plan-2  H35  0.020
 9EC  plan-2  H36  0.020
 9EC  plan-3  C02  0.020
 9EC  plan-3  C04  0.020
 9EC  plan-3  N03  0.020
 9EC  plan-3  H33  0.020
 9EC  plan-4  C02  0.020
 9EC  plan-4  N03  0.020
 9EC  plan-4  O01  0.020
 9EC  plan-4  O16  0.020

