# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 04:47:22 2022
#   Inital geometry file: a 101 line input string
#   Ligand name: (1R,2R,3S,5S,8S)-3-{[(3-hydroxyphenyl)carbonyl]oxy}-8-methyl-8-azoniabicyclo[3.2.1]octane-2-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[NH+]1[C@H]2CC[C@@H]1[C@H]([C@H](C2)OC(=O)c3cccc(O)c3)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
 OBE  OBE  (1R,2R,3S,5S,8S)-3-{[(3-hydroxyphenyl)carbonyl]oxy}-8-methyl-8-azoniabicyclo[3.2.1]octane-2-carboxylate  ligand  41  22  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OBE
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
 OBE  C1    C  CH1    0  -0.142   3.2767  -0.0709  -0.8894
 OBE  C2    C  CH1    0  -0.432   1.8008  -0.4876  -0.9026
 OBE  C3    C  CH1    0   0.046   0.9717   0.6185  -0.2336
 OBE  C4    C  CH2    0  -0.493   1.5589   1.0673   1.1037
 OBE  C5    C  CH1    0  -0.120   3.0619   1.2922   0.9806
 OBE  C6    C  CH2    0  -0.480   3.4338   2.2489  -0.1574
 OBE  C7    C  CH2    0  -0.477   3.5348   1.3481  -1.4073
 OBE  C9    C  CR6    0  -0.085  -2.6712   0.1819   0.0585
 OBE  C10   C  CR16   0  -0.351  -3.8302   0.9260   0.2505
 OBE  C11   C  CR6    0   0.378  -5.0648   0.2892   0.3085
 OBE  C12   C  CR16   0  -0.368  -5.1315  -1.0952   0.1661
 OBE  C13   C  CR16   0  -0.231  -3.9698  -1.8273  -0.0288
 OBE  C14   C  CR16   0  -0.302  -2.7331  -1.2040  -0.0830
 OBE  C15   C  C      0   0.507   1.5820  -1.8544  -0.2082
 OBE  C16   C  CH3    0  -0.534   5.1342  -0.0745   0.7690
 OBE  N1    N  NT1    1  -0.535   3.6828   0.0049   0.5469
 OBE  O1    O  O2     0  -0.472  -0.3462   0.0950  -0.0659
 OBE  O2    O  O      0  -0.443  -1.2894   2.1219  -0.0173
 OBE  O3    O  OC    -1  -0.543   0.8335  -2.6704  -0.7428
 OBE  O4    O  O      0  -0.605   2.2006  -2.0216   0.8870
 OBE  O5    O  OH1    0  -0.630  -6.1549   1.0551   0.5011
 OBE  H1    H  HCH1   0   0.308   3.8840  -0.8235  -1.3924
 OBE  H2    H  HCH1   0   0.285   1.4911  -0.5717  -1.9462
 OBE  H3    H  HCH1   0   0.272   0.9246   1.4748  -0.9118
 OBE  H41   H  HCH2   0   0.270   1.3597   0.3237   1.8780
 OBE  H42   H  HCH2   0   0.282   1.0973   2.0013   1.4242
 OBE  H5    H  HCH1   0   0.303   3.4778   1.5818   1.9443
 OBE  H61   H  HCH2   0   0.275   2.6883   3.0362  -0.2622
 OBE  H62   H  HCH2   0   0.277   4.3844   2.7390   0.0489
 OBE  H71   H  HCH2   0   0.278   2.8141   1.6151  -2.1796
 OBE  H72   H  HCH2   0   0.279   4.5225   1.4150  -1.8610
 OBE  H10   H  HCR6   0   0.270  -3.7793   2.0021   0.3569
 OBE  H12   H  HCR6   0   0.280  -6.0884  -1.6031   0.2057
 OBE  H13   H  HCR6   0   0.269  -4.0357  -2.9013  -0.1404
 OBE  H14   H  HCR6   0   0.269  -1.8391  -1.7906  -0.2432
 OBE  H161  H  HCH3   0   0.283   5.3348   0.0464   1.8300
 OBE  H162  H  HCH3   0   0.282   5.4855  -1.0508   0.4450
 OBE  H163  H  HCH3   0   0.274   5.6568   0.6988   0.2106
 OBE  HN1   H  HNT1   0   0.469   3.1831  -0.8486   0.9780
 OBE  HO5   H  HOH1   0   0.477  -6.9515   0.5129   0.5169
 OBE  C8    C  C      0   0.610  -1.3820   0.9186  -0.0092

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
 OBE  C1   C2    single    1.534  0.020  1.534
 OBE  C1   C7    single    1.532  0.020  1.532
 OBE  C1   N1    single    1.495  0.020  1.495
 OBE  C1   H1    single    0.970  0.020  1.090
 OBE  C2   C3    single    1.536  0.020  1.536
 OBE  C2   C15   single    1.549  0.020  1.549
 OBE  C2   H2    single    0.970  0.020  1.090
 OBE  C3   C4    single    1.528  0.020  1.528
 OBE  C3   O1    single    1.428  0.020  1.428
 OBE  C3   H3    single    0.970  0.020  1.090
 OBE  C4   C5    single    1.525  0.020  1.525
 OBE  C4   H41   single    0.970  0.020  1.090
 OBE  C4   H42   single    0.970  0.020  1.090
 OBE  C5   C6    single    1.533  0.020  1.533
 OBE  C5   N1    single    1.494  0.020  1.494
 OBE  C5   H5    single    0.970  0.020  1.090
 OBE  C6   C7    single    1.544  0.020  1.544
 OBE  C6   H61   single    0.970  0.020  1.090
 OBE  C6   H62   single    0.970  0.020  1.090
 OBE  C7   H71   single    0.970  0.020  1.090
 OBE  C7   H72   single    0.970  0.020  1.090
 OBE  C8   C9    single    1.486  0.020  1.486
 OBE  C8   O1    single    1.325  0.020  1.325
 OBE  C8   O2    double    1.207  0.020  1.207
 OBE  C9   C10   aromatic  1.391  0.020  1.391
 OBE  C9   C14   aromatic  1.395  0.020  1.395
 OBE  C10  C11   aromatic  1.390  0.020  1.390
 OBE  C10  H10   single    0.930  0.020  1.080
 OBE  C11  C12   aromatic  1.393  0.020  1.393
 OBE  C11  O5    single    1.346  0.020  1.346
 OBE  C12  C13   aromatic  1.387  0.020  1.387
 OBE  C12  H12   single    0.930  0.020  1.080
 OBE  C13  C14   aromatic  1.386  0.020  1.386
 OBE  C13  H13   single    0.930  0.020  1.080
 OBE  C14  H14   single    0.930  0.020  1.080
 OBE  C15  O3    deloc     1.230  0.020  1.230
 OBE  C15  O4    deloc     1.269  0.020  1.269
 OBE  C16  N1    single    1.470  0.020  1.470
 OBE  C16  H161  single    0.970  0.020  1.090
 OBE  C16  H162  single    0.970  0.020  1.090
 OBE  C16  H163  single    0.970  0.020  1.090
 OBE  N1   HN1   single    0.890  0.020  1.040
 OBE  O5   HO5   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
 OBE  H1    C1   N1    109.09  3.000
 OBE  H1    C1   C7    112.92  3.000
 OBE  N1    C1   C7    103.42  3.000
 OBE  H1    C1   C2    110.16  3.000
 OBE  N1    C1   C2    106.47  3.000
 OBE  C7    C1   C2    114.25  3.000
 OBE  H2    C2   C15   108.70  3.000
 OBE  H2    C2   C3    108.58  3.000
 OBE  C15   C2   C3    111.35  3.000
 OBE  H2    C2   C1    107.58  3.000
 OBE  C15   C2   C1    111.84  3.000
 OBE  C3    C2   C1    108.67  3.000
 OBE  H3    C3   O1    108.68  3.000
 OBE  H3    C3   C4    109.23  3.000
 OBE  O1    C3   C4    111.07  3.000
 OBE  H3    C3   C2    108.50  3.000
 OBE  O1    C3   C2    106.58  3.000
 OBE  C4    C3   C2    112.66  3.000
 OBE  H42   C4   H41   107.32  3.000
 OBE  H42   C4   C5    108.35  3.000
 OBE  H41   C4   C5    109.73  3.000
 OBE  H42   C4   C3    110.26  3.000
 OBE  H41   C4   C3    110.52  3.000
 OBE  C5    C4   C3    110.58  3.000
 OBE  H5    C5   N1    109.12  3.000
 OBE  H5    C5   C6    113.48  3.000
 OBE  N1    C5   C6    102.80  3.000
 OBE  H5    C5   C4    110.14  3.000
 OBE  N1    C5   C4    107.82  3.000
 OBE  C6    C5   C4    113.03  3.000
 OBE  H62   C6   H61   106.88  3.000
 OBE  H62   C6   C7    111.02  3.000
 OBE  H61   C6   C7    112.86  3.000
 OBE  H62   C6   C5    110.61  3.000
 OBE  H61   C6   C5    110.89  3.000
 OBE  C7    C6   C5    104.64  3.000
 OBE  H72   C7   H71   106.83  3.000
 OBE  H72   C7   C6    111.15  3.000
 OBE  H71   C7   C6    112.81  3.000
 OBE  H72   C7   C1    110.51  3.000
 OBE  H71   C7   C1    110.80  3.000
 OBE  C6    C7   C1    104.81  3.000
 OBE  C14   C9   C10   120.58  3.000
 OBE  C14   C9   C8    121.76  3.000
 OBE  C10   C9   C8    117.65  3.000
 OBE  H10   C10  C11   119.54  3.000
 OBE  H10   C10  C9    120.41  3.000
 OBE  C11   C10  C9    120.05  3.000
 OBE  O5    C11  C12   122.77  3.000
 OBE  O5    C11  C10   117.67  3.000
 OBE  C12   C11  C10   119.56  3.000
 OBE  H12   C12  C13   119.81  3.000
 OBE  H12   C12  C11   120.27  3.000
 OBE  C13   C12  C11   119.92  3.000
 OBE  H13   C13  C14   119.79  3.000
 OBE  H13   C13  C12   119.18  3.000
 OBE  C14   C13  C12   121.03  3.000
 OBE  H14   C14  C13   119.98  3.000
 OBE  H14   C14  C9    121.17  3.000
 OBE  C13   C14  C9    118.86  3.000
 OBE  O4    C15  O3    125.78  3.000
 OBE  O4    C15  C2    115.74  3.000
 OBE  O3    C15  C2    118.48  3.000
 OBE  H163  C16  H162  109.29  3.000
 OBE  H163  C16  H161  109.48  3.000
 OBE  H162  C16  H161  109.35  3.000
 OBE  H163  C16  N1    111.00  3.000
 OBE  H162  C16  N1    108.81  3.000
 OBE  H161  C16  N1    108.88  3.000
 OBE  HN1   N1   C16   110.74  3.000
 OBE  HN1   N1   C5    111.92  3.000
 OBE  C16   N1   C5    114.39  3.000
 OBE  HN1   N1   C1    102.59  3.000
 OBE  C16   N1   C1    114.24  3.000
 OBE  C5    N1   C1    102.11  3.000
 OBE  C8    O1   C3    119.92  3.000
 OBE  HO5   O5   C11   110.59  3.000
 OBE  O2    C8   O1    124.03  3.000
 OBE  O2    C8   C9    124.12  3.000
 OBE  O1    C8   C9    111.84  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
 OBE  CONST_01  C12  C11  C10  C9     0.00   0.0  0
 OBE  CONST_02  C12  C13  C14  C9     0.00   0.0  0
 OBE  CONST_03  C13  C14  C9   C10    0.00   0.0  0
 OBE  CONST_04  C13  C12  C11  C10    0.00   0.0  0
 OBE  CONST_05  C14  C9   C10  C11    0.00   0.0  0
 OBE  CONST_06  C14  C13  C12  C11    0.00   0.0  0
 OBE  CONST_07  C11  C10  C9   C8   180.00   0.0  0
 OBE  CONST_08  C13  C14  C9   C8   180.00   0.0  0
 OBE  CONST_09  O5   C11  C10  C9   180.00   0.0  0
 OBE  CONST_10  O5   C11  C12  C13  180.00   0.0  0
 OBE  CONST_11  H13  C13  C14  C9   180.00   0.0  0
 OBE  CONST_12  H14  C14  C9   C10  180.00   0.0  0
 OBE  CONST_13  H12  C12  C11  C10  180.00   0.0  0
 OBE  CONST_14  H10  C10  C11  C12  180.00   0.0  0
 OBE  Var_01    C5   C6   C7   C1    -2.48  30.0  3
 OBE  Var_02    C9   C8   O1   C3   175.46  30.0  2
 OBE  Var_03    O1   C8   C9   C10  174.01  30.0  2

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
 OBE  chir_01  C1  C2   C7  N1   negativ
 OBE  chir_02  C2  C1   C3  C15  positiv
 OBE  chir_03  C3  O1   C4  C2   negativ
 OBE  chir_04  C5  N1   C4  C6   positiv
 OBE  chir_05  N1  C16  C5  C1   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
 OBE  plan-1  C9   0.020
 OBE  plan-1  C10  0.020
 OBE  plan-1  C11  0.020
 OBE  plan-1  C12  0.020
 OBE  plan-1  C13  0.020
 OBE  plan-1  C14  0.020
 OBE  plan-1  O5   0.020
 OBE  plan-1  H10  0.020
 OBE  plan-1  H12  0.020
 OBE  plan-1  H13  0.020
 OBE  plan-1  H14  0.020
 OBE  plan-1  C8   0.020
 OBE  plan-2  C2   0.020
 OBE  plan-2  C15  0.020
 OBE  plan-2  O3   0.020
 OBE  plan-2  O4   0.020
 OBE  plan-3  C9   0.020
 OBE  plan-3  O1   0.020
 OBE  plan-3  O2   0.020
 OBE  plan-3  C8   0.020

