# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 21:01:32 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: (1R,2R,3S,5S)-3-[(phenylcarbonyl)oxy]-8-azoniabicyclo[3.2.1]octane-2-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-]C(=O)[C@@H]1[C@H]2CC[C@@H](C[C@@H]1OC(=O)c3ccccc3)[NH2+]2
#
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
 RBE  RBE  (1R,2R,3S,5S)-3-[(phenylcarbonyl)oxy]-8-azoniabicyclo[3.2.1]octane-2-carboxylate  ligand  37  20  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RBE
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
 RBE  C1    C  CH1    0  -0.151   3.1995   0.2032   0.7419
 RBE  C2    C  CH1    0  -0.427   1.7006   0.4977   0.8813
 RBE  C3    C  CH1    0   0.049   0.9041  -0.6583   0.2567
 RBE  C4    C  CH2    0  -0.488   1.4222  -1.0848  -1.1174
 RBE  C5    C  CH1    0  -0.133   2.9426  -1.1862  -1.1147
 RBE  C6    C  CH2    0  -0.465   3.4914  -2.0976  -0.0127
 RBE  C7    C  CH2    0  -0.467   3.6139  -1.1884   1.2290
 RBE  C9    C  CR6    0  -0.095  -2.7633  -0.3836   0.0306
 RBE  C10   C  CR16   0  -0.257  -3.8989  -1.1621  -0.1854
 RBE  C11   C  CR16   0  -0.242  -5.1458  -0.5648  -0.2786
 RBE  C12   C  CR16   0  -0.242  -5.2666   0.8133  -0.1515
 RBE  C13   C  CR16   0  -0.242  -4.1380   1.5922   0.0701
 RBE  C14   C  CR16   0  -0.271  -2.8874   1.0002   0.1594
 RBE  C15   C  C      0   0.501   1.3311   1.8546   0.2320
 RBE  N1    N  NT2    1  -0.661   3.4731   0.1486  -0.7221
 RBE  O1    O  O2     0  -0.473  -0.4469  -0.1992   0.1682
 RBE  O2    O  O      0  -0.445  -1.3040  -2.2642   0.1179
 RBE  O3    O  OC    -1  -0.607   1.7683   2.0357  -0.9436
 RBE  O4    O  O      0  -0.549   0.6520   2.6505   0.8803
 RBE  H1    H  HCH1   0   0.309   3.7891   1.0018   1.1883
 RBE  H2    H  HCH1   0   0.282   1.4663   0.5388   1.9469
 RBE  H3    H  HCH1   0   0.272   0.9436  -1.5152   0.9348
 RBE  H41   H  HCH2   0   0.270   1.1028  -0.3726  -1.8807
 RBE  H42   H  HCH2   0   0.280   1.0130  -2.0583  -1.3880
 RBE  H5    H  HCH1   0   0.304   3.3099  -1.4438  -2.1055
 RBE  H61   H  HCH2   0   0.275   4.4683  -2.4842  -0.3022
 RBE  H62   H  HCH2   0   0.269   2.8407  -2.9560   0.1503
 RBE  H71   H  HCH2   0   0.277   4.6407  -1.1672   1.5916
 RBE  H72   H  HCH2   0   0.271   2.9877  -1.5135   2.0596
 RBE  H10   H  HCR6   0   0.263  -3.8074  -2.2352  -0.2855
 RBE  H11   H  HCR6   0   0.265  -6.0227  -1.1737  -0.4537
 RBE  H12   H  HCR6   0   0.267  -6.2399   1.2811  -0.2253
 RBE  H13   H  HCR6   0   0.266  -4.2315   2.6652   0.1721
 RBE  H14   H  HCR6   0   0.270  -2.0173   1.6187   0.3357
 RBE  HN11  H  HNT2   0   0.466   2.9080   0.9590  -1.1329
 RBE  HN12  H  HNT2   0   0.454   4.4633   0.2528  -0.9356
 RBE  C8    C  C      0   0.608  -1.4470  -1.0655   0.1135

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
 RBE  C1   C2    single    1.534  0.020  1.534
 RBE  C1   C7    single    1.532  0.020  1.532
 RBE  C1   N1    single    1.490  0.020  1.490
 RBE  C1   H1    single    0.970  0.020  1.090
 RBE  C2   C3    single    1.537  0.020  1.537
 RBE  C2   C15   single    1.549  0.020  1.549
 RBE  C2   H2    single    0.970  0.020  1.090
 RBE  C3   C4    single    1.529  0.020  1.529
 RBE  C3   O1    single    1.430  0.020  1.430
 RBE  C3   H3    single    0.970  0.020  1.090
 RBE  C4   C5    single    1.524  0.020  1.524
 RBE  C4   H41   single    0.970  0.020  1.090
 RBE  C4   H42   single    0.970  0.020  1.090
 RBE  C5   C6    single    1.532  0.020  1.532
 RBE  C5   N1    single    1.489  0.020  1.489
 RBE  C5   H5    single    0.970  0.020  1.090
 RBE  C6   C7    single    1.544  0.020  1.544
 RBE  C6   H61   single    0.970  0.020  1.090
 RBE  C6   H62   single    0.970  0.020  1.090
 RBE  C7   H71   single    0.970  0.020  1.090
 RBE  C7   H72   single    0.970  0.020  1.090
 RBE  C8   C9    single    1.485  0.020  1.485
 RBE  C8   O1    single    1.324  0.020  1.324
 RBE  C8   O2    double    1.207  0.020  1.207
 RBE  C9   C10   aromatic  1.394  0.020  1.394
 RBE  C9   C14   aromatic  1.395  0.020  1.395
 RBE  C10  C11   aromatic  1.386  0.020  1.386
 RBE  C10  H10   single    0.930  0.020  1.080
 RBE  C11  C12   aromatic  1.389  0.020  1.389
 RBE  C11  H11   single    0.930  0.020  1.080
 RBE  C12  C13   aromatic  1.389  0.020  1.389
 RBE  C12  H12   single    0.930  0.020  1.080
 RBE  C13  C14   aromatic  1.387  0.020  1.387
 RBE  C13  H13   single    0.930  0.020  1.080
 RBE  C14  H14   single    0.930  0.020  1.080
 RBE  C15  O3    deloc     1.267  0.020  1.267
 RBE  C15  O4    deloc     1.231  0.020  1.231
 RBE  N1   HN11  single    0.890  0.020  1.040
 RBE  N1   HN12  single    0.890  0.020  1.040

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
 RBE  H1    C1   N1    109.28  3.000
 RBE  H1    C1   C7    112.93  3.000
 RBE  N1    C1   C7    103.27  3.000
 RBE  H1    C1   C2    110.56  3.000
 RBE  N1    C1   C2    106.01  3.000
 RBE  C7    C1   C2    114.20  3.000
 RBE  H2    C2   C15   108.96  3.000
 RBE  H2    C2   C3    108.29  3.000
 RBE  C15   C2   C3    111.40  3.000
 RBE  H2    C2   C1    107.80  3.000
 RBE  C15   C2   C1    111.30  3.000
 RBE  C3    C2   C1    108.97  3.000
 RBE  H3    C3   O1    108.92  3.000
 RBE  H3    C3   C4    109.05  3.000
 RBE  O1    C3   C4    110.74  3.000
 RBE  H3    C3   C2    108.59  3.000
 RBE  O1    C3   C2    105.87  3.000
 RBE  C4    C3   C2    113.54  3.000
 RBE  H42   C4   H41   107.41  3.000
 RBE  H42   C4   C5    108.39  3.000
 RBE  H41   C4   C5    109.67  3.000
 RBE  H42   C4   C3    110.18  3.000
 RBE  H41   C4   C3    110.32  3.000
 RBE  C5    C4   C3    110.79  3.000
 RBE  H5    C5   N1    109.40  3.000
 RBE  H5    C5   C6    113.17  3.000
 RBE  N1    C5   C6    102.48  3.000
 RBE  H5    C5   C4    110.56  3.000
 RBE  N1    C5   C4    107.24  3.000
 RBE  C6    C5   C4    113.48  3.000
 RBE  H62   C6   H61   107.20  3.000
 RBE  H62   C6   C7    113.03  3.000
 RBE  H61   C6   C7    110.58  3.000
 RBE  H62   C6   C5    111.25  3.000
 RBE  H61   C6   C5    109.94  3.000
 RBE  C7    C6   C5    104.87  3.000
 RBE  H72   C7   H71   107.08  3.000
 RBE  H72   C7   C6    113.06  3.000
 RBE  H71   C7   C6    110.73  3.000
 RBE  H72   C7   C1    110.98  3.000
 RBE  H71   C7   C1    110.08  3.000
 RBE  C6    C7   C1    104.94  3.000
 RBE  C14   C9   C10   119.72  3.000
 RBE  C14   C9   C8    121.95  3.000
 RBE  C10   C9   C8    118.33  3.000
 RBE  H10   C10  C11   119.84  3.000
 RBE  H10   C10  C9    119.97  3.000
 RBE  C11   C10  C9    120.19  3.000
 RBE  H11   C11  C12   120.17  3.000
 RBE  H11   C11  C10   119.84  3.000
 RBE  C12   C11  C10   119.99  3.000
 RBE  H12   C12  C13   119.95  3.000
 RBE  H12   C12  C11   120.04  3.000
 RBE  C13   C12  C11   120.01  3.000
 RBE  H13   C13  C14   119.69  3.000
 RBE  H13   C13  C12   120.06  3.000
 RBE  C14   C13  C12   120.25  3.000
 RBE  H14   C14  C13   119.46  3.000
 RBE  H14   C14  C9    120.69  3.000
 RBE  C13   C14  C9    119.85  3.000
 RBE  O4    C15  O3    125.91  3.000
 RBE  O4    C15  C2    118.51  3.000
 RBE  O3    C15  C2    115.58  3.000
 RBE  HN12  N1   HN11  110.83  3.000
 RBE  HN12  N1   C5    112.52  3.000
 RBE  HN11  N1   C5    112.93  3.000
 RBE  HN12  N1   C1    112.38  3.000
 RBE  HN11  N1   C1    104.62  3.000
 RBE  C5    N1   C1    103.08  3.000
 RBE  C8    O1   C3    120.41  3.000
 RBE  O2    C8   O1    124.05  3.000
 RBE  O2    C8   C9    124.14  3.000
 RBE  O1    C8   C9    111.80  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
 RBE  CONST_01  C12  C11  C10  C9     0.00   0.0  0
 RBE  CONST_02  C12  C13  C14  C9     0.00   0.0  0
 RBE  CONST_03  C13  C14  C9   C10    0.00   0.0  0
 RBE  CONST_04  C13  C12  C11  C10    0.00   0.0  0
 RBE  CONST_05  C14  C9   C10  C11    0.00   0.0  0
 RBE  CONST_06  C14  C13  C12  C11    0.00   0.0  0
 RBE  CONST_07  C11  C10  C9   C8   180.00   0.0  0
 RBE  CONST_08  C13  C14  C9   C8   180.00   0.0  0
 RBE  CONST_09  H11  C11  C10  C9   180.00   0.0  0
 RBE  CONST_10  H13  C13  C14  C9   180.00   0.0  0
 RBE  CONST_11  H14  C14  C9   C10  180.00   0.0  0
 RBE  CONST_12  H12  C12  C11  C10  180.00   0.0  0
 RBE  CONST_13  H10  C10  C11  C12  180.00   0.0  0
 RBE  Var_01    C5   C6   C7   C1    -2.94  30.0  3
 RBE  Var_02    C9   C8   O1   C3   179.78  30.0  2
 RBE  Var_03    O1   C8   C9   C10  172.86  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
 RBE  chir_01  C1  C2  C7  N1   negativ
 RBE  chir_02  C2  C1  C3  C15  positiv
 RBE  chir_03  C3  O1  C4  C2   negativ
 RBE  chir_04  C5  N1  C6  C4   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
 RBE  plan-1  C9   0.020
 RBE  plan-1  C10  0.020
 RBE  plan-1  C11  0.020
 RBE  plan-1  C12  0.020
 RBE  plan-1  C13  0.020
 RBE  plan-1  C14  0.020
 RBE  plan-1  H10  0.020
 RBE  plan-1  H11  0.020
 RBE  plan-1  H12  0.020
 RBE  plan-1  H13  0.020
 RBE  plan-1  H14  0.020
 RBE  plan-1  C8   0.020
 RBE  plan-2  C2   0.020
 RBE  plan-2  C15  0.020
 RBE  plan-2  O3   0.020
 RBE  plan-2  O4   0.020
 RBE  plan-3  C9   0.020
 RBE  plan-3  O1   0.020
 RBE  plan-3  O2   0.020
 RBE  plan-3  C8   0.020

