# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 13:06:49 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: [(7~{S})-6,6-bis(oxidanyl)-5,7,8,9-tetrahydrobenzo[7]annulen-7-yl]azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+][C@H]1CCc2ccccc2CC1(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
 7MK  7MK  '[(7~{S})-6,6-bis(oxidanyl)-5,7,8,9-tetrahydrobenzo[7]annulen-7-yl]azanium'  ligand  30  14  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7MK
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
 7MK  C1   C  CR16  0  -0.297   2.0271  -1.4599  -0.1437
 7MK  C10  C  CH2   0  -0.447  -0.9828   1.7654   0.1919
 7MK  C11  C  CH1   0  -0.154  -1.9750   0.6877  -0.2096
 7MK  C2   C  CR16  0  -0.248   3.5191   0.3158   0.4626
 7MK  C3   C  CR16  0  -0.257   3.2608  -1.0396   0.3389
 7MK  C4   C  CR6   0   0.042   1.0456  -0.5410  -0.5050
 7MK  C5   C  CR6   0   0.133   1.3042   0.8284  -0.3719
 7MK  C6   C  CR16  0  -0.319   2.5422   1.2385   0.1089
 7MK  C7   C  CH2   0  -0.620  -0.2789  -1.0295  -1.0205
 7MK  C8   C  CH2   0  -0.550   0.2501   1.8423  -0.7133
 7MK  C9   C  CT    0   0.525  -1.4752  -0.7625  -0.0922
 7MK  N1   N  NT3   1  -0.793  -3.1870   0.8202   0.6523
 7MK  O1   O  OH1   0  -0.669  -2.5724  -1.5301  -0.4848
 7MK  O2   O  OH1   0  -0.669  -1.1845  -1.0294   1.2481
 7MK  H1   H  HCR6  0   0.259   1.8251  -2.5198  -0.2473
 7MK  H9   H  HCH2  0   0.275  -1.5011   2.7260   0.1407
 7MK  H10  H  HCH2  0   0.260  -0.6737   1.6319   1.2319
 7MK  H11  H  HCH1  0   0.314  -2.3182   0.8676  -1.2302
 7MK  H2   H  HCR6  0   0.258   4.4751   0.6586   0.8359
 7MK  H3   H  HCR6  0   0.258   4.0103  -1.7691   0.6164
 7MK  H4   H  HCR6  0   0.253   2.7454   2.2979   0.2118
 7MK  H6   H  HCH2  0   0.278  -0.5010  -0.5996  -2.0018
 7MK  H5   H  HCH2  0   0.289  -0.2189  -2.1108  -1.1719
 7MK  H8   H  HCH2  0   0.259  -0.0559   1.7427  -1.7602
 7MK  H7   H  HCH2  0   0.276   0.6757   2.8417  -0.6204
 7MK  H15  H  HNT3  0   0.477  -3.6020   1.7482   0.5704
 7MK  H16  H  HNT3  0   0.472  -3.9086   0.1451   0.3952
 7MK  H12  H  HOH1  0   0.464  -2.3591  -2.4676  -0.4003
 7MK  H13  H  HOH1  0   0.468  -0.2437  -1.1989   1.3731
 7MK  H14  H  HNT3  0   0.465  -2.9698   0.6713   1.6393

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
 7MK  C10  C8   single    1.531  0.020  1.531
 7MK  C10  C11  single    1.519  0.020  1.519
 7MK  N1   C11  single    1.493  0.020  1.493
 7MK  C8   C5   single    1.502  0.020  1.502
 7MK  C6   C5   aromatic  1.390  0.020  1.390
 7MK  C6   C2   aromatic  1.389  0.020  1.389
 7MK  C11  C9   single    1.538  0.020  1.538
 7MK  C5   C4   aromatic  1.400  0.020  1.400
 7MK  C2   C3   aromatic  1.385  0.020  1.385
 7MK  O2   C9   single    1.397  0.020  1.397
 7MK  C9   O1   single    1.395  0.020  1.395
 7MK  C9   C7   single    1.538  0.020  1.538
 7MK  C4   C1   aromatic  1.392  0.020  1.392
 7MK  C4   C7   single    1.503  0.020  1.503
 7MK  C3   C1   aromatic  1.390  0.020  1.390
 7MK  C1   H1   single    0.930  0.020  1.080
 7MK  C10  H9   single    0.970  0.020  1.090
 7MK  C10  H10  single    0.970  0.020  1.090
 7MK  C11  H11  single    0.970  0.020  1.090
 7MK  C2   H2   single    0.930  0.020  1.080
 7MK  C3   H3   single    0.930  0.020  1.080
 7MK  C6   H4   single    0.930  0.020  1.080
 7MK  C7   H6   single    0.970  0.020  1.090
 7MK  C7   H5   single    0.970  0.020  1.090
 7MK  C8   H8   single    0.970  0.020  1.090
 7MK  C8   H7   single    0.970  0.020  1.090
 7MK  N1   H15  single    0.890  0.020  1.040
 7MK  N1   H16  single    0.890  0.020  1.040
 7MK  O1   H12  single    0.850  0.020  0.980
 7MK  O2   H13  single    0.850  0.020  0.980
 7MK  H14  N1   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
 7MK  H1   C1   C4   119.29  3.000
 7MK  H1   C1   C3   119.63  3.000
 7MK  C4   C1   C3   121.08  3.000
 7MK  H10  C10  H9   106.63  3.000
 7MK  H10  C10  C8   109.93  3.000
 7MK  H9   C10  C8   108.06  3.000
 7MK  H10  C10  C11  110.46  3.000
 7MK  H9   C10  C11  107.55  3.000
 7MK  C8   C10  C11  113.91  3.000
 7MK  H11  C11  N1   105.66  3.000
 7MK  H11  C11  C9   109.20  3.000
 7MK  N1   C11  C9   107.65  3.000
 7MK  H11  C11  C10  109.61  3.000
 7MK  C9   C11  C10  115.88  3.000
 7MK  N1   C11  C10  108.34  3.000
 7MK  H2   C2   C6   119.91  3.000
 7MK  H2   C2   C3   120.37  3.000
 7MK  C6   C2   C3   119.73  3.000
 7MK  H3   C3   C2   120.50  3.000
 7MK  H3   C3   C1   120.00  3.000
 7MK  C2   C3   C1   119.50  3.000
 7MK  C7   C4   C5   120.89  3.000
 7MK  C7   C4   C1   119.72  3.000
 7MK  C5   C4   C1   119.39  3.000
 7MK  C8   C5   C6   120.30  3.000
 7MK  C6   C5   C4   119.08  3.000
 7MK  C8   C5   C4   120.60  3.000
 7MK  H4   C6   C5   119.23  3.000
 7MK  H4   C6   C2   119.55  3.000
 7MK  C5   C6   C2   121.22  3.000
 7MK  H5   C7   H6   105.99  3.000
 7MK  H5   C7   C9   107.34  3.000
 7MK  H6   C7   C9   108.38  3.000
 7MK  H5   C7   C4   108.70  3.000
 7MK  H6   C7   C4   111.03  3.000
 7MK  C9   C7   C4   114.97  3.000
 7MK  H7   C8   H8   105.89  3.000
 7MK  H7   C8   C5   108.99  3.000
 7MK  H8   C8   C5   110.61  3.000
 7MK  H7   C8   C10  108.06  3.000
 7MK  H8   C8   C10  109.61  3.000
 7MK  C5   C8   C10  113.38  3.000
 7MK  O2   C9   O1   109.17  3.000
 7MK  O1   C9   C7   110.27  3.000
 7MK  O2   C9   C7   112.59  3.000
 7MK  C7   C9   C11  111.74  3.000
 7MK  O1   C9   C11  103.98  3.000
 7MK  O2   C9   C11  108.72  3.000
 7MK  H14  N1   H16  107.29  3.000
 7MK  H14  N1   H15  107.26  3.000
 7MK  H16  N1   H15  107.09  3.000
 7MK  H14  N1   C11  111.85  3.000
 7MK  H16  N1   C11  111.69  3.000
 7MK  H15  N1   C11  111.38  3.000
 7MK  H12  O1   C9   109.62  3.000
 7MK  H13  O2   C9   111.16  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
 7MK  CONST_01  C6  C2  C3  C1    0.00  0.0  0
 7MK  CONST_02  C4  C1  C3  C2    0.00  0.0  0
 7MK  CONST_03  C5  C6  C2  C3    0.00  0.0  0
 7MK  CONST_04  H2  C2  C3  C1  180.00  0.0  0
 7MK  CONST_05  H1  C1  C3  C2  180.00  0.0  0
 7MK  CONST_06  H4  C6  C2  C3  180.00  0.0  0
 7MK  CONST_07  H3  C3  C1  C4  180.00  0.0  0

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
 7MK  chir_01  C11  C10  N1  C9  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
 7MK  plan-1  C1  0.020
 7MK  plan-1  C2  0.020
 7MK  plan-1  C3  0.020
 7MK  plan-1  C4  0.020
 7MK  plan-1  C5  0.020
 7MK  plan-1  C6  0.020
 7MK  plan-1  C7  0.020
 7MK  plan-1  C8  0.020
 7MK  plan-1  H1  0.020
 7MK  plan-1  H2  0.020
 7MK  plan-1  H3  0.020
 7MK  plan-1  H4  0.020

