# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 09:31:57 2021
#   Inital geometry file: a 52 line input string
#   Ligand name: 5-methyl-2-nitrophenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(c(O)c1)[N+]([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
 L3S  L3S  '5-methyl-2-nitrophenol   '  ligand  18  11  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L3S
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
 L3S  C02   C  CR6    0   0.385  17.5014  19.8568   1.5361
 L3S  C03   C  CR16   0  -0.396  18.4959  19.9524   2.5147
 L3S  C04   C  CR6    0   0.126  18.5821  21.0361   3.3663
 L3S  C05   C  CH3    0  -0.724  19.6629  21.1220   4.3961
 L3S  C06   C  CR16   0  -0.304  17.6437  22.0752   3.2467
 L3S  C07   C  CR16   0  -0.279  16.6600  22.0139   2.2951
 L3S  C08   C  CR6    0   0.143  16.5763  20.9138   1.4336
 L3S  N09   N  N      1   0.364  15.5329  20.8905   0.4565
 L3S  O01   O  OH1    0  -0.604  17.5047  18.7707   0.7757
 L3S  O10   O  O      0  -0.372  14.7621  21.8154   0.3900
 L3S  O11   O  O     -1  -0.435  15.4561  19.9207  -0.2892
 L3S  H031  H  HCR6   0   0.277  19.2086  19.1397   2.5863
 L3S  H052  H  HCH3   0   0.262  20.3769  21.9064   4.1375
 L3S  H051  H  HCH3   0   0.257  19.2524  21.3780   5.3724
 L3S  H053  H  HCH3   0   0.254  20.2138  20.1882   4.4888
 L3S  H061  H  HCR6   0   0.267  17.6953  22.9291   3.9093
 L3S  H071  H  HCR6   0   0.298  15.9444  22.8185   2.2099
 L3S  H011  H  HOH1   0   0.482  16.7646  18.8262   0.1435

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
 L3S  O11  N09   single    1.226  0.020  1.226
 L3S  O10  N09   double    1.206  0.020  1.206
 L3S  N09  C08   single    1.430  0.020  1.430
 L3S  O01  C02   single    1.326  0.020  1.326
 L3S  C08  C02   aromatic  1.408  0.020  1.408
 L3S  C08  C07   aromatic  1.400  0.020  1.400
 L3S  C02  C03   aromatic  1.399  0.020  1.399
 L3S  C07  C06   aromatic  1.370  0.020  1.370
 L3S  C03  C04   aromatic  1.381  0.020  1.381
 L3S  C06  C04   aromatic  1.405  0.020  1.405
 L3S  C04  C05   single    1.495  0.020  1.495
 L3S  C03  H031  single    0.930  0.020  1.080
 L3S  C05  H052  single    0.970  0.020  1.090
 L3S  C05  H051  single    0.970  0.020  1.090
 L3S  C05  H053  single    0.970  0.020  1.090
 L3S  C06  H061  single    0.930  0.020  1.080
 L3S  C07  H071  single    0.930  0.020  1.080
 L3S  O01  H011  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
 L3S  O01   C02  C08   125.08  3.000
 L3S  C08   C02  C03   117.82  3.000
 L3S  O01   C02  C03   117.10  3.000
 L3S  H031  C03  C04   120.46  3.000
 L3S  H031  C03  C02   117.57  3.000
 L3S  C04   C03  C02   121.97  3.000
 L3S  C06   C04  C05   119.92  3.000
 L3S  C05   C04  C03   120.99  3.000
 L3S  C06   C04  C03   119.09  3.000
 L3S  H053  C05  H051  108.42  3.000
 L3S  H053  C05  H052  107.80  3.000
 L3S  H051  C05  H052  106.84  3.000
 L3S  H053  C05  C04   112.05  3.000
 L3S  H051  C05  C04   110.99  3.000
 L3S  H052  C05  C04   110.54  3.000
 L3S  H061  C06  C07   119.67  3.000
 L3S  H061  C06  C04   119.97  3.000
 L3S  C07   C06  C04   120.36  3.000
 L3S  H071  C07  C08   119.81  3.000
 L3S  H071  C07  C06   119.81  3.000
 L3S  C08   C07  C06   120.37  3.000
 L3S  N09   C08  C07   118.50  3.000
 L3S  C07   C08  C02   120.38  3.000
 L3S  N09   C08  C02   121.12  3.000
 L3S  O11   N09  O10   122.23  3.000
 L3S  O10   N09  C08   119.45  3.000
 L3S  O11   N09  C08   118.32  3.000
 L3S  H011  O01  C02   108.87  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
 L3S  CONST_01  C06   C07  C08  C02    0.00   0.0  0
 L3S  CONST_02  C06   C04  C03  C02    0.00   0.0  0
 L3S  CONST_03  C07   C08  C02  C03    0.00   0.0  0
 L3S  CONST_04  C07   C06  C04  C03    0.00   0.0  0
 L3S  CONST_05  C08   C02  C03  C04    0.00   0.0  0
 L3S  CONST_06  C08   C07  C06  C04    0.00   0.0  0
 L3S  CONST_07  C05   C04  C03  C02  180.00   0.0  0
 L3S  CONST_08  N09   C08  C02  C03  180.00   0.0  0
 L3S  CONST_09  O01   C02  C03  C04  180.00   0.0  0
 L3S  CONST_10  C07   C06  C04  C05  180.00   0.0  0
 L3S  CONST_11  N09   C08  C07  C06  180.00   0.0  0
 L3S  CONST_12  O01   C02  C08  C07  180.00   0.0  0
 L3S  CONST_13  H071  C07  C08  C02  180.00   0.0  0
 L3S  CONST_14  H061  C06  C04  C03  180.00   0.0  0
 L3S  CONST_15  H031  C03  C04  C06  180.00   0.0  0
 L3S  CONST_16  O11   N09  C08  C02    0.00   0.0  0
 L3S  CONST_17  O10   N09  C08  C02  180.00   0.0  0
 L3S  CONST_18  O11   N09  C08  C07  180.00   0.0  0
 L3S  CONST_19  O10   N09  C08  C07    0.00   0.0  0
 L3S  Var_01    H052  C05  C04  C03  110.26  30.0  2

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
 L3S  plan-1  C02   0.020
 L3S  plan-1  C03   0.020
 L3S  plan-1  C04   0.020
 L3S  plan-1  C05   0.020
 L3S  plan-1  C06   0.020
 L3S  plan-1  C07   0.020
 L3S  plan-1  C08   0.020
 L3S  plan-1  N09   0.020
 L3S  plan-1  O01   0.020
 L3S  plan-1  H031  0.020
 L3S  plan-1  H061  0.020
 L3S  plan-1  H071  0.020
 L3S  plan-2  C08   0.020
 L3S  plan-2  N09   0.020
 L3S  plan-2  O10   0.020
 L3S  plan-2  O11   0.020

