# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 06:56:47 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 2-methyl-4-nitrophenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(ccc1O)[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
 MYJ  MYJ  '2-methyl-4-nitrophenol   '  ligand  18  11  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MYJ
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
 MYJ  C1  C  CH3    0  -0.771   2.3305   1.8818   0.1356
 MYJ  C2  C  CR6    0  -0.002   1.3747   0.7261   0.0932
 MYJ  C3  C  CR6    0   0.350   1.8501  -0.5952   0.0542
 MYJ  C4  C  CR16   0  -0.331   0.9626  -1.6714   0.0123
 MYJ  C5  C  CR16   0  -0.270  -0.3981  -1.4551   0.0090
 MYJ  C6  C  CR6    0   0.243  -0.8706  -0.1494   0.0483
 MYJ  C7  C  CR16   0  -0.315   0.0066   0.9286   0.0898
 MYJ  N1  N  N      1   0.325  -2.2925   0.0940   0.0451
 MYJ  O1  O  O     -1  -0.392  -2.6802   1.2413   0.0775
 MYJ  O2  O  O      0  -0.392  -3.0383  -0.8601   0.0100
 MYJ  O3  O  OH1    0  -0.603   3.1534  -0.8884   0.0544
 MYJ  H1  H  HCH3   0   0.262   2.9817   1.9054  -0.7412
 MYJ  H2  H  HCH3   0   0.275   1.7923   2.8269   0.1589
 MYJ  H3  H  HCH3   0   0.261   2.9672   1.8541   1.0229
 MYJ  H4  H  HCR6   0   0.283   1.3517  -2.6807  -0.0181
 MYJ  H5  H  HCR6   0   0.296  -1.0722  -2.2982  -0.0236
 MYJ  H6  H  HCR6   0   0.291  -0.3717   1.9410   0.1201
 MYJ  H7  H  HOH1   0   0.490   3.7030  -0.0969   0.0951

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
 MYJ  C1  C2  single    1.500  0.020  1.500
 MYJ  O1  N1  single    1.212  0.020  1.212
 MYJ  C7  C2  aromatic  1.383  0.020  1.383
 MYJ  C7  C6  aromatic  1.390  0.020  1.390
 MYJ  C2  C3  aromatic  1.405  0.020  1.405
 MYJ  N1  C6  single    1.443  0.020  1.443
 MYJ  N1  O2  double    1.211  0.020  1.211
 MYJ  C6  C5  aromatic  1.389  0.020  1.389
 MYJ  C3  O3  single    1.336  0.020  1.336
 MYJ  C3  C4  aromatic  1.396  0.020  1.396
 MYJ  C5  C4  aromatic  1.378  0.020  1.378
 MYJ  C1  H1  single    0.970  0.020  1.090
 MYJ  C1  H2  single    0.970  0.020  1.090
 MYJ  C1  H3  single    0.970  0.020  1.090
 MYJ  C4  H4  single    0.930  0.020  1.080
 MYJ  C5  H5  single    0.930  0.020  1.080
 MYJ  C7  H6  single    0.930  0.020  1.080
 MYJ  O3  H7  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
 MYJ  H3  C1  H2  107.04  3.000
 MYJ  H3  C1  H1  107.76  3.000
 MYJ  H2  C1  H1  107.06  3.000
 MYJ  H3  C1  C2  112.01  3.000
 MYJ  H2  C1  C2  110.77  3.000
 MYJ  H1  C1  C2  111.95  3.000
 MYJ  C7  C2  C3  118.19  3.000
 MYJ  C3  C2  C1  120.64  3.000
 MYJ  C7  C2  C1  121.17  3.000
 MYJ  O3  C3  C4  116.82  3.000
 MYJ  C4  C3  C2  120.72  3.000
 MYJ  O3  C3  C2  122.45  3.000
 MYJ  H4  C4  C5  120.09  3.000
 MYJ  H4  C4  C3  119.43  3.000
 MYJ  C5  C4  C3  120.47  3.000
 MYJ  H5  C5  C6  121.49  3.000
 MYJ  H5  C5  C4  119.60  3.000
 MYJ  C6  C5  C4  118.91  3.000
 MYJ  N1  C6  C7  119.42  3.000
 MYJ  N1  C6  C5  119.59  3.000
 MYJ  C7  C6  C5  120.99  3.000
 MYJ  H6  C7  C6  120.40  3.000
 MYJ  H6  C7  C2  118.89  3.000
 MYJ  C6  C7  C2  120.71  3.000
 MYJ  O2  N1  O1  123.34  3.000
 MYJ  O2  N1  C6  118.29  3.000
 MYJ  O1  N1  C6  118.37  3.000
 MYJ  H7  O3  C3  112.07  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
 MYJ  CONST_01  C5  C6  C7  C2    0.00   0.0  0
 MYJ  CONST_02  C5  C4  C3  C2    0.00   0.0  0
 MYJ  CONST_03  C6  C7  C2  C3    0.00   0.0  0
 MYJ  CONST_04  C6  C5  C4  C3    0.00   0.0  0
 MYJ  CONST_05  C7  C2  C3  C4    0.00   0.0  0
 MYJ  CONST_06  C7  C6  C5  C4    0.00   0.0  0
 MYJ  CONST_07  C6  C7  C2  C1  180.00   0.0  0
 MYJ  CONST_08  C4  C3  C2  C1  180.00   0.0  0
 MYJ  CONST_09  N1  C6  C7  C2  180.00   0.0  0
 MYJ  CONST_10  N1  C6  C5  C4  180.00   0.0  0
 MYJ  CONST_11  O3  C3  C4  C5  180.00   0.0  0
 MYJ  CONST_12  O3  C3  C2  C7  180.00   0.0  0
 MYJ  CONST_13  H4  C4  C3  C2  180.00   0.0  0
 MYJ  CONST_14  H6  C7  C2  C3  180.00   0.0  0
 MYJ  CONST_15  H5  C5  C4  C3  180.00   0.0  0
 MYJ  CONST_16  O1  N1  C6  C5  180.00   0.0  0
 MYJ  CONST_17  O2  N1  C6  C5    0.00   0.0  0
 MYJ  CONST_18  O1  N1  C6  C7    0.00   0.0  0
 MYJ  CONST_19  O2  N1  C6  C7  180.00   0.0  0
 MYJ  Var_01    H1  C1  C2  C3   60.40  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
 MYJ  plan-1  C1  0.020
 MYJ  plan-1  C2  0.020
 MYJ  plan-1  C3  0.020
 MYJ  plan-1  C4  0.020
 MYJ  plan-1  C5  0.020
 MYJ  plan-1  C6  0.020
 MYJ  plan-1  C7  0.020
 MYJ  plan-1  N1  0.020
 MYJ  plan-1  O3  0.020
 MYJ  plan-1  H4  0.020
 MYJ  plan-1  H5  0.020
 MYJ  plan-1  H6  0.020
 MYJ  plan-2  C6  0.020
 MYJ  plan-2  N1  0.020
 MYJ  plan-2  O1  0.020
 MYJ  plan-2  O2  0.020

