# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 23:22:00 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 4-methyl-2-nitrophenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(O)c(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
 NCR  NCR  '4-methyl-2-nitrophenol   '  ligand  18  11  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NCR
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
 NCR  C1   C  CR6    0   0.090  -0.3798  -0.0079   2.0423
 NCR  C2   C  CR16   0  -0.353  -0.9183  -0.0882   0.7789
 NCR  C3   C  CR6    0   0.180  -0.0992  -0.1344  -0.3563
 NCR  C4   C  CR6    0   0.350   1.3015  -0.0992  -0.2445
 NCR  C5   C  CR16   0  -0.333   1.8360  -0.0177   1.0465
 NCR  C6   C  CR16   0  -0.255   1.0192   0.0263   2.1510
 NCR  C7   C  CH3    0  -0.720  -1.2443   0.0406   3.2661
 NCR  N3   N  N      1   0.362  -0.7308  -0.2196  -1.6414
 NCR  O1N  O  O     -1  -0.431  -0.0177  -0.2576  -2.6367
 NCR  O2N  O  O      0  -0.368  -1.9337  -0.2518  -1.7091
 NCR  O4   O  OH1    0  -0.604   2.1589  -0.1365  -1.2563
 NCR  H2   H  HCR6   0   0.292  -1.9923  -0.1147   0.6575
 NCR  H5   H  HCR6   0   0.285   2.9121   0.0099   1.1567
 NCR  H6   H  HCR6   0   0.272   1.4736   0.0904   3.1324
 NCR  H71  H  HCH3   0   0.251  -1.0511   0.9406   3.8513
 NCR  H72  H  HCH3   0   0.249  -2.3017   0.0322   3.0071
 NCR  H73  H  HCH3   0   0.251  -1.0546  -0.8133   3.9180
 NCR  HO4  H  HOH1   0   0.482   1.6587  -0.1880  -2.0911

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
 NCR  C1  C2   aromatic  1.376  0.020  1.376
 NCR  C1  C6   aromatic  1.404  0.020  1.404
 NCR  C1  C7   single    1.499  0.020  1.499
 NCR  C2  C3   aromatic  1.401  0.020  1.401
 NCR  C2  H2   single    0.930  0.020  1.080
 NCR  C3  C4   aromatic  1.406  0.020  1.406
 NCR  C3  N3   single    1.434  0.020  1.434
 NCR  C4  C5   aromatic  1.400  0.020  1.400
 NCR  C4  O4   single    1.327  0.020  1.327
 NCR  C5  C6   aromatic  1.374  0.020  1.374
 NCR  C5  H5   single    0.930  0.020  1.080
 NCR  C6  H6   single    0.930  0.020  1.080
 NCR  C7  H71  single    0.970  0.020  1.090
 NCR  C7  H72  single    0.970  0.020  1.090
 NCR  C7  H73  single    0.970  0.020  1.090
 NCR  N3  O1N  single    1.225  0.020  1.225
 NCR  N3  O2N  double    1.205  0.020  1.205
 NCR  O4  HO4  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
 NCR  C7   C1  C6   120.72  3.000
 NCR  C7   C1  C2   121.72  3.000
 NCR  C6   C1  C2   117.56  3.000
 NCR  H2   C2  C3   119.28  3.000
 NCR  H2   C2  C1   119.56  3.000
 NCR  C3   C2  C1   121.15  3.000
 NCR  N3   C3  C4   120.76  3.000
 NCR  N3   C3  C2   118.07  3.000
 NCR  C4   C3  C2   121.16  3.000
 NCR  O4   C4  C5   117.28  3.000
 NCR  O4   C4  C3   125.64  3.000
 NCR  C5   C4  C3   117.09  3.000
 NCR  H5   C5  C6   120.55  3.000
 NCR  H5   C5  C4   118.37  3.000
 NCR  C6   C5  C4   121.08  3.000
 NCR  H6   C6  C5   118.72  3.000
 NCR  H6   C6  C1   119.32  3.000
 NCR  C5   C6  C1   121.96  3.000
 NCR  H73  C7  H72  107.76  3.000
 NCR  H73  C7  H71  107.12  3.000
 NCR  H72  C7  H71  107.82  3.000
 NCR  H73  C7  C1   111.24  3.000
 NCR  H72  C7  C1   111.45  3.000
 NCR  H71  C7  C1   111.25  3.000
 NCR  O2N  N3  O1N  122.31  3.000
 NCR  O2N  N3  C3   119.43  3.000
 NCR  O1N  N3  C3   118.26  3.000
 NCR  HO4  O4  C4   108.85  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
 NCR  CONST_01  C4   C3  C2  C1     0.00   0.0  0
 NCR  CONST_02  C4   C5  C6  C1     0.00   0.0  0
 NCR  CONST_03  C5   C6  C1  C2     0.00   0.0  0
 NCR  CONST_04  C5   C4  C3  C2     0.00   0.0  0
 NCR  CONST_05  C6   C1  C2  C3     0.00   0.0  0
 NCR  CONST_06  C6   C5  C4  C3     0.00   0.0  0
 NCR  CONST_07  N3   C3  C2  C1   180.00   0.0  0
 NCR  CONST_08  O4   C4  C3  C2   180.00   0.0  0
 NCR  CONST_09  C7   C1  C2  C3   180.00   0.0  0
 NCR  CONST_10  N3   C3  C4  C5   180.00   0.0  0
 NCR  CONST_11  C7   C1  C6  C5   180.00   0.0  0
 NCR  CONST_12  O4   C4  C5  C6   180.00   0.0  0
 NCR  CONST_13  H5   C5  C6  C1   180.00   0.0  0
 NCR  CONST_14  H6   C6  C1  C2   180.00   0.0  0
 NCR  CONST_15  H2   C2  C3  C4   180.00   0.0  0
 NCR  CONST_16  O1N  N3  C3  C2   180.00   0.0  0
 NCR  CONST_17  O2N  N3  C3  C2     0.00   0.0  0
 NCR  CONST_18  O1N  N3  C3  C4     0.00   0.0  0
 NCR  CONST_19  O2N  N3  C3  C4   180.00   0.0  0
 NCR  Var_01    H71  C7  C1  C2  -121.96  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
 NCR  plan-1  C1   0.020
 NCR  plan-1  C2   0.020
 NCR  plan-1  C3   0.020
 NCR  plan-1  C4   0.020
 NCR  plan-1  C5   0.020
 NCR  plan-1  C6   0.020
 NCR  plan-1  C7   0.020
 NCR  plan-1  N3   0.020
 NCR  plan-1  O4   0.020
 NCR  plan-1  H2   0.020
 NCR  plan-1  H5   0.020
 NCR  plan-1  H6   0.020
 NCR  plan-2  C3   0.020
 NCR  plan-2  N3   0.020
 NCR  plan-2  O1N  0.020
 NCR  plan-2  O2N  0.020

