# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 04:00:28 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: 4-methyl-2,6-dinitro-phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(c(O)c(c1)[N+]([O-])=O)[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
 6J1  6J1  4-methyl-2,6-dinitro-phenol  ligand  20  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_6J1
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
 6J1  O10   O  O      0  -0.349   3.4059  -0.0494   0.0517
 6J1  C01   C  CH3    0  -0.716   0.0042   3.6387  -0.0247
 6J1  C02   C  CR6    0   0.085  -0.0135   2.1405  -0.0041
 6J1  C03   C  CR16   0  -0.289  -1.2185   1.4434  -0.0003
 6J1  C04   C  CR6    0   0.184  -1.2506   0.0651   0.0557
 6J1  C05   C  CR6    0   0.354  -0.0829  -0.7170   0.0759
 6J1  C06   C  CR6    0   0.200   1.1249   0.0086   0.0484
 6J1  C07   C  CR16   0  -0.333   1.1513   1.4003   0.0174
 6J1  N08   N  N      1   0.367   2.3870  -0.6863   0.0445
 6J1  O09   O  O     -1  -0.421   2.3723  -1.9096   0.0342
 6J1  N12   N  N      1   0.341  -2.5544  -0.5742   0.0832
 6J1  O13   O  O     -1  -0.373  -3.4388  -0.0523  -0.5542
 6J1  O14   O  O      0  -0.363  -2.6900  -1.5676   0.7528
 6J1  H011  H  HCH3   0   0.261  -0.2853   4.0455   0.9451
 6J1  H013  H  HCH3   0   0.256   0.9956   4.0190  -0.2633
 6J1  H012  H  HCH3   0   0.257  -0.6942   4.0295  -0.7641
 6J1  H031  H  HCR6   0   0.308  -2.1493   1.9953  -0.0263
 6J1  H071  H  HCR6   0   0.310   2.1041   1.9109   0.0026
 6J1  H111  H  HOH1   0   0.493   0.7303  -2.4007   0.0475
 6J1  O11   O  OH1    0  -0.573  -0.1746  -2.0279   0.0781

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
 6J1  O11  C05   single    1.314  0.020  1.314
 6J1  O10  N08   double    1.202  0.020  1.202
 6J1  O14  N12   double    1.206  0.020  1.206
 6J1  C05  C06   aromatic  1.409  0.020  1.409
 6J1  C05  C04   aromatic  1.406  0.020  1.406
 6J1  N08  C06   single    1.441  0.020  1.441
 6J1  N08  O09   single    1.224  0.020  1.224
 6J1  N12  O13   single    1.209  0.020  1.209
 6J1  N12  C04   single    1.452  0.020  1.452
 6J1  C06  C07   aromatic  1.392  0.020  1.392
 6J1  C04  C03   aromatic  1.380  0.020  1.380
 6J1  C07  C02   aromatic  1.380  0.020  1.380
 6J1  C03  C02   aromatic  1.392  0.020  1.392
 6J1  C02  C01   single    1.499  0.020  1.499
 6J1  C01  H011  single    0.970  0.020  1.090
 6J1  C01  H013  single    0.970  0.020  1.090
 6J1  C01  H012  single    0.970  0.020  1.090
 6J1  C03  H031  single    0.930  0.020  1.080
 6J1  C07  H071  single    0.930  0.020  1.080
 6J1  O11  H111  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
 6J1  H012  C01  H013  108.05  3.000
 6J1  H012  C01  H011  107.43  3.000
 6J1  H013  C01  H011  107.84  3.000
 6J1  H012  C01  C02   111.12  3.000
 6J1  H013  C01  C02   111.29  3.000
 6J1  H011  C01  C02   110.95  3.000
 6J1  C07   C02  C03   117.51  3.000
 6J1  C03   C02  C01   120.72  3.000
 6J1  C07   C02  C01   121.76  3.000
 6J1  H031  C03  C04   119.36  3.000
 6J1  H031  C03  C02   119.28  3.000
 6J1  C04   C03  C02   121.36  3.000
 6J1  N12   C04  C05   120.04  3.000
 6J1  N12   C04  C03   117.47  3.000
 6J1  C05   C04  C03   122.48  3.000
 6J1  O11   C05  C06   124.99  3.000
 6J1  C06   C05  C04   115.17  3.000
 6J1  O11   C05  C04   119.81  3.000
 6J1  N08   C06  C07   117.74  3.000
 6J1  C07   C06  C05   122.09  3.000
 6J1  N08   C06  C05   120.16  3.000
 6J1  H071  C07  C06   119.28  3.000
 6J1  H071  C07  C02   119.36  3.000
 6J1  C06   C07  C02   121.36  3.000
 6J1  O09   N08  C06   118.15  3.000
 6J1  O09   N08  O10   122.70  3.000
 6J1  C06   N08  O10   119.15  3.000
 6J1  O14   N12  O13   124.50  3.000
 6J1  O13   N12  C04   117.19  3.000
 6J1  O14   N12  C04   118.30  3.000
 6J1  H111  O11  C05   108.38  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
 6J1  CONST_01  C05   C06  C07  C02    0.00   0.0  0
 6J1  CONST_02  C05   C04  C03  C02    0.00   0.0  0
 6J1  CONST_03  C06   C05  C04  C03    0.00   0.0  0
 6J1  CONST_04  C06   C07  C02  C03    0.00   0.0  0
 6J1  CONST_05  C07   C06  C05  C04    0.00   0.0  0
 6J1  CONST_06  C07   C02  C03  C04    0.00   0.0  0
 6J1  CONST_07  C06   C07  C02  C01  180.00   0.0  0
 6J1  CONST_08  C04   C03  C02  C01  180.00   0.0  0
 6J1  CONST_09  N08   C06  C07  C02  180.00   0.0  0
 6J1  CONST_10  N12   C04  C03  C02  180.00   0.0  0
 6J1  CONST_11  O11   C05  C04  C03  180.00   0.0  0
 6J1  CONST_12  N08   C06  C05  C04  180.00   0.0  0
 6J1  CONST_13  N12   C04  C05  C06  180.00   0.0  0
 6J1  CONST_14  O11   C05  C06  C07  180.00   0.0  0
 6J1  CONST_15  H071  C07  C02  C03  180.00   0.0  0
 6J1  CONST_16  H031  C03  C04  C05  180.00   0.0  0
 6J1  CONST_17  C05   C06  N08  O10  180.00   0.0  0
 6J1  CONST_18  C07   C06  N08  O10    0.00   0.0  0
 6J1  CONST_21  O09   N08  C06  C05    0.00   0.0  0
 6J1  CONST_24  O09   N08  C06  C07  180.00   0.0  0
 6J1  Var_01    H011  C01  C02  C03   73.50  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
 6J1  plan-1  C01   0.020
 6J1  plan-1  C02   0.020
 6J1  plan-1  C03   0.020
 6J1  plan-1  C04   0.020
 6J1  plan-1  C05   0.020
 6J1  plan-1  C06   0.020
 6J1  plan-1  C07   0.020
 6J1  plan-1  N08   0.020
 6J1  plan-1  N12   0.020
 6J1  plan-1  H031  0.020
 6J1  plan-1  H071  0.020
 6J1  plan-1  O11   0.020
 6J1  plan-2  O10   0.020
 6J1  plan-2  C06   0.020
 6J1  plan-2  N08   0.020
 6J1  plan-2  O09   0.020
 6J1  plan-3  C04   0.020
 6J1  plan-3  N12   0.020
 6J1  plan-3  O13   0.020
 6J1  plan-3  O14   0.020

