# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 16:21:06 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 2-[(4-hydroxybenzyl)amino]-5-nitrobenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cc(ccc1NCc2ccc(O)cc2)[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
 19Z  19Z  2-[(4-hydroxybenzyl)amino]-5-nitrobenzamide  ligand  34  21  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_19Z
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
 19Z  N01   N  NH1    0  -0.673   0.5293   0.2749  -0.0385
 19Z  N02   N  NH2    0  -0.806  -1.7114  -3.2454  -0.2334
 19Z  N03   N  N      1   0.320  -5.0293   0.5838   0.1372
 19Z  C04   C  CR16   0  -0.317  -2.9803  -0.7394   0.1328
 19Z  C05   C  CR6    0  -0.121  -1.6044  -0.8551   0.0725
 19Z  C06   C  CR6    0   0.413  -0.8054   0.3265  -0.0295
 19Z  C07   C  CR16   0  -0.360  -1.4747   1.5694  -0.1451
 19Z  C08   C  CR16   0  -0.256  -2.8401   1.6564  -0.1002
 19Z  C09   C  CR6    0   0.236  -3.6031   0.4983   0.0550
 19Z  C11   C  CH2    0  -0.349   1.3993   1.4281  -0.1733
 19Z  C12   C  CR6    0   0.038   2.8326   0.9834  -0.1428
 19Z  C13   C  CR16   0  -0.271   3.4944   0.6256  -1.3147
 19Z  C14   C  CR16   0  -0.325   4.8027   0.1729  -1.2932
 19Z  C15   C  CR6    0   0.348   5.4789   0.0646  -0.0795
 19Z  C16   C  CR16   0  -0.371   4.8295   0.4176   1.1011
 19Z  C17   C  CR16   0  -0.271   3.5192   0.8699   1.0608
 19Z  O18   O  O      0  -0.498   0.1923  -2.3414   0.5402
 19Z  O19   O  OH1    0  -0.630   6.7503  -0.3791  -0.1045
 19Z  O20   O  O     -1  -0.405  -5.6651  -0.4385   0.2964
 19Z  O21   O  O      0  -0.402  -5.5466   1.6782   0.0447
 19Z  HN01  H  HNH1   0   0.412   0.9477  -0.6250   0.1541
 19Z  HN02  H  HNH2   0   0.416  -2.5754  -3.1451  -0.7361
 19Z  HN0A  H  HNH2   0   0.410  -1.3083  -4.1682  -0.2083
 19Z  H04   H  HCR6   0   0.292  -3.5881  -1.6242   0.2598
 19Z  H07   H  HCR6   0   0.295  -0.9019   2.4788  -0.2553
 19Z  H08   H  HCR6   0   0.297  -3.3096   2.6268  -0.1759
 19Z  H11   H  HCH2   0   0.259   1.1866   1.9466  -1.1128
 19Z  H11A  H  HCH2   0   0.259   1.2095   2.1427   0.6340
 19Z  H13   H  HCR6   0   0.255   2.9822   0.7078  -2.2661
 19Z  H14   H  HCR6   0   0.265   5.3041  -0.0956  -2.2146
 19Z  H16   H  HCR6   0   0.273   5.3439   0.3404   2.0523
 19Z  H17   H  HCR6   0   0.259   3.0301   1.1416   1.9887
 19Z  HO19  H  HOH1   0   0.475   7.1066  -0.4284   0.7894
 19Z  C10   C  C      0   0.534  -0.9636  -2.1993   0.1444

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
 19Z  N01  C06   single    1.336  0.020  1.336
 19Z  N01  C11   single    1.451  0.020  1.451
 19Z  N01  HN01  single    0.860  0.020  1.020
 19Z  N02  C10   single    1.340  0.020  1.340
 19Z  N02  HN02  single    0.860  0.020  1.020
 19Z  N02  HN0A  single    0.860  0.020  1.020
 19Z  N03  C09   single    1.431  0.020  1.431
 19Z  N03  O20   single    1.214  0.020  1.214
 19Z  N03  O21   double    1.214  0.020  1.214
 19Z  C04  C05   aromatic  1.382  0.020  1.382
 19Z  C04  C09   aromatic  1.388  0.020  1.388
 19Z  C04  H04   single    0.930  0.020  1.080
 19Z  C05  C06   aromatic  1.430  0.020  1.430
 19Z  C05  C10   single    1.491  0.020  1.491
 19Z  C06  C07   aromatic  1.416  0.020  1.416
 19Z  C07  C08   aromatic  1.369  0.020  1.369
 19Z  C07  H07   single    0.930  0.020  1.080
 19Z  C08  C09   aromatic  1.395  0.020  1.395
 19Z  C08  H08   single    0.930  0.020  1.080
 19Z  C10  O18   double    1.230  0.020  1.230
 19Z  C11  C12   single    1.501  0.020  1.501
 19Z  C11  H11   single    0.970  0.020  1.090
 19Z  C11  H11A  single    0.970  0.020  1.090
 19Z  C12  C13   aromatic  1.393  0.020  1.393
 19Z  C12  C17   aromatic  1.390  0.020  1.390
 19Z  C13  C14   aromatic  1.385  0.020  1.385
 19Z  C13  H13   single    0.930  0.020  1.080
 19Z  C14  C15   aromatic  1.394  0.020  1.394
 19Z  C14  H14   single    0.930  0.020  1.080
 19Z  C15  C16   aromatic  1.393  0.020  1.393
 19Z  C15  O19   single    1.347  0.020  1.347
 19Z  C16  C17   aromatic  1.387  0.020  1.387
 19Z  C16  H16   single    0.930  0.020  1.080
 19Z  C17  H17   single    0.930  0.020  1.080
 19Z  O19  HO19  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
 19Z  HN01  N01  C11   118.50  3.000
 19Z  HN01  N01  C06   116.53  3.000
 19Z  C11   N01  C06   124.69  3.000
 19Z  HN0A  N02  HN02  116.62  3.000
 19Z  HN0A  N02  C10   119.00  3.000
 19Z  HN02  N02  C10   122.89  3.000
 19Z  O21   N03  O20   123.08  3.000
 19Z  O21   N03  C09   118.30  3.000
 19Z  O20   N03  C09   118.62  3.000
 19Z  H04   C04  C09   118.97  3.000
 19Z  H04   C04  C05   119.76  3.000
 19Z  C09   C04  C05   121.26  3.000
 19Z  C10   C05  C06   120.55  3.000
 19Z  C10   C05  C04   120.08  3.000
 19Z  C06   C05  C04   119.35  3.000
 19Z  C07   C06  C05   117.83  3.000
 19Z  C07   C06  N01   120.37  3.000
 19Z  C05   C06  N01   121.79  3.000
 19Z  H07   C07  C08   118.60  3.000
 19Z  H07   C07  C06   119.76  3.000
 19Z  C08   C07  C06   121.63  3.000
 19Z  H08   C08  C09   121.02  3.000
 19Z  H08   C08  C07   119.22  3.000
 19Z  C09   C08  C07   119.75  3.000
 19Z  C08   C09  C04   120.07  3.000
 19Z  C08   C09  N03   120.11  3.000
 19Z  C04   C09  N03   119.82  3.000
 19Z  H11A  C11  H11   106.87  3.000
 19Z  H11A  C11  C12   110.12  3.000
 19Z  H11   C11  C12   110.09  3.000
 19Z  H11A  C11  N01   110.27  3.000
 19Z  H11   C11  N01   109.88  3.000
 19Z  C12   C11  N01   109.59  3.000
 19Z  C17   C12  C13   118.22  3.000
 19Z  C17   C12  C11   120.89  3.000
 19Z  C13   C12  C11   120.85  3.000
 19Z  H13   C13  C14   119.02  3.000
 19Z  H13   C13  C12   119.65  3.000
 19Z  C14   C13  C12   121.33  3.000
 19Z  H14   C14  C15   119.81  3.000
 19Z  H14   C14  C13   120.36  3.000
 19Z  C15   C14  C13   119.83  3.000
 19Z  O19   C15  C16   122.64  3.000
 19Z  O19   C15  C14   117.87  3.000
 19Z  C16   C15  C14   119.49  3.000
 19Z  H16   C16  C17   119.81  3.000
 19Z  H16   C16  C15   120.29  3.000
 19Z  C17   C16  C15   119.90  3.000
 19Z  H17   C17  C16   118.91  3.000
 19Z  H17   C17  C12   119.86  3.000
 19Z  C16   C17  C12   121.22  3.000
 19Z  HO19  O19  C15   110.41  3.000
 19Z  O18   C10  C05   121.57  3.000
 19Z  O18   C10  N02   121.66  3.000
 19Z  C05   C10  N02   116.77  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
 19Z  CONST_01  C07   C06  C05  C04     0.00   0.0  0
 19Z  CONST_02  C07   C08  C09  C04     0.00   0.0  0
 19Z  CONST_03  C08   C09  C04  C05     0.00   0.0  0
 19Z  CONST_04  C08   C07  C06  C05     0.00   0.0  0
 19Z  CONST_05  C09   C04  C05  C06     0.00   0.0  0
 19Z  CONST_06  C09   C08  C07  C06     0.00   0.0  0
 19Z  CONST_07  C15   C14  C13  C12     0.00   0.0  0
 19Z  CONST_08  C15   C16  C17  C12     0.00   0.0  0
 19Z  CONST_09  C16   C17  C12  C13     0.00   0.0  0
 19Z  CONST_10  C16   C15  C14  C13     0.00   0.0  0
 19Z  CONST_11  C17   C12  C13  C14     0.00   0.0  0
 19Z  CONST_12  C17   C16  C15  C14     0.00   0.0  0
 19Z  CONST_13  C04   C05  C06  N01   180.00   0.0  0
 19Z  CONST_14  C08   C07  C06  N01   180.00   0.0  0
 19Z  CONST_15  C05   C04  C09  N03   180.00   0.0  0
 19Z  CONST_16  C07   C08  C09  N03   180.00   0.0  0
 19Z  CONST_17  C10   C05  C06  C07   180.00   0.0  0
 19Z  CONST_18  C10   C05  C04  C09   180.00   0.0  0
 19Z  CONST_19  C14   C13  C12  C11   180.00   0.0  0
 19Z  CONST_20  C16   C17  C12  C11   180.00   0.0  0
 19Z  CONST_21  O19   C15  C14  C13   180.00   0.0  0
 19Z  CONST_22  O19   C15  C16  C17   180.00   0.0  0
 19Z  CONST_23  H08   C08  C09  C04   180.00   0.0  0
 19Z  CONST_24  H07   C07  C06  C05   180.00   0.0  0
 19Z  CONST_25  H04   C04  C05  C06   180.00   0.0  0
 19Z  CONST_26  H14   C14  C13  C12   180.00   0.0  0
 19Z  CONST_27  H16   C16  C17  C12   180.00   0.0  0
 19Z  CONST_28  H17   C17  C12  C13   180.00   0.0  0
 19Z  CONST_29  H13   C13  C14  C15   180.00   0.0  0
 19Z  CONST_30  O20   N03  C09  C04     0.00   0.0  0
 19Z  CONST_31  O21   N03  C09  C04   180.00   0.0  0
 19Z  CONST_32  C11   N01  C06  C05   180.00   0.0  0
 19Z  CONST_33  C11   N01  C06  C07     0.00   0.0  0
 19Z  CONST_34  O20   N03  C09  C08   180.00   0.0  0
 19Z  CONST_35  O21   N03  C09  C08     0.00   0.0  0
 19Z  CONST_36  HN01  N01  C06  C05     0.00   0.0  0
 19Z  CONST_37  HN02  N02  C10  C05     0.00   0.0  0
 19Z  CONST_38  HN0A  N02  C10  C05   180.00   0.0  0
 19Z  Var_01    C13   C12  C11  N01    89.08  30.0  2
 19Z  Var_02    C04   C05  C10  N02    24.41  30.0  2
 19Z  Var_03    C12   C11  N01  C06  -179.91  30.0  3

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
 19Z  plan-1  N01   0.020
 19Z  plan-1  N03   0.020
 19Z  plan-1  C04   0.020
 19Z  plan-1  C05   0.020
 19Z  plan-1  C06   0.020
 19Z  plan-1  C07   0.020
 19Z  plan-1  C08   0.020
 19Z  plan-1  C09   0.020
 19Z  plan-1  H04   0.020
 19Z  plan-1  H07   0.020
 19Z  plan-1  H08   0.020
 19Z  plan-1  C10   0.020
 19Z  plan-2  C11   0.020
 19Z  plan-2  C12   0.020
 19Z  plan-2  C13   0.020
 19Z  plan-2  C14   0.020
 19Z  plan-2  C15   0.020
 19Z  plan-2  C16   0.020
 19Z  plan-2  C17   0.020
 19Z  plan-2  O19   0.020
 19Z  plan-2  H13   0.020
 19Z  plan-2  H14   0.020
 19Z  plan-2  H16   0.020
 19Z  plan-2  H17   0.020
 19Z  plan-3  N02   0.020
 19Z  plan-3  C05   0.020
 19Z  plan-3  O18   0.020
 19Z  plan-3  HN02  0.020
 19Z  plan-3  HN0A  0.020
 19Z  plan-3  C10   0.020
 19Z  plan-4  N01   0.020
 19Z  plan-4  C06   0.020
 19Z  plan-4  C11   0.020
 19Z  plan-4  HN01  0.020
 19Z  plan-5  N03   0.020
 19Z  plan-5  C09   0.020
 19Z  plan-5  O20   0.020
 19Z  plan-5  O21   0.020

