# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 02:45:55 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 4-[(3-hydroxypropyl)amino]-5-nitro-2-[(pyridin-3-ylmethyl)amino]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cc(c(NCCCO)cc1NCc2cccnc2)[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
 X84  X84  4-[(3-hydroxypropyl)amino]-5-nitro-2-[(pyridin-3-ylmethyl)amino]benzamide  ligand  44  25  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X84
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
 X84  N01   N  NH1    0  -0.696   1.7604  -0.2293  -0.1277
 X84  N02   N  NH2    0  -0.809   1.1119  -4.2984   0.5425
 X84  N03   N  N      0  -0.400   5.6836   1.9993  -1.0249
 X84  N04   N  NH1    0  -0.683  -2.9088   0.6439  -0.0258
 X84  N05   N  N      1   0.339  -3.4253  -2.2562  -0.0046
 X84  C06   C  CR16   0  -0.354  -1.0437  -2.5381   0.0079
 X84  C07   C  CR6    0  -0.149   0.2595  -2.1116  -0.0051
 X84  C08   C  CR6    0   0.456   0.5034  -0.6962  -0.0822
 X84  C09   C  CR16   0  -0.557  -0.5857   0.1742  -0.0794
 X84  C10   C  CR6    0   0.458  -1.9192  -0.2558  -0.0317
 X84  C11   C  CR6    0   0.176  -2.1380  -1.6719  -0.0059
 X84  C13   C  CH2    0  -0.342   2.1100   1.1696  -0.1987
 X84  C14   C  CR6    0  -0.017   3.5955   1.3288  -0.0536
 X84  C15   C  CR16   0  -0.096   4.3668   1.8402  -1.0893
 X84  C16   C  CR16   0  -0.065   6.2964   1.6408   0.0956
 X84  C17   C  CR16   0  -0.318   5.6266   1.1153   1.1924
 X84  C18   C  CR16   0  -0.170   4.2537   0.9583   1.1149
 X84  C19   C  CH2    0  -0.267  -2.7171   2.0751  -0.0675
 X84  C20   C  CH2    0  -0.505  -4.0634   2.7741   0.0253
 X84  C21   C  CH2    0  -0.136  -3.9108   4.2810  -0.0396
 X84  O22   O  O      0  -0.505   2.4950  -2.8118  -0.4118
 X84  O23   O  OH1    0  -0.672  -5.1922   4.8631   0.0483
 X84  O24   O  O     -1  -0.419  -3.5318  -3.4690  -0.0092
 X84  O25   O  O      0  -0.445  -4.4135  -1.5310   0.0029
 X84  HN01  H  HNH1   0   0.411   2.4788  -0.9182  -0.3086
 X84  H102  H  HNH2   0   0.414   0.2854  -4.4922   1.0798
 X84  H202  H  HNH2   0   0.407   1.8502  -4.9819   0.5860
 X84  HN04  H  HNH1   0   0.412  -3.8513   0.2896  -0.0134
 X84  H06   H  HCR6   0   0.289  -1.2512  -3.5983   0.0097
 X84  H09   H  HCR6   0   0.304  -0.4025   1.2357  -0.1417
 X84  H113  H  HCH2   0   0.259   1.7778   1.6202  -1.1413
 X84  H213  H  HCH2   0   0.262   1.6078   1.7157   0.6057
 X84  H15   H  HCR6   0   0.263   3.8886   2.1374  -2.0177
 X84  H16   H  HCR6   0   0.267   7.3719   1.7753   0.1264
 X84  H17   H  HCR6   0   0.275   6.1723   0.8378   2.0837
 X84  H18   H  HCR6   0   0.275   3.7009   0.5539   1.9542
 X84  H119  H  HCH2   0   0.239  -2.0770   2.3956   0.7614
 X84  H219  H  HCH2   0   0.239  -2.2077   2.3648  -0.9936
 X84  H120  H  HCH2   0   0.242  -4.7056   2.4369  -0.7934
 X84  H220  H  HCH2   0   0.243  -4.5509   2.4937   0.9630
 X84  H121  H  HCH2   0   0.195  -3.2592   4.6173   0.7777
 X84  H221  H  HCH2   0   0.195  -3.4095   4.5550  -0.9772
 X84  HO23  H  HOH1   0   0.455  -5.0901   5.8185   0.0211
 X84  C12   C  C      0   0.531   1.3765  -3.0891   0.0247

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
 X84  N01  C08   single    1.342  0.020  1.342
 X84  N01  C13   single    1.444  0.020  1.444
 X84  N01  HN01  single    0.860  0.020  1.020
 X84  N02  C12   single    1.342  0.020  1.342
 X84  N02  H102  single    0.860  0.020  1.020
 X84  N02  H202  single    0.860  0.020  1.020
 X84  N04  C19   single    1.445  0.020  1.445
 X84  N04  HN04  single    0.860  0.020  1.020
 X84  N05  O24   single    1.218  0.020  1.218
 X84  C06  C11   aromatic  1.396  0.020  1.396
 X84  C06  H06   single    0.930  0.020  1.080
 X84  C07  C06   aromatic  1.371  0.020  1.371
 X84  C07  C08   aromatic  1.438  0.020  1.438
 X84  C08  C09   aromatic  1.394  0.020  1.394
 X84  C09  C10   aromatic  1.402  0.020  1.402
 X84  C09  H09   single    0.930  0.020  1.080
 X84  C10  N04   single    1.338  0.020  1.338
 X84  C11  N05   single    1.414  0.020  1.414
 X84  C11  C10   aromatic  1.433  0.020  1.433
 X84  C12  C07   single    1.485  0.020  1.485
 X84  C13  C14   single    1.501  0.020  1.501
 X84  C13  H113  single    0.970  0.020  1.090
 X84  C13  H213  single    0.970  0.020  1.090
 X84  C14  C15   aromatic  1.389  0.020  1.389
 X84  C15  N03   aromatic  1.328  0.020  1.328
 X84  C15  H15   single    0.930  0.020  1.080
 X84  C16  N03   aromatic  1.327  0.020  1.327
 X84  C16  H16   single    0.930  0.020  1.080
 X84  C17  C16   aromatic  1.388  0.020  1.388
 X84  C17  H17   single    0.930  0.020  1.080
 X84  C18  C14   aromatic  1.391  0.020  1.391
 X84  C18  C17   aromatic  1.384  0.020  1.384
 X84  C18  H18   single    0.930  0.020  1.080
 X84  C19  C20   single    1.520  0.020  1.520
 X84  C19  H119  single    0.970  0.020  1.090
 X84  C19  H219  single    0.970  0.020  1.090
 X84  C20  C21   single    1.516  0.020  1.516
 X84  C20  H120  single    0.970  0.020  1.090
 X84  C20  H220  single    0.970  0.020  1.090
 X84  C21  O23   single    1.410  0.020  1.410
 X84  C21  H121  single    0.970  0.020  1.090
 X84  C21  H221  single    0.970  0.020  1.090
 X84  O22  C12   double    1.232  0.020  1.232
 X84  O23  HO23  single    0.850  0.020  0.980
 X84  O25  N05   double    1.226  0.020  1.226

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
 X84  HN01  N01  C13   118.63  3.000
 X84  HN01  N01  C08   115.74  3.000
 X84  C13   N01  C08   124.46  3.000
 X84  H202  N02  H102  116.68  3.000
 X84  H202  N02  C12   118.93  3.000
 X84  H102  N02  C12   122.85  3.000
 X84  C16   N03  C15   117.82  3.000
 X84  HN04  N04  C19   118.24  3.000
 X84  HN04  N04  C10   117.12  3.000
 X84  C19   N04  C10   124.62  3.000
 X84  O25   N05  O24   121.25  3.000
 X84  O25   N05  C11   119.32  3.000
 X84  O24   N05  C11   119.43  3.000
 X84  H06   C06  C11   117.29  3.000
 X84  H06   C06  C07   119.19  3.000
 X84  C11   C06  C07   123.51  3.000
 X84  C12   C07  C08   121.43  3.000
 X84  C12   C07  C06   120.67  3.000
 X84  C08   C07  C06   117.88  3.000
 X84  C09   C08  C07   118.80  3.000
 X84  C09   C08  N01   120.97  3.000
 X84  C07   C08  N01   120.21  3.000
 X84  H09   C09  C10   117.73  3.000
 X84  H09   C09  C08   118.78  3.000
 X84  C10   C09  C08   123.48  3.000
 X84  C11   C10  C09   116.68  3.000
 X84  C11   C10  N04   123.48  3.000
 X84  C09   C10  N04   119.84  3.000
 X84  C10   C11  C06   119.58  3.000
 X84  C10   C11  N05   123.19  3.000
 X84  C06   C11  N05   117.22  3.000
 X84  H213  C13  H113  106.73  3.000
 X84  H213  C13  C14   109.28  3.000
 X84  H113  C13  C14   109.85  3.000
 X84  H213  C13  N01   109.65  3.000
 X84  H113  C13  N01   111.54  3.000
 X84  C14   C13  N01   109.73  3.000
 X84  C18   C14  C15   117.49  3.000
 X84  C18   C14  C13   121.41  3.000
 X84  C15   C14  C13   121.10  3.000
 X84  H15   C15  C14   119.60  3.000
 X84  H15   C15  N03   116.44  3.000
 X84  C14   C15  N03   123.96  3.000
 X84  H16   C16  C17   120.20  3.000
 X84  C17   C16  N03   123.14  3.000
 X84  H16   C16  N03   116.66  3.000
 X84  H17   C17  C18   121.17  3.000
 X84  C18   C17  C16   118.50  3.000
 X84  H17   C17  C16   120.32  3.000
 X84  H18   C18  C17   120.34  3.000
 X84  H18   C18  C14   120.57  3.000
 X84  C17   C18  C14   119.09  3.000
 X84  H219  C19  H119  106.89  3.000
 X84  H219  C19  C20   109.98  3.000
 X84  H119  C19  C20   109.69  3.000
 X84  H219  C19  N04   110.36  3.000
 X84  H119  C19  N04   110.22  3.000
 X84  C20   C19  N04   109.65  3.000
 X84  H220  C20  H120  107.52  3.000
 X84  H220  C20  C21   109.66  3.000
 X84  H120  C20  C21   109.48  3.000
 X84  H220  C20  C19   109.23  3.000
 X84  H120  C20  C19   109.43  3.000
 X84  C21   C20  C19   111.43  3.000
 X84  H221  C21  H121  106.76  3.000
 X84  H221  C21  O23   111.41  3.000
 X84  H121  C21  O23   111.50  3.000
 X84  H221  C21  C20   109.30  3.000
 X84  H121  C21  C20   109.41  3.000
 X84  O23   C21  C20   108.43  3.000
 X84  HO23  O23  C21   108.18  3.000
 X84  O22   C12  C07   121.85  3.000
 X84  O22   C12  N02   121.23  3.000
 X84  C07   C12  N02   116.92  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
 X84  CONST_01  C18   C14  C15  N03     0.00   0.0  0
 X84  CONST_02  C18   C17  C16  N03     0.00   0.0  0
 X84  CONST_03  C09   C10  C11  C06     0.00   0.0  0
 X84  CONST_04  C09   C08  C07  C06     0.00   0.0  0
 X84  CONST_05  C10   C11  C06  C07     0.00   0.0  0
 X84  CONST_06  C10   C09  C08  C07     0.00   0.0  0
 X84  CONST_07  C11   C06  C07  C08     0.00   0.0  0
 X84  CONST_08  C11   C10  C09  C08     0.00   0.0  0
 X84  CONST_09  C16   N03  C15  C14     0.00   0.0  0
 X84  CONST_10  C16   C17  C18  C14     0.00   0.0  0
 X84  CONST_11  C17   C18  C14  C15     0.00   0.0  0
 X84  CONST_12  C17   C16  N03  C15     0.00   0.0  0
 X84  CONST_13  C06   C07  C08  N01   180.00   0.0  0
 X84  CONST_14  C10   C09  C08  N01   180.00   0.0  0
 X84  CONST_15  C13   C14  C15  N03   180.00   0.0  0
 X84  CONST_16  C08   C09  C10  N04   180.00   0.0  0
 X84  CONST_17  C06   C11  C10  N04   180.00   0.0  0
 X84  CONST_18  C07   C06  C11  N05   180.00   0.0  0
 X84  CONST_19  C09   C10  C11  N05   180.00   0.0  0
 X84  CONST_20  C12   C07  C08  C09   180.00   0.0  0
 X84  CONST_21  C12   C07  C06  C11   180.00   0.0  0
 X84  CONST_22  C17   C18  C14  C13   180.00   0.0  0
 X84  CONST_23  H17   C17  C16  N03   180.00   0.0  0
 X84  CONST_24  H09   C09  C08  C07   180.00   0.0  0
 X84  CONST_25  H06   C06  C07  C08   180.00   0.0  0
 X84  CONST_26  H18   C18  C14  C15   180.00   0.0  0
 X84  CONST_27  H16   C16  N03  C15   180.00   0.0  0
 X84  CONST_28  H15   C15  N03  C16   180.00   0.0  0
 X84  CONST_29  O24   N05  C11  C06     0.00   0.0  0
 X84  CONST_30  O25   N05  C11  C06   180.00   0.0  0
 X84  CONST_31  C13   N01  C08  C07   180.00   0.0  0
 X84  CONST_32  C13   N01  C08  C09     0.00   0.0  0
 X84  CONST_33  C19   N04  C10  C09     0.00   0.0  0
 X84  CONST_34  O24   N05  C11  C10   180.00   0.0  0
 X84  CONST_35  O25   N05  C11  C10     0.00   0.0  0
 X84  CONST_36  C19   N04  C10  C11   180.00   0.0  0
 X84  CONST_37  HN01  N01  C08  C07     0.00   0.0  0
 X84  CONST_38  HN04  N04  C10  C09   180.00   0.0  0
 X84  CONST_39  H102  N02  C12  C07     0.00   0.0  0
 X84  CONST_40  H202  N02  C12  C07   180.00   0.0  0
 X84  Var_01    C15   C14  C13  N01   116.02  30.0  2
 X84  Var_02    C06   C07  C12  N02   -23.68  30.0  2
 X84  Var_03    C14   C13  N01  C08   172.65  30.0  3
 X84  Var_04    C20   C19  N04  C10  -177.14  30.0  3
 X84  Var_05    C21   C20  C19  N04  -178.99  30.0  3
 X84  Var_06    O23   C21  C20  C19   179.86  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
 X84  plan-1  N01   0.020
 X84  plan-1  N04   0.020
 X84  plan-1  N05   0.020
 X84  plan-1  C06   0.020
 X84  plan-1  C07   0.020
 X84  plan-1  C08   0.020
 X84  plan-1  C09   0.020
 X84  plan-1  C10   0.020
 X84  plan-1  C11   0.020
 X84  plan-1  H06   0.020
 X84  plan-1  H09   0.020
 X84  plan-1  C12   0.020
 X84  plan-2  N03   0.020
 X84  plan-2  C13   0.020
 X84  plan-2  C14   0.020
 X84  plan-2  C15   0.020
 X84  plan-2  C16   0.020
 X84  plan-2  C17   0.020
 X84  plan-2  C18   0.020
 X84  plan-2  H15   0.020
 X84  plan-2  H16   0.020
 X84  plan-2  H17   0.020
 X84  plan-2  H18   0.020
 X84  plan-3  N02   0.020
 X84  plan-3  C07   0.020
 X84  plan-3  O22   0.020
 X84  plan-3  H102  0.020
 X84  plan-3  H202  0.020
 X84  plan-3  C12   0.020
 X84  plan-4  N01   0.020
 X84  plan-4  C08   0.020
 X84  plan-4  C13   0.020
 X84  plan-4  HN01  0.020
 X84  plan-5  N04   0.020
 X84  plan-5  C10   0.020
 X84  plan-5  C19   0.020
 X84  plan-5  HN04  0.020
 X84  plan-6  N05   0.020
 X84  plan-6  C11   0.020
 X84  plan-6  O24   0.020
 X84  plan-6  O25   0.020

