# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 01:51:58 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 4-({4-carbamoyl-2-nitro-5-[(pyridin-3-ylmethyl)amino]phenyl}amino)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cc(c(NCCCC(O)=O)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
 24Z  24Z  '4-({4-carbamoyl-2-nitro-5-[(pyridin-3-ylmethyl)amino]phenyl}amino)butanoic acid'  ligand  45  27  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_24Z
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
 24Z  N01   N  NH1    0  -0.690   2.2885   0.0788  -0.1023
 24Z  N02   N  NH2    0  -0.814   2.9733  -4.0352   0.4170
 24Z  N03   N  N      0  -0.401   5.3136   3.0678   1.1940
 24Z  N04   N  NH1    0  -0.682  -2.4059  -0.5997  -0.1229
 24Z  N05   N  N      1   0.339  -1.9590  -3.5137  -0.2199
 24Z  C06   C  C1     0  -0.359   0.3843  -3.0161  -0.1137
 24Z  C07   C  C      0  -0.147   1.4832  -2.1963  -0.0582
 24Z  C08   C  C      0   0.455   1.2565  -0.7756  -0.0968
 24Z  C09   C  C1     0  -0.561  -0.0553  -0.3018  -0.1072
 24Z  C10   C  C      0   0.455  -1.1814  -1.1358  -0.1260
 24Z  C11   C  C      0   0.179  -0.9293  -2.5474  -0.1557
 24Z  C13   C  CH2    0  -0.348   2.1534   1.5174  -0.1164
 24Z  C14   C  CR6    0  -0.028   3.5126   2.1524  -0.0984
 24Z  C15   C  CR16   0  -0.081   4.1077   2.5230   1.1025
 24Z  C16   C  CR16   0  -0.064   5.9907   3.2659   0.0688
 24Z  C17   C  CR16   0  -0.320   5.4967   2.9320  -1.1837
 24Z  C18   C  CR16   0  -0.168   4.2354   2.3646  -1.2658
 24Z  C19   C  CH2    0  -0.255  -2.6793   0.8194  -0.0580
 24Z  C20   C  CH2    0  -0.460  -4.1761   1.0706   0.0293
 24Z  C21   C  CH2    0  -0.584  -4.4815   2.5570   0.1040
 24Z  C22   C  C      0   0.416  -5.9733   2.9263   0.1962
 24Z  O23   O  O      0  -0.508   3.8496  -2.0907  -0.2696
 24Z  O24   O  OC    -1  -0.631  -6.2269   4.1480   0.2473
 24Z  O25   O  O      0  -0.607  -6.8039   1.9973   0.2095
 24Z  O26   O  O     -1  -0.444  -3.1274  -3.1446  -0.2303
 24Z  O27   O  O      0  -0.421  -1.6698  -4.6959  -0.2636
 24Z  HN01  H  HNH1   0   0.411   3.2091  -0.3350  -0.1723
 24Z  H102  H  HNH2   0   0.414   2.2195  -4.5546   0.8298
 24Z  H202  H  HNH2   0   0.407   3.8936  -4.4355   0.4986
 24Z  HN04  H  HNH1   0   0.410  -3.1874  -1.2333  -0.1496
 24Z  H06   H  H      0   0.285   0.5206  -4.0875  -0.1414
 24Z  H09   H  H      0   0.303  -0.2137   0.7651  -0.1159
 24Z  H113  H  HCH2   0   0.260   1.6040   1.8461  -1.0055
 24Z  H213  H  HCH2   0   0.260   1.5790   1.8534   0.7530
 24Z  H15   H  HCR6   0   0.263   3.5719   2.3736   2.0353
 24Z  H16   H  HCR6   0   0.267   6.9729   3.7149   0.1663
 24Z  H17   H  HCR6   0   0.275   6.0871   3.1158  -2.0706
 24Z  H18   H  HCR6   0   0.275   3.8149   2.0953  -2.2272
 24Z  H119  H  HCH2   0   0.231  -2.1819   1.2542   0.8163
 24Z  H219  H  HCH2   0   0.231  -2.2681   1.3265  -0.9388
 24Z  H120  H  HCH2   0   0.226  -4.6710   0.6303  -0.8404
 24Z  H220  H  HCH2   0   0.225  -4.5744   0.5598   0.9099
 24Z  H121  H  HCH2   0   0.225  -3.9659   2.9968   0.9656
 24Z  H221  H  HCH2   0   0.225  -4.0598   3.0660  -0.7703
 24Z  C12   C  C      0   0.538   2.8544  -2.7590   0.0194

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
 24Z  N01  C08   single    1.340  0.020  1.340
 24Z  N01  C13   single    1.445  0.020  1.445
 24Z  N01  HN01  single    0.860  0.020  1.020
 24Z  N02  C12   single    1.342  0.020  1.342
 24Z  N02  H102  single    0.860  0.020  1.020
 24Z  N02  H202  single    0.860  0.020  1.020
 24Z  N03  C16   aromatic  1.328  0.020  1.328
 24Z  N04  C19   single    1.447  0.020  1.447
 24Z  N04  HN04  single    0.860  0.020  1.020
 24Z  N05  O27   double    1.218  0.020  1.218
 24Z  C06  C11   aromatic  1.395  0.020  1.395
 24Z  C06  H06   single    0.930  0.020  1.080
 24Z  C07  C06   aromatic  1.372  0.020  1.372
 24Z  C07  C08   aromatic  1.439  0.020  1.439
 24Z  C08  C09   aromatic  1.395  0.020  1.395
 24Z  C09  C10   aromatic  1.401  0.020  1.401
 24Z  C09  H09   single    0.930  0.020  1.080
 24Z  C10  N04   single    1.337  0.020  1.337
 24Z  C11  N05   single    1.414  0.020  1.414
 24Z  C11  C10   aromatic  1.434  0.020  1.434
 24Z  C12  C07   single    1.484  0.020  1.484
 24Z  C13  C14   single    1.500  0.020  1.500
 24Z  C13  H113  single    0.970  0.020  1.090
 24Z  C13  H213  single    0.970  0.020  1.090
 24Z  C14  C18   aromatic  1.389  0.020  1.389
 24Z  C15  C14   aromatic  1.391  0.020  1.391
 24Z  C15  N03   aromatic  1.326  0.020  1.326
 24Z  C15  H15   single    0.930  0.020  1.080
 24Z  C16  C17   aromatic  1.387  0.020  1.387
 24Z  C16  H16   single    0.930  0.020  1.080
 24Z  C17  H17   single    0.930  0.020  1.080
 24Z  C18  C17   aromatic  1.386  0.020  1.386
 24Z  C18  H18   single    0.930  0.020  1.080
 24Z  C19  C20   single    1.520  0.020  1.520
 24Z  C19  H119  single    0.970  0.020  1.090
 24Z  C19  H219  single    0.970  0.020  1.090
 24Z  C20  C21   single    1.519  0.020  1.519
 24Z  C20  H120  single    0.970  0.020  1.090
 24Z  C20  H220  single    0.970  0.020  1.090
 24Z  C21  C22   single    1.540  0.020  1.540
 24Z  C21  H121  single    0.970  0.020  1.090
 24Z  C21  H221  single    0.970  0.020  1.090
 24Z  C22  O25   deloc     1.246  0.020  1.246
 24Z  C22  O24   deloc     1.249  0.020  1.249
 24Z  O23  C12   double    1.233  0.020  1.233
 24Z  O26  N05   single    1.225  0.020  1.225

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
 24Z  HN01  N01  C13   119.45  3.000
 24Z  HN01  N01  C08   116.13  3.000
 24Z  C13   N01  C08   124.25  3.000
 24Z  H202  N02  H102  116.56  3.000
 24Z  H202  N02  C12   118.88  3.000
 24Z  H102  N02  C12   123.17  3.000
 24Z  C16   N03  C15   117.80  3.000
 24Z  HN04  N04  C19   118.17  3.000
 24Z  HN04  N04  C10   117.30  3.000
 24Z  C19   N04  C10   124.52  3.000
 24Z  O27   N05  O26   121.24  3.000
 24Z  O26   N05  C11   119.27  3.000
 24Z  O27   N05  C11   119.49  3.000
 24Z  H06   C06  C11   116.82  3.000
 24Z  H06   C06  C07   119.50  3.000
 24Z  C11   C06  C07   123.67  3.000
 24Z  C12   C07  C08   121.42  3.000
 24Z  C12   C07  C06   121.03  3.000
 24Z  C08   C07  C06   117.55  3.000
 24Z  C09   C08  C07   118.93  3.000
 24Z  C09   C08  N01   120.52  3.000
 24Z  C07   C08  N01   120.54  3.000
 24Z  H09   C09  C10   118.07  3.000
 24Z  H09   C09  C08   118.30  3.000
 24Z  C10   C09  C08   123.62  3.000
 24Z  C11   C10  C09   116.41  3.000
 24Z  C11   C10  N04   123.77  3.000
 24Z  C09   C10  N04   119.82  3.000
 24Z  C10   C11  C06   119.70  3.000
 24Z  C10   C11  N05   123.07  3.000
 24Z  C06   C11  N05   117.22  3.000
 24Z  H213  C13  H113  106.81  3.000
 24Z  H213  C13  C14   109.62  3.000
 24Z  H113  C13  C14   109.70  3.000
 24Z  H213  C13  N01   110.30  3.000
 24Z  H113  C13  N01   110.70  3.000
 24Z  C14   C13  N01   109.67  3.000
 24Z  C18   C14  C15   117.54  3.000
 24Z  C15   C14  C13   120.72  3.000
 24Z  C18   C14  C13   121.72  3.000
 24Z  H15   C15  C14   119.60  3.000
 24Z  H15   C15  N03   116.47  3.000
 24Z  C14   C15  N03   123.93  3.000
 24Z  H16   C16  C17   120.23  3.000
 24Z  H16   C16  N03   116.58  3.000
 24Z  C17   C16  N03   123.20  3.000
 24Z  H17   C17  C18   121.20  3.000
 24Z  C18   C17  C16   118.45  3.000
 24Z  H17   C17  C16   120.36  3.000
 24Z  H18   C18  C17   120.52  3.000
 24Z  H18   C18  C14   120.39  3.000
 24Z  C17   C18  C14   119.10  3.000
 24Z  H219  C19  H119  106.69  3.000
 24Z  H219  C19  C20   109.82  3.000
 24Z  H119  C19  C20   109.60  3.000
 24Z  H219  C19  N04   110.29  3.000
 24Z  H119  C19  N04   109.83  3.000
 24Z  C20   C19  N04   110.54  3.000
 24Z  H220  C20  H120  106.71  3.000
 24Z  H220  C20  C21   110.14  3.000
 24Z  H120  C20  C21   110.01  3.000
 24Z  H220  C20  C19   109.14  3.000
 24Z  H120  C20  C19   109.48  3.000
 24Z  C21   C20  C19   111.25  3.000
 24Z  H221  C21  H121  105.05  3.000
 24Z  H221  C21  C22   108.01  3.000
 24Z  H121  C21  C22   108.21  3.000
 24Z  H221  C21  C20   109.74  3.000
 24Z  H121  C21  C20   109.67  3.000
 24Z  C22   C21  C20   115.62  3.000
 24Z  O25   C22  O24   126.40  3.000
 24Z  O24   C22  C21   115.71  3.000
 24Z  O25   C22  C21   117.88  3.000
 24Z  O23   C12  C07   121.86  3.000
 24Z  O23   C12  N02   120.89  3.000
 24Z  C07   C12  N02   117.25  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
 24Z  CONST_01  C18   C17  C16  N03     0.00   0.0  0
 24Z  CONST_02  C18   C14  C15  N03     0.00   0.0  0
 24Z  CONST_03  C09   C10  C11  C06     0.00   0.0  0
 24Z  CONST_04  C09   C08  C07  C06     0.00   0.0  0
 24Z  CONST_05  C10   C11  C06  C07     0.00   0.0  0
 24Z  CONST_06  C10   C09  C08  C07     0.00   0.0  0
 24Z  CONST_07  C11   C06  C07  C08     0.00   0.0  0
 24Z  CONST_08  C11   C10  C09  C08     0.00   0.0  0
 24Z  CONST_09  C16   C17  C18  C14     0.00   0.0  0
 24Z  CONST_10  C16   N03  C15  C14     0.00   0.0  0
 24Z  CONST_11  C17   C18  C14  C15     0.00   0.0  0
 24Z  CONST_12  C17   C16  N03  C15     0.00   0.0  0
 24Z  CONST_13  C06   C07  C08  N01   180.00   0.0  0
 24Z  CONST_14  C10   C09  C08  N01   180.00   0.0  0
 24Z  CONST_15  C13   C14  C15  N03   180.00   0.0  0
 24Z  CONST_16  C08   C09  C10  N04   180.00   0.0  0
 24Z  CONST_17  C06   C11  C10  N04   180.00   0.0  0
 24Z  CONST_18  C07   C06  C11  N05   180.00   0.0  0
 24Z  CONST_19  C09   C10  C11  N05   180.00   0.0  0
 24Z  CONST_20  C12   C07  C08  C09   180.00   0.0  0
 24Z  CONST_21  C12   C07  C06  C11   180.00   0.0  0
 24Z  CONST_22  C17   C18  C14  C13   180.00   0.0  0
 24Z  CONST_23  H17   C17  C16  N03   180.00   0.0  0
 24Z  CONST_24  H09   C09  C08  C07   180.00   0.0  0
 24Z  CONST_25  H06   C06  C07  C08   180.00   0.0  0
 24Z  CONST_26  H18   C18  C14  C15   180.00   0.0  0
 24Z  CONST_27  H16   C16  N03  C15   180.00   0.0  0
 24Z  CONST_28  H15   C15  N03  C16   180.00   0.0  0
 24Z  CONST_29  O27   N05  C11  C06     0.00   0.0  0
 24Z  CONST_30  O26   N05  C11  C06   180.00   0.0  0
 24Z  CONST_31  C13   N01  C08  C07   180.00   0.0  0
 24Z  CONST_32  C13   N01  C08  C09     0.00   0.0  0
 24Z  CONST_33  C19   N04  C10  C09     0.00   0.0  0
 24Z  CONST_34  O27   N05  C11  C10   180.00   0.0  0
 24Z  CONST_35  O26   N05  C11  C10     0.00   0.0  0
 24Z  CONST_36  C19   N04  C10  C11   180.00   0.0  0
 24Z  CONST_37  HN01  N01  C08  C07     0.00   0.0  0
 24Z  CONST_38  HN04  N04  C10  C09   180.00   0.0  0
 24Z  CONST_39  H102  N02  C12  C07     0.00   0.0  0
 24Z  CONST_40  H202  N02  C12  C07   180.00   0.0  0
 24Z  Var_01    C18   C14  C13  N01    85.32  30.0  2
 24Z  Var_02    C06   C07  C12  N02   -18.77  30.0  2
 24Z  Var_03    C14   C13  N01  C08   179.16  30.0  3
 24Z  Var_04    C20   C19  N04  C10  -175.84  30.0  3
 24Z  Var_05    C21   C20  C19  N04   179.77  30.0  3
 24Z  Var_06    C22   C21  C20  C19  -179.98  30.0  3
 24Z  Var_07    O25   C22  C21  C20     0.36  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
 24Z  plan-1  N03   0.020
 24Z  plan-1  C13   0.020
 24Z  plan-1  C14   0.020
 24Z  plan-1  C15   0.020
 24Z  plan-1  C16   0.020
 24Z  plan-1  C17   0.020
 24Z  plan-1  C18   0.020
 24Z  plan-1  H15   0.020
 24Z  plan-1  H16   0.020
 24Z  plan-1  H17   0.020
 24Z  plan-1  H18   0.020
 24Z  plan-2  N01   0.020
 24Z  plan-2  N04   0.020
 24Z  plan-2  N05   0.020
 24Z  plan-2  C06   0.020
 24Z  plan-2  C07   0.020
 24Z  plan-2  C08   0.020
 24Z  plan-2  C09   0.020
 24Z  plan-2  C10   0.020
 24Z  plan-2  C11   0.020
 24Z  plan-2  H06   0.020
 24Z  plan-2  H09   0.020
 24Z  plan-2  C12   0.020
 24Z  plan-3  N02   0.020
 24Z  plan-3  C07   0.020
 24Z  plan-3  O23   0.020
 24Z  plan-3  H102  0.020
 24Z  plan-3  H202  0.020
 24Z  plan-3  C12   0.020
 24Z  plan-4  N01   0.020
 24Z  plan-4  C08   0.020
 24Z  plan-4  C13   0.020
 24Z  plan-4  HN01  0.020
 24Z  plan-5  N04   0.020
 24Z  plan-5  C10   0.020
 24Z  plan-5  C19   0.020
 24Z  plan-5  HN04  0.020
 24Z  plan-6  N05   0.020
 24Z  plan-6  C11   0.020
 24Z  plan-6  O26   0.020
 24Z  plan-6  O27   0.020
 24Z  plan-7  C21   0.020
 24Z  plan-7  C22   0.020
 24Z  plan-7  O24   0.020
 24Z  plan-7  O25   0.020

