# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 10:14:35 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 4-[(3-methoxypropyl)amino]-5-nitro-2-[(pyridin-3-ylmethyl)amino]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCCNc1cc(NCc2cccnc2)c(cc1[N+]([O-])=O)C(N)=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
 X86  X86  4-[(3-methoxypropyl)amino]-5-nitro-2-[(pyridin-3-ylmethyl)amino]benzamide  ligand  47  26  .  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_X86
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
 X86  N01   N  NH1    0  -0.690   2.0272  -0.0711   0.0517
 X86  N02   N  NH2    0  -0.813   2.2193  -4.2461   0.4613
 X86  N03   N  N      0  -0.402   5.4438   2.6527   1.0872
 X86  N04   N  NH1    0  -0.685  -2.7168  -0.2116  -0.1008
 X86  N05   N  N      1   0.339  -2.5968  -3.1463  -0.3141
 X86  C06   C  CR16   0  -0.357  -0.2173  -2.9246  -0.1156
 X86  C07   C  CR6    0  -0.149   0.9643  -2.2370   0.0005
 X86  C08   C  CR6    0   0.455   0.9036  -0.7992   0.0091
 X86  C09   C  CR16   0  -0.560  -0.3467  -0.1794  -0.0052
 X86  C10   C  CR6    0   0.459  -1.5571  -0.8791  -0.0914
 X86  C11   C  CR6    0   0.179  -1.4674  -2.3075  -0.1744
 X86  C13   C  CH2    0  -0.348   2.0636   1.3738   0.0560
 X86  C14   C  CR6    0  -0.026   3.4860   1.8420  -0.0352
 X86  C15   C  CR16   0  -0.084   4.1795   2.2496   1.0982
 X86  C16   C  CR16   0  -0.064   6.0806   2.6625  -0.0774
 X86  C17   C  CR16   0  -0.319   5.4879   2.2747  -1.2708
 X86  C18   C  CR16   0  -0.168   4.1679   1.8563  -1.2464
 X86  C19   C  CH2    0  -0.266  -2.8326   1.2256  -0.0165
 X86  C20   C  CH2    0  -0.513  -4.2975   1.6292  -0.0217
 X86  C21   C  CH2    0  -0.119  -4.4441   3.1366   0.0602
 X86  C22   C  CH3    0  -0.397  -6.0350   4.8484   0.1169
 X86  O23   O  O      0  -0.507   3.3297  -2.4044  -0.1710
 X86  O24   O  O      0  -0.419  -2.4402  -4.3496  -0.4123
 X86  O25   O  O     -1  -0.445  -3.7162  -2.6472  -0.3338
 X86  O26   O  O2     0  -0.486  -5.8100   3.4638   0.0526
 X86  HN01  H  HNH1   0   0.412   2.8942  -0.5891  -0.0109
 X86  H102  H  HNH2   0   0.414   1.4073  -4.6727   0.8705
 X86  H202  H  HNH2   0   0.407   3.0871  -4.7471   0.5609
 X86  HN04  H  HNH1   0   0.413  -3.5587  -0.7574  -0.1859
 X86  H06   H  HCR6   0   0.287  -0.1989  -4.0026  -0.1832
 X86  H09   H  HCR6   0   0.303  -0.3874   0.8974   0.0414
 X86  H113  H  HCH2   0   0.260   1.4934   1.7711  -0.7905
 X86  H213  H  HCH2   0   0.261   1.5979   1.7682   0.9653
 X86  H15   H  HCR6   0   0.263   3.6785   2.2515   2.0619
 X86  H16   H  HCR6   0   0.268   7.1118   2.9974  -0.0643
 X86  H17   H  HCR6   0   0.275   6.0496   2.3069  -2.1941
 X86  H18   H  HCR6   0   0.275   3.6718   1.5514  -2.1600
 X86  H119  H  HCH2   0   0.240  -2.3514   1.5887   0.8982
 X86  H219  H  HCH2   0   0.239  -2.3148   1.6986  -0.8587
 X86  H120  H  HCH2   0   0.245  -4.7750   1.2636  -0.9351
 X86  H220  H  HCH2   0   0.245  -4.8080   1.1645   0.8267
 X86  H121  H  HCH2   0   0.199  -3.9594   3.5106   0.9744
 X86  H221  H  HCH2   0   0.199  -3.9263   3.6103  -0.7872
 X86  H122  H  HCH3   0   0.204  -5.5969   5.3780  -0.7380
 X86  H222  H  HCH3   0   0.234  -7.1116   5.0156   0.1084
 X86  H322  H  HCH3   0   0.203  -5.6242   5.2914   1.0323
 X86  C12   C  C      0   0.536   2.2589  -2.9569   0.0887

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
 X86  N01  C08   single    1.340  0.020  1.340
 X86  N01  C13   single    1.445  0.020  1.445
 X86  N01  HN01  single    0.860  0.020  1.020
 X86  N02  C12   single    1.342  0.020  1.342
 X86  N02  H102  single    0.860  0.020  1.020
 X86  N02  H202  single    0.860  0.020  1.020
 X86  N03  C16   aromatic  1.327  0.020  1.327
 X86  N04  C19   single    1.444  0.020  1.444
 X86  N04  HN04  single    0.860  0.020  1.020
 X86  N05  O24   double    1.217  0.020  1.217
 X86  C06  C11   aromatic  1.395  0.020  1.395
 X86  C06  H06   single    0.930  0.020  1.080
 X86  C07  C06   aromatic  1.372  0.020  1.372
 X86  C07  C08   aromatic  1.439  0.020  1.439
 X86  C08  C09   aromatic  1.396  0.020  1.396
 X86  C09  C10   aromatic  1.401  0.020  1.401
 X86  C09  H09   single    0.930  0.020  1.080
 X86  C10  N04   single    1.338  0.020  1.338
 X86  C11  N05   single    1.414  0.020  1.414
 X86  C11  C10   aromatic  1.434  0.020  1.434
 X86  C12  C07   single    1.484  0.020  1.484
 X86  C13  C14   single    1.500  0.020  1.500
 X86  C13  H113  single    0.970  0.020  1.090
 X86  C13  H213  single    0.970  0.020  1.090
 X86  C14  C18   aromatic  1.390  0.020  1.390
 X86  C15  C14   aromatic  1.390  0.020  1.390
 X86  C15  N03   aromatic  1.327  0.020  1.327
 X86  C15  H15   single    0.930  0.020  1.080
 X86  C16  C17   aromatic  1.388  0.020  1.388
 X86  C16  H16   single    0.930  0.020  1.080
 X86  C17  H17   single    0.930  0.020  1.080
 X86  C18  C17   aromatic  1.385  0.020  1.385
 X86  C18  H18   single    0.930  0.020  1.080
 X86  C19  C20   single    1.519  0.020  1.519
 X86  C19  H119  single    0.970  0.020  1.090
 X86  C19  H219  single    0.970  0.020  1.090
 X86  C20  C21   single    1.517  0.020  1.517
 X86  C20  H120  single    0.970  0.020  1.090
 X86  C20  H220  single    0.970  0.020  1.090
 X86  C21  H121  single    0.970  0.020  1.090
 X86  C21  H221  single    0.970  0.020  1.090
 X86  C22  H122  single    0.970  0.020  1.090
 X86  C22  H222  single    0.970  0.020  1.090
 X86  C22  H322  single    0.970  0.020  1.090
 X86  O23  C12   double    1.233  0.020  1.233
 X86  O25  N05   single    1.226  0.020  1.226
 X86  O26  C22   single    1.404  0.020  1.404
 X86  O26  C21   single    1.405  0.020  1.405

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
 X86  HN01  N01  C13   119.36  3.000
 X86  HN01  N01  C08   116.00  3.000
 X86  C13   N01  C08   124.38  3.000
 X86  H202  N02  H102  116.43  3.000
 X86  H202  N02  C12   118.68  3.000
 X86  H102  N02  C12   123.01  3.000
 X86  C16   N03  C15   117.81  3.000
 X86  HN04  N04  C19   118.50  3.000
 X86  HN04  N04  C10   117.05  3.000
 X86  C19   N04  C10   124.44  3.000
 X86  O25   N05  O24   121.24  3.000
 X86  O25   N05  C11   119.31  3.000
 X86  O24   N05  C11   119.45  3.000
 X86  H06   C06  C11   117.00  3.000
 X86  H06   C06  C07   119.38  3.000
 X86  C11   C06  C07   123.61  3.000
 X86  C12   C07  C08   121.41  3.000
 X86  C12   C07  C06   120.88  3.000
 X86  C08   C07  C06   117.70  3.000
 X86  C09   C08  C07   118.78  3.000
 X86  C09   C08  N01   120.69  3.000
 X86  C07   C08  N01   120.53  3.000
 X86  H09   C09  C10   117.96  3.000
 X86  H09   C09  C08   118.47  3.000
 X86  C10   C09  C08   123.57  3.000
 X86  C11   C10  C09   116.56  3.000
 X86  C11   C10  N04   123.42  3.000
 X86  C09   C10  N04   120.01  3.000
 X86  C10   C11  C06   119.62  3.000
 X86  C10   C11  N05   123.15  3.000
 X86  C06   C11  N05   117.22  3.000
 X86  H213  C13  H113  106.84  3.000
 X86  H213  C13  C14   109.95  3.000
 X86  H113  C13  C14   109.48  3.000
 X86  H213  C13  N01   110.60  3.000
 X86  H113  C13  N01   110.32  3.000
 X86  C14   C13  N01   109.61  3.000
 X86  C18   C14  C15   117.56  3.000
 X86  C15   C14  C13   121.00  3.000
 X86  C18   C14  C13   121.42  3.000
 X86  H15   C15  C14   119.59  3.000
 X86  H15   C15  N03   116.51  3.000
 X86  C14   C15  N03   123.90  3.000
 X86  H16   C16  C17   120.20  3.000
 X86  H16   C16  N03   116.60  3.000
 X86  C17   C16  N03   123.20  3.000
 X86  H17   C17  C18   121.27  3.000
 X86  C18   C17  C16   118.45  3.000
 X86  H17   C17  C16   120.28  3.000
 X86  H18   C18  C17   120.44  3.000
 X86  H18   C18  C14   120.48  3.000
 X86  C17   C18  C14   119.08  3.000
 X86  H219  C19  H119  106.92  3.000
 X86  H219  C19  C20   109.77  3.000
 X86  H119  C19  C20   109.78  3.000
 X86  H219  C19  N04   110.29  3.000
 X86  H119  C19  N04   110.08  3.000
 X86  C20   C19  N04   109.96  3.000
 X86  H220  C20  H120  107.58  3.000
 X86  H220  C20  C21   109.59  3.000
 X86  H120  C20  C21   109.58  3.000
 X86  H220  C20  C19   109.54  3.000
 X86  H120  C20  C19   109.57  3.000
 X86  C21   C20  C19   110.91  3.000
 X86  H221  C21  H121  106.63  3.000
 X86  H221  C21  O26   110.68  3.000
 X86  H121  C21  O26   110.72  3.000
 X86  O26   C21  C20   108.98  3.000
 X86  H221  C21  C20   109.93  3.000
 X86  H121  C21  C20   109.88  3.000
 X86  H322  C22  H222  108.34  3.000
 X86  H322  C22  H122  107.81  3.000
 X86  H222  C22  H122  108.34  3.000
 X86  H322  C22  O26   112.11  3.000
 X86  H222  C22  O26   108.01  3.000
 X86  H122  C22  O26   112.10  3.000
 X86  C22   O26  C21   112.66  3.000
 X86  O23   C12  C07   121.86  3.000
 X86  O23   C12  N02   120.97  3.000
 X86  C07   C12  N02   117.17  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
 X86  CONST_01  C18   C17  C16  N03     0.00   0.0  0
 X86  CONST_02  C18   C14  C15  N03     0.00   0.0  0
 X86  CONST_03  C09   C10  C11  C06     0.00   0.0  0
 X86  CONST_04  C09   C08  C07  C06     0.00   0.0  0
 X86  CONST_05  C10   C11  C06  C07     0.00   0.0  0
 X86  CONST_06  C10   C09  C08  C07     0.00   0.0  0
 X86  CONST_07  C11   C06  C07  C08     0.00   0.0  0
 X86  CONST_08  C11   C10  C09  C08     0.00   0.0  0
 X86  CONST_09  C16   C17  C18  C14     0.00   0.0  0
 X86  CONST_10  C16   N03  C15  C14     0.00   0.0  0
 X86  CONST_11  C17   C18  C14  C15     0.00   0.0  0
 X86  CONST_12  C17   C16  N03  C15     0.00   0.0  0
 X86  CONST_13  C06   C07  C08  N01   180.00   0.0  0
 X86  CONST_14  C10   C09  C08  N01   180.00   0.0  0
 X86  CONST_15  C13   C14  C15  N03   180.00   0.0  0
 X86  CONST_16  C08   C09  C10  N04   180.00   0.0  0
 X86  CONST_17  C06   C11  C10  N04   180.00   0.0  0
 X86  CONST_18  C07   C06  C11  N05   180.00   0.0  0
 X86  CONST_19  C09   C10  C11  N05   180.00   0.0  0
 X86  CONST_20  C12   C07  C08  C09   180.00   0.0  0
 X86  CONST_21  C12   C07  C06  C11   180.00   0.0  0
 X86  CONST_22  C17   C18  C14  C13   180.00   0.0  0
 X86  CONST_23  H17   C17  C16  N03   180.00   0.0  0
 X86  CONST_24  H09   C09  C08  C07   180.00   0.0  0
 X86  CONST_25  H06   C06  C07  C08   180.00   0.0  0
 X86  CONST_26  H18   C18  C14  C15   180.00   0.0  0
 X86  CONST_27  H16   C16  N03  C15   180.00   0.0  0
 X86  CONST_28  H15   C15  N03  C16   180.00   0.0  0
 X86  CONST_29  O24   N05  C11  C06     0.00   0.0  0
 X86  CONST_30  O25   N05  C11  C06   180.00   0.0  0
 X86  CONST_31  C13   N01  C08  C07   180.00   0.0  0
 X86  CONST_32  C13   N01  C08  C09     0.00   0.0  0
 X86  CONST_33  C19   N04  C10  C09     0.00   0.0  0
 X86  CONST_34  O24   N05  C11  C10   180.00   0.0  0
 X86  CONST_35  O25   N05  C11  C10     0.00   0.0  0
 X86  CONST_36  C19   N04  C10  C11   180.00   0.0  0
 X86  CONST_37  HN01  N01  C08  C07     0.00   0.0  0
 X86  CONST_38  HN04  N04  C10  C09   180.00   0.0  0
 X86  CONST_39  H102  N02  C12  C07     0.00   0.0  0
 X86  CONST_40  H202  N02  C12  C07   180.00   0.0  0
 X86  Var_01    C18   C14  C13  N01    78.89  30.0  2
 X86  Var_02    C06   C07  C12  N02   -20.00  30.0  2
 X86  Var_03    C14   C13  N01  C08  -174.14  30.0  3
 X86  Var_04    C20   C19  N04  C10  -178.64  30.0  3
 X86  Var_05    C21   C20  C19  N04  -179.76  30.0  3
 X86  Var_06    O26   C21  C20  C19   180.00  30.0  3
 X86  Var_07    H122  C22  O26  C21    60.83  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
 X86  plan-1  N03   0.020
 X86  plan-1  C13   0.020
 X86  plan-1  C14   0.020
 X86  plan-1  C15   0.020
 X86  plan-1  C16   0.020
 X86  plan-1  C17   0.020
 X86  plan-1  C18   0.020
 X86  plan-1  H15   0.020
 X86  plan-1  H16   0.020
 X86  plan-1  H17   0.020
 X86  plan-1  H18   0.020
 X86  plan-2  N01   0.020
 X86  plan-2  N04   0.020
 X86  plan-2  N05   0.020
 X86  plan-2  C06   0.020
 X86  plan-2  C07   0.020
 X86  plan-2  C08   0.020
 X86  plan-2  C09   0.020
 X86  plan-2  C10   0.020
 X86  plan-2  C11   0.020
 X86  plan-2  H06   0.020
 X86  plan-2  H09   0.020
 X86  plan-2  C12   0.020
 X86  plan-3  N02   0.020
 X86  plan-3  C07   0.020
 X86  plan-3  O23   0.020
 X86  plan-3  H102  0.020
 X86  plan-3  H202  0.020
 X86  plan-3  C12   0.020
 X86  plan-4  N01   0.020
 X86  plan-4  C08   0.020
 X86  plan-4  C13   0.020
 X86  plan-4  HN01  0.020
 X86  plan-5  N04   0.020
 X86  plan-5  C10   0.020
 X86  plan-5  C19   0.020
 X86  plan-5  HN04  0.020
 X86  plan-6  N05   0.020
 X86  plan-6  C11   0.020
 X86  plan-6  O24   0.020
 X86  plan-6  O25   0.020

