# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 23:32:37 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 2-{[(2-aminopyrimidin-5-yl)methyl]amino}-4-[(2-hydroxyethyl)amino]-5-nitrobenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cc(c(NCCO)cc1NCc2cnc(N)nc2)[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
 X63  X63  2-{[(2-aminopyrimidin-5-yl)methyl]amino}-4-[(2-hydroxyethyl)amino]-5-nitrobenzamide  ligand  42  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_X63
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
 X63  N01   N  NH1    0  -0.686  -1.2132  -0.2825   0.0290
 X63  N02   N  NH2    0  -0.810   0.2670  -4.1428  -0.6152
 X63  N03   N  N      0  -0.452  -5.3366   0.6631  -1.1729
 X63  N04   N  N      0  -0.452  -5.4013   0.7124   1.2040
 X63  N05   N  NH1    0  -0.676   3.1880   1.4984   0.1655
 X63  N06   N  NH2    0  -0.818  -7.3175   0.4882  -0.0335
 X63  N07   N  N      1   0.339   4.2702  -1.2396   0.1281
 X63  C08   C  CR16   0  -0.355   1.9960  -1.9899   0.0117
 X63  C09   C  CR6    0  -0.146   0.6342  -1.8339  -0.0323
 X63  C10   C  CR6    0   0.450   0.1099  -0.4968   0.0334
 X63  C11   C  CR16   0  -0.556   1.0035   0.5748   0.0686
 X63  C12   C  CR6    0   0.457   2.3963   0.4214   0.0970
 X63  C13   C  CR6    0   0.176   2.8931  -0.9227   0.0777
 X63  C15   C  CH2    0  -0.353  -1.8233   1.0279   0.1036
 X63  C16   C  CR6    0  -0.094  -3.3126   0.9054   0.0672
 X63  C17   C  CR16   0  -0.019  -4.0259   0.8042  -1.1210
 X63  C18   C  CR6    0   0.555  -5.9806   0.6162   0.0009
 X63  C19   C  CR16   0  -0.024  -4.0887   0.8526   1.2170
 X63  C20   C  CH2    0  -0.303   2.7171   2.8628   0.1417
 X63  C21   C  CH2    0  -0.187   3.8547   3.8120   0.4460
 X63  O22   O  O      0  -0.505  -1.4299  -2.9734   0.2726
 X63  O23   O  OH1    0  -0.670   4.8683   3.6318  -0.5170
 X63  O24   O  O      0  -0.420   4.6140  -2.4070   0.1677
 X63  O25   O  O     -1  -0.444   5.0954  -0.3335   0.1280
 X63  HN01  H  HNH1   0   0.407  -1.7995  -1.0984   0.1392
 X63  H102  H  HNH2   0   0.414   1.1343  -4.1602  -1.1224
 X63  H202  H  HNH2   0   0.407  -0.3145  -4.9621  -0.6880
 X63  HN05  H  HNH1   0   0.403   4.1793   1.3465   0.0718
 X63  H106  H  HNH2   0   0.399  -7.7690   0.2601  -0.9017
 X63  H206  H  HNH2   0   0.399  -7.8163   0.2937   0.8168
 X63  H08   H  HCR6   0   0.288   2.4133  -2.9864   0.0132
 X63  H11   H  HCR6   0   0.303   0.6035   1.5768   0.0874
 X63  H115  H  HCH2   0   0.257  -1.5138   1.5439   1.0196
 X63  H215  H  HCH2   0   0.260  -1.4799   1.6430  -0.7337
 X63  H17   H  HCR6   0   0.269  -3.5065   0.8441  -2.0748
 X63  H19   H  HCR6   0   0.269  -3.6221   0.9336   2.1950
 X63  H120  H  HCH2   0   0.246   2.2668   3.1078  -0.8273
 X63  H220  H  HCH2   0   0.247   1.9473   3.0164   0.9017
 X63  H121  H  HCH2   0   0.221   3.4535   4.8323   0.4366
 X63  H221  H  HCH2   0   0.215   4.2235   3.6168   1.4597
 X63  HO23  H  HOH1   0   0.461   5.6555   4.0958  -0.2190
 X63  C14   C  C      0   0.528  -0.2604  -3.0154  -0.1125

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
 X63  N01  HN01  single    0.860  0.020  1.020
 X63  N02  C14   single    1.342  0.020  1.342
 X63  N02  H102  single    0.860  0.020  1.020
 X63  N02  H202  single    0.860  0.020  1.020
 X63  N03  C18   aromatic  1.340  0.020  1.340
 X63  N05  C12   single    1.338  0.020  1.338
 X63  N05  HN05  single    0.860  0.020  1.020
 X63  N06  H106  single    0.890  0.020  1.040
 X63  N06  H206  single    0.890  0.020  1.040
 X63  N07  O25   single    1.226  0.020  1.226
 X63  N07  C13   single    1.414  0.020  1.414
 X63  C08  C09   aromatic  1.371  0.020  1.371
 X63  C08  H08   single    0.930  0.020  1.080
 X63  C09  C14   single    1.484  0.020  1.484
 X63  C10  C09   aromatic  1.438  0.020  1.438
 X63  C10  N01   single    1.340  0.020  1.340
 X63  C11  C10   aromatic  1.396  0.020  1.396
 X63  C11  H11   single    0.930  0.020  1.080
 X63  C12  C13   aromatic  1.433  0.020  1.433
 X63  C12  C11   aromatic  1.401  0.020  1.401
 X63  C13  C08   aromatic  1.396  0.020  1.396
 X63  C14  O22   double    1.232  0.020  1.232
 X63  C15  N01   single    1.447  0.020  1.447
 X63  C15  C16   single    1.495  0.020  1.495
 X63  C15  H115  single    0.970  0.020  1.090
 X63  C15  H215  single    0.970  0.020  1.090
 X63  C16  C19   aromatic  1.388  0.020  1.388
 X63  C17  C16   aromatic  1.390  0.020  1.390
 X63  C17  N03   aromatic  1.319  0.020  1.319
 X63  C17  H17   single    0.930  0.020  1.080
 X63  C18  N04   aromatic  1.339  0.020  1.339
 X63  C18  N06   single    1.343  0.020  1.343
 X63  C19  N04   aromatic  1.320  0.020  1.320
 X63  C19  H19   single    0.930  0.020  1.080
 X63  C20  C21   single    1.512  0.020  1.512
 X63  C20  N05   single    1.444  0.020  1.444
 X63  C20  H120  single    0.970  0.020  1.090
 X63  C20  H220  single    0.970  0.020  1.090
 X63  C21  H121  single    0.970  0.020  1.090
 X63  C21  H221  single    0.970  0.020  1.090
 X63  O23  C21   single    1.410  0.020  1.410
 X63  O23  HO23  single    0.850  0.020  0.980
 X63  O24  N07   double    1.218  0.020  1.218

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
 X63  HN01  N01  C15   118.74  3.000
 X63  C15   N01  C10   124.10  3.000
 X63  HN01  N01  C10   116.30  3.000
 X63  H202  N02  H102  116.60  3.000
 X63  H202  N02  C14   118.91  3.000
 X63  H102  N02  C14   122.86  3.000
 X63  C18   N03  C17   116.54  3.000
 X63  C19   N04  C18   116.53  3.000
 X63  HN05  N05  C20   117.52  3.000
 X63  C20   N05  C12   124.52  3.000
 X63  HN05  N05  C12   117.13  3.000
 X63  H206  N06  H106  117.66  3.000
 X63  H206  N06  C18   119.39  3.000
 X63  H106  N06  C18   119.40  3.000
 X63  O25   N07  O24   121.24  3.000
 X63  O24   N07  C13   119.41  3.000
 X63  O25   N07  C13   119.34  3.000
 X63  H08   C08  C13   117.19  3.000
 X63  C13   C08  C09   123.56  3.000
 X63  H08   C08  C09   119.24  3.000
 X63  C14   C09  C10   121.53  3.000
 X63  C10   C09  C08   117.80  3.000
 X63  C14   C09  C08   120.65  3.000
 X63  C11   C10  C09   118.80  3.000
 X63  C11   C10  N01   120.62  3.000
 X63  C09   C10  N01   120.56  3.000
 X63  H11   C11  C12   118.01  3.000
 X63  C12   C11  C10   123.56  3.000
 X63  H11   C11  C10   118.43  3.000
 X63  C13   C12  C11   116.55  3.000
 X63  C11   C12  N05   120.06  3.000
 X63  C13   C12  N05   123.39  3.000
 X63  C12   C13  C08   119.66  3.000
 X63  C08   C13  N07   117.15  3.000
 X63  C12   C13  N07   123.19  3.000
 X63  H215  C15  H115  106.63  3.000
 X63  H215  C15  C16   109.88  3.000
 X63  H115  C15  C16   109.90  3.000
 X63  H215  C15  N01   109.71  3.000
 X63  H115  C15  N01   110.50  3.000
 X63  C16   C15  N01   110.15  3.000
 X63  C19   C16  C17   114.74  3.000
 X63  C17   C16  C15   122.56  3.000
 X63  C19   C16  C15   122.68  3.000
 X63  H17   C17  C16   120.16  3.000
 X63  H17   C17  N03   116.38  3.000
 X63  C16   C17  N03   123.46  3.000
 X63  N06   C18  N04   117.42  3.000
 X63  N06   C18  N03   117.34  3.000
 X63  N04   C18  N03   125.23  3.000
 X63  H19   C19  C16   120.17  3.000
 X63  H19   C19  N04   116.34  3.000
 X63  C16   C19  N04   123.48  3.000
 X63  H220  C20  H120  107.10  3.000
 X63  H220  C20  C21   107.56  3.000
 X63  H120  C20  C21   110.27  3.000
 X63  H220  C20  N05   110.57  3.000
 X63  H120  C20  N05   111.08  3.000
 X63  C21   C20  N05   110.15  3.000
 X63  H221  C21  H121  107.26  3.000
 X63  H221  C21  O23   111.54  3.000
 X63  H121  C21  O23   112.10  3.000
 X63  O23   C21  C20   108.85  3.000
 X63  H221  C21  C20   109.11  3.000
 X63  H121  C21  C20   107.88  3.000
 X63  HO23  O23  C21   108.38  3.000
 X63  O22   C14  C09   121.88  3.000
 X63  O22   C14  N02   121.24  3.000
 X63  C09   C14  N02   116.87  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
 X63  CONST_01  C19   N04  C18  N03    0.00   0.0  0
 X63  CONST_02  C19   C16  C17  N03    0.00   0.0  0
 X63  CONST_03  C17   N03  C18  N04    0.00   0.0  0
 X63  CONST_04  C17   C16  C19  N04    0.00   0.0  0
 X63  CONST_05  C11   C10  C09  C08    0.00   0.0  0
 X63  CONST_06  C11   C12  C13  C08    0.00   0.0  0
 X63  CONST_07  C12   C13  C08  C09    0.00   0.0  0
 X63  CONST_08  C12   C11  C10  C09    0.00   0.0  0
 X63  CONST_09  C13   C08  C09  C10    0.00   0.0  0
 X63  CONST_10  C13   C12  C11  C10    0.00   0.0  0
 X63  CONST_11  C18   N04  C19  C16    0.00   0.0  0
 X63  CONST_12  C18   N03  C17  C16    0.00   0.0  0
 X63  CONST_13  C08   C09  C10  N01  180.00   0.0  0
 X63  CONST_14  C12   C11  C10  N01  180.00   0.0  0
 X63  CONST_15  C15   C16  C17  N03  180.00   0.0  0
 X63  CONST_16  C15   C16  C19  N04  180.00   0.0  0
 X63  CONST_17  C08   C13  C12  N05  180.00   0.0  0
 X63  CONST_18  C10   C11  C12  N05  180.00   0.0  0
 X63  CONST_19  C17   N03  C18  N06  180.00   0.0  0
 X63  CONST_20  C19   N04  C18  N06  180.00   0.0  0
 X63  CONST_21  C11   C12  C13  N07  180.00   0.0  0
 X63  CONST_22  C09   C08  C13  N07  180.00   0.0  0
 X63  CONST_23  C14   C09  C10  C11  180.00   0.0  0
 X63  CONST_24  C14   C09  C08  C13  180.00   0.0  0
 X63  CONST_25  H11   C11  C10  C09  180.00   0.0  0
 X63  CONST_26  H08   C08  C09  C10  180.00   0.0  0
 X63  CONST_27  H19   C19  C16  C17  180.00   0.0  0
 X63  CONST_28  H17   C17  N03  C18  180.00   0.0  0
 X63  CONST_29  O25   N07  C13  C08  180.00   0.0  0
 X63  CONST_30  O24   N07  C13  C08    0.00   0.0  0
 X63  CONST_31  C15   N01  C10  C09  180.00   0.0  0
 X63  CONST_32  C15   N01  C10  C11    0.00   0.0  0
 X63  CONST_33  C20   N05  C12  C11    0.00   0.0  0
 X63  CONST_34  O25   N07  C13  C12    0.00   0.0  0
 X63  CONST_35  O24   N07  C13  C12  180.00   0.0  0
 X63  CONST_36  C20   N05  C12  C13  180.00   0.0  0
 X63  CONST_37  H106  N06  C18  N03    0.00   0.0  0
 X63  CONST_38  H206  N06  C18  N03  180.00   0.0  0
 X63  CONST_39  HN01  N01  C10  C09    0.00   0.0  0
 X63  CONST_40  HN05  N05  C12  C11  180.00   0.0  0
 X63  CONST_41  H102  N02  C14  C09    0.00   0.0  0
 X63  CONST_42  H202  N02  C14  C09  180.00   0.0  0
 X63  Var_01    C19   C16  C15  N01   94.19  30.0  2
 X63  Var_02    C08   C09  C14  N02  -23.44  30.0  2
 X63  Var_03    C16   C15  N01  C10  179.65  30.0  1
 X63  Var_04    C21   C20  N05  C12  171.48  30.0  1
 X63  Var_05    O23   C21  C20  N05   59.16  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
 X63  plan-1  N03   0.020
 X63  plan-1  N04   0.020
 X63  plan-1  N06   0.020
 X63  plan-1  C15   0.020
 X63  plan-1  C16   0.020
 X63  plan-1  C17   0.020
 X63  plan-1  C18   0.020
 X63  plan-1  C19   0.020
 X63  plan-1  H17   0.020
 X63  plan-1  H19   0.020
 X63  plan-2  N01   0.020
 X63  plan-2  N05   0.020
 X63  plan-2  N07   0.020
 X63  plan-2  C08   0.020
 X63  plan-2  C09   0.020
 X63  plan-2  C10   0.020
 X63  plan-2  C11   0.020
 X63  plan-2  C12   0.020
 X63  plan-2  C13   0.020
 X63  plan-2  H08   0.020
 X63  plan-2  H11   0.020
 X63  plan-2  C14   0.020
 X63  plan-3  N02   0.020
 X63  plan-3  C09   0.020
 X63  plan-3  O22   0.020
 X63  plan-3  H102  0.020
 X63  plan-3  H202  0.020
 X63  plan-3  C14   0.020
 X63  plan-4  N01   0.020
 X63  plan-4  C10   0.020
 X63  plan-4  C15   0.020
 X63  plan-4  HN01  0.020
 X63  plan-5  N05   0.020
 X63  plan-5  C12   0.020
 X63  plan-5  C20   0.020
 X63  plan-5  HN05  0.020
 X63  plan-6  N06   0.020
 X63  plan-6  C18   0.020
 X63  plan-6  H106  0.020
 X63  plan-6  H206  0.020
 X63  plan-7  N07   0.020
 X63  plan-7  C13   0.020
 X63  plan-7  O24   0.020
 X63  plan-7  O25   0.020

