# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 08:40:36 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 2-({2-[(4-carbamoylphenyl)amino]pyrimidin-4-yl}amino)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc(Nc2nccc(Nc3ccccc3C(N)=O)n2)cc1
#
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
 NHU  NHU  2-({2-[(4-carbamoylphenyl)amino]pyrimidin-4-yl}amino)benzamide  ligand  42  26  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NHU
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
 NHU  N01   N  NH1   0  -0.770   1.6206   0.9187   0.2672
 NHU  N02   N  N     0  -0.522  -0.6315   1.0332   0.1664
 NHU  N03   N  N     0  -0.490   0.5118  -0.6256  -1.0848
 NHU  N04   N  NH1   0  -0.748  -2.8891   1.2742   0.1484
 NHU  C05   C  CR16  0  -0.259   4.7512  -0.8492  -0.6457
 NHU  N05   N  NH2   0  -0.789  -3.9390  -2.6410   0.4523
 NHU  C06   C  CR6   0  -0.061   5.6951  -0.0627   0.0079
 NHU  N06   N  NH2   0  -0.819   7.9634   0.1092   0.8089
 NHU  C07   C  CR16  0  -0.271   5.2371   1.0531   0.7097
 NHU  C08   C  CR16  0  -0.345   3.8921   1.3516   0.7661
 NHU  C09   C  CR6   0   0.372   2.9427   0.5426   0.1255
 NHU  C10   C  CR16  0  -0.303   3.3967  -0.5698  -0.5917
 NHU  C12   C  CR6   0   0.605   0.4645   0.4030  -0.2514
 NHU  C13   C  CR6   0   0.514  -1.8004   0.6027  -0.2920
 NHU  C14   C  CR16  0  -0.434  -1.8693  -0.4603  -1.2121
 NHU  C15   C  CR16  0  -0.004  -0.6699  -1.0287  -1.5556
 NHU  C16   C  CR6   0   0.303  -4.2301   0.9064  -0.0287
 NHU  C17   C  CR16  0  -0.295  -5.1155   1.8648  -0.5124
 NHU  C18   C  CR16  0  -0.254  -6.4573   1.5662  -0.6893
 NHU  C19   C  CR16  0  -0.247  -6.9249   0.2893  -0.4162
 NHU  C20   C  CR16  0  -0.276  -6.0457  -0.6723   0.0571
 NHU  C21   C  CR6   0  -0.068  -4.7018  -0.3768   0.2758
 NHU  C22   C  C     0   0.476  -3.8329  -1.3998   0.9465
 NHU  O23   O  O     0  -0.466  -3.1227  -1.1097   1.8965
 NHU  O25   O  O     0  -0.489   7.5281  -1.2054  -0.9647
 NHU  HN01  H  HNH1  0   0.409   1.4607   1.7128   0.8689
 NHU  HN04  H  HNH1  0   0.402  -2.7013   2.1139   0.6757
 NHU  H05   H  HCR6  0   0.259   5.0757  -1.7166  -1.2053
 NHU  HN05  H  HNH2  0   0.413  -4.4449  -2.8364  -0.3946
 NHU  HN0A  H  HNH2  0   0.406  -3.3890  -3.3891   0.8433
 NHU  HN06  H  HNH2  0   0.411   7.6377   0.6194   1.6108
 NHU  HN0B  H  HNH2  0   0.403   8.9399  -0.1357   0.7949
 NHU  H07   H  HCR6  0   0.257   5.9233   1.7252   1.2095
 NHU  H08   H  HCR6  0   0.273   3.5668   2.2303   1.3102
 NHU  H10   H  HCR6  0   0.287   2.6974  -1.2092  -1.1040
 NHU  H14   H  HCR6  0   0.285  -2.7947  -0.8053  -1.6467
 NHU  H15   H  HCR6  0   0.269  -0.6462  -1.8544  -2.2577
 NHU  H17   H  HCR6  0   0.274  -4.7410   2.8506  -0.7578
 NHU  H18   H  HCR6  0   0.268  -7.1315   2.3291  -1.0558
 NHU  H19   H  HCR6  0   0.265  -7.9683   0.0442  -0.5605
 NHU  H20   H  HCR6  0   0.271  -6.4202  -1.6594   0.2973
 NHU  C11   C  C     0   0.486   7.1331  -0.4374  -0.0950

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
 NHU  C09  N01   single    1.382  0.020  1.382
 NHU  N01  C12   single    1.368  0.020  1.368
 NHU  N01  HN01  single    0.860  0.020  1.020
 NHU  N02  C13   aromatic  1.327  0.020  1.327
 NHU  N02  C12   aromatic  1.331  0.020  1.331
 NHU  C12  N03   aromatic  1.325  0.020  1.325
 NHU  N03  C15   aromatic  1.334  0.020  1.334
 NHU  C16  N04   single    1.402  0.020  1.402
 NHU  N04  C13   single    1.353  0.020  1.353
 NHU  N04  HN04  single    0.860  0.020  1.020
 NHU  C06  C05   aromatic  1.392  0.020  1.392
 NHU  C05  C10   aromatic  1.384  0.020  1.384
 NHU  C05  H05   single    0.930  0.020  1.080
 NHU  N05  C22   single    1.340  0.020  1.340
 NHU  N05  HN05  single    0.860  0.020  1.020
 NHU  N05  HN0A  single    0.860  0.020  1.020
 NHU  C11  C06   single    1.490  0.020  1.490
 NHU  C06  C07   aromatic  1.395  0.020  1.395
 NHU  N06  C11   single    1.344  0.020  1.344
 NHU  N06  HN06  single    0.860  0.020  1.020
 NHU  N06  HN0B  single    0.860  0.020  1.020
 NHU  C07  C08   aromatic  1.379  0.020  1.379
 NHU  C07  H07   single    0.930  0.020  1.080
 NHU  C08  C09   aromatic  1.402  0.020  1.402
 NHU  C08  H08   single    0.930  0.020  1.080
 NHU  C10  C09   aromatic  1.399  0.020  1.399
 NHU  C10  H10   single    0.930  0.020  1.080
 NHU  O25  C11   double    1.226  0.020  1.226
 NHU  C13  C14   aromatic  1.408  0.020  1.408
 NHU  C14  C15   aromatic  1.371  0.020  1.371
 NHU  C14  H14   single    0.930  0.020  1.080
 NHU  C15  H15   single    0.930  0.020  1.080
 NHU  C17  C16   aromatic  1.392  0.020  1.392
 NHU  C21  C16   aromatic  1.401  0.020  1.401
 NHU  C18  C17   aromatic  1.386  0.020  1.386
 NHU  C17  H17   single    0.930  0.020  1.080
 NHU  C19  C18   aromatic  1.387  0.020  1.387
 NHU  C18  H18   single    0.930  0.020  1.080
 NHU  C19  C20   aromatic  1.386  0.020  1.386
 NHU  C19  H19   single    0.930  0.020  1.080
 NHU  C20  C21   aromatic  1.393  0.020  1.393
 NHU  C20  H20   single    0.930  0.020  1.080
 NHU  C21  C22   single    1.500  0.020  1.500
 NHU  C22  O23   double    1.221  0.020  1.221

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
 NHU  HN01  N01  C12   112.88  3.000
 NHU  HN01  N01  C09   115.27  3.000
 NHU  C12   N01  C09   131.85  3.000
 NHU  C13   N02  C12   117.58  3.000
 NHU  C15   N03  C12   115.15  3.000
 NHU  HN04  N04  C16   117.54  3.000
 NHU  HN04  N04  C13   115.68  3.000
 NHU  C16   N04  C13   126.77  3.000
 NHU  H05   C05  C10   118.39  3.000
 NHU  H05   C05  C06   119.50  3.000
 NHU  C10   C05  C06   122.10  3.000
 NHU  HN0A  N05  HN05  117.21  3.000
 NHU  HN0A  N05  C22   120.09  3.000
 NHU  HN05  N05  C22   122.02  3.000
 NHU  C11   C06  C07   123.56  3.000
 NHU  C07   C06  C05   117.74  3.000
 NHU  C11   C06  C05   118.70  3.000
 NHU  HN0B  N06  HN06  116.68  3.000
 NHU  HN0B  N06  C11   119.41  3.000
 NHU  HN06  N06  C11   122.91  3.000
 NHU  H07   C07  C08   117.71  3.000
 NHU  H07   C07  C06   121.36  3.000
 NHU  C08   C07  C06   120.92  3.000
 NHU  H08   C08  C09   119.61  3.000
 NHU  H08   C08  C07   119.27  3.000
 NHU  C09   C08  C07   121.12  3.000
 NHU  C10   C09  C08   118.24  3.000
 NHU  C10   C09  N01   125.40  3.000
 NHU  C08   C09  N01   116.36  3.000
 NHU  H10   C10  C09   120.34  3.000
 NHU  H10   C10  C05   119.79  3.000
 NHU  C09   C10  C05   119.87  3.000
 NHU  N03   C12  N02   126.46  3.000
 NHU  N03   C12  N01   120.07  3.000
 NHU  N02   C12  N01   113.47  3.000
 NHU  C14   C13  N04   123.25  3.000
 NHU  C14   C13  N02   120.92  3.000
 NHU  N04   C13  N02   115.81  3.000
 NHU  H14   C14  C15   121.12  3.000
 NHU  H14   C14  C13   123.15  3.000
 NHU  C15   C14  C13   115.73  3.000
 NHU  H15   C15  C14   119.81  3.000
 NHU  H15   C15  N03   116.05  3.000
 NHU  C14   C15  N03   124.13  3.000
 NHU  C21   C16  C17   119.49  3.000
 NHU  C21   C16  N04   122.35  3.000
 NHU  C17   C16  N04   118.16  3.000
 NHU  H17   C17  C18   120.14  3.000
 NHU  H17   C17  C16   119.06  3.000
 NHU  C18   C17  C16   120.79  3.000
 NHU  H18   C18  C19   120.38  3.000
 NHU  H18   C18  C17   119.64  3.000
 NHU  C19   C18  C17   119.98  3.000
 NHU  H19   C19  C20   120.02  3.000
 NHU  H19   C19  C18   120.51  3.000
 NHU  C20   C19  C18   119.47  3.000
 NHU  H20   C20  C21   119.48  3.000
 NHU  H20   C20  C19   119.26  3.000
 NHU  C21   C20  C19   121.22  3.000
 NHU  C22   C21  C20   118.96  3.000
 NHU  C22   C21  C16   121.79  3.000
 NHU  C20   C21  C16   119.01  3.000
 NHU  O23   C22  C21   121.51  3.000
 NHU  O23   C22  N05   123.57  3.000
 NHU  C21   C22  N05   114.88  3.000
 NHU  O25   C11  N06   122.22  3.000
 NHU  O25   C11  C06   121.18  3.000
 NHU  N06   C11  C06   116.60  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
 NHU  CONST_01  C15   C14  C13  N02     0.00   0.0  0
 NHU  CONST_02  C15   N03  C12  N02     0.00   0.0  0
 NHU  CONST_03  C13   N02  C12  N03     0.00   0.0  0
 NHU  CONST_04  C13   C14  C15  N03     0.00   0.0  0
 NHU  CONST_05  C08   C07  C06  C05     0.00   0.0  0
 NHU  CONST_06  C08   C09  C10  C05     0.00   0.0  0
 NHU  CONST_07  C09   C10  C05  C06     0.00   0.0  0
 NHU  CONST_08  C09   C08  C07  C06     0.00   0.0  0
 NHU  CONST_09  C10   C05  C06  C07     0.00   0.0  0
 NHU  CONST_10  C10   C09  C08  C07     0.00   0.0  0
 NHU  CONST_11  C14   C13  N02  C12     0.00   0.0  0
 NHU  CONST_12  C14   C15  N03  C12     0.00   0.0  0
 NHU  CONST_13  C19   C18  C17  C16     0.00   0.0  0
 NHU  CONST_14  C19   C20  C21  C16     0.00   0.0  0
 NHU  CONST_15  C20   C21  C16  C17     0.00   0.0  0
 NHU  CONST_16  C20   C19  C18  C17     0.00   0.0  0
 NHU  CONST_17  C21   C16  C17  C18     0.00   0.0  0
 NHU  CONST_18  C21   C20  C19  C18     0.00   0.0  0
 NHU  CONST_19  C07   C08  C09  N01   180.00   0.0  0
 NHU  CONST_20  C05   C10  C09  N01   180.00   0.0  0
 NHU  CONST_21  C13   N02  C12  N01   180.00   0.0  0
 NHU  CONST_22  C15   N03  C12  N01   180.00   0.0  0
 NHU  CONST_23  C18   C17  C16  N04   180.00   0.0  0
 NHU  CONST_24  C20   C21  C16  N04   180.00   0.0  0
 NHU  CONST_25  C12   N02  C13  N04   180.00   0.0  0
 NHU  CONST_26  C15   C14  C13  N04   180.00   0.0  0
 NHU  CONST_27  C11   C06  C07  C08   180.00   0.0  0
 NHU  CONST_28  C11   C06  C05  C10   180.00   0.0  0
 NHU  CONST_29  C22   C21  C16  C17   180.00   0.0  0
 NHU  CONST_30  C22   C21  C20  C19   180.00   0.0  0
 NHU  CONST_31  H14   C14  C13  N02   180.00   0.0  0
 NHU  CONST_32  H07   C07  C06  C05   180.00   0.0  0
 NHU  CONST_33  H10   C10  C05  C06   180.00   0.0  0
 NHU  CONST_34  H08   C08  C07  C06   180.00   0.0  0
 NHU  CONST_35  H05   C05  C06  C07   180.00   0.0  0
 NHU  CONST_36  H15   C15  N03  C12   180.00   0.0  0
 NHU  CONST_37  H18   C18  C17  C16   180.00   0.0  0
 NHU  CONST_38  H20   C20  C21  C16   180.00   0.0  0
 NHU  CONST_39  H19   C19  C18  C17   180.00   0.0  0
 NHU  CONST_40  H17   C17  C18  C19   180.00   0.0  0
 NHU  CONST_41  HN06  N06  C11  C06     0.00   0.0  0
 NHU  CONST_42  HN0B  N06  C11  C06   180.00   0.0  0
 NHU  CONST_43  HN05  N05  C22  C21     0.00   0.0  0
 NHU  CONST_44  HN0A  N05  C22  C21   180.00   0.0  0
 NHU  Var_01    C16   N04  C13  N02  -170.18  30.0  3
 NHU  Var_02    C09   N01  C12  N02   177.84  30.0  2
 NHU  Var_03    C12   N01  C09  C08   177.15  30.0  2
 NHU  Var_04    C17   C16  N04  C13  -130.46  30.0  3
 NHU  Var_05    N06   C11  C06  C05  -162.99  30.0  2
 NHU  Var_06    C16   C21  C22  N05  -138.03  30.0  2

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
 NHU  plan-1  N01   0.020
 NHU  plan-1  N02   0.020
 NHU  plan-1  N03   0.020
 NHU  plan-1  N04   0.020
 NHU  plan-1  C12   0.020
 NHU  plan-1  C13   0.020
 NHU  plan-1  C14   0.020
 NHU  plan-1  C15   0.020
 NHU  plan-1  H14   0.020
 NHU  plan-1  H15   0.020
 NHU  plan-2  N01   0.020
 NHU  plan-2  C05   0.020
 NHU  plan-2  C06   0.020
 NHU  plan-2  C07   0.020
 NHU  plan-2  C08   0.020
 NHU  plan-2  C09   0.020
 NHU  plan-2  C10   0.020
 NHU  plan-2  H05   0.020
 NHU  plan-2  H07   0.020
 NHU  plan-2  H08   0.020
 NHU  plan-2  H10   0.020
 NHU  plan-2  C11   0.020
 NHU  plan-3  N04   0.020
 NHU  plan-3  C16   0.020
 NHU  plan-3  C17   0.020
 NHU  plan-3  C18   0.020
 NHU  plan-3  C19   0.020
 NHU  plan-3  C20   0.020
 NHU  plan-3  C21   0.020
 NHU  plan-3  C22   0.020
 NHU  plan-3  H17   0.020
 NHU  plan-3  H18   0.020
 NHU  plan-3  H19   0.020
 NHU  plan-3  H20   0.020
 NHU  plan-4  N05   0.020
 NHU  plan-4  C21   0.020
 NHU  plan-4  C22   0.020
 NHU  plan-4  O23   0.020
 NHU  plan-4  HN05  0.020
 NHU  plan-4  HN0A  0.020
 NHU  plan-5  C06   0.020
 NHU  plan-5  N06   0.020
 NHU  plan-5  O25   0.020
 NHU  plan-5  HN06  0.020
 NHU  plan-5  HN0B  0.020
 NHU  plan-5  C11   0.020

