# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 20:23:01 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: N-{4-methyl-3-[(4-pyridin-3-ylpyrimidin-2-yl)amino]phenyl}pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(NC(=O)c2cccnc2)cc1Nc3nccc(n3)c4cccnc4
#
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
 PRC  PRC  N-{4-methyl-3-[(4-pyridin-3-ylpyrimidin-2-yl)amino]phenyl}pyridine-3-carboxamide  ligand  47  29  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PRC
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
 PRC  C1    C  CR16  0  -0.283   0.3346   0.4399  -7.4212
 PRC  C2    C  CR16  0  -0.044  -0.7916   0.0198  -8.1133
 PRC  N3    N  N     0  -0.398  -1.9035  -0.3857  -7.5123
 PRC  C4    C  CR16  0  -0.082  -1.9327  -0.3711  -6.1881
 PRC  C5    C  CR6   0  -0.037  -0.8668   0.0402  -5.3913
 PRC  C6    C  CR16  0  -0.143   0.2977   0.4438  -6.0398
 PRC  C7    C  CR6   0   0.302  -0.9481   0.0357  -3.9188
 PRC  N8    N  N     0  -0.489   0.1999   0.0132  -3.2654
 PRC  C9    C  CR6   0   0.623   0.1608   0.0082  -1.9301
 PRC  N10   N  N     0  -0.454  -0.9422   0.0289  -1.1898
 PRC  C11   C  CR16  0   0.034  -2.0856   0.0618  -1.8563
 PRC  C12   C  CR16  0  -0.384  -2.1645   0.0684  -3.2339
 PRC  N13   N  NH1   0  -0.782   1.3898  -0.0253  -1.3494
 PRC  C14   C  CR6   0   0.347   1.8002  -0.0620  -0.0191
 PRC  C15   C  CR16  0  -0.434   0.9213  -0.0120   1.0548
 PRC  C16   C  CR6   0   0.435   1.3908  -0.0503   2.3675
 PRC  C17   C  CR16  0  -0.303   2.7542  -0.1420   2.6166
 PRC  C18   C  CR16  0  -0.260   3.6157  -0.1873   1.5309
 PRC  C19   C  CR6   0   0.043   3.1852  -0.1494   0.2160
 PRC  C20   C  CH3   0  -0.757   4.1754  -0.1960  -0.9119
 PRC  N21   N  NH1   0  -0.768   0.4088   0.0222   3.3632
 PRC  C22   C  C     0   0.533   0.5470  -0.0443   4.7147
 PRC  C23   C  CR6   0  -0.140  -0.7273   0.1420   5.4745
 PRC  C25   C  CR16  0  -0.130  -0.8513  -0.4518   6.7262
 PRC  C26   C  CR16  0  -0.299  -2.0211  -0.2700   7.4389
 PRC  C27   C  CR16  0  -0.034  -3.0206   0.5171   6.8831
 PRC  N28   N  N     0  -0.359  -2.9049   1.1154   5.7073
 PRC  C29   C  CR16  0  -0.068  -1.7844   0.9299   5.0275
 PRC  O29   O  O     0  -0.411   1.5925  -0.2488   5.2932
 PRC  HC1   H  HCR6  0   0.256   1.2167   0.7594  -7.9568
 PRC  HC2   H  HCR6  0   0.254  -0.7939   0.0091  -9.1969
 PRC  HC4   H  HCR6  0   0.236  -2.8509  -0.7286  -5.7350
 PRC  HC6   H  HCR6  0   0.256   1.1549   0.7613  -5.4625
 PRC  H11C  H  HCR6  0   0.245  -2.9871   0.0903  -1.2544
 PRC  H12C  H  HCR6  0   0.238  -3.1184   0.1218  -3.7354
 PRC  H13N  H  HNH1  0   0.395   2.1239  -0.0461  -2.0373
 PRC  H15C  H  HCR6  0   0.278  -0.1391   0.0578   0.8645
 PRC  H17C  H  HCR6  0   0.280   3.1456  -0.1806   3.6187
 PRC  H18C  H  HCR6  0   0.218   4.6794  -0.2575   1.7230
 PRC  H201  H  HCH3  0   0.233   4.0215  -1.0538  -1.5723
 PRC  H202  H  HCH3  0   0.232   4.1455   0.7052  -1.5309
 PRC  H203  H  HCH3  0   0.256   5.1899  -0.2757  -0.5267
 PRC  H21N  H  HNH1  0   0.384  -0.5332   0.0686   3.0116
 PRC  H25C  H  HCR6  0   0.266  -0.0411  -1.0474   7.1250
 PRC  H26C  H  HCR6  0   0.245  -2.1605  -0.7235   8.4102
 PRC  H27C  H  HCR6  0   0.245  -3.9520   0.6776   7.4145
 PRC  H29C  H  HCR6  0   0.229  -1.7183   1.4707   4.0876

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
 PRC  C1   C2    aromatic  1.387  0.020  1.387
 PRC  C1   C6    aromatic  1.382  0.020  1.382
 PRC  C1   HC1   single    0.930  0.020  1.080
 PRC  C2   N3    aromatic  1.327  0.020  1.327
 PRC  C2   HC2   single    0.930  0.020  1.080
 PRC  N3   C4    aromatic  1.325  0.020  1.325
 PRC  C4   C5    aromatic  1.393  0.020  1.393
 PRC  C4   HC4   single    0.930  0.020  1.080
 PRC  C5   C6    aromatic  1.393  0.020  1.393
 PRC  C5   C7    single    1.475  0.020  1.475
 PRC  C6   HC6   single    0.930  0.020  1.080
 PRC  C7   N8    aromatic  1.321  0.020  1.321
 PRC  C7   C12   aromatic  1.396  0.020  1.396
 PRC  N8   C9    aromatic  1.336  0.020  1.336
 PRC  C9   N10   aromatic  1.329  0.020  1.329
 PRC  C9   N13   single    1.360  0.020  1.360
 PRC  N10  C11   aromatic  1.324  0.020  1.324
 PRC  C11  C12   aromatic  1.380  0.020  1.380
 PRC  C11  H11C  single    0.930  0.020  1.080
 PRC  C12  H12C  single    0.930  0.020  1.080
 PRC  N13  C14   single    1.393  0.020  1.393
 PRC  N13  H13N  single    0.860  0.020  1.020
 PRC  C14  C15   aromatic  1.389  0.020  1.389
 PRC  C14  C19   aromatic  1.408  0.020  1.408
 PRC  C15  C16   aromatic  1.395  0.020  1.395
 PRC  C15  H15C  single    0.930  0.020  1.080
 PRC  C16  C17   aromatic  1.389  0.020  1.389
 PRC  C16  N21   single    1.400  0.020  1.400
 PRC  C17  C18   aromatic  1.387  0.020  1.387
 PRC  C17  H17C  single    0.930  0.020  1.080
 PRC  C18  C19   aromatic  1.384  0.020  1.384
 PRC  C18  H18C  single    0.930  0.020  1.080
 PRC  C19  C20   single    1.502  0.020  1.502
 PRC  C20  H201  single    0.970  0.020  1.090
 PRC  C20  H202  single    0.970  0.020  1.090
 PRC  C20  H203  single    0.970  0.020  1.090
 PRC  N21  C22   single    1.360  0.020  1.360
 PRC  N21  H21N  single    0.860  0.020  1.020
 PRC  C22  C23   single    1.495  0.020  1.495
 PRC  C22  O29   double    1.212  0.020  1.212
 PRC  C23  C25   aromatic  1.391  0.020  1.391
 PRC  C23  C29   aromatic  1.392  0.020  1.392
 PRC  C25  C26   aromatic  1.382  0.020  1.382
 PRC  C25  H25C  single    0.930  0.020  1.080
 PRC  C26  C27   aromatic  1.388  0.020  1.388
 PRC  C26  H26C  single    0.930  0.020  1.080
 PRC  C27  N28   aromatic  1.324  0.020  1.324
 PRC  C27  H27C  single    0.930  0.020  1.080
 PRC  N28  C29   aromatic  1.324  0.020  1.324
 PRC  C29  H29C  single    0.930  0.020  1.080

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
 PRC  HC1   C1   C6    121.11  3.000
 PRC  HC1   C1   C2    120.34  3.000
 PRC  C6    C1   C2    118.55  3.000
 PRC  HC2   C2   N3    116.62  3.000
 PRC  HC2   C2   C1    120.24  3.000
 PRC  N3    C2   C1    123.14  3.000
 PRC  C4    N3   C2    117.89  3.000
 PRC  HC4   C4   C5    120.42  3.000
 PRC  HC4   C4   N3    115.64  3.000
 PRC  C5    C4   N3    123.93  3.000
 PRC  C7    C5   C6    120.79  3.000
 PRC  C7    C5   C4    121.87  3.000
 PRC  C6    C5   C4    117.33  3.000
 PRC  HC6   C6   C5    119.96  3.000
 PRC  HC6   C6   C1    120.89  3.000
 PRC  C5    C6   C1    119.14  3.000
 PRC  C12   C7   N8    120.98  3.000
 PRC  C12   C7   C5    122.53  3.000
 PRC  N8    C7   C5    116.49  3.000
 PRC  C9    N8   C7    117.98  3.000
 PRC  N13   C9   N10   120.85  3.000
 PRC  N13   C9   N8    113.62  3.000
 PRC  N10   C9   N8    125.54  3.000
 PRC  C11   N10  C9    115.90  3.000
 PRC  H11C  C11  C12   120.44  3.000
 PRC  H11C  C11  N10   116.05  3.000
 PRC  C12   C11  N10   123.51  3.000
 PRC  H12C  C12  C11   120.98  3.000
 PRC  H12C  C12  C7    122.91  3.000
 PRC  C11   C12  C7    116.09  3.000
 PRC  H13N  N13  C14   115.94  3.000
 PRC  H13N  N13  C9    111.58  3.000
 PRC  C14   N13  C9    132.46  3.000
 PRC  C19   C14  C15   119.73  3.000
 PRC  C19   C14  N13   116.82  3.000
 PRC  C15   C14  N13   123.45  3.000
 PRC  H15C  C15  C16   119.89  3.000
 PRC  H15C  C15  C14   119.19  3.000
 PRC  C16   C15  C14   120.92  3.000
 PRC  N21   C16  C17   124.35  3.000
 PRC  N21   C16  C15   115.58  3.000
 PRC  C17   C16  C15   120.07  3.000
 PRC  H17C  C17  C18   120.11  3.000
 PRC  H17C  C17  C16   121.75  3.000
 PRC  C18   C17  C16   118.13  3.000
 PRC  H18C  C18  C19   118.40  3.000
 PRC  H18C  C18  C17   118.25  3.000
 PRC  C19   C18  C17   123.35  3.000
 PRC  C20   C19  C18   120.51  3.000
 PRC  C20   C19  C14   121.69  3.000
 PRC  C18   C19  C14   117.80  3.000
 PRC  H203  C20  H202  106.63  3.000
 PRC  H203  C20  H201  106.71  3.000
 PRC  H202  C20  H201  107.50  3.000
 PRC  H203  C20  C19   110.56  3.000
 PRC  H202  C20  C19   112.43  3.000
 PRC  H201  C20  C19   112.65  3.000
 PRC  H21N  N21  C22   116.39  3.000
 PRC  H21N  N21  C16   114.22  3.000
 PRC  C22   N21  C16   129.25  3.000
 PRC  O29   C22  C23   120.90  3.000
 PRC  O29   C22  N21   124.75  3.000
 PRC  C23   C22  N21   114.34  3.000
 PRC  C29   C23  C25   117.58  3.000
 PRC  C29   C23  C22   123.68  3.000
 PRC  C25   C23  C22   118.68  3.000
 PRC  H25C  C25  C26   121.09  3.000
 PRC  H25C  C25  C23   120.01  3.000
 PRC  C26   C25  C23   118.91  3.000
 PRC  H26C  C26  C27   120.31  3.000
 PRC  H26C  C26  C25   121.16  3.000
 PRC  C27   C26  C25   118.53  3.000
 PRC  H27C  C27  N28   116.31  3.000
 PRC  H27C  C27  C26   120.40  3.000
 PRC  N28   C27  C26   123.28  3.000
 PRC  C29   N28  C27   117.82  3.000
 PRC  H29C  C29  N28   115.22  3.000
 PRC  H29C  C29  C23   120.88  3.000
 PRC  N28   C29  C23   123.86  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
 PRC  CONST_01  C4    N3   C2   C1      0.00   0.0  0
 PRC  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 PRC  CONST_03  C7    C5   C6   C1    180.00   0.0  0
 PRC  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 PRC  CONST_05  C5    C4   N3   C2      0.00   0.0  0
 PRC  CONST_06  C6    C1   C2   N3      0.00   0.0  0
 PRC  CONST_07  C6    C5   C4   N3      0.00   0.0  0
 PRC  CONST_08  C7    C5   C4   N3    180.00   0.0  0
 PRC  CONST_11  C9    N8   C7   C5    180.00   0.0  0
 PRC  CONST_12  C11   C12  C7   C5    180.00   0.0  0
 PRC  CONST_15  N10   C9   N8   C7      0.00   0.0  0
 PRC  CONST_16  N10   C11  C12  C7      0.00   0.0  0
 PRC  CONST_17  C11   C12  C7   N8      0.00   0.0  0
 PRC  CONST_18  C11   N10  C9   N8      0.00   0.0  0
 PRC  CONST_19  C12   C7   N8   C9      0.00   0.0  0
 PRC  CONST_20  C12   C11  N10  C9      0.00   0.0  0
 PRC  CONST_21  C17   C16  C15  C14     0.00   0.0  0
 PRC  CONST_22  C17   C18  C19  C14     0.00   0.0  0
 PRC  CONST_23  C18   C19  C14  C15     0.00   0.0  0
 PRC  CONST_24  C18   C17  C16  C15     0.00   0.0  0
 PRC  CONST_25  C19   C14  C15  C16     0.00   0.0  0
 PRC  CONST_26  C19   C18  C17  C16     0.00   0.0  0
 PRC  CONST_27  C27   C26  C25  C23     0.00   0.0  0
 PRC  CONST_28  C27   N28  C29  C23     0.00   0.0  0
 PRC  CONST_29  N28   C29  C23  C25     0.00   0.0  0
 PRC  CONST_30  N28   C27  C26  C25     0.00   0.0  0
 PRC  CONST_31  C29   C23  C25  C26     0.00   0.0  0
 PRC  CONST_32  C29   N28  C27  C26     0.00   0.0  0
 PRC  CONST_33  N13   C9   N8   C7    180.00   0.0  0
 PRC  CONST_34  N13   C9   N10  C11   180.00   0.0  0
 PRC  CONST_35  C16   C15  C14  N13   180.00   0.0  0
 PRC  CONST_36  C18   C19  C14  N13   180.00   0.0  0
 PRC  CONST_37  N21   C16  C15  C14   180.00   0.0  0
 PRC  CONST_38  C20   C19  C14  C15   180.00   0.0  0
 PRC  CONST_39  C20   C19  C18  C17   180.00   0.0  0
 PRC  CONST_40  N21   C16  C17  C18   180.00   0.0  0
 PRC  CONST_41  C26   C25  C23  C22   180.00   0.0  0
 PRC  CONST_42  N28   C29  C23  C22   180.00   0.0  0
 PRC  CONST_43  HC6   C6   C1   C2    180.00   0.0  0
 PRC  CONST_44  HC4   C4   N3   C2    180.00   0.0  0
 PRC  CONST_45  HC1   C1   C2   N3    180.00   0.0  0
 PRC  CONST_46  HC2   C2   N3   C4    180.00   0.0  0
 PRC  CONST_47  H12C  C12  C7   C5      0.00   0.0  0
 PRC  CONST_48  H11C  C11  C12  C7    180.00   0.0  0
 PRC  CONST_49  H18C  C18  C19  C14   180.00   0.0  0
 PRC  CONST_50  H17C  C17  C16  C15   180.00   0.0  0
 PRC  CONST_51  H15C  C15  C16  C17   180.00   0.0  0
 PRC  CONST_52  H26C  C26  C25  C23   180.00   0.0  0
 PRC  CONST_53  H29C  C29  C23  C25   180.00   0.0  0
 PRC  CONST_54  H27C  C27  C26  C25   180.00   0.0  0
 PRC  CONST_55  H25C  C25  C26  C27   180.00   0.0  0
 PRC  CONST_56  C23   C22  N21  C16   180.00   0.0  0
 PRC  CONST_57  C22   N21  C16  C15   180.00   0.0  0
 PRC  CONST_58  C22   N21  C16  C17     0.00   0.0  0
 PRC  CONST_59  H21N  N21  C16  C15     0.00   0.0  0
 PRC  CONST_60  O29   C22  N21  C16     0.00   0.0  0
 PRC  Var_01    C14   N13  C9   N8   -178.86  30.0  2
 PRC  Var_02    C15   C14  N13  C9     -2.94  30.0  2
 PRC  Var_03    C25   C23  C22  N21   152.36  30.0  2
 PRC  Var_04    H201  C20  C19  C14   -59.97  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
 PRC  plan-1  C1    0.020
 PRC  plan-1  C2    0.020
 PRC  plan-1  N3    0.020
 PRC  plan-1  C4    0.020
 PRC  plan-1  C5    0.020
 PRC  plan-1  C6    0.020
 PRC  plan-1  C7    0.020
 PRC  plan-1  HC1   0.020
 PRC  plan-1  HC2   0.020
 PRC  plan-1  HC4   0.020
 PRC  plan-1  HC6   0.020
 PRC  plan-2  C5    0.020
 PRC  plan-2  C7    0.020
 PRC  plan-2  N8    0.020
 PRC  plan-2  C9    0.020
 PRC  plan-2  N10   0.020
 PRC  plan-2  C11   0.020
 PRC  plan-2  C12   0.020
 PRC  plan-2  N13   0.020
 PRC  plan-2  H11C  0.020
 PRC  plan-2  H12C  0.020
 PRC  plan-3  N13   0.020
 PRC  plan-3  C14   0.020
 PRC  plan-3  C15   0.020
 PRC  plan-3  C16   0.020
 PRC  plan-3  C17   0.020
 PRC  plan-3  C18   0.020
 PRC  plan-3  C19   0.020
 PRC  plan-3  C20   0.020
 PRC  plan-3  N21   0.020
 PRC  plan-3  H15C  0.020
 PRC  plan-3  H17C  0.020
 PRC  plan-3  H18C  0.020
 PRC  plan-4  C22   0.020
 PRC  plan-4  C23   0.020
 PRC  plan-4  C25   0.020
 PRC  plan-4  C26   0.020
 PRC  plan-4  C27   0.020
 PRC  plan-4  N28   0.020
 PRC  plan-4  C29   0.020
 PRC  plan-4  H25C  0.020
 PRC  plan-4  H26C  0.020
 PRC  plan-4  H27C  0.020
 PRC  plan-4  H29C  0.020
 PRC  plan-5  C16   0.020
 PRC  plan-5  N21   0.020
 PRC  plan-5  C22   0.020
 PRC  plan-5  C23   0.020
 PRC  plan-5  O29   0.020
 PRC  plan-5  H21N  0.020

