# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 04:59:18 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 2-{[(1R,2S)-2-aminocyclohexyl]amino}-4-[(3-methylphenyl)amino]pyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(Nc2nc(N[C@@H]3CCCC[C@@H]3N)ncc2C(N)=O)c1
#
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
 P5C  P5C  2-{[(1R,2S)-2-aminocyclohexyl]amino}-4-[(3-methylphenyl)amino]pyrimidine-5-carboxamide  ligand  49  25  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_P5C
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
 P5C  C2    C  CR6   0   0.626   1.2120   0.7074   0.0931
 P5C  C3    C  CR16  0  -0.021   0.3419   2.7456  -0.2830
 P5C  N1    N  N     0  -0.530   0.0158   0.1101   0.1023
 P5C  C4    C  CR6   0  -0.304  -0.9587   2.2647  -0.2704
 P5C  C6    C  CR6   0   0.570  -1.0620   0.8475  -0.0924
 P5C  C8    C  C     0   0.541  -2.1330   3.1362  -0.4574
 P5C  C12   C  CR6   0   0.390  -2.6649  -1.0690   0.0262
 P5C  C13   C  CR16  0  -0.333  -1.8230  -2.1319   0.3606
 P5C  C14   C  CR16  0  -0.322  -3.7077  -3.6526   0.2818
 P5C  C15   C  CR6   0   0.114  -4.5607  -2.6010  -0.0515
 P5C  C16   C  CR16  0  -0.232  -2.3596  -3.4070   0.4837
 P5C  C17   C  CR16  0  -0.423  -4.0270  -1.3269  -0.1757
 P5C  C18   C  CH3   0  -0.722  -6.0306  -2.8330  -0.2504
 P5C  O10   O  O     0  -0.519  -3.2582   2.6725  -0.6770
 P5C  N9    N  NH2   0  -0.819  -1.9444   4.4620  -0.3851
 P5C  N11   N  NH1   0  -0.797  -2.2765   0.2608  -0.1240
 P5C  N5    N  N     0  -0.484   1.4268   2.0150  -0.1126
 P5C  N7    N  NH1   0  -0.644   2.2669  -0.0862   0.2994
 P5C  C19   C  CH1   0  -0.072   3.6451   0.3527   0.4124
 P5C  C24   C  CH1   0  -0.106   4.4741  -0.7886   1.0174
 P5C  N25   N  NH2   0  -0.800   3.8583  -1.2522   2.2508
 P5C  C23   C  CH2   0  -0.438   4.6170  -1.9590   0.0459
 P5C  C22   C  CH2   0  -0.436   5.1924  -1.5180  -1.2944
 P5C  C21   C  CH2   0  -0.433   4.3624  -0.3938  -1.9031
 P5C  C20   C  CH2   0  -0.445   4.2384   0.7748  -0.9343
 P5C  H3    H  HCR6  0   0.258   0.5318   3.7993  -0.4600
 P5C  H13   H  HCR6  0   0.285  -0.7698  -1.9720   0.5156
 P5C  H14   H  HCR6  0   0.244  -4.0984  -4.6585   0.3788
 P5C  H16   H  HCR6  0   0.252  -1.6989  -4.2259   0.7399
 P5C  H17   H  HCR6  0   0.254  -4.6861  -0.5051  -0.4373
 P5C  H18   H  HCH3  0   0.249  -6.5711  -2.7465   0.6943
 P5C  H18A  H  HCH3  0   0.243  -6.4633  -2.1078  -0.9389
 P5C  H18B  H  HCH3  0   0.244  -6.2264  -3.8304  -0.6430
 P5C  HN9   H  HNH2  0   0.414  -1.0866   4.8887  -0.0844
 P5C  HN9A  H  HNH2  0   0.407  -2.7315   5.0746  -0.5204
 P5C  HN11  H  HNH1  0   0.432  -3.0202   0.9236  -0.3385
 P5C  HN7   H  HNH1  0   0.391   2.0546  -1.0216   0.6116
 P5C  H19   H  HCH1  0   0.248   3.6877   1.2091   1.0956
 P5C  H24   H  HCH1  0   0.219   5.4789  -0.3674   1.1775
 P5C  HN25  H  HNH2  0   0.349   4.4186  -1.9971   2.6465
 P5C  HN2A  H  HNH2  0   0.346   3.8595  -0.5085   2.9388
 P5C  H23   H  HCH2  0   0.235   5.2565  -2.7214   0.5002
 P5C  H23A  H  HCH2  0   0.215   3.6413  -2.4327  -0.1088
 P5C  H22   H  HCH2  0   0.212   6.2218  -1.1711  -1.1540
 P5C  H22A  H  HCH2  0   0.231   5.2427  -2.3700  -1.9759
 P5C  H21   H  HCH2  0   0.231   4.8138  -0.0538  -2.8380
 P5C  H21A  H  HCH2  0   0.215   3.3675  -0.7701  -2.1595
 P5C  H20   H  HCH2  0   0.245   3.6351   1.5772  -1.3591
 P5C  H20A  H  HCH2  0   0.221   5.2307   1.1979  -0.7441

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
 P5C  C2   N1    aromatic  1.337  0.020  1.337
 P5C  C2   N5    aromatic  1.341  0.020  1.341
 P5C  C2   N7    single    1.336  0.020  1.336
 P5C  C3   C4    aromatic  1.387  0.020  1.387
 P5C  C3   N5    aromatic  1.319  0.020  1.319
 P5C  N1   C6    aromatic  1.320  0.020  1.320
 P5C  C4   C6    aromatic  1.432  0.020  1.432
 P5C  C4   C8    single    1.474  0.020  1.474
 P5C  C6   N11   single    1.349  0.020  1.349
 P5C  C8   O10   double    1.237  0.020  1.237
 P5C  C8   N9    single    1.341  0.020  1.341
 P5C  C12  C13   aromatic  1.396  0.020  1.396
 P5C  C12  C17   aromatic  1.401  0.020  1.401
 P5C  C12  N11   single    1.393  0.020  1.393
 P5C  C13  C16   aromatic  1.389  0.020  1.389
 P5C  C14  C15   aromatic  1.394  0.020  1.394
 P5C  C14  C16   aromatic  1.385  0.020  1.385
 P5C  C15  C17   aromatic  1.387  0.020  1.387
 P5C  C15  C18   single    1.501  0.020  1.501
 P5C  N7   C19   single    1.451  0.020  1.451
 P5C  C19  C24   single    1.535  0.020  1.535
 P5C  C19  C20   single    1.531  0.020  1.531
 P5C  C24  N25   single    1.454  0.020  1.454
 P5C  C24  C23   single    1.528  0.020  1.528
 P5C  C23  C22   single    1.524  0.020  1.524
 P5C  C22  C21   single    1.524  0.020  1.524
 P5C  C21  C20   single    1.523  0.020  1.523
 P5C  C3   H3    single    0.930  0.020  1.080
 P5C  C13  H13   single    0.930  0.020  1.080
 P5C  C14  H14   single    0.930  0.020  1.080
 P5C  C16  H16   single    0.930  0.020  1.080
 P5C  C17  H17   single    0.930  0.020  1.080
 P5C  C18  H18   single    0.970  0.020  1.090
 P5C  C18  H18A  single    0.970  0.020  1.090
 P5C  C18  H18B  single    0.970  0.020  1.090
 P5C  N9   HN9   single    0.860  0.020  1.020
 P5C  N9   HN9A  single    0.860  0.020  1.020
 P5C  N11  HN11  single    0.860  0.020  1.020
 P5C  N7   HN7   single    0.860  0.020  1.020
 P5C  C19  H19   single    0.970  0.020  1.090
 P5C  C24  H24   single    0.970  0.020  1.090
 P5C  N25  HN25  single    0.890  0.020  1.040
 P5C  N25  HN2A  single    0.890  0.020  1.040
 P5C  C23  H23   single    0.970  0.020  1.090
 P5C  C23  H23A  single    0.970  0.020  1.090
 P5C  C22  H22   single    0.970  0.020  1.090
 P5C  C22  H22A  single    0.970  0.020  1.090
 P5C  C21  H21   single    0.970  0.020  1.090
 P5C  C21  H21A  single    0.970  0.020  1.090
 P5C  C20  H20   single    0.970  0.020  1.090
 P5C  C20  H20A  single    0.970  0.020  1.090

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
 P5C  N7    C2   N5    118.45  3.000
 P5C  N7    C2   N1    116.10  3.000
 P5C  N5    C2   N1    125.45  3.000
 P5C  H3    C3   N5    114.51  3.000
 P5C  H3    C3   C4    120.15  3.000
 P5C  N5    C3   C4    125.33  3.000
 P5C  C6    N1   C2    118.67  3.000
 P5C  C8    C4   C6    122.91  3.000
 P5C  C8    C4   C3    122.75  3.000
 P5C  C6    C4   C3    114.33  3.000
 P5C  N11   C6   C4    119.50  3.000
 P5C  N11   C6   N1    119.70  3.000
 P5C  C4    C6   N1    120.80  3.000
 P5C  N9    C8   O10   120.54  3.000
 P5C  N9    C8   C4    117.75  3.000
 P5C  O10   C8   C4    121.71  3.000
 P5C  N11   C12  C17   115.54  3.000
 P5C  N11   C12  C13   125.74  3.000
 P5C  C17   C12  C13   118.72  3.000
 P5C  H13   C13  C16   120.10  3.000
 P5C  H13   C13  C12   120.75  3.000
 P5C  C16   C13  C12   119.15  3.000
 P5C  H14   C14  C16   120.17  3.000
 P5C  H14   C14  C15   120.07  3.000
 P5C  C16   C14  C15   119.76  3.000
 P5C  C18   C15  C17   120.45  3.000
 P5C  C18   C15  C14   120.93  3.000
 P5C  C17   C15  C14   118.61  3.000
 P5C  H16   C16  C14   119.61  3.000
 P5C  H16   C16  C13   118.66  3.000
 P5C  C14   C16  C13   121.73  3.000
 P5C  H17   C17  C15   118.91  3.000
 P5C  H17   C17  C12   119.06  3.000
 P5C  C15   C17  C12   122.03  3.000
 P5C  H18B  C18  H18A  108.07  3.000
 P5C  H18B  C18  H18   107.18  3.000
 P5C  H18A  C18  H18   107.30  3.000
 P5C  H18B  C18  C15   111.41  3.000
 P5C  H18A  C18  C15   111.70  3.000
 P5C  H18   C18  C15   110.97  3.000
 P5C  HN9A  N9   HN9   116.72  3.000
 P5C  HN9A  N9   C8    118.98  3.000
 P5C  HN9   N9   C8    123.81  3.000
 P5C  HN11  N11  C12   116.11  3.000
 P5C  HN11  N11  C6    112.27  3.000
 P5C  C12   N11  C6    131.56  3.000
 P5C  C3    N5   C2    115.35  3.000
 P5C  HN7   N7   C19   117.16  3.000
 P5C  HN7   N7   C2    115.62  3.000
 P5C  C19   N7   C2    125.61  3.000
 P5C  H19   C19  C20   108.53  3.000
 P5C  H19   C19  C24   108.32  3.000
 P5C  C20   C19  C24   110.02  3.000
 P5C  H19   C19  N7    108.77  3.000
 P5C  C20   C19  N7    112.52  3.000
 P5C  C24   C19  N7    108.59  3.000
 P5C  H24   C24  C23   107.47  3.000
 P5C  H24   C24  N25   112.64  3.000
 P5C  C23   C24  N25   109.55  3.000
 P5C  H24   C24  C19   105.41  3.000
 P5C  C23   C24  C19   111.69  3.000
 P5C  N25   C24  C19   110.03  3.000
 P5C  HN2A  N25  HN25  105.89  3.000
 P5C  HN2A  N25  C24   109.96  3.000
 P5C  HN25  N25  C24   109.37  3.000
 P5C  H23A  C23  H23   106.13  3.000
 P5C  H23A  C23  C22   109.71  3.000
 P5C  H23   C23  C22   110.26  3.000
 P5C  H23A  C23  C24   109.74  3.000
 P5C  H23   C23  C24   108.94  3.000
 P5C  C22   C23  C24   111.90  3.000
 P5C  H22A  C22  H22   106.49  3.000
 P5C  H22A  C22  C21   110.56  3.000
 P5C  H22   C22  C21   109.23  3.000
 P5C  H22A  C22  C23   109.90  3.000
 P5C  H22   C22  C23   109.50  3.000
 P5C  C21   C22  C23   111.04  3.000
 P5C  H21A  C21  H21   106.39  3.000
 P5C  H21A  C21  C20   109.81  3.000
 P5C  H21   C21  C20   109.83  3.000
 P5C  H21A  C21  C22   109.58  3.000
 P5C  H21   C21  C22   110.26  3.000
 P5C  C20   C21  C22   110.87  3.000
 P5C  H20A  C20  H20   106.54  3.000
 P5C  H20A  C20  C21   109.46  3.000
 P5C  H20   C20  C21   111.22  3.000
 P5C  H20A  C20  C19   107.74  3.000
 P5C  H20   C20  C19   109.34  3.000
 P5C  C21   C20  C19   112.31  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
 P5C  CONST_01  C4    C6   N1   C2     0.00   0.0  0
 P5C  CONST_02  C4    C3   N5   C2     0.00   0.0  0
 P5C  CONST_03  N1    C6   C4   C3     0.00   0.0  0
 P5C  CONST_04  N1    C2   N5   C3     0.00   0.0  0
 P5C  CONST_05  N5    C2   N1   C6     0.00   0.0  0
 P5C  CONST_06  N5    C3   C4   C6     0.00   0.0  0
 P5C  CONST_07  C14   C16  C13  C12    0.00   0.0  0
 P5C  CONST_08  C14   C15  C17  C12    0.00   0.0  0
 P5C  CONST_09  C15   C17  C12  C13    0.00   0.0  0
 P5C  CONST_10  C15   C14  C16  C13    0.00   0.0  0
 P5C  CONST_11  C17   C12  C13  C16    0.00   0.0  0
 P5C  CONST_12  C17   C15  C14  C16    0.00   0.0  0
 P5C  CONST_13  N11   C6   N1   C2   180.00   0.0  0
 P5C  CONST_14  N11   C6   C4   C3   180.00   0.0  0
 P5C  CONST_15  N7    C2   N5   C3   180.00   0.0  0
 P5C  CONST_16  C8    C4   C6   N1   180.00   0.0  0
 P5C  CONST_17  N7    C2   N1   C6   180.00   0.0  0
 P5C  CONST_18  N5    C3   C4   C8   180.00   0.0  0
 P5C  CONST_19  C18   C15  C17  C12  180.00   0.0  0
 P5C  CONST_20  N11   C12  C17  C15  180.00   0.0  0
 P5C  CONST_21  N11   C12  C13  C16  180.00   0.0  0
 P5C  CONST_22  C18   C15  C14  C16  180.00   0.0  0
 P5C  CONST_23  C19   N7   C2   N1   180.00   0.0  0
 P5C  CONST_24  C19   N7   C2   N5     0.00   0.0  0
 P5C  CONST_25  H3    C3   N5   C2   180.00   0.0  0
 P5C  CONST_26  H16   C16  C13  C12  180.00   0.0  0
 P5C  CONST_27  H17   C17  C12  C13  180.00   0.0  0
 P5C  CONST_28  H14   C14  C16  C13  180.00   0.0  0
 P5C  CONST_29  H13   C13  C16  C14  180.00   0.0  0
 P5C  CONST_30  HN7   N7   C2   N1     0.00   0.0  0
 P5C  CONST_31  HN9   N9   C8   C4     0.00   0.0  0
 P5C  CONST_32  HN9A  N9   C8   C4   180.00   0.0  0
 P5C  Var_01    C22   C21  C20  C19  -56.36  30.0  1
 P5C  Var_02    C21   C22  C23  C24  -55.06  30.0  1
 P5C  Var_03    C20   C21  C22  C23   55.33  30.0  1
 P5C  Var_04    C12   N11  C6   N1     0.49  30.0  2
 P5C  Var_05    C13   C12  N11  C6     5.31  30.0  2
 P5C  Var_06    O10   C8   C4   C3   167.10  30.0  2
 P5C  Var_07    H18   C18  C15  C14   87.98  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 P5C  chir_01  C19  N7   C24  C20  negativ
 P5C  chir_02  C24  N25  C23  C19  negativ

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
 P5C  plan-1  C2    0.020
 P5C  plan-1  C3    0.020
 P5C  plan-1  N1    0.020
 P5C  plan-1  C4    0.020
 P5C  plan-1  C6    0.020
 P5C  plan-1  C8    0.020
 P5C  plan-1  N11   0.020
 P5C  plan-1  N5    0.020
 P5C  plan-1  N7    0.020
 P5C  plan-1  H3    0.020
 P5C  plan-2  C12   0.020
 P5C  plan-2  C13   0.020
 P5C  plan-2  C14   0.020
 P5C  plan-2  C15   0.020
 P5C  plan-2  C16   0.020
 P5C  plan-2  C17   0.020
 P5C  plan-2  C18   0.020
 P5C  plan-2  N11   0.020
 P5C  plan-2  H13   0.020
 P5C  plan-2  H14   0.020
 P5C  plan-2  H16   0.020
 P5C  plan-2  H17   0.020
 P5C  plan-3  C4    0.020
 P5C  plan-3  C8    0.020
 P5C  plan-3  O10   0.020
 P5C  plan-3  N9    0.020
 P5C  plan-3  HN9   0.020
 P5C  plan-3  HN9A  0.020
 P5C  plan-4  C2    0.020
 P5C  plan-4  N7    0.020
 P5C  plan-4  C19   0.020
 P5C  plan-4  HN7   0.020

