# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 11:00:57 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: (2E)-3-(3-{6-[(trans-4-aminocyclohexyl)amino]pyrazin-2-yl}phenyl)prop-2-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1CC[C@H](CC1)Nc2cncc(n2)c3cccc(\C=C\C(O)=O)c3
#
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
 XJ1  XJ1  '(2E)-3-(3-{6-[(trans-4-aminocyclohexyl)amino]pyrazin-2-yl}phenyl)prop-2-enoic acid'  ligand  46  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_XJ1
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
 XJ1  C3    C  CH2    0  -0.452  -5.3179  -1.0581   1.0797
 XJ1  C4    C  CH2    0  -0.438  -6.7632  -0.5758   1.1089
 XJ1  C5    C  CH1    0  -0.052  -7.2807  -0.2469  -0.2868
 XJ1  N8    N  NH2    0  -0.807  -8.6388   0.2707  -0.1984
 XJ1  C6    C  CH2    0  -0.441  -6.3710   0.7809  -0.9497
 XJ1  C7    C  CH2    0  -0.441  -4.9270   0.2952  -0.9983
 XJ1  C2    C  CH1    0  -0.062  -4.4115  -0.0338   0.4043
 XJ1  N1    N  NH1    0  -0.677  -3.0496  -0.5251   0.4048
 XJ1  C9    C  CR6    0   0.459  -1.9501   0.2300   0.1985
 XJ1  N10   N  N      0  -0.455  -0.7891  -0.4082   0.0798
 XJ1  C14   C  CR16   0  -0.174  -1.9833   1.6427   0.1346
 XJ1  N13   N  N      0  -0.347  -0.8844   2.3361  -0.0567
 XJ1  C12   C  CR16   0  -0.165   0.2701   1.6887  -0.1819
 XJ1  C11   C  CR6    0   0.208   0.3208   0.3001  -0.1003
 XJ1  C15   C  CR6    0   0.085   1.5868  -0.4539  -0.2176
 XJ1  C16   C  CR16   0  -0.410   2.8214   0.1690  -0.0394
 XJ1  C20   C  CR16   0  -0.301   1.5632  -1.8188  -0.5006
 XJ1  C19   C  CR16   0  -0.216   2.7507  -2.5286  -0.6090
 XJ1  C18   C  CR16   0  -0.331   3.9700  -1.8980  -0.4319
 XJ1  C17   C  CR6    0   0.187   4.0231  -0.5321  -0.1378
 XJ1  C21   C  C1     0  -0.251   5.2759   0.1961   0.0760
 XJ1  C22   C  C1     0  -0.439   6.5039  -0.3212   0.1501
 XJ1  C23   C  C      0   0.404   7.7406   0.5184   0.3791
 XJ1  O25   O  O      0  -0.599   7.5968   1.7536   0.4736
 XJ1  O24   O  OC    -1  -0.616   8.8127  -0.1170   0.4550
 XJ1  H31C  H  HCH2   0   0.247  -4.9621  -1.2533   2.0938
 XJ1  H32C  H  HCH2   0   0.223  -5.2585  -2.0070   0.5337
 XJ1  H41C  H  HCH2   0   0.235  -7.3960  -1.3380   1.5723
 XJ1  H42C  H  HCH2   0   0.216  -6.8414   0.3205   1.7332
 XJ1  H2    H  HCH1   0   0.234  -4.4415   0.8791   1.0109
 XJ1  H5    H  HCH1   0   0.188  -7.2241  -1.1705  -0.8880
 XJ1  H81N  H  HNH2   0   0.340  -8.9859   0.4671  -1.1299
 XJ1  H82N  H  HNH2   0   0.341  -9.2482  -0.4507   0.1692
 XJ1  H61C  H  HCH2   0   0.234  -6.7247   0.9982  -1.9616
 XJ1  H62C  H  HCH2   0   0.215  -6.4281   1.7206  -0.3888
 XJ1  H71C  H  HCH2   0   0.222  -4.8538  -0.6042  -1.6186
 XJ1  H72C  H  HCH2   0   0.239  -4.2931   1.0509  -1.4691
 XJ1  H1    H  HNH1   0   0.381  -2.9137  -1.5196   0.3005
 XJ1  H14   H  HCR6   0   0.269  -2.9085   2.1968   0.2361
 XJ1  H12   H  HCR6   0   0.259   1.1512   2.2899  -0.3638
 XJ1  H16   H  HCR6   0   0.250   2.8687   1.2239   0.2019
 XJ1  H20   H  HCR6   0   0.256   0.6168  -2.3220  -0.6435
 XJ1  H19   H  HCR6   0   0.260   2.7225  -3.5862  -0.8370
 XJ1  H18   H  HCR6   0   0.255   4.8818  -2.4734  -0.5276
 XJ1  H21   H  H      0   0.237   5.1729   1.2713   0.1914
 XJ1  H22   H  H      0   0.230   6.6576  -1.3923   0.0545

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
 XJ1  C3   C4    single    1.524  0.020  1.524
 XJ1  C3   C2    single    1.525  0.020  1.525
 XJ1  C4   C5    single    1.524  0.020  1.524
 XJ1  C5   N8    single    1.456  0.020  1.456
 XJ1  C5   C6    single    1.524  0.020  1.524
 XJ1  C6   C7    single    1.524  0.020  1.524
 XJ1  C7   C2    single    1.530  0.020  1.530
 XJ1  C2   N1    single    1.448  0.020  1.448
 XJ1  N1   C9    single    1.350  0.020  1.350
 XJ1  C9   N10   aromatic  1.330  0.020  1.330
 XJ1  C9   C14   aromatic  1.415  0.020  1.415
 XJ1  N10  C11   aromatic  1.329  0.020  1.329
 XJ1  C14  N13   aromatic  1.313  0.020  1.313
 XJ1  N13  C12   aromatic  1.330  0.020  1.330
 XJ1  C12  C11   aromatic  1.392  0.020  1.392
 XJ1  C11  C15   single    1.478  0.020  1.478
 XJ1  C15  C16   aromatic  1.394  0.020  1.394
 XJ1  C15  C20   aromatic  1.394  0.020  1.394
 XJ1  C16  C17   aromatic  1.395  0.020  1.395
 XJ1  C20  C19   aromatic  1.388  0.020  1.388
 XJ1  C19  C18   aromatic  1.384  0.020  1.384
 XJ1  C18  C17   aromatic  1.398  0.020  1.398
 XJ1  C17  C21   single    1.465  0.020  1.465
 XJ1  C21  C22   double    1.335  0.020  1.335
 XJ1  C22  C23   single    1.512  0.020  1.512
 XJ1  C23  O25   deloc     1.247  0.020  1.247
 XJ1  C23  O24   deloc     1.248  0.020  1.248
 XJ1  C3   H31C  single    0.970  0.020  1.090
 XJ1  C3   H32C  single    0.970  0.020  1.090
 XJ1  C4   H41C  single    0.970  0.020  1.090
 XJ1  C4   H42C  single    0.970  0.020  1.090
 XJ1  C2   H2    single    0.970  0.020  1.090
 XJ1  C5   H5    single    0.970  0.020  1.090
 XJ1  N8   H81N  single    0.890  0.020  1.040
 XJ1  N8   H82N  single    0.890  0.020  1.040
 XJ1  C6   H61C  single    0.970  0.020  1.090
 XJ1  C6   H62C  single    0.970  0.020  1.090
 XJ1  C7   H71C  single    0.970  0.020  1.090
 XJ1  C7   H72C  single    0.970  0.020  1.090
 XJ1  N1   H1    single    0.860  0.020  1.020
 XJ1  C14  H14   single    0.930  0.020  1.080
 XJ1  C12  H12   single    0.930  0.020  1.080
 XJ1  C16  H16   single    0.930  0.020  1.080
 XJ1  C20  H20   single    0.930  0.020  1.080
 XJ1  C19  H19   single    0.930  0.020  1.080
 XJ1  C18  H18   single    0.930  0.020  1.080
 XJ1  C21  H21   single    0.930  0.020  1.080
 XJ1  C22  H22   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
 XJ1  H32C  C3   H31C  106.86  3.000
 XJ1  H32C  C3   C2    109.18  3.000
 XJ1  H31C  C3   C2    109.72  3.000
 XJ1  H32C  C3   C4    109.56  3.000
 XJ1  H31C  C3   C4    110.35  3.000
 XJ1  C2    C3   C4    111.07  3.000
 XJ1  H42C  C4   H41C  106.71  3.000
 XJ1  H42C  C4   C5    108.73  3.000
 XJ1  H41C  C4   C5    110.00  3.000
 XJ1  H42C  C4   C3    109.73  3.000
 XJ1  H41C  C4   C3    109.65  3.000
 XJ1  C5    C4   C3    111.88  3.000
 XJ1  H5    C5   C6    107.27  3.000
 XJ1  H5    C5   N8    112.24  3.000
 XJ1  C6    C5   N8    110.08  3.000
 XJ1  H5    C5   C4    107.51  3.000
 XJ1  C6    C5   C4    109.94  3.000
 XJ1  N8    C5   C4    109.74  3.000
 XJ1  H82N  N8   H81N  105.40  3.000
 XJ1  H82N  N8   C5    109.26  3.000
 XJ1  H81N  N8   C5    109.43  3.000
 XJ1  H62C  C6   H61C  106.64  3.000
 XJ1  H62C  C6   C7    109.81  3.000
 XJ1  H61C  C6   C7    109.88  3.000
 XJ1  H62C  C6   C5    108.94  3.000
 XJ1  H61C  C6   C5    110.08  3.000
 XJ1  C7    C6   C5    111.37  3.000
 XJ1  H72C  C7   H71C  106.57  3.000
 XJ1  H72C  C7   C2    110.37  3.000
 XJ1  H71C  C7   C2    108.67  3.000
 XJ1  H72C  C7   C6    110.06  3.000
 XJ1  H71C  C7   C6    110.07  3.000
 XJ1  C2    C7   C6    111.00  3.000
 XJ1  H2    C2   N1    107.94  3.000
 XJ1  H2    C2   C7    108.60  3.000
 XJ1  N1    C2   C7    112.96  3.000
 XJ1  H2    C2   C3    107.33  3.000
 XJ1  N1    C2   C3    109.33  3.000
 XJ1  C7    C2   C3    110.49  3.000
 XJ1  H1    N1   C9    115.20  3.000
 XJ1  H1    N1   C2    117.46  3.000
 XJ1  C9    N1   C2    125.20  3.000
 XJ1  C14   C9   N10   119.71  3.000
 XJ1  C14   C9   N1    123.12  3.000
 XJ1  N10   C9   N1    117.15  3.000
 XJ1  C11   N10  C9    119.03  3.000
 XJ1  H14   C14  N13   117.27  3.000
 XJ1  H14   C14  C9    121.79  3.000
 XJ1  N13   C14  C9    120.95  3.000
 XJ1  C12   N13  C14   118.89  3.000
 XJ1  H12   C12  C11   122.31  3.000
 XJ1  H12   C12  N13   116.89  3.000
 XJ1  C11   C12  N13   120.79  3.000
 XJ1  C15   C11  C12   122.38  3.000
 XJ1  C15   C11  N10   117.01  3.000
 XJ1  C12   C11  N10   120.61  3.000
 XJ1  C20   C15  C16   118.57  3.000
 XJ1  C20   C15  C11   120.07  3.000
 XJ1  C16   C15  C11   121.35  3.000
 XJ1  H16   C16  C17   117.88  3.000
 XJ1  H16   C16  C15   120.15  3.000
 XJ1  C17   C16  C15   121.96  3.000
 XJ1  H20   C20  C19   120.03  3.000
 XJ1  H20   C20  C15   119.82  3.000
 XJ1  C19   C20  C15   120.15  3.000
 XJ1  H19   C19  C18   119.68  3.000
 XJ1  H19   C19  C20   119.61  3.000
 XJ1  C18   C19  C20   120.71  3.000
 XJ1  H18   C18  C17   120.39  3.000
 XJ1  H18   C18  C19   119.25  3.000
 XJ1  C17   C18  C19   120.36  3.000
 XJ1  C21   C17  C18   123.29  3.000
 XJ1  C21   C17  C16   118.47  3.000
 XJ1  C18   C17  C16   118.24  3.000
 XJ1  H21   C21  C22   117.71  3.000
 XJ1  H21   C21  C17   115.24  3.000
 XJ1  C22   C21  C17   127.05  3.000
 XJ1  H22   C22  C23   116.43  3.000
 XJ1  H22   C22  C21   120.49  3.000
 XJ1  C23   C22  C21   123.07  3.000
 XJ1  O24   C23  O25   126.76  3.000
 XJ1  O24   C23  C22   115.40  3.000
 XJ1  O25   C23  C22   117.84  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
 XJ1  CONST_01  C12  C11  N10  C9      0.00   0.0  0
 XJ1  CONST_02  C15  C11  N10  C9    180.00   0.0  0
 XJ1  CONST_03  C12  N13  C14  C9      0.00   0.0  0
 XJ1  CONST_04  N13  C14  C9   N10     0.00   0.0  0
 XJ1  CONST_05  N13  C12  C11  N10     0.00   0.0  0
 XJ1  CONST_08  C11  N10  C9   C14     0.00   0.0  0
 XJ1  CONST_09  C11  C12  N13  C14     0.00   0.0  0
 XJ1  CONST_10  C15  C11  C12  N13   180.00   0.0  0
 XJ1  CONST_13  C17  C16  C15  C11   180.00   0.0  0
 XJ1  CONST_14  C19  C20  C15  C11   180.00   0.0  0
 XJ1  CONST_15  C18  C17  C16  C15     0.00   0.0  0
 XJ1  CONST_16  C18  C19  C20  C15     0.00   0.0  0
 XJ1  CONST_17  C19  C20  C15  C16     0.00   0.0  0
 XJ1  CONST_18  C19  C18  C17  C16     0.00   0.0  0
 XJ1  CONST_19  C17  C16  C15  C20     0.00   0.0  0
 XJ1  CONST_20  C17  C18  C19  C20     0.00   0.0  0
 XJ1  CONST_21  C11  N10  C9   N1    180.00   0.0  0
 XJ1  CONST_22  N13  C14  C9   N1    180.00   0.0  0
 XJ1  CONST_23  C21  C17  C16  C15   180.00   0.0  0
 XJ1  CONST_24  C21  C17  C18  C19   180.00   0.0  0
 XJ1  CONST_25  N10  C9   N1   C2    180.00   0.0  0
 XJ1  CONST_26  C14  C9   N1   C2      0.00   0.0  0
 XJ1  CONST_27  H14  C14  C9   N10   180.00   0.0  0
 XJ1  CONST_28  H12  C12  C11  N10   180.00   0.0  0
 XJ1  CONST_29  H16  C16  C15  C11     0.00   0.0  0
 XJ1  CONST_30  H20  C20  C15  C11     0.00   0.0  0
 XJ1  CONST_31  H19  C19  C20  C15   180.00   0.0  0
 XJ1  CONST_32  H18  C18  C17  C16   180.00   0.0  0
 XJ1  CONST_33  H1   N1   C9   N10     0.00   0.0  0
 XJ1  Var_01    C2   C3   C4   C5     56.14  30.0  1
 XJ1  Var_02    C2   C7   C6   C5    -57.03  30.0  1
 XJ1  Var_03    C22  C21  C17  C16   173.08  30.0  2
 XJ1  Var_04    C23  C22  C21  C17  -179.80   0.0  2
 XJ1  Var_05    O25  C23  C22  C21    -1.55  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
 XJ1  chir_01  C5  C4  N8  C6  negativ
 XJ1  chir_02  C2  N1  C7  C3  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
 XJ1  plan-1  N1   0.020
 XJ1  plan-1  C9   0.020
 XJ1  plan-1  N10  0.020
 XJ1  plan-1  C14  0.020
 XJ1  plan-1  N13  0.020
 XJ1  plan-1  C12  0.020
 XJ1  plan-1  C11  0.020
 XJ1  plan-1  C15  0.020
 XJ1  plan-1  H14  0.020
 XJ1  plan-1  H12  0.020
 XJ1  plan-2  C11  0.020
 XJ1  plan-2  C15  0.020
 XJ1  plan-2  C16  0.020
 XJ1  plan-2  C20  0.020
 XJ1  plan-2  C19  0.020
 XJ1  plan-2  C18  0.020
 XJ1  plan-2  C17  0.020
 XJ1  plan-2  C21  0.020
 XJ1  plan-2  H16  0.020
 XJ1  plan-2  H20  0.020
 XJ1  plan-2  H19  0.020
 XJ1  plan-2  H18  0.020
 XJ1  plan-3  C2   0.020
 XJ1  plan-3  N1   0.020
 XJ1  plan-3  C9   0.020
 XJ1  plan-3  H1   0.020
 XJ1  plan-4  C22  0.020
 XJ1  plan-4  C23  0.020
 XJ1  plan-4  O25  0.020
 XJ1  plan-4  O24  0.020
 XJ1  plan-5  C17  0.020
 XJ1  plan-5  C21  0.020
 XJ1  plan-5  C22  0.020
 XJ1  plan-5  C23  0.020
 XJ1  plan-5  H21  0.020
 XJ1  plan-5  H22  0.020

