# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 05:33:43 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 3-amino-N-{4-[(3S)-3-aminopiperidin-1-yl]pyridin-3-yl}pyrazine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CCCN(C1)c2ccncc2NC(=O)c3nccnc3N
#
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
 2HW  2HW  3-amino-N-{4-[(3S)-3-aminopiperidin-1-yl]pyridin-3-yl}pyrazine-2-carboxamide  ligand  42  23  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2HW
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
 2HW  O    O  O     0  -0.477   2.1904  -2.0255   0.5769
 2HW  C10  C  C     0   0.554   1.7005  -0.9769   0.1774
 2HW  C11  C  CR6   0  -0.006   2.4550   0.3053   0.1704
 2HW  C14  C  CR6   0   0.477   3.8079   0.3990   0.5988
 2HW  N6   N  NH2   0  -0.833   4.5250  -0.6355   1.0445
 2HW  N5   N  N     0  -0.412   4.4228   1.5910   0.5670
 2HW  C13  C  CR16  0  -0.080   3.7442   2.6357   0.1445
 2HW  C12  C  CR16  0  -0.154   2.4183   2.5479  -0.2691
 2HW  N4   N  N     0  -0.382   1.8066   1.3803  -0.2463
 2HW  N3   N  NH1   0  -0.743   0.4379  -0.8597  -0.2854
 2HW  C9   C  CR6   0   0.236  -0.5589  -1.8313  -0.3274
 2HW  C8   C  CR16  0  -0.118  -0.3155  -3.1859  -0.5250
 2HW  N2   N  N     0  -0.409  -1.2802  -4.0909  -0.6515
 2HW  C7   C  CR16  0  -0.083  -2.5358  -3.6699  -0.6083
 2HW  C6   C  CR16  0  -0.391  -2.8913  -2.3449  -0.4141
 2HW  C5   C  CR6   0   0.362  -1.8952  -1.3897  -0.2460
 2HW  N1   N  NT    0  -0.516  -2.1454  -0.0323  -0.0471
 2HW  C3   C  CH2   0  -0.323  -1.8248   0.4770   1.2899
 2HW  C2   C  CH2   0  -0.448  -1.7169   1.9906   1.2616
 2HW  C1   C  CH2   0  -0.445  -2.9906   2.6110   0.7033
 2HW  C4   C  CH2   0  -0.297  -3.4123   0.4863  -0.5315
 2HW  C    C  CH1   0  -0.072  -3.3436   2.0063  -0.6491
 2HW  N    N  NH2   0  -0.804  -4.6368   2.4971  -1.0983
 2HW  H18  H  HNH2  0   0.417   4.1339  -1.5610   1.0718
 2HW  H17  H  HNH2  0   0.398   5.4876  -0.4896   1.2963
 2HW  H16  H  HCR6  0   0.279   4.2624   3.5878   0.1302
 2HW  H15  H  HCR6  0   0.273   1.8677   3.4135  -0.6117
 2HW  H14  H  HNH1  0   0.418   0.1442   0.0801  -0.5315
 2HW  H13  H  HCR6  0   0.272   0.6992  -3.5507  -0.6052
 2HW  H12  H  HCR6  0   0.262  -3.3077  -4.4219  -0.7275
 2HW  H11  H  HCR6  0   0.279  -3.9373  -2.0724  -0.3758
 2HW  H7   H  HCH2  0   0.231  -2.6090   0.1742   1.9998
 2HW  H8   H  HCH2  0   0.260  -0.8935   0.0353   1.6419
 2HW  H5   H  HCH2  0   0.240  -1.5299   2.3521   2.2747
 2HW  H6   H  HCH2  0   0.227  -0.8531   2.2806   0.6562
 2HW  H4   H  HCH2  0   0.216  -3.8218   2.4313   1.3940
 2HW  H3   H  HCH2  0   0.238  -2.8795   3.6950   0.6128
 2HW  H10  H  HCH2  0   0.254  -3.6205   0.0499  -1.5113
 2HW  H9   H  HCH2  0   0.210  -4.2488   0.2230   0.1341
 2HW  H    H  HCH1  0   0.200  -2.5288   2.2413  -1.3516
 2HW  H1   H  HNH2  0   0.347  -4.6152   3.5089  -1.1356
 2HW  H2   H  HNH2  0   0.344  -4.8023   2.1951  -2.0511

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
 2HW  N    C    single    1.454  0.020  1.454
 2HW  C1   C    single    1.523  0.020  1.523
 2HW  C1   C2   single    1.523  0.020  1.523
 2HW  C    C4   single    1.526  0.020  1.526
 2HW  C2   C3   single    1.518  0.020  1.518
 2HW  C4   N1   single    1.452  0.020  1.452
 2HW  C3   N1   single    1.466  0.020  1.466
 2HW  N1   C5   single    1.394  0.020  1.394
 2HW  C6   C5   aromatic  1.390  0.020  1.390
 2HW  C6   C7   aromatic  1.386  0.020  1.386
 2HW  C5   C9   aromatic  1.410  0.020  1.410
 2HW  C12  N4   aromatic  1.318  0.020  1.318
 2HW  C12  C13  aromatic  1.392  0.020  1.392
 2HW  N4   C11  aromatic  1.323  0.020  1.323
 2HW  C7   N2   aromatic  1.325  0.020  1.325
 2HW  C9   N3   single    1.393  0.020  1.393
 2HW  C9   C8   aromatic  1.390  0.020  1.390
 2HW  C13  N5   aromatic  1.315  0.020  1.315
 2HW  N3   C10  single    1.350  0.020  1.350
 2HW  C11  C10  single    1.488  0.020  1.488
 2HW  C11  C14  aromatic  1.422  0.020  1.422
 2HW  N2   C8   aromatic  1.329  0.020  1.329
 2HW  C10  O    double    1.224  0.020  1.224
 2HW  N5   C14  aromatic  1.342  0.020  1.342
 2HW  C14  N6   single    1.335  0.020  1.335
 2HW  N6   H18  single    0.860  0.020  1.020
 2HW  N6   H17  single    0.860  0.020  1.020
 2HW  C13  H16  single    0.930  0.020  1.080
 2HW  C12  H15  single    0.930  0.020  1.080
 2HW  N3   H14  single    0.860  0.020  1.020
 2HW  C8   H13  single    0.930  0.020  1.080
 2HW  C7   H12  single    0.930  0.020  1.080
 2HW  C6   H11  single    0.930  0.020  1.080
 2HW  C3   H7   single    0.970  0.020  1.090
 2HW  C3   H8   single    0.970  0.020  1.090
 2HW  C2   H5   single    0.970  0.020  1.090
 2HW  C2   H6   single    0.970  0.020  1.090
 2HW  C1   H4   single    0.970  0.020  1.090
 2HW  C1   H3   single    0.970  0.020  1.090
 2HW  C4   H10  single    0.970  0.020  1.090
 2HW  C4   H9   single    0.970  0.020  1.090
 2HW  C    H    single    0.970  0.020  1.090
 2HW  N    H1   single    0.890  0.020  1.040
 2HW  N    H2   single    0.890  0.020  1.040

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
 2HW  N3   C10  C11  113.45  3.000
 2HW  C11  C10  O    122.45  3.000
 2HW  N3   C10  O    124.09  3.000
 2HW  N4   C11  C14  120.50  3.000
 2HW  C14  C11  C10  122.54  3.000
 2HW  N4   C11  C10  116.95  3.000
 2HW  N5   C14  N6   116.75  3.000
 2HW  N6   C14  C11  124.08  3.000
 2HW  N5   C14  C11  119.17  3.000
 2HW  H17  N6   H18  119.95  3.000
 2HW  H17  N6   C14  119.03  3.000
 2HW  H18  N6   C14  120.89  3.000
 2HW  C13  N5   C14  118.48  3.000
 2HW  H16  C13  C12  120.45  3.000
 2HW  H16  C13  N5   117.08  3.000
 2HW  C12  C13  N5   122.47  3.000
 2HW  H15  C12  N4   118.56  3.000
 2HW  H15  C12  C13  121.91  3.000
 2HW  N4   C12  C13  119.52  3.000
 2HW  C12  N4   C11  119.85  3.000
 2HW  H14  N3   C9   115.57  3.000
 2HW  H14  N3   C10  115.74  3.000
 2HW  C9   N3   C10  128.27  3.000
 2HW  C5   C9   C8   118.65  3.000
 2HW  C8   C9   N3   123.96  3.000
 2HW  C5   C9   N3   117.27  3.000
 2HW  H13  C8   N2   116.39  3.000
 2HW  H13  C8   C9   120.24  3.000
 2HW  N2   C8   C9   123.36  3.000
 2HW  C7   N2   C8   117.94  3.000
 2HW  H12  C7   C6   119.74  3.000
 2HW  H12  C7   N2   116.79  3.000
 2HW  C6   C7   N2   123.47  3.000
 2HW  H11  C6   C5   121.04  3.000
 2HW  H11  C6   C7   119.60  3.000
 2HW  C5   C6   C7   119.35  3.000
 2HW  N1   C5   C6   123.88  3.000
 2HW  C6   C5   C9   117.19  3.000
 2HW  N1   C5   C9   118.90  3.000
 2HW  C4   N1   C3   111.77  3.000
 2HW  C3   N1   C5   115.40  3.000
 2HW  C4   N1   C5   117.17  3.000
 2HW  H8   C3   H7   106.82  3.000
 2HW  H8   C3   C2   110.47  3.000
 2HW  H7   C3   C2   109.71  3.000
 2HW  H8   C3   N1   109.92  3.000
 2HW  H7   C3   N1   109.69  3.000
 2HW  C2   C3   N1   110.18  3.000
 2HW  H6   C2   H5   106.89  3.000
 2HW  H6   C2   C1   110.46  3.000
 2HW  H5   C2   C1   110.40  3.000
 2HW  H6   C2   C3   109.32  3.000
 2HW  H5   C2   C3   108.97  3.000
 2HW  C1   C2   C3   110.71  3.000
 2HW  H3   C1   H4   106.97  3.000
 2HW  H3   C1   C    110.10  3.000
 2HW  H4   C1   C    108.60  3.000
 2HW  H3   C1   C2   110.44  3.000
 2HW  H4   C1   C2   109.67  3.000
 2HW  C    C1   C2   110.96  3.000
 2HW  H9   C4   H10  107.57  3.000
 2HW  H9   C4   C    108.60  3.000
 2HW  H10  C4   C    109.71  3.000
 2HW  H9   C4   N1   112.08  3.000
 2HW  H10  C4   N1   108.83  3.000
 2HW  C    C4   N1   110.01  3.000
 2HW  H    C    N    112.89  3.000
 2HW  H    C    C4   107.16  3.000
 2HW  N    C    C4   108.66  3.000
 2HW  H    C    C1   108.08  3.000
 2HW  C4   C    C1   109.72  3.000
 2HW  N    C    C1   110.27  3.000
 2HW  H2   N    H1   105.46  3.000
 2HW  H2   N    C    109.58  3.000
 2HW  H1   N    C    109.24  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
 2HW  CONST_01  C13  C12  N4   C11     0.00   0.0  0
 2HW  CONST_02  C13  N5   C14  C11     0.00   0.0  0
 2HW  CONST_03  C12  N4   C11  C14     0.00   0.0  0
 2HW  CONST_04  C12  C13  N5   C14     0.00   0.0  0
 2HW  CONST_05  N4   C12  C13  N5      0.00   0.0  0
 2HW  CONST_06  N4   C11  C14  N5      0.00   0.0  0
 2HW  CONST_07  C7   C6   C5   C9      0.00   0.0  0
 2HW  CONST_08  C7   N2   C8   C9      0.00   0.0  0
 2HW  CONST_09  C6   C5   C9   C8      0.00   0.0  0
 2HW  CONST_10  C6   C7   N2   C8      0.00   0.0  0
 2HW  CONST_11  C5   C6   C7   N2      0.00   0.0  0
 2HW  CONST_12  C5   C9   C8   N2      0.00   0.0  0
 2HW  CONST_13  N1   C5   C9   C8    180.00   0.0  0
 2HW  CONST_14  N1   C5   C6   C7    180.00   0.0  0
 2HW  CONST_15  C12  N4   C11  C10   180.00   0.0  0
 2HW  CONST_16  N5   C14  C11  C10   180.00   0.0  0
 2HW  CONST_17  N4   C11  C14  N6    180.00   0.0  0
 2HW  CONST_18  C13  N5   C14  N6    180.00   0.0  0
 2HW  CONST_19  N1   C5   C9   N3      0.00   0.0  0
 2HW  CONST_20  C6   C5   C9   N3    180.00   0.0  0
 2HW  CONST_21  N2   C8   C9   N3    180.00   0.0  0
 2HW  CONST_22  H15  C12  N4   C11   180.00   0.0  0
 2HW  CONST_23  H16  C13  N5   C14   180.00   0.0  0
 2HW  CONST_24  H11  C6   C5   C9    180.00   0.0  0
 2HW  CONST_25  H12  C7   N2   C8    180.00   0.0  0
 2HW  CONST_26  H13  C8   N2   C7    180.00   0.0  0
 2HW  CONST_27  C9   N3   C10  C11   180.00   0.0  0
 2HW  CONST_30  H18  N6   C14  C11     0.00   0.0  0
 2HW  CONST_31  H17  N6   C14  C11   180.00   0.0  0
 2HW  CONST_33  C9   N3   C10  O       0.00   0.0  0
 2HW  Var_01    C4   N1   C5   C9    153.82  30.0  2
 2HW  Var_02    C    C4   N1   C5   -161.81  30.0  1
 2HW  Var_03    C2   C3   N1   C5    162.21  30.0  1
 2HW  Var_04    C1   C2   C3   N1     55.47  30.0  1
 2HW  Var_05    C    C1   C2   C3    -53.27  30.0  1
 2HW  Var_06    N4   C11  C10  O    -177.98  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
 2HW  chir_01  C  N  C1  C4  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
 2HW  plan-1  C10  0.020
 2HW  plan-1  C11  0.020
 2HW  plan-1  C14  0.020
 2HW  plan-1  N6   0.020
 2HW  plan-1  N5   0.020
 2HW  plan-1  C13  0.020
 2HW  plan-1  C12  0.020
 2HW  plan-1  N4   0.020
 2HW  plan-1  H16  0.020
 2HW  plan-1  H15  0.020
 2HW  plan-2  N3   0.020
 2HW  plan-2  C9   0.020
 2HW  plan-2  C8   0.020
 2HW  plan-2  N2   0.020
 2HW  plan-2  C7   0.020
 2HW  plan-2  C6   0.020
 2HW  plan-2  C5   0.020
 2HW  plan-2  N1   0.020
 2HW  plan-2  H13  0.020
 2HW  plan-2  H12  0.020
 2HW  plan-2  H11  0.020
 2HW  plan-3  O    0.020
 2HW  plan-3  C10  0.020
 2HW  plan-3  C11  0.020
 2HW  plan-3  N3   0.020
 2HW  plan-3  C9   0.020
 2HW  plan-3  H14  0.020
 2HW  plan-4  C14  0.020
 2HW  plan-4  N6   0.020
 2HW  plan-4  H18  0.020
 2HW  plan-4  H17  0.020

