# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 15:01:58 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 6-(4-azanyl-4-methyl-piperidin-1-yl)-3-[2,3-bis(chloranyl)phenyl]pyrazin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(N)CCN(CC1)c2cnc(c(N)n2)c3cccc(Cl)c3Cl
#
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
 5OD  5OD  6-(4-azanyl-4-methyl-piperidin-1-yl)-3-[2,3-bis(chloranyl)phenyl]pyrazin-2-amine  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_5OD
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
 5OD  C1   C   CR6   0   0.068   0.9816  -0.4885   0.2077
 5OD  C3   C   CR16  0  -0.239  -0.8843   0.4922   1.1031
 5OD  C11  C   CH2   0  -0.403  -5.0936   1.2900   0.6847
 5OD  C12  C   CT    0   0.042  -5.9891   0.2331   0.0404
 5OD  C13  C   CH2   0  -0.419  -5.1814  -0.3809  -1.1110
 5OD  C14  C   CH2   0  -0.307  -3.8435  -0.9375  -0.6605
 5OD  C15  C   CR6   0  -0.064   3.3679   0.3002   0.1618
 5OD  C16  C   CR6   0   0.020   4.7304   0.0391   0.2792
 5OD  C17  C   CR16  0  -0.234   5.1824  -1.2494   0.5172
 5OD  C18  C   CR16  0  -0.236   4.2666  -2.2815   0.6363
 5OD  C19  C   CR16  0  -0.294   2.9106  -2.0226   0.5255
 5OD  C23  C   CH3   0  -0.639  -7.2511   0.8858  -0.5087
 5OD  N2   N   N     0  -0.336   0.4176   0.2920   1.1123
 5OD  C4   C   CR6   0   0.506  -1.6982  -0.1196   0.1229
 5OD  N5   N   N     0  -0.479  -1.1333  -0.8997  -0.7951
 5OD  C6   C   CR6   0   0.406   0.1776  -1.0914  -0.7821
 5OD  N7   N   NH2   0  -0.831   0.6917  -1.9150  -1.7324
 5OD  C8   C   CR6   0   0.117   2.4373  -0.7325   0.2931
 5OD  N9   N   NT    0  -0.500  -3.0501   0.0558   0.0555
 5OD  C10  C   CH2   0  -0.320  -3.7376   0.7572   1.1279
 5OD  CL2  CL  CL    0  -0.097   5.8816   1.3124   0.1196
 5OD  N22  N   NH2   0  -0.799  -6.3958  -0.7384   1.0545
 5OD  H1   H   HCR6  0   0.258  -1.2817   1.1211   1.8869
 5OD  H2   H   HCH2  0   0.228  -4.9345   2.0960  -0.0368
 5OD  H3   H   HCH2  0   0.241  -5.5911   1.7289   1.5529
 5OD  H4   H   HCH2  0   0.235  -5.7504  -1.1874  -1.5823
 5OD  H5   H   HCH2  0   0.221  -5.0125   0.3790  -1.8804
 5OD  H6   H   HCH2  0   0.215  -3.9899  -1.8238  -0.0274
 5OD  H7   H   HCH2  0   0.269  -3.2823  -1.2724  -1.5275
 5OD  H8   H   HCR6  0   0.290   6.2432  -1.4389   0.6065
 5OD  H9   H   HCR6  0   0.275   4.6148  -3.2877   0.8247
 5OD  H10  H   HCR6  0   0.271   2.1982  -2.8302   0.6322
 5OD  H11  H   HCH3  0   0.222  -7.0072   1.6392  -1.2591
 5OD  H12  H   HCH3  0   0.225  -7.8988   0.1443  -0.9832
 5OD  H13  H   HCH3  0   0.228  -7.8192   1.3688   0.2878
 5OD  H14  H   HNH2  0   0.395   1.6697  -1.8429  -1.9567
 5OD  H15  H   HNH2  0   0.389   0.0946  -2.1153  -2.5181
 5OD  H16  H   HCH2  0   0.262  -3.1446   1.6144   1.4413
 5OD  H17  H   HCH2  0   0.226  -3.8375   0.1115   2.0114
 5OD  H18  H   HNH2  0   0.341  -6.9499  -1.4676   0.6187
 5OD  H19  H   HNH2  0   0.343  -5.5933  -1.2115   1.4514
 5OD  CL1  CL  CL    0  -0.095   2.8356   1.9009  -0.1819

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
 5OD  C23  C12  single    1.523  0.020  1.523
 5OD  C14  C13  single    1.517  0.020  1.517
 5OD  C14  N9   single    1.459  0.020  1.459
 5OD  C13  C12  single    1.535  0.020  1.535
 5OD  N9   C10  single    1.454  0.020  1.454
 5OD  N9   C4   single    1.365  0.020  1.365
 5OD  C12  C11  single    1.528  0.020  1.528
 5OD  C12  N22  single    1.462  0.020  1.462
 5OD  C10  C11  single    1.523  0.020  1.523
 5OD  C3   C4   aromatic  1.413  0.020  1.413
 5OD  C3   N2   aromatic  1.317  0.020  1.317
 5OD  C4   N5   aromatic  1.331  0.020  1.331
 5OD  N2   C1   aromatic  1.321  0.020  1.321
 5OD  N5   C6   aromatic  1.325  0.020  1.325
 5OD  C19  C18  aromatic  1.385  0.020  1.385
 5OD  C19  C8   aromatic  1.394  0.020  1.394
 5OD  C1   C6   aromatic  1.410  0.020  1.410
 5OD  C1   C8   single    1.479  0.020  1.479
 5OD  C18  C17  aromatic  1.385  0.020  1.385
 5OD  C6   N7   single    1.359  0.020  1.359
 5OD  C8   C15  aromatic  1.396  0.020  1.396
 5OD  C17  C16  aromatic  1.386  0.020  1.386
 5OD  C15  C16  aromatic  1.392  0.020  1.392
 5OD  C15  CL1  single    1.722  0.020  1.722
 5OD  C16  CL2  single    1.724  0.020  1.724
 5OD  C3   H1   single    0.930  0.020  1.080
 5OD  C11  H2   single    0.970  0.020  1.090
 5OD  C11  H3   single    0.970  0.020  1.090
 5OD  C13  H4   single    0.970  0.020  1.090
 5OD  C13  H5   single    0.970  0.020  1.090
 5OD  C14  H6   single    0.970  0.020  1.090
 5OD  C14  H7   single    0.970  0.020  1.090
 5OD  C17  H8   single    0.930  0.020  1.080
 5OD  C18  H9   single    0.930  0.020  1.080
 5OD  C19  H10  single    0.930  0.020  1.080
 5OD  C23  H11  single    0.970  0.020  1.090
 5OD  C23  H12  single    0.970  0.020  1.090
 5OD  C23  H13  single    0.970  0.020  1.090
 5OD  N7   H14  single    0.890  0.020  1.040
 5OD  N7   H15  single    0.890  0.020  1.040
 5OD  C10  H16  single    0.970  0.020  1.090
 5OD  C10  H17  single    0.970  0.020  1.090
 5OD  N22  H18  single    0.890  0.020  1.040
 5OD  N22  H19  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
 5OD  C8   C1   C6   122.09  3.000
 5OD  C8   C1   N2   118.57  3.000
 5OD  C6   C1   N2   119.31  3.000
 5OD  H1   C3   C4   122.90  3.000
 5OD  H1   C3   N2   116.54  3.000
 5OD  C4   C3   N2   120.55  3.000
 5OD  H3   C11  H2   107.13  3.000
 5OD  H3   C11  C10  108.35  3.000
 5OD  H2   C11  C10  108.68  3.000
 5OD  H3   C11  C12  110.25  3.000
 5OD  H2   C11  C12  108.48  3.000
 5OD  C10  C11  C12  113.74  3.000
 5OD  N22  C12  C23  107.72  3.000
 5OD  N22  C12  C13  113.64  3.000
 5OD  C23  C12  C13  109.70  3.000
 5OD  N22  C12  C11  109.28  3.000
 5OD  C13  C12  C11  106.54  3.000
 5OD  C23  C12  C11  109.95  3.000
 5OD  H5   C13  H4   106.82  3.000
 5OD  H5   C13  C14  109.11  3.000
 5OD  H4   C13  C14  108.43  3.000
 5OD  H5   C13  C12  109.32  3.000
 5OD  H4   C13  C12  110.15  3.000
 5OD  C14  C13  C12  112.83  3.000
 5OD  H7   C14  H6   106.27  3.000
 5OD  H7   C14  N9   108.71  3.000
 5OD  H6   C14  N9   109.80  3.000
 5OD  H7   C14  C13  109.37  3.000
 5OD  H6   C14  C13  110.45  3.000
 5OD  N9   C14  C13  112.05  3.000
 5OD  CL1  C15  C8   120.03  3.000
 5OD  CL1  C15  C16  119.59  3.000
 5OD  C8   C15  C16  120.37  3.000
 5OD  CL2  C16  C17  119.00  3.000
 5OD  CL2  C16  C15  120.47  3.000
 5OD  C17  C16  C15  120.53  3.000
 5OD  H8   C17  C18  120.73  3.000
 5OD  H8   C17  C16  119.80  3.000
 5OD  C18  C17  C16  119.46  3.000
 5OD  H9   C18  C19  120.21  3.000
 5OD  H9   C18  C17  119.70  3.000
 5OD  C19  C18  C17  120.08  3.000
 5OD  H10  C19  C8   118.92  3.000
 5OD  H10  C19  C18  119.82  3.000
 5OD  C8   C19  C18  121.26  3.000
 5OD  H13  C23  H12  107.98  3.000
 5OD  H13  C23  H11  108.23  3.000
 5OD  H12  C23  H11  107.61  3.000
 5OD  H13  C23  C12  110.97  3.000
 5OD  H12  C23  C12  110.90  3.000
 5OD  H11  C23  C12  111.02  3.000
 5OD  C3   N2   C1   120.46  3.000
 5OD  N9   C4   N5   117.50  3.000
 5OD  N5   C4   C3   119.20  3.000
 5OD  N9   C4   C3   123.30  3.000
 5OD  C6   N5   C4   119.87  3.000
 5OD  N7   C6   N5   117.08  3.000
 5OD  N7   C6   C1   122.29  3.000
 5OD  N5   C6   C1   120.60  3.000
 5OD  H15  N7   H14  114.62  3.000
 5OD  H15  N7   C6   116.23  3.000
 5OD  H14  N7   C6   118.72  3.000
 5OD  C19  C8   C15  118.29  3.000
 5OD  C15  C8   C1   121.92  3.000
 5OD  C19  C8   C1   119.79  3.000
 5OD  C10  N9   C4   119.59  3.000
 5OD  C4   N9   C14  118.38  3.000
 5OD  C10  N9   C14  115.67  3.000
 5OD  H17  C10  H16  106.31  3.000
 5OD  H17  C10  N9   110.64  3.000
 5OD  H16  C10  N9   109.55  3.000
 5OD  H17  C10  C11  111.02  3.000
 5OD  H16  C10  C11  107.06  3.000
 5OD  N9   C10  C11  112.03  3.000
 5OD  H19  N22  H18  105.39  3.000
 5OD  H19  N22  C12  111.22  3.000
 5OD  H18  N22  C12  109.37  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
 5OD  CONST_01  C4   C3   N2   C1      0.00   0.0  0
 5OD  CONST_02  C4   N5   C6   C1      0.00   0.0  0
 5OD  CONST_03  C18  C19  C8   C1    180.00   0.0  0
 5OD  CONST_04  C16  C15  C8   C1    180.00   0.0  0
 5OD  CONST_05  C6   N5   C4   C3      0.00   0.0  0
 5OD  CONST_06  C6   C1   N2   C3      0.00   0.0  0
 5OD  CONST_07  C8   C1   N2   C3    180.00   0.0  0
 5OD  CONST_08  C18  C19  C8   C15     0.00   0.0  0
 5OD  CONST_11  C18  C17  C16  C15     0.00   0.0  0
 5OD  CONST_12  C19  C18  C17  C16     0.00   0.0  0
 5OD  CONST_13  C19  C8   C15  C16     0.00   0.0  0
 5OD  CONST_14  C8   C19  C18  C17     0.00   0.0  0
 5OD  CONST_15  C8   C15  C16  C17     0.00   0.0  0
 5OD  CONST_18  N5   C4   C3   N2      0.00   0.0  0
 5OD  CONST_19  N5   C6   C1   N2      0.00   0.0  0
 5OD  CONST_20  C8   C1   C6   N5    180.00   0.0  0
 5OD  CONST_21  N9   C4   C3   N2    180.00   0.0  0
 5OD  CONST_22  N9   C4   N5   C6    180.00   0.0  0
 5OD  CONST_23  CL1  C15  C8   C1      0.00   0.0  0
 5OD  CONST_24  CL1  C15  C16  C17   180.00   0.0  0
 5OD  CONST_25  CL2  C16  C17  C18   180.00   0.0  0
 5OD  CONST_26  CL1  C15  C8   C19   180.00   0.0  0
 5OD  CONST_27  N7   C6   C1   N2    180.00   0.0  0
 5OD  CONST_28  N7   C6   N5   C4    180.00   0.0  0
 5OD  CONST_29  C8   C1   C6   N7      0.00   0.0  0
 5OD  CONST_30  CL2  C16  C15  C8    180.00   0.0  0
 5OD  CONST_31  H1   C3   N2   C1    180.00   0.0  0
 5OD  CONST_32  H10  C19  C8   C1      0.00   0.0  0
 5OD  CONST_33  H8   C17  C16  C15   180.00   0.0  0
 5OD  CONST_34  H9   C18  C17  C16   180.00   0.0  0
 5OD  CONST_36  H15  N7   C6   C1    180.00   0.0  0
 5OD  Var_01    C14  N9   C4   C3   -159.16  30.0  1
 5OD  Var_02    N9   C14  C13  C12   -54.17  30.0  1
 5OD  Var_03    N9   C10  C11  C12    52.33  30.0  1

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
 5OD  chir_01  C12  C13  C11  N22  positiv

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
 5OD  plan-1  C1   0.020
 5OD  plan-1  C3   0.020
 5OD  plan-1  N2   0.020
 5OD  plan-1  C4   0.020
 5OD  plan-1  N5   0.020
 5OD  plan-1  C6   0.020
 5OD  plan-1  N7   0.020
 5OD  plan-1  C8   0.020
 5OD  plan-1  N9   0.020
 5OD  plan-1  H1   0.020
 5OD  plan-2  C1   0.020
 5OD  plan-2  C15  0.020
 5OD  plan-2  C16  0.020
 5OD  plan-2  C17  0.020
 5OD  plan-2  C18  0.020
 5OD  plan-2  C19  0.020
 5OD  plan-2  C8   0.020
 5OD  plan-2  CL2  0.020
 5OD  plan-2  H8   0.020
 5OD  plan-2  H9   0.020
 5OD  plan-2  H10  0.020
 5OD  plan-2  CL1  0.020
 5OD  plan-3  C6   0.020
 5OD  plan-3  N7   0.020
 5OD  plan-3  H14  0.020
 5OD  plan-3  H15  0.020

