# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 22:59:04 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 3-(5-amino-6-{[(1R)-1-phenylethyl]amino}pyrazin-2-yl)-4-chlorobenzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](Nc1nc(cnc1N)c2cc(ccc2Cl)C(O)=O)c3ccccc3
#
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
 22Y  22Y  '3-(5-amino-6-{[(1R)-1-phenylethyl]amino}pyrazin-2-yl)-4-chlorobenzoic acid'  ligand  42  26  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_22Y
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
 22Y  C1   C   CH3    0  -0.656   2.5129   1.0864  -1.5541
 22Y  C2   C   CH1    0  -0.121   2.6868   0.3955  -0.2033
 22Y  C4   C   CR6    0   0.107   4.0993   0.5658   0.3012
 22Y  C5   C   CR16   0  -0.319   4.3683   1.4530   1.3381
 22Y  C6   C   CR16   0  -0.238   5.6683   1.6496   1.7869
 22Y  C7   C   CR16   0  -0.269   6.7181   0.9534   1.2044
 22Y  C8   C   CR16   0  -0.238   6.4592   0.0625   0.1700
 22Y  C9   C   CR16   0  -0.303   5.1605  -0.1267  -0.2811
 22Y  N10  N   NH1    0  -0.701   2.3816  -1.0273  -0.2958
 22Y  C11  C   CR6    0   0.413   1.0843  -1.4612  -0.3351
 22Y  C12  C   CR6    0   0.357   0.8293  -2.8737  -0.3197
 22Y  N13  N   N      0  -0.404  -0.3985  -3.3240  -0.3016
 22Y  C14  C   CR16   0  -0.151  -1.4022  -2.4340  -0.3363
 22Y  C15  C   CR6    0   0.146  -1.1636  -1.0837  -0.4115
 22Y  N16  N   N      0  -0.417   0.0949  -0.6088  -0.3963
 22Y  C17  C   CR6    0   0.165  -2.2731  -0.1104  -0.4691
 22Y  C18  C   CR16   0  -0.361  -3.2521  -0.1168   0.5230
 22Y  C19  C   CR6    0  -0.065  -4.3149   0.7791   0.5264
 22Y  C20  C   CR16   0  -0.313  -4.3924   1.7137  -0.5008
 22Y  C21  C   CR16   0  -0.186  -3.4446   1.7386  -1.5112
 22Y  C22  C   CR6    0  -0.124  -2.3983   0.8297  -1.4916
 22Y  CL1  CL  CL     0  -0.126  -1.2806   0.8454  -2.8176
 22Y  C24  C   C      0   0.400  -5.3639   0.7411   1.6321
 22Y  O25  O   OC    -1  -0.590  -6.2553   1.6087   1.5790
 22Y  O26  O   O      0  -0.589  -5.2385  -0.1542   2.4885
 22Y  N27  N   NH2    0  -0.836   1.8822  -3.7493  -0.2668
 22Y  H1   H   HCH3   0   0.223   3.1770   0.6501  -2.3012
 22Y  H2   H   HCH3   0   0.246   1.4872   0.9980  -1.9080
 22Y  H3   H   HCH3   0   0.231   2.7498   2.1468  -1.4639
 22Y  H4   H   HCH1   0   0.245   2.0061   0.8726   0.5119
 22Y  H5   H   HCR6   0   0.252   3.5523   1.9955   1.8008
 22Y  H6   H   HCR6   0   0.256   5.8567   2.3420   2.5973
 22Y  H7   H   HCR6   0   0.256   7.7310   1.1000   1.5560
 22Y  H8   H   HCR6   0   0.256   7.2710  -0.4877  -0.2882
 22Y  H9   H   HCR6   0   0.257   4.9780  -0.8228  -1.0920
 22Y  H10  H   HNH1   0   0.389   2.9931  -1.6201   0.2481
 22Y  H11  H   HCR6   0   0.257  -2.4107  -2.8294  -0.3312
 22Y  H12  H   HCR6   0   0.248  -3.1690  -0.8383   1.3256
 22Y  H13  H   HCR6   0   0.256  -5.2058   2.4258  -0.5189
 22Y  H14  H   HCR6   0   0.273  -3.5233   2.4559  -2.3173
 22Y  H16  H   HNH2   0   0.387   2.6866  -3.5074  -0.8272
 22Y  H17  H   HNH2   0   0.387   1.6188  -4.7160  -0.3872

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
 22Y  C8   C9   aromatic  1.388  0.020  1.388
 22Y  C8   C7   aromatic  1.389  0.020  1.389
 22Y  C9   C4   aromatic  1.395  0.020  1.395
 22Y  C21  C20  aromatic  1.386  0.020  1.386
 22Y  C21  C22  aromatic  1.386  0.020  1.386
 22Y  C20  C19  aromatic  1.391  0.020  1.391
 22Y  CL1  C22  single    1.734  0.020  1.734
 22Y  C7   C6   aromatic  1.388  0.020  1.388
 22Y  C1   C2   single    1.527  0.020  1.527
 22Y  C22  C17  aromatic  1.395  0.020  1.395
 22Y  O26  C24  deloc     1.245  0.020  1.245
 22Y  C4   C2   single    1.510  0.020  1.510
 22Y  C4   C5   aromatic  1.391  0.020  1.391
 22Y  C2   N10  single    1.458  0.020  1.458
 22Y  C19  C24  single    1.525  0.020  1.525
 22Y  C19  C18  aromatic  1.390  0.020  1.390
 22Y  C24  O25  deloc     1.245  0.020  1.245
 22Y  C6   C5   aromatic  1.389  0.020  1.389
 22Y  C17  C18  aromatic  1.394  0.020  1.394
 22Y  C17  C15  single    1.477  0.020  1.477
 22Y  N16  C15  aromatic  1.345  0.020  1.345
 22Y  N16  C11  aromatic  1.307  0.020  1.307
 22Y  N10  C11  single    1.368  0.020  1.368
 22Y  C15  C14  aromatic  1.373  0.020  1.373
 22Y  C11  C12  aromatic  1.435  0.020  1.435
 22Y  C14  N13  aromatic  1.342  0.020  1.342
 22Y  C12  N13  aromatic  1.308  0.020  1.308
 22Y  C12  N27  single    1.370  0.020  1.370
 22Y  C1   H1   single    0.970  0.020  1.090
 22Y  C1   H2   single    0.970  0.020  1.090
 22Y  C1   H3   single    0.970  0.020  1.090
 22Y  C2   H4   single    0.970  0.020  1.090
 22Y  C5   H5   single    0.930  0.020  1.080
 22Y  C6   H6   single    0.930  0.020  1.080
 22Y  C7   H7   single    0.930  0.020  1.080
 22Y  C8   H8   single    0.930  0.020  1.080
 22Y  C9   H9   single    0.930  0.020  1.080
 22Y  N10  H10  single    0.890  0.020  1.040
 22Y  C14  H11  single    0.930  0.020  1.080
 22Y  C18  H12  single    0.930  0.020  1.080
 22Y  C20  H13  single    0.930  0.020  1.080
 22Y  C21  H14  single    0.930  0.020  1.080
 22Y  N27  H16  single    0.890  0.020  1.040
 22Y  N27  H17  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
 22Y  H3   C1   H2   108.09  3.000
 22Y  H3   C1   H1   108.27  3.000
 22Y  H2   C1   H1   108.58  3.000
 22Y  H3   C1   C2   110.00  3.000
 22Y  H2   C1   C2   110.98  3.000
 22Y  H1   C1   C2   110.83  3.000
 22Y  H4   C2   N10  109.63  3.000
 22Y  H4   C2   C4   108.28  3.000
 22Y  N10  C2   C4   109.10  3.000
 22Y  H4   C2   C1   108.03  3.000
 22Y  N10  C2   C1   111.19  3.000
 22Y  C4   C2   C1   110.56  3.000
 22Y  C9   C4   C5   118.74  3.000
 22Y  C5   C4   C2   120.14  3.000
 22Y  C9   C4   C2   121.09  3.000
 22Y  H5   C5   C6   119.72  3.000
 22Y  H5   C5   C4   119.47  3.000
 22Y  C6   C5   C4   120.81  3.000
 22Y  H6   C6   C7   120.23  3.000
 22Y  H6   C6   C5   119.69  3.000
 22Y  C7   C6   C5   120.08  3.000
 22Y  H7   C7   C8   120.21  3.000
 22Y  H7   C7   C6   120.24  3.000
 22Y  C8   C7   C6   119.55  3.000
 22Y  H8   C8   C9   119.66  3.000
 22Y  H8   C8   C7   120.09  3.000
 22Y  C9   C8   C7   120.25  3.000
 22Y  H9   C9   C8   119.22  3.000
 22Y  H9   C9   C4   120.21  3.000
 22Y  C8   C9   C4   120.57  3.000
 22Y  H10  N10  C11  113.77  3.000
 22Y  H10  N10  C2   114.31  3.000
 22Y  C11  N10  C2   120.64  3.000
 22Y  N16  C11  C12  120.51  3.000
 22Y  C12  C11  N10  118.69  3.000
 22Y  N16  C11  N10  120.80  3.000
 22Y  N27  C12  N13  120.05  3.000
 22Y  N27  C12  C11  119.52  3.000
 22Y  N13  C12  C11  120.37  3.000
 22Y  C14  N13  C12  118.26  3.000
 22Y  H11  C14  C15  121.39  3.000
 22Y  H11  C14  N13  117.01  3.000
 22Y  C15  C14  N13  121.58  3.000
 22Y  C17  C15  N16  118.07  3.000
 22Y  N16  C15  C14  120.60  3.000
 22Y  C17  C15  C14  121.30  3.000
 22Y  C15  N16  C11  118.58  3.000
 22Y  C22  C17  C18  117.51  3.000
 22Y  C18  C17  C15  119.79  3.000
 22Y  C22  C17  C15  122.70  3.000
 22Y  H12  C18  C19  119.11  3.000
 22Y  H12  C18  C17  118.48  3.000
 22Y  C19  C18  C17  122.40  3.000
 22Y  C24  C19  C20  120.93  3.000
 22Y  C24  C19  C18  120.79  3.000
 22Y  C20  C19  C18  118.28  3.000
 22Y  H13  C20  C21  119.38  3.000
 22Y  H13  C20  C19  119.79  3.000
 22Y  C21  C20  C19  120.83  3.000
 22Y  H14  C21  C22  120.02  3.000
 22Y  H14  C21  C20  120.36  3.000
 22Y  C22  C21  C20  119.62  3.000
 22Y  CL1  C22  C21  118.02  3.000
 22Y  CL1  C22  C17  120.58  3.000
 22Y  C21  C22  C17  121.34  3.000
 22Y  O26  C24  O25  127.04  3.000
 22Y  O25  C24  C19  116.38  3.000
 22Y  O26  C24  C19  116.57  3.000
 22Y  H17  N27  H16  111.79  3.000
 22Y  H17  N27  C12  114.02  3.000
 22Y  H16  N27  C12  115.95  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
 22Y  CONST_01  C7   C8   C9   C4     0.00   0.0  0
 22Y  CONST_02  C7   C6   C5   C4     0.00   0.0  0
 22Y  CONST_03  C8   C9   C4   C5     0.00   0.0  0
 22Y  CONST_04  C8   C7   C6   C5     0.00   0.0  0
 22Y  CONST_05  C9   C8   C7   C6     0.00   0.0  0
 22Y  CONST_06  C9   C4   C5   C6     0.00   0.0  0
 22Y  CONST_07  C17  C15  N16  C11  180.00   0.0  0
 22Y  CONST_08  C14  C15  N16  C11    0.00   0.0  0
 22Y  CONST_09  C14  N13  C12  C11    0.00   0.0  0
 22Y  CONST_10  C15  N16  C11  C12    0.00   0.0  0
 22Y  CONST_11  C15  C14  N13  C12    0.00   0.0  0
 22Y  CONST_12  C17  C15  C14  N13  180.00   0.0  0
 22Y  CONST_13  N16  C15  C14  N13    0.00   0.0  0
 22Y  CONST_14  N16  C11  C12  N13    0.00   0.0  0
 22Y  CONST_17  C21  C22  C17  C15  180.00   0.0  0
 22Y  CONST_18  C19  C18  C17  C15  180.00   0.0  0
 22Y  CONST_21  C20  C21  C22  C17    0.00   0.0  0
 22Y  CONST_22  C20  C19  C18  C17    0.00   0.0  0
 22Y  CONST_23  C21  C20  C19  C18    0.00   0.0  0
 22Y  CONST_24  C21  C22  C17  C18    0.00   0.0  0
 22Y  CONST_25  C22  C21  C20  C19    0.00   0.0  0
 22Y  CONST_26  C22  C17  C18  C19    0.00   0.0  0
 22Y  CONST_27  C8   C9   C4   C2   180.00   0.0  0
 22Y  CONST_28  C6   C5   C4   C2   180.00   0.0  0
 22Y  CONST_29  C15  N16  C11  N10  180.00   0.0  0
 22Y  CONST_30  N13  C12  C11  N10  180.00   0.0  0
 22Y  CONST_31  N27  C12  N13  C14  180.00   0.0  0
 22Y  CONST_32  CL1  C22  C17  C15    0.00   0.0  0
 22Y  CONST_33  N27  C12  C11  N16  180.00   0.0  0
 22Y  CONST_34  C24  C19  C18  C17  180.00   0.0  0
 22Y  CONST_35  CL1  C22  C17  C18  180.00   0.0  0
 22Y  CONST_36  CL1  C22  C21  C20  180.00   0.0  0
 22Y  CONST_37  C24  C19  C20  C21  180.00   0.0  0
 22Y  CONST_38  H8   C8   C9   C4   180.00   0.0  0
 22Y  CONST_39  H6   C6   C5   C4   180.00   0.0  0
 22Y  CONST_40  H9   C9   C4   C5   180.00   0.0  0
 22Y  CONST_41  H7   C7   C6   C5   180.00   0.0  0
 22Y  CONST_42  H5   C5   C6   C7   180.00   0.0  0
 22Y  CONST_43  H11  C14  N13  C12  180.00   0.0  0
 22Y  CONST_44  H12  C18  C17  C15    0.00   0.0  0
 22Y  CONST_45  H14  C21  C22  C17  180.00   0.0  0
 22Y  CONST_46  H13  C20  C19  C18  180.00   0.0  0
 22Y  CONST_47  N16  C11  N10  C2     0.00   0.0  0
 22Y  CONST_48  C12  C11  N10  C2   180.00   0.0  0
 22Y  CONST_50  H17  N27  C12  C11  180.00   0.0  0
 22Y  Var_01    O26  C24  C19  C18   -2.41  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
 22Y  chir_01  C2  C1  C4  N10  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
 22Y  plan-1  C2   0.020
 22Y  plan-1  C4   0.020
 22Y  plan-1  C5   0.020
 22Y  plan-1  C6   0.020
 22Y  plan-1  C7   0.020
 22Y  plan-1  C8   0.020
 22Y  plan-1  C9   0.020
 22Y  plan-1  H5   0.020
 22Y  plan-1  H6   0.020
 22Y  plan-1  H7   0.020
 22Y  plan-1  H8   0.020
 22Y  plan-1  H9   0.020
 22Y  plan-2  N10  0.020
 22Y  plan-2  C11  0.020
 22Y  plan-2  C12  0.020
 22Y  plan-2  N13  0.020
 22Y  plan-2  C14  0.020
 22Y  plan-2  C15  0.020
 22Y  plan-2  N16  0.020
 22Y  plan-2  C17  0.020
 22Y  plan-2  N27  0.020
 22Y  plan-2  H11  0.020
 22Y  plan-3  C15  0.020
 22Y  plan-3  C17  0.020
 22Y  plan-3  C18  0.020
 22Y  plan-3  C19  0.020
 22Y  plan-3  C20  0.020
 22Y  plan-3  C21  0.020
 22Y  plan-3  C22  0.020
 22Y  plan-3  CL1  0.020
 22Y  plan-3  C24  0.020
 22Y  plan-3  H12  0.020
 22Y  plan-3  H13  0.020
 22Y  plan-3  H14  0.020
 22Y  plan-4  C2   0.020
 22Y  plan-4  N10  0.020
 22Y  plan-4  C11  0.020
 22Y  plan-4  H10  0.020
 22Y  plan-5  C12  0.020
 22Y  plan-5  N27  0.020
 22Y  plan-5  H16  0.020
 22Y  plan-5  H17  0.020
 22Y  plan-6  C19  0.020
 22Y  plan-6  C24  0.020
 22Y  plan-6  O25  0.020
 22Y  plan-6  O26  0.020

