# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 12:04:19 2022
#   Inital geometry file: a 59 line input string
#   Ligand name: 2-(pyridin-2-ylmethylamino)ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CNCc1ccccn1
#
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
 SGK  SGK  "2-(pyridin-2-ylmethylamino)ethanoic acid"  ligand  21  12  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SGK
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
 SGK  C    C  C      0   0.390  -23.0756  57.1014  -36.2204
 SGK  O    O  O      0  -0.601  -23.9966  56.2630  -36.2608
 SGK  CH3  C  CH2    0  -0.407  -23.3761  58.5093  -36.7740
 SGK  C2   C  CH2    0  -0.350  -25.0818  59.9177  -37.7476
 SGK  C3   C  CR6    0   0.247  -24.2190  60.6811  -38.7211
 SGK  C4   C  CR16   0  -0.340  -23.4689  61.7786  -38.3125
 SGK  C5   C  CR16   0  -0.149  -22.6707  62.4365  -39.2366
 SGK  C6   C  CR16   0  -0.329  -22.6486  61.9758  -40.5429
 SGK  C7   C  CR16   0  -0.081  -23.4351  60.8764  -40.8585
 SGK  N1   N  NH1    0  -0.589  -24.5897  58.5710  -37.5582
 SGK  N8   N  N      0  -0.411  -24.1989  60.2431  -39.9792
 SGK  O1   O  OC    -1  -0.615  -21.9338  56.9451  -35.7460
 SGK  H1   H  HCH2   0   0.213  -22.5248  58.8391  -37.3780
 SGK  H2   H  HCH2   0   0.187  -23.4026  59.1974  -35.9084
 SGK  H3   H  HCH2   0   0.202  -25.1413  60.4899  -36.8076
 SGK  H4   H  HCH2   0   0.244  -26.0963  59.8621  -38.1511
 SGK  H5   H  HCR6   0   0.262  -23.5073  62.1063  -37.2816
 SGK  H6   H  HCR6   0   0.269  -22.0748  63.2899  -38.9394
 SGK  H7   H  HCR6   0   0.265  -22.0423  62.4511  -41.3018
 SGK  H8   H  HCR6   0   0.256  -23.4478  60.4919  -41.8731
 SGK  H9   H  HNH1   0   0.338  -25.2931  58.0047  -37.1030

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
 SGK  C7   C6   aromatic  1.388  0.020  1.388
 SGK  C7   N8   aromatic  1.326  0.020  1.326
 SGK  C6   C5   aromatic  1.385  0.020  1.385
 SGK  N8   C3   aromatic  1.332  0.020  1.332
 SGK  C5   C4   aromatic  1.387  0.020  1.387
 SGK  C3   C4   aromatic  1.391  0.020  1.391
 SGK  C3   C2   single    1.508  0.020  1.508
 SGK  C2   N1   single    1.446  0.020  1.446
 SGK  N1   CH3  single    1.446  0.020  1.446
 SGK  O    C    deloc     1.246  0.020  1.246
 SGK  CH3  C    single    1.542  0.020  1.542
 SGK  C    O1   deloc     1.246  0.020  1.246
 SGK  CH3  H1   single    0.970  0.020  1.090
 SGK  CH3  H2   single    0.970  0.020  1.090
 SGK  C2   H3   single    0.970  0.020  1.090
 SGK  C2   H4   single    0.970  0.020  1.090
 SGK  C4   H5   single    0.930  0.020  1.080
 SGK  C5   H6   single    0.930  0.020  1.080
 SGK  C6   H7   single    0.930  0.020  1.080
 SGK  C7   H8   single    0.930  0.020  1.080
 SGK  N1   H9   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
 SGK  O1   C    CH3  115.45  3.000
 SGK  O1   C    O    127.23  3.000
 SGK  CH3  C    O    117.29  3.000
 SGK  H2   CH3  H1   105.25  3.000
 SGK  H2   CH3  N1   112.19  3.000
 SGK  H1   CH3  N1   109.91  3.000
 SGK  H2   CH3  C    106.95  3.000
 SGK  H1   CH3  C    108.76  3.000
 SGK  N1   CH3  C    113.39  3.000
 SGK  H4   C2   H3   106.92  3.000
 SGK  H4   C2   N1   108.47  3.000
 SGK  H3   C2   N1   112.96  3.000
 SGK  H4   C2   C3   108.56  3.000
 SGK  H3   C2   C3   108.57  3.000
 SGK  N1   C2   C3   111.17  3.000
 SGK  N8   C3   C4   121.92  3.000
 SGK  C4   C3   C2   121.22  3.000
 SGK  N8   C3   C2   116.85  3.000
 SGK  H5   C4   C5   120.75  3.000
 SGK  H5   C4   C3   119.97  3.000
 SGK  C5   C4   C3   119.27  3.000
 SGK  H6   C5   C6   120.81  3.000
 SGK  H6   C5   C4   120.52  3.000
 SGK  C6   C5   C4   118.66  3.000
 SGK  H7   C6   C7   120.41  3.000
 SGK  H7   C6   C5   121.64  3.000
 SGK  C7   C6   C5   117.95  3.000
 SGK  H8   C7   N8   116.37  3.000
 SGK  H8   C7   C6   119.99  3.000
 SGK  N8   C7   C6   123.64  3.000
 SGK  H9   N1   C2   110.10  3.000
 SGK  H9   N1   CH3  108.41  3.000
 SGK  C2   N1   CH3  113.35  3.000
 SGK  C7   N8   C3   118.55  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
 SGK  CONST_01  C6  C7   N8   C3      0.00   0.0  0
 SGK  CONST_02  C6  C5   C4   C3      0.00   0.0  0
 SGK  CONST_03  C7  C6   C5   C4      0.00   0.0  0
 SGK  CONST_04  C7  N8   C3   C4      0.00   0.0  0
 SGK  CONST_05  N8  C7   C6   C5      0.00   0.0  0
 SGK  CONST_06  N8  C3   C4   C5      0.00   0.0  0
 SGK  CONST_07  C7  N8   C3   C2    180.00   0.0  0
 SGK  CONST_08  C5  C4   C3   C2    180.00   0.0  0
 SGK  CONST_09  H8  C7   N8   C3    180.00   0.0  0
 SGK  CONST_10  H6  C5   C4   C3    180.00   0.0  0
 SGK  CONST_11  H7  C6   C5   C4    180.00   0.0  0
 SGK  CONST_12  H8  C7   C6   C5    180.00   0.0  0
 SGK  CONST_13  H5  C4   C5   C6    180.00   0.0  0
 SGK  CONST_14  H6  C5   C6   C7    180.00   0.0  0
 SGK  CONST_15  H7  C6   C7   N8    180.00   0.0  0
 SGK  CONST_16  H5  C4   C3   N8    180.00   0.0  0
 SGK  Var_01    N1  C2   C3   C4   -114.10  30.0  2
 SGK  Var_02    N8  C3   C2   N1     65.07  30.0  2
 SGK  Var_03    H3  C2   C3   C4     10.76  30.0  2
 SGK  Var_04    H4  C2   C3   C4    126.66  30.0  2
 SGK  Var_05    H3  C2   C3   N8   -170.07  30.0  2
 SGK  Var_06    H4  C2   C3   N8    -54.18  30.0  2
 SGK  Var_07    C3  C2   N1   CH3    72.91  30.0  1
 SGK  Var_08    H9  N1   C2   C3   -165.48  30.0  3
 SGK  Var_09    C2  N1   CH3  C     163.02  30.0  1
 SGK  Var_10    N1  CH3  C    O     -14.08  30.0  2
 SGK  Var_11    O1  C    CH3  N1    167.77  30.0  3
 SGK  Var_12    H9  N1   CH3  C      40.47  30.0  1
 SGK  Var_13    H1  CH3  C    O    -136.67  30.0  2
 SGK  Var_14    H2  CH3  C    O     110.13  30.0  2
 SGK  Var_15    H3  C2   N1   CH3   -49.44  30.0  1
 SGK  Var_16    H4  C2   N1   CH3  -167.80  30.0  1
 SGK  Var_17    H1  CH3  N1   C2    -75.02  30.0  3
 SGK  Var_18    H2  CH3  N1   C2     41.72  30.0  3
 SGK  Var_19    H1  CH3  C    O1     45.17  30.0  2
 SGK  Var_20    H2  CH3  C    O1    -68.03  30.0  2

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
 SGK  plan-1  C2   0.020
 SGK  plan-1  C3   0.020
 SGK  plan-1  C4   0.020
 SGK  plan-1  C5   0.020
 SGK  plan-1  C6   0.020
 SGK  plan-1  C7   0.020
 SGK  plan-1  N8   0.020
 SGK  plan-1  H5   0.020
 SGK  plan-1  H6   0.020
 SGK  plan-1  H7   0.020
 SGK  plan-1  H8   0.020
 SGK  plan-2  C    0.020
 SGK  plan-2  O    0.020
 SGK  plan-2  CH3  0.020
 SGK  plan-2  O1   0.020

