# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 04:32:40 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: ~{N}-(phenylmethyl)pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C(Nc1ccccn1)c2ccccc2
#
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
 9VO  9VO  "N-(phenylmethyl)pyridin-2-amine"
  ligand  26  14  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_9VO
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
 9VO  C1   C  CR16  0  -0.367  27.8038   0.5646  -1.2269
 9VO  C2   C  CR16  0  -0.065  26.4372   0.4623  -1.0662
 9VO  C3   C  CR16  0  -0.151  28.4987  -0.6037  -1.5480
 9VO  C4   C  CR16  0  -0.397  27.8138  -1.7874  -1.6862
 9VO  C5   C  CR6   0   0.527  26.4163  -1.7825  -1.4961
 9VO  C8   C  CH2   0  -0.335  24.2761  -2.9883  -1.5083
 9VO  C11  C  CR16  0  -0.240  23.3691  -1.8896  -5.0457
 9VO  C12  C  CR16  0  -0.270  22.0761  -1.4162  -4.8666
 9VO  C13  C  CR16  0  -0.241  21.5114  -1.4378  -3.5979
 9VO  C14  C  CR16  0  -0.301  22.2373  -1.9277  -2.5209
 9VO  N6   N  N     0  -0.468  25.7496  -0.6702  -1.1973
 9VO  C10  C  CR16  0  -0.294  24.0906  -2.3839  -3.9663
 9VO  C9   C  CR6   0   0.098  23.5325  -2.4093  -2.6924
 9VO  N7   N  NH1   0  -0.676  25.7075  -2.9356  -1.5992
 9VO  H1   H  HCR6  0   0.254  28.3073   1.5135  -1.1096
 9VO  H2   H  HCR6  0   0.249  25.8511   1.3417  -0.8193
 9VO  H3   H  HCR6  0   0.263  29.5718  -0.5829  -1.6900
 9VO  H4   H  HCR6  0   0.262  28.3284  -2.7074  -1.9340
 9VO  H5   H  HCH2  0   0.247  23.9416  -2.4878  -0.5970
 9VO  H6   H  HCH2  0   0.269  24.0038  -4.0399  -1.3970
 9VO  H8   H  HCR6  0   0.250  21.5150  -1.0290  -5.7074
 9VO  H9   H  HCR6  0   0.251  20.5056  -1.0674  -3.4448
 9VO  H10  H  HCR6  0   0.244  21.7917  -1.9340  -1.5324
 9VO  H11  H  HCR6  0   0.242  25.0990  -2.7479  -4.1222
 9VO  H12  H  HNH1  0   0.395  26.1963  -3.7611  -1.8988
 9VO  H7   H  HCR6  0   0.250  23.8203  -1.8740  -6.0298

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
 9VO  C12  C11  aromatic  1.389  0.020  1.389
 9VO  C12  C13  aromatic  1.389  0.020  1.389
 9VO  C11  C10  aromatic  1.389  0.020  1.389
 9VO  C13  C14  aromatic  1.388  0.020  1.388
 9VO  C10  C9   aromatic  1.391  0.020  1.391
 9VO  C14  C9   aromatic  1.392  0.020  1.392
 9VO  C9   C8   single    1.513  0.020  1.513
 9VO  C4   C3   aromatic  1.375  0.020  1.375
 9VO  C4   C5   aromatic  1.410  0.020  1.410
 9VO  N7   C8   single    1.435  0.020  1.435
 9VO  N7   C5   single    1.357  0.020  1.357
 9VO  C3   C1   aromatic  1.397  0.020  1.397
 9VO  C5   N6   aromatic  1.331  0.020  1.331
 9VO  C1   C2   aromatic  1.380  0.020  1.380
 9VO  N6   C2   aromatic  1.331  0.020  1.331
 9VO  C1   H1   single    0.930  0.020  1.080
 9VO  C2   H2   single    0.930  0.020  1.080
 9VO  C3   H3   single    0.930  0.020  1.080
 9VO  C4   H4   single    0.930  0.020  1.080
 9VO  C8   H5   single    0.970  0.020  1.090
 9VO  C8   H6   single    0.970  0.020  1.090
 9VO  C11  H7   single    0.930  0.020  1.080
 9VO  C12  H8   single    0.930  0.020  1.080
 9VO  C13  H9   single    0.930  0.020  1.080
 9VO  C14  H10  single    0.930  0.020  1.080
 9VO  C10  H11  single    0.930  0.020  1.080
 9VO  N7   H12  single    0.860  0.020  1.020

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
 9VO  H1   C1   C3   121.85  3.000
 9VO  H1   C1   C2   120.93  3.000
 9VO  C3   C1   C2   117.22  3.000
 9VO  H2   C2   N6   115.64  3.000
 9VO  H2   C2   C1   120.09  3.000
 9VO  N6   C2   C1   124.27  3.000
 9VO  H3   C3   C4   119.81  3.000
 9VO  H3   C3   C1   120.48  3.000
 9VO  C4   C3   C1   119.71  3.000
 9VO  H4   C4   C5   120.31  3.000
 9VO  H4   C4   C3   121.19  3.000
 9VO  C5   C4   C3   118.50  3.000
 9VO  N7   C5   N6   117.74  3.000
 9VO  N6   C5   C4   121.98  3.000
 9VO  N7   C5   C4   120.28  3.000
 9VO  H6   C8   H5   106.25  3.000
 9VO  H6   C8   N7   106.89  3.000
 9VO  H5   C8   N7   109.96  3.000
 9VO  H6   C8   C9   109.01  3.000
 9VO  H5   C8   C9   109.09  3.000
 9VO  N7   C8   C9   115.24  3.000
 9VO  H7   C11  C10  119.66  3.000
 9VO  H7   C11  C12  120.03  3.000
 9VO  C10  C11  C12  120.31  3.000
 9VO  H8   C12  C13  120.29  3.000
 9VO  H8   C12  C11  120.30  3.000
 9VO  C13  C12  C11  119.42  3.000
 9VO  H9   C13  C14  119.79  3.000
 9VO  H9   C13  C12  120.10  3.000
 9VO  C14  C13  C12  120.10  3.000
 9VO  H10  C14  C9   119.51  3.000
 9VO  H10  C14  C13  119.63  3.000
 9VO  C9   C14  C13  120.86  3.000
 9VO  C5   N6   C2   118.31  3.000
 9VO  H11  C10  C9   119.94  3.000
 9VO  H11  C10  C11  119.42  3.000
 9VO  C9   C10  C11  120.64  3.000
 9VO  C10  C9   C14  118.66  3.000
 9VO  C14  C9   C8   119.54  3.000
 9VO  C10  C9   C8   121.76  3.000
 9VO  H12  N7   C8   118.27  3.000
 9VO  H12  N7   C5   117.80  3.000
 9VO  C8   N7   C5   123.17  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
 9VO  CONST_01  C5   C4   C3   C1      0.00   0.0  0
 9VO  CONST_02  C5   N6   C2   C1      0.00   0.0  0
 9VO  CONST_03  C4   C3   C1   C2      0.00   0.0  0
 9VO  CONST_04  C4   C5   N6   C2      0.00   0.0  0
 9VO  CONST_05  N6   C5   C4   C3      0.00   0.0  0
 9VO  CONST_06  N6   C2   C1   C3      0.00   0.0  0
 9VO  CONST_07  C14  C13  C12  C11     0.00   0.0  0
 9VO  CONST_08  C14  C9   C10  C11     0.00   0.0  0
 9VO  CONST_09  C9   C10  C11  C12     0.00   0.0  0
 9VO  CONST_10  C9   C14  C13  C12     0.00   0.0  0
 9VO  CONST_11  C10  C11  C12  C13     0.00   0.0  0
 9VO  CONST_12  C10  C9   C14  C13     0.00   0.0  0
 9VO  CONST_13  N7   C5   N6   C2    180.00   0.0  0
 9VO  CONST_14  N7   C5   C4   C3    180.00   0.0  0
 9VO  CONST_15  C11  C10  C9   C8    180.00   0.0  0
 9VO  CONST_16  C13  C14  C9   C8    180.00   0.0  0
 9VO  CONST_17  H4   C4   C3   C1    180.00   0.0  0
 9VO  CONST_18  H3   C3   C1   C2    180.00   0.0  0
 9VO  CONST_19  H2   C2   C1   C3    180.00   0.0  0
 9VO  CONST_20  H1   C1   C3   C4    180.00   0.0  0
 9VO  CONST_21  H3   C3   C4   C5    180.00   0.0  0
 9VO  CONST_22  H2   C2   N6   C5    180.00   0.0  0
 9VO  CONST_23  H9   C13  C12  C11   180.00   0.0  0
 9VO  CONST_24  H11  C10  C11  C12   180.00   0.0  0
 9VO  CONST_25  H10  C14  C13  C12   180.00   0.0  0
 9VO  CONST_26  H7   C11  C12  C13   180.00   0.0  0
 9VO  CONST_27  H8   C12  C13  C14   180.00   0.0  0
 9VO  CONST_28  H11  C10  C9   C14   180.00   0.0  0
 9VO  CONST_29  H4   C4   C5   N6    180.00   0.0  0
 9VO  CONST_30  H1   C1   C2   N6    180.00   0.0  0
 9VO  CONST_31  H8   C12  C11  C10   180.00   0.0  0
 9VO  CONST_32  H10  C14  C9   C10   180.00   0.0  0
 9VO  CONST_33  H7   C11  C10  C9    180.00   0.0  0
 9VO  CONST_34  H9   C13  C14  C9    180.00   0.0  0
 9VO  CONST_35  C8   N7   C5   C4    180.00   0.0  0
 9VO  CONST_36  N6   C5   N7   C8      0.00   0.0  0
 9VO  CONST_37  H12  N7   C5   C4      0.00   0.0  0
 9VO  CONST_38  H12  N7   C5   N6    180.00   0.0  0
 9VO  Var_01    C9   C8   N7   C5     71.33  30.0  3
 9VO  Var_02    N7   C8   C9   C14  -154.88  30.0  2
 9VO  Var_03    N7   C8   C9   C10    27.33  30.0  2
 9VO  Var_04    H5   C8   C9   C14   -30.64  30.0  2
 9VO  Var_05    H6   C8   C9   C14    84.98  30.0  2
 9VO  Var_06    H5   C8   C9   C10   151.56  30.0  2
 9VO  Var_07    H6   C8   C9   C10   -92.82  30.0  2
 9VO  Var_08    H5   C8   N7   C5    -52.45  30.0  3
 9VO  Var_09    H6   C8   N7   C5   -167.37  30.0  3
 9VO  Var_10    H12  N7   C8   C9    -98.51  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
 9VO  plan-1  C1   0.020
 9VO  plan-1  C2   0.020
 9VO  plan-1  C3   0.020
 9VO  plan-1  C4   0.020
 9VO  plan-1  C5   0.020
 9VO  plan-1  N6   0.020
 9VO  plan-1  N7   0.020
 9VO  plan-1  H1   0.020
 9VO  plan-1  H2   0.020
 9VO  plan-1  H3   0.020
 9VO  plan-1  H4   0.020
 9VO  plan-2  C8   0.020
 9VO  plan-2  C11  0.020
 9VO  plan-2  C12  0.020
 9VO  plan-2  C13  0.020
 9VO  plan-2  C14  0.020
 9VO  plan-2  C10  0.020
 9VO  plan-2  C9   0.020
 9VO  plan-2  H8   0.020
 9VO  plan-2  H9   0.020
 9VO  plan-2  H10  0.020
 9VO  plan-2  H11  0.020
 9VO  plan-2  H7   0.020
 9VO  plan-3  C5   0.020
 9VO  plan-3  C8   0.020
 9VO  plan-3  N7   0.020
 9VO  plan-3  H12  0.020

