# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 20:48:14 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: 3-(benzyloxy)pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncccc1OCc2ccccc2
#
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
 3IP  3IP  3-(benzyloxy)pyridin-2-amine  ligand  27  15  .  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_3IP
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
 3IP  N1    N  NH2   0  -0.839   2.1321  -0.0132   1.9084
 3IP  C2    C  CR6   0   0.387   0.8907  -0.0091   2.4440
 3IP  N3    N  N     0  -0.453   0.7699  -0.0126   3.7608
 3IP  C4    C  CR16  0  -0.094  -0.4523  -0.0111   4.3023
 3IP  C5    C  CR16  0  -0.347  -1.6088  -0.0053   3.5614
 3IP  C6    C  CR16  0  -0.292  -1.4966  -0.0004   2.1637
 3IP  C7    C  CR6   0   0.257  -0.2482  -0.0025   1.5906
 3IP  O8    O  O2    0  -0.473   0.0267   0.0019   0.2684
 3IP  C9    C  CH2   0  -0.264  -1.0614  -0.0070  -0.6453
 3IP  C10   C  CR6   0   0.099  -0.4795  -0.0107  -2.0257
 3IP  C11   C  CR16  0  -0.292  -0.1904  -1.2121  -2.6657
 3IP  C12   C  CR16  0  -0.242   0.3900  -1.2178  -3.9268
 3IP  C13   C  CR16  0  -0.261   0.6915  -0.0178  -4.5580
 3IP  C14   C  CR16  0  -0.243   0.4053   1.1859  -3.9261
 3IP  C15   C  CR16  0  -0.291  -0.1753   1.1875  -2.6653
 3IP  H1N1  H  HNH2  0   0.390   2.9331  -0.0062   2.5135
 3IP  H1N2  H  HNH2  0   0.398   2.2823   0.0003   0.9172
 3IP  H4    H  HCR6  0   0.248  -0.4909  -0.0150   5.3859
 3IP  H5    H  HCR6  0   0.256  -2.5785  -0.0037   4.0384
 3IP  H6    H  HCR6  0   0.287  -2.3915   0.0048   1.5553
 3IP  H9C1  H  HCH2  0   0.242  -1.6850  -0.8931  -0.4836
 3IP  H9C2  H  HCH2  0   0.242  -1.6930   0.8749  -0.4919
 3IP  H11   H  HCR6  0   0.255  -0.4243  -2.1508  -2.1779
 3IP  H12   H  HCR6  0   0.258   0.6066  -2.1585  -4.4161
 3IP  H13   H  HCR6  0   0.259   1.1442  -0.0202  -5.5411
 3IP  H14   H  HCR6  0   0.258   0.6328   2.1237  -4.4160
 3IP  H15   H  HCR6  0   0.255  -0.3982   2.1291  -2.1779

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
 3IP  N1   C2    single    1.352  0.020  1.352
 3IP  N1   H1N1  single    0.860  0.020  1.020
 3IP  N1   H1N2  single    0.860  0.020  1.020
 3IP  C2   N3    aromatic  1.322  0.020  1.322
 3IP  C2   C7    aromatic  1.423  0.020  1.423
 3IP  N3   C4    aromatic  1.337  0.020  1.337
 3IP  C4   C5    aromatic  1.373  0.020  1.373
 3IP  C4   H4    single    0.930  0.020  1.080
 3IP  C5   C6    aromatic  1.402  0.020  1.402
 3IP  C5   H5    single    0.930  0.020  1.080
 3IP  C6   C7    aromatic  1.374  0.020  1.374
 3IP  C6   H6    single    0.930  0.020  1.080
 3IP  C7   O8    single    1.350  0.020  1.350
 3IP  O8   C9    single    1.421  0.020  1.421
 3IP  C9   C10   single    1.498  0.020  1.498
 3IP  C9   H9C1  single    0.970  0.020  1.090
 3IP  C9   H9C2  single    0.970  0.020  1.090
 3IP  C10  C11   aromatic  1.392  0.020  1.392
 3IP  C10  C15   aromatic  1.392  0.020  1.392
 3IP  C11  C12   aromatic  1.388  0.020  1.388
 3IP  C11  H11   single    0.930  0.020  1.080
 3IP  C12  C13   aromatic  1.389  0.020  1.389
 3IP  C12  H12   single    0.930  0.020  1.080
 3IP  C13  C14   aromatic  1.389  0.020  1.389
 3IP  C13  H13   single    0.930  0.020  1.080
 3IP  C14  C15   aromatic  1.388  0.020  1.388
 3IP  C14  H14   single    0.930  0.020  1.080
 3IP  C15  H15   single    0.930  0.020  1.080

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
 3IP  H1N2  N1   H1N1  118.44  3.000
 3IP  H1N2  N1   C2    121.95  3.000
 3IP  H1N1  N1   C2    119.59  3.000
 3IP  C7    C2   N3    121.61  3.000
 3IP  C7    C2   N1    119.82  3.000
 3IP  N3    C2   N1    118.58  3.000
 3IP  C4    N3   C2    119.14  3.000
 3IP  H4    C4   C5    120.61  3.000
 3IP  H4    C4   N3    115.93  3.000
 3IP  C5    C4   N3    123.45  3.000
 3IP  H5    C5   C6    120.78  3.000
 3IP  H5    C5   C4    121.16  3.000
 3IP  C6    C5   C4    118.06  3.000
 3IP  H6    C6   C7    121.13  3.000
 3IP  H6    C6   C5    119.62  3.000
 3IP  C7    C6   C5    119.25  3.000
 3IP  O8    C7   C6    126.41  3.000
 3IP  O8    C7   C2    115.10  3.000
 3IP  C6    C7   C2    118.49  3.000
 3IP  C9    O8   C7    118.27  3.000
 3IP  H9C2  C9   H9C1  107.60  3.000
 3IP  H9C2  C9   C10   110.79  3.000
 3IP  H9C1  C9   C10   110.80  3.000
 3IP  H9C2  C9   O8    110.27  3.000
 3IP  H9C1  C9   O8    110.24  3.000
 3IP  C10   C9   O8    107.16  3.000
 3IP  C15   C10  C11   119.11  3.000
 3IP  C15   C10  C9    120.42  3.000
 3IP  C11   C10  C9    120.44  3.000
 3IP  H11   C11  C12   119.72  3.000
 3IP  H11   C11  C10   119.74  3.000
 3IP  C12   C11  C10   120.54  3.000
 3IP  H12   C12  C13   120.14  3.000
 3IP  H12   C12  C11   119.86  3.000
 3IP  C13   C12  C11   120.00  3.000
 3IP  H13   C13  C14   120.08  3.000
 3IP  H13   C13  C12   120.11  3.000
 3IP  C14   C13  C12   119.81  3.000
 3IP  H14   C14  C15   119.87  3.000
 3IP  H14   C14  C13   120.11  3.000
 3IP  C15   C14  C13   120.02  3.000
 3IP  H15   C15  C14   119.71  3.000
 3IP  H15   C15  C10   119.77  3.000
 3IP  C14   C15  C10   120.52  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
 3IP  CONST_01  C5    C4   N3   C2      0.00   0.0  0
 3IP  CONST_02  C5    C6   C7   C2      0.00   0.0  0
 3IP  CONST_03  C6    C7   C2   N3      0.00   0.0  0
 3IP  CONST_04  C6    C5   C4   N3      0.00   0.0  0
 3IP  CONST_05  C7    C2   N3   C4      0.00   0.0  0
 3IP  CONST_06  C7    C6   C5   C4      0.00   0.0  0
 3IP  CONST_07  C13   C12  C11  C10     0.00   0.0  0
 3IP  CONST_08  C13   C14  C15  C10     0.00   0.0  0
 3IP  CONST_09  C14   C15  C10  C11     0.00   0.0  0
 3IP  CONST_10  C14   C13  C12  C11     0.00   0.0  0
 3IP  CONST_11  C15   C10  C11  C12     0.00   0.0  0
 3IP  CONST_12  C15   C14  C13  C12     0.00   0.0  0
 3IP  CONST_13  C4    N3   C2   N1    180.00   0.0  0
 3IP  CONST_14  C6    C7   C2   N1    180.00   0.0  0
 3IP  CONST_15  O8    C7   C2   N3    180.00   0.0  0
 3IP  CONST_16  O8    C7   C6   C5    180.00   0.0  0
 3IP  CONST_17  C12   C11  C10  C9    180.00   0.0  0
 3IP  CONST_18  C14   C15  C10  C9    180.00   0.0  0
 3IP  CONST_19  H4    C4   N3   C2    180.00   0.0  0
 3IP  CONST_20  H6    C6   C7   C2    180.00   0.0  0
 3IP  CONST_21  H5    C5   C4   N3    180.00   0.0  0
 3IP  CONST_22  H12   C12  C11  C10   180.00   0.0  0
 3IP  CONST_23  H14   C14  C15  C10   180.00   0.0  0
 3IP  CONST_24  H15   C15  C10  C11   180.00   0.0  0
 3IP  CONST_25  H13   C13  C12  C11   180.00   0.0  0
 3IP  CONST_26  H11   C11  C12  C13   180.00   0.0  0
 3IP  CONST_27  H1N1  N1   C2   N3      0.00   0.0  0
 3IP  CONST_28  H1N2  N1   C2   N3    180.00   0.0  0
 3IP  Var_01    C10   C9   O8   C7   -179.56  30.0  3
 3IP  Var_02    C11   C10  C9   O8     89.48  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
 3IP  plan-1  N1    0.020
 3IP  plan-1  C2    0.020
 3IP  plan-1  N3    0.020
 3IP  plan-1  C4    0.020
 3IP  plan-1  C5    0.020
 3IP  plan-1  C6    0.020
 3IP  plan-1  C7    0.020
 3IP  plan-1  O8    0.020
 3IP  plan-1  H4    0.020
 3IP  plan-1  H5    0.020
 3IP  plan-1  H6    0.020
 3IP  plan-2  C9    0.020
 3IP  plan-2  C10   0.020
 3IP  plan-2  C11   0.020
 3IP  plan-2  C12   0.020
 3IP  plan-2  C13   0.020
 3IP  plan-2  C14   0.020
 3IP  plan-2  C15   0.020
 3IP  plan-2  H11   0.020
 3IP  plan-2  H12   0.020
 3IP  plan-2  H13   0.020
 3IP  plan-2  H14   0.020
 3IP  plan-2  H15   0.020
 3IP  plan-3  N1    0.020
 3IP  plan-3  C2    0.020
 3IP  plan-3  H1N1  0.020
 3IP  plan-3  H1N2  0.020

