# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 16:26:40 2022
#   Inital geometry file: a 83 line input string
#   Ligand name: 5-azanyl-2-(pyridin-3-ylmethylamino)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc(NCc2cccnc2)c(c1)C(O)=O
#
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
 T2E  T2E  "5-azanyl-2-(pyridin-3-ylmethylamino)benzoic acid"  ligand  30  18  .  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_T2E
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
 T2E  C10  C  CR16   0  -0.281   5.1450  -6.2660  6.2552
 T2E  C13  C  CR16   0  -0.375   6.7178  -4.7882  7.9497
 T2E  C15  C  C      0   0.356   6.6240  -2.7517  6.5032
 T2E  C01  C  CR16   0  -0.321   1.1538  -5.5204  6.9957
 T2E  C02  C  CR16   0  -0.172   2.2074  -4.6869  6.6540
 T2E  C03  C  CR6    0   0.014   2.4794  -4.4453  5.3114
 T2E  C04  C  CR16   0  -0.102   1.6529  -5.0654  4.3789
 T2E  C06  C  CR16   0  -0.075   0.4008  -6.0859  5.9774
 T2E  C07  C  CH2    0  -0.406   3.6516  -3.6086  4.8745
 T2E  C09  C  CR6    0   0.178   5.4052  -4.9350  5.9340
 T2E  C11  C  CR16   0  -0.341   5.6506  -6.8588  7.4013
 T2E  C12  C  CR6    0   0.295   6.4352  -6.1150  8.2848
 T2E  C14  C  CR6    0  -0.028   6.2159  -4.1891  6.7994
 T2E  N05  N  N      0  -0.401   0.6382  -5.8629  4.6897
 T2E  N08  N  NH1    0  -0.647   4.9022  -4.3592  4.7368
 T2E  N18  N  NH2    0  -0.864   6.8897  -6.6611  9.4768
 T2E  O16  O  OC    -1  -0.592   7.8268  -2.5805  6.2357
 T2E  O17  O  O      0  -0.588   5.7355  -1.8818  6.5857
 T2E  H1   H  HCR6   0   0.239   4.5330  -6.8602  5.5851
 T2E  H2   H  HCR6   0   0.238   7.3585  -4.2114  8.6096
 T2E  H5   H  HCR6   0   0.252   1.8245  -4.8981  3.3187
 T2E  H6   H  HCR6   0   0.257  -0.4313  -6.7412  6.2112
 T2E  H7   H  HCH2   0   0.262   3.8258  -2.8026  5.5841
 T2E  H8   H  HCH2   0   0.239   3.4338  -3.1506  3.9069
 T2E  H9   H  HCR6   0   0.243   5.4278  -7.8978  7.6153
 T2E  H10  H  HNH1   0   0.350   4.7749  -5.0803  4.0372
 T2E  H11  H  HNH2   0   0.370   6.9889  -7.6643  9.4698
 T2E  H12  H  HNH2   0   0.370   7.7179  -6.2239  9.8503
 T2E  H3   H  HCR6   0   0.265   0.9155  -5.7285  8.0301
 T2E  H4   H  HCR6   0   0.264   2.8102  -4.2211  7.4244

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
 T2E  N05  C04  aromatic  1.327  0.020  1.327
 T2E  N05  C06  aromatic  1.328  0.020  1.328
 T2E  C04  C03  aromatic  1.392  0.020  1.392
 T2E  C06  C01  aromatic  1.387  0.020  1.387
 T2E  O17  C15  deloc     1.246  0.020  1.246
 T2E  N08  C07  single    1.465  0.020  1.465
 T2E  N08  C09  single    1.421  0.020  1.421
 T2E  C03  C07  single    1.505  0.020  1.505
 T2E  C03  C02  aromatic  1.391  0.020  1.391
 T2E  O16  C15  deloc     1.244  0.020  1.244
 T2E  C15  C14  single    1.523  0.020  1.523
 T2E  C01  C02  aromatic  1.386  0.020  1.386
 T2E  C09  C14  aromatic  1.401  0.020  1.401
 T2E  C09  C10  aromatic  1.394  0.020  1.394
 T2E  C14  C13  aromatic  1.391  0.020  1.391
 T2E  C10  C11  aromatic  1.386  0.020  1.386
 T2E  C13  C12  aromatic  1.397  0.020  1.397
 T2E  C11  C12  aromatic  1.396  0.020  1.396
 T2E  C12  N18  single    1.388  0.020  1.388
 T2E  C10  H1   single    0.930  0.020  1.080
 T2E  C13  H2   single    0.930  0.020  1.080
 T2E  C01  H3   single    0.930  0.020  1.080
 T2E  C02  H4   single    0.930  0.020  1.080
 T2E  C04  H5   single    0.930  0.020  1.080
 T2E  C06  H6   single    0.930  0.020  1.080
 T2E  C07  H7   single    0.970  0.020  1.090
 T2E  C07  H8   single    0.970  0.020  1.090
 T2E  C11  H9   single    0.930  0.020  1.080
 T2E  N08  H10  single    0.890  0.020  1.040
 T2E  N18  H11  single    0.890  0.020  1.040
 T2E  N18  H12  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
 T2E  H1   C10  C11  118.84  3.000
 T2E  H1   C10  C09  119.09  3.000
 T2E  C11  C10  C09  122.07  3.000
 T2E  H2   C13  C14  119.14  3.000
 T2E  H2   C13  C12  118.56  3.000
 T2E  C14  C13  C12  122.30  3.000
 T2E  O17  C15  O16  127.41  3.000
 T2E  O16  C15  C14  115.51  3.000
 T2E  O17  C15  C14  117.06  3.000
 T2E  H3   C01  C06  120.27  3.000
 T2E  H3   C01  C02  121.25  3.000
 T2E  C06  C01  C02  118.48  3.000
 T2E  H4   C02  C03  120.19  3.000
 T2E  H4   C02  C01  120.41  3.000
 T2E  C03  C02  C01  119.40  3.000
 T2E  C07  C03  C04  121.05  3.000
 T2E  C07  C03  C02  121.94  3.000
 T2E  C04  C03  C02  116.95  3.000
 T2E  H5   C04  N05  116.21  3.000
 T2E  H5   C04  C03  119.41  3.000
 T2E  N05  C04  C03  124.38  3.000
 T2E  H6   C06  N05  116.59  3.000
 T2E  H6   C06  C01  120.30  3.000
 T2E  N05  C06  C01  123.11  3.000
 T2E  H8   C07  H7   107.40  3.000
 T2E  H8   C07  N08  107.56  3.000
 T2E  H7   C07  N08  107.71  3.000
 T2E  H8   C07  C03  109.57  3.000
 T2E  H7   C07  C03  110.32  3.000
 T2E  N08  C07  C03  114.04  3.000
 T2E  N08  C09  C14  120.65  3.000
 T2E  C14  C09  C10  118.30  3.000
 T2E  N08  C09  C10  121.01  3.000
 T2E  H9   C11  C12  120.08  3.000
 T2E  H9   C11  C10  119.89  3.000
 T2E  C12  C11  C10  120.03  3.000
 T2E  N18  C12  C11  121.20  3.000
 T2E  N18  C12  C13  120.89  3.000
 T2E  C11  C12  C13  117.89  3.000
 T2E  C09  C14  C15  122.50  3.000
 T2E  C09  C14  C13  119.37  3.000
 T2E  C15  C14  C13  118.07  3.000
 T2E  C06  N05  C04  117.68  3.000
 T2E  H10  N08  C09  109.76  3.000
 T2E  H10  N08  C07  108.81  3.000
 T2E  C09  N08  C07  115.52  3.000
 T2E  H12  N18  H11  110.68  3.000
 T2E  H12  N18  C12  114.62  3.000
 T2E  H11  N18  C12  114.70  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
 T2E  CONST_01  C13  C14  C09  C10     0.00   0.0  0
 T2E  CONST_02  C13  C12  C11  C10     0.00   0.0  0
 T2E  CONST_03  C04  N05  C06  C01     0.00   0.0  0
 T2E  CONST_04  C04  C03  C02  C01     0.00   0.0  0
 T2E  CONST_05  N05  C04  C03  C02     0.00   0.0  0
 T2E  CONST_06  N05  C06  C01  C02     0.00   0.0  0
 T2E  CONST_07  C06  N05  C04  C03     0.00   0.0  0
 T2E  CONST_08  C06  C01  C02  C03     0.00   0.0  0
 T2E  CONST_09  C12  C13  C14  C09     0.00   0.0  0
 T2E  CONST_10  C12  C11  C10  C09     0.00   0.0  0
 T2E  CONST_11  C14  C09  C10  C11     0.00   0.0  0
 T2E  CONST_12  C14  C13  C12  C11     0.00   0.0  0
 T2E  CONST_13  C15  C14  C09  C10   180.00   0.0  0
 T2E  CONST_14  N18  C12  C11  C10   180.00   0.0  0
 T2E  CONST_15  N08  C09  C14  C13   180.00   0.0  0
 T2E  CONST_16  C12  C13  C14  C15   180.00   0.0  0
 T2E  CONST_17  C07  C03  C02  C01   180.00   0.0  0
 T2E  CONST_18  N05  C04  C03  C07   180.00   0.0  0
 T2E  CONST_19  N08  C09  C10  C11   180.00   0.0  0
 T2E  CONST_20  N18  C12  C13  C14   180.00   0.0  0
 T2E  CONST_21  H9   C11  C12  C13   180.00   0.0  0
 T2E  CONST_22  H5   C04  C03  C02   180.00   0.0  0
 T2E  CONST_23  H6   C06  C01  C02   180.00   0.0  0
 T2E  CONST_24  H3   C01  C02  C03   180.00   0.0  0
 T2E  CONST_25  H6   C06  N05  C04   180.00   0.0  0
 T2E  CONST_26  H4   C02  C03  C04   180.00   0.0  0
 T2E  CONST_27  H5   C04  N05  C06   180.00   0.0  0
 T2E  CONST_28  H4   C02  C01  C06   180.00   0.0  0
 T2E  CONST_29  H2   C13  C14  C09   180.00   0.0  0
 T2E  CONST_30  H9   C11  C10  C09   180.00   0.0  0
 T2E  CONST_31  H2   C13  C12  C11   180.00   0.0  0
 T2E  CONST_32  H1   C10  C11  C12   180.00   0.0  0
 T2E  CONST_33  H1   C10  C09  C14   180.00   0.0  0
 T2E  CONST_34  H3   C01  C06  N05   180.00   0.0  0
 T2E  Var_01    O17  C15  C14  C13  -111.59  30.0  2
 T2E  Var_02    O16  C15  C14  C13    66.73  30.0  2
 T2E  Var_03    N08  C07  C03  C02    86.53  30.0  2
 T2E  Var_04    C09  N08  C07  C03   -63.35  30.0  2
 T2E  Var_05    N08  C07  C03  C04   -90.41  30.0  2
 T2E  Var_06    O17  C15  C14  C09    71.01  30.0  2
 T2E  Var_07    O16  C15  C14  C09  -110.66  30.0  2
 T2E  Var_08    H7   C07  C03  C02   -34.82  30.0  2
 T2E  Var_09    H8   C07  C03  C02  -152.86  30.0  2
 T2E  Var_10    H7   C07  C03  C04   148.24  30.0  2
 T2E  Var_11    H8   C07  C03  C04    30.20  30.0  2
 T2E  Var_12    H10  N08  C07  C03    60.59  30.0  2
 T2E  Var_13    H7   C07  N08  C09    59.43  30.0  3
 T2E  Var_14    H8   C07  N08  C09   174.92  30.0  3

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
 T2E  plan-1  C10  0.020
 T2E  plan-1  C13  0.020
 T2E  plan-1  C15  0.020
 T2E  plan-1  C09  0.020
 T2E  plan-1  C11  0.020
 T2E  plan-1  C12  0.020
 T2E  plan-1  C14  0.020
 T2E  plan-1  N08  0.020
 T2E  plan-1  N18  0.020
 T2E  plan-1  H1   0.020
 T2E  plan-1  H2   0.020
 T2E  plan-1  H9   0.020
 T2E  plan-2  C01  0.020
 T2E  plan-2  C02  0.020
 T2E  plan-2  C03  0.020
 T2E  plan-2  C04  0.020
 T2E  plan-2  C06  0.020
 T2E  plan-2  C07  0.020
 T2E  plan-2  N05  0.020
 T2E  plan-2  H5   0.020
 T2E  plan-2  H6   0.020
 T2E  plan-2  H3   0.020
 T2E  plan-2  H4   0.020
 T2E  plan-3  C07  0.020
 T2E  plan-3  C09  0.020
 T2E  plan-3  N08  0.020
 T2E  plan-3  H10  0.020
 T2E  plan-4  C12  0.020
 T2E  plan-4  N18  0.020
 T2E  plan-4  H11  0.020
 T2E  plan-4  H12  0.020
 T2E  plan-5  C15  0.020
 T2E  plan-5  C14  0.020
 T2E  plan-5  O16  0.020
 T2E  plan-5  O17  0.020

