# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 23:10:19 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 2-[(pyridin-3-ylmethyl)amino]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccccc1NCc2cccnc2
#
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
 X76  X76  2-[(pyridin-3-ylmethyl)amino]benzamide  ligand  30  17  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X76
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
 X76  N01   N  NH1   0  -0.699  -0.0261   0.2961   0.0214
 X76  N02   N  NH2   0  -0.805  -2.8428  -2.7413  -0.3390
 X76  N03   N  N     0  -0.401   4.4687   0.1370   1.0401
 X76  C04   C  CR16  0  -0.284  -3.6927  -0.0488   0.0115
 X76  C05   C  CR6   0  -0.133  -2.3458  -0.4126   0.0377
 X76  C06   C  CR6   0   0.375  -1.3526   0.6027   0.0049
 X76  C07   C  CR16  0  -0.359  -1.7822   1.9388  -0.0881
 X76  C08   C  CR16  0  -0.239  -3.1251   2.2607  -0.1288
 X76  C09   C  CR16  0  -0.283  -4.0985   1.2707  -0.0713
 X76  C11   C  CH2   0  -0.336   1.0123   1.2947   0.1081
 X76  C12   C  CR6   0  -0.015   2.3578   0.6354   0.0134
 X76  C13   C  CR16  0  -0.100   3.2665   0.7019   1.0620
 X76  C14   C  CR16  0  -0.067   4.8171  -0.5345  -0.0492
 X76  C15   C  CR16  0  -0.319   3.9883  -0.6698  -1.1551
 X76  C16   C  CR16  0  -0.170   2.7390  -0.0750  -1.1207
 X76  O17   O  O     0  -0.505  -0.8929  -2.2079   0.6301
 X76  HN01  H  HNH1  0   0.398   0.1930  -0.6260   0.3682
 X76  H102  H  HNH2  0   0.412  -3.6463  -2.4810  -0.8826
 X76  H202  H  HNH2  0   0.405  -2.6180  -3.7220  -0.2977
 X76  H04   H  HCR6  0   0.256  -4.4546  -0.8146   0.0835
 X76  H07   H  HCR6  0   0.275  -1.0564   2.7392  -0.1145
 X76  H08   H  HCR6  0   0.259  -3.4120   3.3029  -0.1923
 X76  H09   H  HCR6  0   0.252  -5.1503   1.5204  -0.0814
 X76  H111  H  HCH2  0   0.254   0.9056   2.0099  -0.7128
 X76  H211  H  HCH2  0   0.245   0.9528   1.8764   1.0369
 X76  H13   H  HCR6  0   0.260   3.0043   1.2431   1.9663
 X76  H14   H  HCR6  0   0.265   5.8013  -0.9898  -0.0463
 X76  H15   H  HCR6  0   0.273   4.3200  -1.2282  -2.0197
 X76  H16   H  HCR6  0   0.272   2.0661  -0.1585  -1.9655
 X76  C10   C  C     0   0.514  -1.9611  -1.8473   0.1343

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
 X76  N02  C10   single    1.342  0.020  1.342
 X76  O17  C10   double    1.232  0.020  1.232
 X76  C10  C05   single    1.488  0.020  1.488
 X76  C05  C04   aromatic  1.395  0.020  1.395
 X76  C05  C06   aromatic  1.421  0.020  1.421
 X76  C04  C09   aromatic  1.383  0.020  1.383
 X76  N01  C06   single    1.362  0.020  1.362
 X76  N01  C11   single    1.443  0.020  1.443
 X76  C06  C07   aromatic  1.407  0.020  1.407
 X76  C11  C12   single    1.501  0.020  1.501
 X76  C09  C08   aromatic  1.390  0.020  1.390
 X76  C13  C12   aromatic  1.389  0.020  1.389
 X76  C13  N03   aromatic  1.328  0.020  1.328
 X76  C07  C08   aromatic  1.382  0.020  1.382
 X76  C12  C16   aromatic  1.392  0.020  1.392
 X76  N03  C14   aromatic  1.326  0.020  1.326
 X76  C16  C15   aromatic  1.384  0.020  1.384
 X76  C14  C15   aromatic  1.389  0.020  1.389
 X76  N01  HN01  single    0.890  0.020  1.040
 X76  N02  H102  single    0.860  0.020  1.020
 X76  N02  H202  single    0.860  0.020  1.020
 X76  C04  H04   single    0.930  0.020  1.080
 X76  C07  H07   single    0.930  0.020  1.080
 X76  C08  H08   single    0.930  0.020  1.080
 X76  C09  H09   single    0.930  0.020  1.080
 X76  C11  H111  single    0.970  0.020  1.090
 X76  C11  H211  single    0.970  0.020  1.090
 X76  C13  H13   single    0.930  0.020  1.080
 X76  C14  H14   single    0.930  0.020  1.080
 X76  C15  H15   single    0.930  0.020  1.080
 X76  C16  H16   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
 X76  HN01  N01  C11   117.09  3.000
 X76  HN01  N01  C06   114.92  3.000
 X76  C11   N01  C06   123.09  3.000
 X76  H202  N02  H102  116.95  3.000
 X76  H202  N02  C10   119.19  3.000
 X76  H102  N02  C10   122.94  3.000
 X76  C14   N03  C13   117.81  3.000
 X76  H04   C04  C09   118.19  3.000
 X76  H04   C04  C05   119.58  3.000
 X76  C09   C04  C05   122.21  3.000
 X76  C10   C05  C06   120.64  3.000
 X76  C06   C05  C04   119.22  3.000
 X76  C10   C05  C04   120.12  3.000
 X76  C07   C06  C05   117.83  3.000
 X76  C07   C06  N01   120.81  3.000
 X76  C05   C06  N01   121.33  3.000
 X76  H07   C07  C08   118.65  3.000
 X76  H07   C07  C06   120.00  3.000
 X76  C08   C07  C06   121.35  3.000
 X76  H08   C08  C09   120.17  3.000
 X76  H08   C08  C07   118.92  3.000
 X76  C09   C08  C07   120.91  3.000
 X76  H09   C09  C08   121.11  3.000
 X76  H09   C09  C04   120.42  3.000
 X76  C08   C09  C04   118.47  3.000
 X76  H211  C11  H111  106.45  3.000
 X76  H211  C11  C12   109.55  3.000
 X76  H111  C11  C12   109.10  3.000
 X76  H211  C11  N01   112.25  3.000
 X76  H111  C11  N01   109.70  3.000
 X76  C12   C11  N01   109.70  3.000
 X76  C16   C12  C13   117.41  3.000
 X76  C16   C12  C11   121.41  3.000
 X76  C13   C12  C11   121.17  3.000
 X76  H13   C13  C12   119.63  3.000
 X76  H13   C13  N03   116.36  3.000
 X76  C12   C13  N03   124.00  3.000
 X76  H14   C14  C15   120.19  3.000
 X76  H14   C14  N03   116.67  3.000
 X76  C15   C14  N03   123.14  3.000
 X76  H15   C15  C16   121.24  3.000
 X76  H15   C15  C14   120.27  3.000
 X76  C16   C15  C14   118.49  3.000
 X76  H16   C16  C15   120.55  3.000
 X76  H16   C16  C12   120.31  3.000
 X76  C15   C16  C12   119.14  3.000
 X76  O17   C10  C05   122.17  3.000
 X76  C05   C10  N02   116.71  3.000
 X76  O17   C10  N02   121.11  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
 X76  CONST_01  C16   C12  C13  N03     0.00   0.0  0
 X76  CONST_02  C16   C15  C14  N03     0.00   0.0  0
 X76  CONST_03  C07   C06  C05  C04     0.00   0.0  0
 X76  CONST_04  C07   C08  C09  C04     0.00   0.0  0
 X76  CONST_05  C08   C09  C04  C05     0.00   0.0  0
 X76  CONST_06  C08   C07  C06  C05     0.00   0.0  0
 X76  CONST_07  C09   C04  C05  C06     0.00   0.0  0
 X76  CONST_08  C09   C08  C07  C06     0.00   0.0  0
 X76  CONST_09  C14   N03  C13  C12     0.00   0.0  0
 X76  CONST_10  C14   C15  C16  C12     0.00   0.0  0
 X76  CONST_11  C15   C16  C12  C13     0.00   0.0  0
 X76  CONST_12  C15   C14  N03  C13     0.00   0.0  0
 X76  CONST_13  C04   C05  C06  N01   180.00   0.0  0
 X76  CONST_14  C08   C07  C06  N01   180.00   0.0  0
 X76  CONST_15  C11   C12  C13  N03   180.00   0.0  0
 X76  CONST_16  C10   C05  C06  C07   180.00   0.0  0
 X76  CONST_17  C10   C05  C04  C09   180.00   0.0  0
 X76  CONST_18  C15   C16  C12  C11   180.00   0.0  0
 X76  CONST_19  H15   C15  C14  N03   180.00   0.0  0
 X76  CONST_20  H08   C08  C09  C04   180.00   0.0  0
 X76  CONST_21  H09   C09  C04  C05   180.00   0.0  0
 X76  CONST_22  H07   C07  C06  C05   180.00   0.0  0
 X76  CONST_23  H04   C04  C05  C06   180.00   0.0  0
 X76  CONST_24  H16   C16  C12  C13   180.00   0.0  0
 X76  CONST_25  H14   C14  N03  C13   180.00   0.0  0
 X76  CONST_26  H13   C13  N03  C14   180.00   0.0  0
 X76  CONST_27  C11   N01  C06  C05   180.00   0.0  0
 X76  CONST_28  C11   N01  C06  C07     0.00   0.0  0
 X76  CONST_30  H102  N02  C10  C05     0.00   0.0  0
 X76  CONST_31  H202  N02  C10  C05   180.00   0.0  0
 X76  Var_01    C13   C12  C11  N01  -117.71  30.0  2
 X76  Var_02    C04   C05  C10  N02    26.28  30.0  2
 X76  Var_03    C12   C11  N01  C06  -176.33  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
 X76  plan-1  N01   0.020
 X76  plan-1  C04   0.020
 X76  plan-1  C05   0.020
 X76  plan-1  C06   0.020
 X76  plan-1  C07   0.020
 X76  plan-1  C08   0.020
 X76  plan-1  C09   0.020
 X76  plan-1  H04   0.020
 X76  plan-1  H07   0.020
 X76  plan-1  H08   0.020
 X76  plan-1  H09   0.020
 X76  plan-1  C10   0.020
 X76  plan-2  N03   0.020
 X76  plan-2  C11   0.020
 X76  plan-2  C12   0.020
 X76  plan-2  C13   0.020
 X76  plan-2  C14   0.020
 X76  plan-2  C15   0.020
 X76  plan-2  C16   0.020
 X76  plan-2  H13   0.020
 X76  plan-2  H14   0.020
 X76  plan-2  H15   0.020
 X76  plan-2  H16   0.020
 X76  plan-3  N02   0.020
 X76  plan-3  C05   0.020
 X76  plan-3  O17   0.020
 X76  plan-3  H102  0.020
 X76  plan-3  H202  0.020
 X76  plan-3  C10   0.020
 X76  plan-4  N01   0.020
 X76  plan-4  C06   0.020
 X76  plan-4  C11   0.020
 X76  plan-4  HN01  0.020

