# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun 10 09:29:05 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 4-[2-amino-5-(1,3-benzodioxol-4-yl)pyridin-3-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc(cc1)c2cc(cnc2N)c3cccc4OCOc34
#
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
 ZZK  ZZK  4-[2-amino-5-(1,3-benzodioxol-4-yl)pyridin-3-yl]benzamide  ligand  40  25  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ZZK
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
 ZZK  N01   N  NH2   0  -0.812   6.4925   1.8836  -1.2009
 ZZK  C02   C  C     0   0.487   6.0997   1.2831  -0.0678
 ZZK  O03   O  O     0  -0.481   6.8136   1.2023   0.9227
 ZZK  C04   C  CR6   0  -0.049   4.7185   0.7086  -0.0664
 ZZK  C05   C  CR16  0  -0.250   4.4194  -0.2918   0.8550
 ZZK  C06   C  CR16  0  -0.289   3.1534  -0.8475   0.9101
 ZZK  C07   C  CR6   0   0.047   2.1399  -0.4016   0.0589
 ZZK  C08   C  CR6   0  -0.038   0.7676  -0.9385   0.1455
 ZZK  C09   C  CR16  0  -0.240  -0.3080  -0.0776   0.2504
 ZZK  C10   C  CR6   0   0.004  -1.6173  -0.5528   0.3444
 ZZK  C11   C  CR6   0  -0.018  -2.7570   0.3645   0.4867
 ZZK  C12   C  CR16  0  -0.335  -2.6814   1.5228   1.2845
 ZZK  C13   C  CR16  0  -0.259  -3.7406   2.4042   1.4043
 ZZK  C14   C  CR16  0  -0.355  -4.9512   2.1881   0.7348
 ZZK  C15   C  CR56  0   0.311  -5.0217   1.0585  -0.0420
 ZZK  O16   O  O     0  -0.486  -6.0456   0.6376  -0.8258
 ZZK  C17   C  CH2   0   0.065  -5.6928  -0.6682  -1.2581
 ZZK  O18   O  O     0  -0.481  -4.2977  -0.8101  -1.0338
 ZZK  C19   C  CR56  0   0.243  -3.9597   0.1760  -0.1637
 ZZK  C20   C  CR16  0  -0.096  -1.7653  -1.9341   0.3320
 ZZK  N21   N  N     0  -0.446  -0.7597  -2.7863   0.2120
 ZZK  C22   C  CR6   0   0.409   0.4846  -2.3253   0.1086
 ZZK  N23   N  NH2   0  -0.827   1.4679  -3.2577  -0.0109
 ZZK  C24   C  CR16  0  -0.285   2.4395   0.6118  -0.8510
 ZZK  C25   C  CR16  0  -0.267   3.7105   1.1593  -0.9149
 ZZK  H011  H  HNH2  0   0.406   7.4143   2.2854  -1.2592
 ZZK  H012  H  HNH2  0   0.414   5.9659   1.8284  -2.0552
 ZZK  H05   H  HCR6  0   0.264   5.1830  -0.6421   1.5365
 ZZK  H25   H  HCR6  0   0.262   3.8904   1.9554  -1.6263
 ZZK  H06   H  HCR6  0   0.267   2.9499  -1.6207   1.6400
 ZZK  H24   H  HCR6  0   0.263   1.6726   0.9768  -1.5224
 ZZK  H09   H  HCR6  0   0.265  -0.1246   0.9908   0.2639
 ZZK  H20   H  HCR6  0   0.257  -2.7477  -2.3816   0.4362
 ZZK  H12   H  HCR6  0   0.255  -1.7697   1.7159   1.8358
 ZZK  H13   H  HCR6  0   0.260  -3.6370   3.2750   2.0375
 ZZK  H14   H  HCR6  0   0.273  -5.7820   2.8744   0.8238
 ZZK  H171  H  HCH2  0   0.232  -6.2414  -1.4154  -0.6734
 ZZK  H172  H  HCH2  0   0.248  -5.9088  -0.7784  -2.3200
 ZZK  H231  H  HNH2  0   0.396   2.3445  -2.9863  -0.4243
 ZZK  H232  H  HNH2  0   0.388   1.1633  -4.1860  -0.2558

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
 ZZK  N01  C02   single    1.341  0.020  1.341
 ZZK  C02  O03   double    1.224  0.020  1.224
 ZZK  C02  C04   single    1.496  0.020  1.496
 ZZK  C04  C05   aromatic  1.393  0.020  1.393
 ZZK  C04  C25   aromatic  1.392  0.020  1.392
 ZZK  C05  C06   aromatic  1.384  0.020  1.384
 ZZK  C06  C07   aromatic  1.397  0.020  1.397
 ZZK  C07  C08   single    1.476  0.020  1.476
 ZZK  C07  C24   aromatic  1.395  0.020  1.395
 ZZK  C08  C09   aromatic  1.382  0.020  1.382
 ZZK  C08  C22   aromatic  1.416  0.020  1.416
 ZZK  C09  C10   aromatic  1.396  0.020  1.396
 ZZK  C10  C11   single    1.470  0.020  1.470
 ZZK  C10  C20   aromatic  1.389  0.020  1.389
 ZZK  C11  C12   aromatic  1.408  0.020  1.408
 ZZK  C11  C19   aromatic  1.380  0.020  1.380
 ZZK  C12  C13   aromatic  1.383  0.020  1.383
 ZZK  C13  C14   aromatic  1.400  0.020  1.400
 ZZK  C14  C15   aromatic  1.373  0.020  1.373
 ZZK  C15  O16   single    1.356  0.020  1.356
 ZZK  C15  C19   aromatic  1.386  0.020  1.386
 ZZK  O16  C17   single    1.420  0.020  1.420
 ZZK  C17  O18   single    1.420  0.020  1.420
 ZZK  O18  C19   single    1.358  0.020  1.358
 ZZK  C20  N21   aromatic  1.324  0.020  1.324
 ZZK  N21  C22   aromatic  1.331  0.020  1.331
 ZZK  C22  N23   single    1.360  0.020  1.360
 ZZK  C24  C25   aromatic  1.385  0.020  1.385
 ZZK  N01  H011  single    0.860  0.020  1.020
 ZZK  N01  H012  single    0.860  0.020  1.020
 ZZK  C05  H05   single    0.930  0.020  1.080
 ZZK  C25  H25   single    0.930  0.020  1.080
 ZZK  C06  H06   single    0.930  0.020  1.080
 ZZK  C24  H24   single    0.930  0.020  1.080
 ZZK  C09  H09   single    0.930  0.020  1.080
 ZZK  C20  H20   single    0.930  0.020  1.080
 ZZK  C12  H12   single    0.930  0.020  1.080
 ZZK  C13  H13   single    0.930  0.020  1.080
 ZZK  C14  H14   single    0.930  0.020  1.080
 ZZK  C17  H171  single    0.970  0.020  1.090
 ZZK  C17  H172  single    0.970  0.020  1.090
 ZZK  N23  H231  single    0.890  0.020  1.040
 ZZK  N23  H232  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
 ZZK  H012  N01  H011  116.89  3.000
 ZZK  H012  N01  C02   122.69  3.000
 ZZK  H011  N01  C02   119.70  3.000
 ZZK  C04   C02  O03   120.84  3.000
 ZZK  C04   C02  N01   116.31  3.000
 ZZK  O03   C02  N01   122.86  3.000
 ZZK  C25   C04  C05   118.70  3.000
 ZZK  C25   C04  C02   122.92  3.000
 ZZK  C05   C04  C02   118.35  3.000
 ZZK  H05   C05  C06   119.39  3.000
 ZZK  H05   C05  C04   119.86  3.000
 ZZK  C06   C05  C04   120.75  3.000
 ZZK  H06   C06  C07   120.17  3.000
 ZZK  H06   C06  C05   119.05  3.000
 ZZK  C07   C06  C05   120.76  3.000
 ZZK  C24   C07  C08   120.16  3.000
 ZZK  C24   C07  C06   118.28  3.000
 ZZK  C08   C07  C06   121.52  3.000
 ZZK  C22   C08  C09   117.17  3.000
 ZZK  C22   C08  C07   122.72  3.000
 ZZK  C09   C08  C07   120.10  3.000
 ZZK  H09   C09  C10   119.56  3.000
 ZZK  H09   C09  C08   118.90  3.000
 ZZK  C10   C09  C08   121.54  3.000
 ZZK  C20   C10  C11   122.59  3.000
 ZZK  C20   C10  C09   115.96  3.000
 ZZK  C11   C10  C09   121.42  3.000
 ZZK  C19   C11  C12   115.21  3.000
 ZZK  C19   C11  C10   123.01  3.000
 ZZK  C12   C11  C10   121.76  3.000
 ZZK  H12   C12  C13   119.15  3.000
 ZZK  H12   C12  C11   118.70  3.000
 ZZK  C13   C12  C11   122.14  3.000
 ZZK  H13   C13  C14   119.15  3.000
 ZZK  H13   C13  C12   119.36  3.000
 ZZK  C14   C13  C12   121.49  3.000
 ZZK  H14   C14  C15   121.97  3.000
 ZZK  H14   C14  C13   121.80  3.000
 ZZK  C15   C14  C13   116.23  3.000
 ZZK  C19   C15  O16   109.27  3.000
 ZZK  C19   C15  C14   122.29  3.000
 ZZK  O16   C15  C14   128.40  3.000
 ZZK  C17   O16  C15   105.89  3.000
 ZZK  H172  C17  H171  110.60  3.000
 ZZK  H172  C17  O18   109.80  3.000
 ZZK  H171  C17  O18   109.84  3.000
 ZZK  H172  C17  O16   109.91  3.000
 ZZK  H171  C17  O16   109.88  3.000
 ZZK  O18   C17  O16   106.73  3.000
 ZZK  C19   O18  C17   105.86  3.000
 ZZK  O18   C19  C15   109.14  3.000
 ZZK  O18   C19  C11   128.17  3.000
 ZZK  C15   C19  C11   122.64  3.000
 ZZK  H20   C20  N21   115.54  3.000
 ZZK  H20   C20  C10   120.40  3.000
 ZZK  N21   C20  C10   124.06  3.000
 ZZK  C22   N21  C20   119.62  3.000
 ZZK  N23   C22  N21   116.43  3.000
 ZZK  N23   C22  C08   121.95  3.000
 ZZK  N21   C22  C08   121.61  3.000
 ZZK  H232  N23  H231  114.34  3.000
 ZZK  H232  N23  C22   115.75  3.000
 ZZK  H231  N23  C22   118.74  3.000
 ZZK  H24   C24  C25   119.22  3.000
 ZZK  H24   C24  C07   119.82  3.000
 ZZK  C25   C24  C07   120.96  3.000
 ZZK  H25   C25  C24   118.25  3.000
 ZZK  H25   C25  C04   121.20  3.000
 ZZK  C24   C25  C04   120.54  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
 ZZK  CONST_01  C07   C06  C05  C04    0.00   0.0  0
 ZZK  CONST_02  C07   C24  C25  C04    0.00   0.0  0
 ZZK  CONST_03  C24   C25  C04  C05    0.00   0.0  0
 ZZK  CONST_04  C08   C07  C06  C05  180.00   0.0  0
 ZZK  CONST_05  C24   C07  C06  C05    0.00   0.0  0
 ZZK  CONST_06  C25   C04  C05  C06    0.00   0.0  0
 ZZK  CONST_09  C25   C24  C07  C06    0.00   0.0  0
 ZZK  CONST_10  C10   C09  C08  C07  180.00   0.0  0
 ZZK  CONST_11  N21   C22  C08  C07  180.00   0.0  0
 ZZK  CONST_12  C25   C24  C07  C08  180.00   0.0  0
 ZZK  CONST_13  C11   C10  C09  C08  180.00   0.0  0
 ZZK  CONST_14  C20   C10  C09  C08    0.00   0.0  0
 ZZK  CONST_15  C20   N21  C22  C08    0.00   0.0  0
 ZZK  CONST_17  N21   C22  C08  C09    0.00   0.0  0
 ZZK  CONST_20  N21   C20  C10  C09    0.00   0.0  0
 ZZK  CONST_21  C22   C08  C09  C10    0.00   0.0  0
 ZZK  CONST_22  C13   C12  C11  C10  180.00   0.0  0
 ZZK  CONST_23  C15   C19  C11  C10  180.00   0.0  0
 ZZK  CONST_24  C22   N21  C20  C10    0.00   0.0  0
 ZZK  CONST_25  N21   C20  C10  C11  180.00   0.0  0
 ZZK  CONST_26  C14   C13  C12  C11    0.00   0.0  0
 ZZK  CONST_27  C14   C15  C19  C11    0.00   0.0  0
 ZZK  CONST_29  C15   C19  C11  C12    0.00   0.0  0
 ZZK  CONST_30  C15   C14  C13  C12    0.00   0.0  0
 ZZK  CONST_31  C19   C11  C12  C13    0.00   0.0  0
 ZZK  CONST_32  C19   C15  C14  C13    0.00   0.0  0
 ZZK  CONST_35  O18   C19  C11  C10    0.00   0.0  0
 ZZK  CONST_36  C06   C05  C04  C02  180.00   0.0  0
 ZZK  CONST_37  C24   C25  C04  C02  180.00   0.0  0
 ZZK  CONST_38  N23   C22  C08  C07    0.00   0.0  0
 ZZK  CONST_39  N23   C22  C08  C09  180.00   0.0  0
 ZZK  CONST_40  N23   C22  N21  C20  180.00   0.0  0
 ZZK  CONST_41  H06   C06  C05  C04  180.00   0.0  0
 ZZK  CONST_42  H24   C24  C25  C04  180.00   0.0  0
 ZZK  CONST_43  H25   C25  C04  C05  180.00   0.0  0
 ZZK  CONST_44  H05   C05  C06  C07  180.00   0.0  0
 ZZK  CONST_45  H09   C09  C08  C07    0.00   0.0  0
 ZZK  CONST_46  H20   C20  C10  C09  180.00   0.0  0
 ZZK  CONST_47  H12   C12  C11  C10    0.00   0.0  0
 ZZK  CONST_48  H13   C13  C12  C11  180.00   0.0  0
 ZZK  CONST_49  H14   C14  C13  C12  180.00   0.0  0
 ZZK  CONST_51  H232  N23  C22  C08  180.00   0.0  0
 ZZK  CONST_52  H011  N01  C02  C04  180.00   0.0  0
 ZZK  CONST_53  H012  N01  C02  C04    0.00   0.0  0
 ZZK  Var_01    O18   C17  O16  C15  -17.05  30.0  1
 ZZK  Var_02    C19   C15  O16  C17   10.45  30.0  1
 ZZK  Var_03    C05   C04  C02  N01  158.32  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
 ZZK  plan-1  C02   0.020
 ZZK  plan-1  C04   0.020
 ZZK  plan-1  C05   0.020
 ZZK  plan-1  C06   0.020
 ZZK  plan-1  C07   0.020
 ZZK  plan-1  C08   0.020
 ZZK  plan-1  C24   0.020
 ZZK  plan-1  C25   0.020
 ZZK  plan-1  H05   0.020
 ZZK  plan-1  H25   0.020
 ZZK  plan-1  H06   0.020
 ZZK  plan-1  H24   0.020
 ZZK  plan-2  C07   0.020
 ZZK  plan-2  C08   0.020
 ZZK  plan-2  C09   0.020
 ZZK  plan-2  C10   0.020
 ZZK  plan-2  C11   0.020
 ZZK  plan-2  C20   0.020
 ZZK  plan-2  N21   0.020
 ZZK  plan-2  C22   0.020
 ZZK  plan-2  N23   0.020
 ZZK  plan-2  H09   0.020
 ZZK  plan-2  H20   0.020
 ZZK  plan-3  C10   0.020
 ZZK  plan-3  C11   0.020
 ZZK  plan-3  C12   0.020
 ZZK  plan-3  C13   0.020
 ZZK  plan-3  C14   0.020
 ZZK  plan-3  C15   0.020
 ZZK  plan-3  O16   0.020
 ZZK  plan-3  O18   0.020
 ZZK  plan-3  C19   0.020
 ZZK  plan-3  H12   0.020
 ZZK  plan-3  H13   0.020
 ZZK  plan-3  H14   0.020
 ZZK  plan-4  N01   0.020
 ZZK  plan-4  C02   0.020
 ZZK  plan-4  O03   0.020
 ZZK  plan-4  C04   0.020
 ZZK  plan-4  H011  0.020
 ZZK  plan-4  H012  0.020
 ZZK  plan-5  C22   0.020
 ZZK  plan-5  N23   0.020
 ZZK  plan-5  H231  0.020
 ZZK  plan-5  H232  0.020

