# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 07:46:13 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 5-cyano-N-(2,5-dimethoxybenzyl)-6-ethoxypyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOc1nc(ccc1C#N)C(=O)NCc2cc(OC)ccc2OC
#
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
 893  893  5-cyano-N-(2,5-dimethoxybenzyl)-6-ethoxypyridine-2-carboxamide  ligand  44  25  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_893
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
 893  C1    C  CR16  0  -0.369  -3.7955   0.6285  -1.2749
 893  C2    C  CR6   0   0.350  -2.8516  -0.3723  -1.1025
 893  C3    C  CR6   0  -0.028  -2.6838  -0.9473   0.1679
 893  C4    C  CR16  0  -0.375  -3.4624  -0.5040   1.2206
 893  C5    C  CR6   0   0.375  -4.4168   0.5013   1.0505
 893  C6    C  CR16  0  -0.377  -4.5760   1.0657  -0.2057
 893  C9    C  CH2   0  -0.308  -1.6644  -2.0288   0.3867
 893  N1    N  NH1   0  -0.637  -0.3235  -1.4810   0.3203
 893  C8    C  C     0   0.553   0.7672  -2.2369   0.4251
 893  C14   C  CR6   0   0.158   2.0640  -1.4768   0.3351
 893  N16   N  N     0  -0.502   1.9808  -0.1756   0.0659
 893  C17   C  CR6   0   0.577   3.0782   0.5357  -0.0193
 893  C18   C  CR6   0  -0.159   4.3525  -0.0369   0.1788
 893  C19   C  CR16  0  -0.110   4.4297  -1.3913   0.4585
 893  C20   C  CR16  0  -0.318   3.2619  -2.1363   0.5346
 893  O22   O  O2    0  -0.477  -5.1221   0.8484   2.1495
 893  C23   C  CH3   0  -0.436  -6.0855   1.8732   2.0265
 893  O27   O  O2    0  -0.467  -2.0560  -0.8516  -2.0820
 893  C28   C  CH3   0  -0.435  -2.1960  -0.3194  -3.3821
 893  C34   C  CSP   0   0.063   5.5163   0.7728   0.0858
 893  N35   N  NS    0  -0.240   6.4652   1.4217   0.0100
 893  O36   O  O2    0  -0.453   3.0340   1.8229  -0.2960
 893  C37   C  CH2   0  -0.181   1.7617   2.4323  -0.5712
 893  C7    C  CH3   0  -0.686   2.0135   3.8858  -0.8850
 893  O1    O  O     0  -0.483   0.7567  -3.4490   0.5893
 893  H1    H  HCR6  0   0.283  -3.9493   1.0914  -2.2402
 893  H4    H  HCR6  0   0.263  -3.3326  -0.9467   2.2016
 893  H6    H  HCR6  0   0.282  -5.3005   1.8480  -0.3867
 893  H91   H  HCH2  0   0.260  -1.7736  -2.8205  -0.3584
 893  H92   H  HCH2  0   0.263  -1.8269  -2.4884   1.3641
 893  HN1   H  HNH1  0   0.409  -0.1966  -0.4878   0.1958
 893  H19   H  HCR6  0   0.302   5.3928  -1.8572   0.6153
 893  H20   H  HCR6  0   0.287   3.2900  -3.1942   0.7467
 893  H231  H  HCH3  0   0.258  -6.5358   1.9963   3.0085
 893  H232  H  HCH3  0   0.226  -5.6368   2.8238   1.7244
 893  H233  H  HCH3  0   0.226  -6.8713   1.6146   1.3111
 893  H281  H  HCH3  0   0.227  -3.1993  -0.4827  -3.7852
 893  H282  H  HCH3  0   0.226  -1.9769   0.7515  -3.4126
 893  H283  H  HCH3  0   0.259  -1.4771  -0.8404  -4.0097
 893  H371  H  HCH2  0   0.241   1.1060   2.3214   0.2945
 893  H372  H  HCH2  0   0.236   1.2918   1.9226  -1.4148
 893  H71   H  HCH3  0   0.239   2.6689   4.0010  -1.7482
 893  H72   H  HCH3  0   0.243   1.0643   4.3669  -1.1190
 893  H73   H  HCH3  0   0.239   2.4542   4.4105  -0.0377

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
 893  C1   C2    aromatic  1.386  0.020  1.386
 893  C1   C6    aromatic  1.394  0.020  1.394
 893  C1   H1    single    0.930  0.020  1.080
 893  C2   C3    aromatic  1.405  0.020  1.405
 893  C2   O27   single    1.350  0.020  1.350
 893  C3   C4    aromatic  1.382  0.020  1.382
 893  C3   C9    single    1.502  0.020  1.502
 893  C4   C5    aromatic  1.397  0.020  1.397
 893  C4   H4    single    0.930  0.020  1.080
 893  C5   C6    aromatic  1.386  0.020  1.386
 893  C5   O22   single    1.351  0.020  1.351
 893  C6   H6    single    0.930  0.020  1.080
 893  C9   N1    single    1.450  0.020  1.450
 893  C9   H91   single    0.970  0.020  1.090
 893  C9   H92   single    0.970  0.020  1.090
 893  N1   C8    single    1.331  0.020  1.331
 893  N1   HN1   single    0.860  0.020  1.020
 893  C8   C14   single    1.506  0.020  1.506
 893  C8   O1    double    1.223  0.020  1.223
 893  C14  N16   aromatic  1.331  0.020  1.331
 893  C14  C20   aromatic  1.382  0.020  1.382
 893  N16  C17   aromatic  1.311  0.020  1.311
 893  C17  C18   aromatic  1.411  0.020  1.411
 893  C17  O36   single    1.317  0.020  1.317
 893  C18  C19   aromatic  1.385  0.020  1.385
 893  C18  C34   single    1.421  0.020  1.421
 893  C19  C20   aromatic  1.387  0.020  1.387
 893  C19  H19   single    0.930  0.020  1.080
 893  C20  H20   single    0.930  0.020  1.080
 893  O22  C23   single    1.412  0.020  1.412
 893  C23  H231  single    0.970  0.020  1.090
 893  C23  H232  single    0.970  0.020  1.090
 893  C23  H233  single    0.970  0.020  1.090
 893  O27  C28   single    1.412  0.020  1.412
 893  C28  H281  single    0.970  0.020  1.090
 893  C28  H282  single    0.970  0.020  1.090
 893  C28  H283  single    0.970  0.020  1.090
 893  C34  N35   triple    1.152  0.020  1.152
 893  O36  C37   single    1.437  0.020  1.437
 893  C37  C7    single    1.508  0.020  1.508
 893  C37  H371  single    0.970  0.020  1.090
 893  C37  H372  single    0.970  0.020  1.090
 893  C7   H71   single    0.970  0.020  1.090
 893  C7   H72   single    0.970  0.020  1.090
 893  C7   H73   single    0.970  0.020  1.090

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
 893  H1    C1   C6    118.08  3.000
 893  H1    C1   C2    121.11  3.000
 893  C6    C1   C2    120.81  3.000
 893  O27   C2   C3    116.14  3.000
 893  O27   C2   C1    124.57  3.000
 893  C3    C2   C1    119.29  3.000
 893  C9    C3   C4    120.14  3.000
 893  C9    C3   C2    120.50  3.000
 893  C4    C3   C2    119.36  3.000
 893  H4    C4   C5    119.08  3.000
 893  H4    C4   C3    119.39  3.000
 893  C5    C4   C3    121.53  3.000
 893  O22   C5   C6    124.93  3.000
 893  O22   C5   C4    116.26  3.000
 893  C6    C5   C4    118.81  3.000
 893  H6    C6   C5    121.54  3.000
 893  H6    C6   C1    118.27  3.000
 893  C5    C6   C1    120.20  3.000
 893  H92   C9   H91   106.89  3.000
 893  H92   C9   N1    109.73  3.000
 893  H91   C9   N1    109.57  3.000
 893  H92   C9   C3    109.41  3.000
 893  H91   C9   C3    110.76  3.000
 893  N1    C9   C3    110.42  3.000
 893  HN1   N1   C8    117.75  3.000
 893  HN1   N1   C9    119.59  3.000
 893  C8    N1   C9    122.65  3.000
 893  O1    C8   C14   121.04  3.000
 893  O1    C8   N1    124.49  3.000
 893  C14   C8   N1    114.47  3.000
 893  C20   C14  N16   123.35  3.000
 893  C20   C14  C8    119.80  3.000
 893  N16   C14  C8    116.85  3.000
 893  C17   N16  C14   119.42  3.000
 893  O36   C17  C18   117.15  3.000
 893  O36   C17  N16   121.06  3.000
 893  C18   C17  N16   121.79  3.000
 893  C34   C18  C19   121.65  3.000
 893  C34   C18  C17   119.95  3.000
 893  C19   C18  C17   118.39  3.000
 893  H19   C19  C20   120.69  3.000
 893  H19   C19  C18   120.02  3.000
 893  C20   C19  C18   119.29  3.000
 893  H20   C20  C19   121.01  3.000
 893  H20   C20  C14   121.25  3.000
 893  C19   C20  C14   117.74  3.000
 893  C23   O22  C5    118.15  3.000
 893  H233  C23  H232  108.63  3.000
 893  H233  C23  H231  108.67  3.000
 893  H232  C23  H231  108.72  3.000
 893  H233  C23  O22   112.07  3.000
 893  H232  C23  O22   112.02  3.000
 893  H231  C23  O22   106.63  3.000
 893  C28   O27  C2    118.42  3.000
 893  H283  C28  H282  108.71  3.000
 893  H283  C28  H281  108.80  3.000
 893  H282  C28  H281  108.65  3.000
 893  H283  C28  O27   106.58  3.000
 893  H282  C28  O27   112.02  3.000
 893  H281  C28  O27   111.97  3.000
 893  N35   C34  C18   180.00  3.000
 893  C37   O36  C17   118.96  3.000
 893  H372  C37  H371  107.87  3.000
 893  H372  C37  C7    111.16  3.000
 893  H371  C37  C7    111.29  3.000
 893  H372  C37  O36   109.33  3.000
 893  H371  C37  O36   109.68  3.000
 893  C7    C37  O36   107.50  3.000
 893  H73   C7   H72   107.86  3.000
 893  H73   C7   H71   108.77  3.000
 893  H72   C7   H71   107.89  3.000
 893  H73   C7   C37   111.70  3.000
 893  H72   C7   C37   108.95  3.000
 893  H71   C7   C37   111.53  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
 893  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 893  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 893  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 893  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 893  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 893  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 893  CONST_07  C18   C17  N16  C14     0.00   0.0  0
 893  CONST_08  C18   C19  C20  C14     0.00   0.0  0
 893  CONST_09  C19   C20  C14  N16     0.00   0.0  0
 893  CONST_10  C19   C18  C17  N16     0.00   0.0  0
 893  CONST_11  C20   C14  N16  C17     0.00   0.0  0
 893  CONST_12  C20   C19  C18  C17     0.00   0.0  0
 893  CONST_13  C9    C3   C2   C1    180.00   0.0  0
 893  CONST_14  O22   C5   C6   C1    180.00   0.0  0
 893  CONST_15  O22   C5   C4   C3    180.00   0.0  0
 893  CONST_16  O27   C2   C3   C4    180.00   0.0  0
 893  CONST_17  C9    C3   C4   C5    180.00   0.0  0
 893  CONST_18  O27   C2   C1   C6    180.00   0.0  0
 893  CONST_19  C17   N16  C14  C8    180.00   0.0  0
 893  CONST_20  C19   C20  C14  C8    180.00   0.0  0
 893  CONST_21  O36   C17  N16  C14   180.00   0.0  0
 893  CONST_22  C34   C18  C17  N16   180.00   0.0  0
 893  CONST_23  O36   C17  C18  C19   180.00   0.0  0
 893  CONST_24  C34   C18  C19  C20   180.00   0.0  0
 893  CONST_25  H6    C6   C1   C2    180.00   0.0  0
 893  CONST_26  H4    C4   C3   C2    180.00   0.0  0
 893  CONST_27  H1    C1   C2   C3    180.00   0.0  0
 893  CONST_28  H19   C19  C20  C14   180.00   0.0  0
 893  CONST_29  H20   C20  C14  N16   180.00   0.0  0
 893  CONST_30  C14   C8   N1   C9    180.00   0.0  0
 893  CONST_31  HN1   N1   C8   C14     0.00   0.0  0
 893  CONST_32  O1    C8   N1   C9      0.00   0.0  0
 893  Var_01    N1    C9   C3   C2     71.02  30.0  2
 893  Var_02    N16   C14  C8   N1     -4.81  30.0  2
 893  Var_03    C8    N1   C9   C3   -177.12  30.0  3
 893  Var_04    C7    C37  O36  C17  -178.60  30.0  3
 893  Var_05    H281  C28  O27  C2    -60.77  30.0  3
 893  Var_06    H231  C23  O22  C5    179.87  30.0  3
 893  Var_07    H71   C7   C37  O36    59.81  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
 893  plan-1  C1   0.020
 893  plan-1  C2   0.020
 893  plan-1  C3   0.020
 893  plan-1  C4   0.020
 893  plan-1  C5   0.020
 893  plan-1  C6   0.020
 893  plan-1  C9   0.020
 893  plan-1  O22  0.020
 893  plan-1  O27  0.020
 893  plan-1  H1   0.020
 893  plan-1  H4   0.020
 893  plan-1  H6   0.020
 893  plan-2  C8   0.020
 893  plan-2  C14  0.020
 893  plan-2  N16  0.020
 893  plan-2  C17  0.020
 893  plan-2  C18  0.020
 893  plan-2  C19  0.020
 893  plan-2  C20  0.020
 893  plan-2  C34  0.020
 893  plan-2  N35  0.020
 893  plan-2  O36  0.020
 893  plan-2  H19  0.020
 893  plan-2  H20  0.020
 893  plan-3  C9   0.020
 893  plan-3  N1   0.020
 893  plan-3  C8   0.020
 893  plan-3  C14  0.020
 893  plan-3  O1   0.020
 893  plan-3  HN1  0.020

