# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 12:11:56 2021
#   Inital geometry file: a 115 line input string
#   Ligand name: N-[(3-methoxyphenyl)methyl]-5H-[1]benzopyrano[3,4-c]pyridine-8-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(CNC(=O)c2ccc3c(OCc4cnccc34)c2)c1
#
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
 VFA  VFA  N-[(3-methoxyphenyl)methyl]-5H-[1]benzopyrano[3,4-c]pyridine-8-carboxamide  ligand  44  26  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VFA
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
 VFA  C1   C  CR16  0  -0.437  47.1232  72.6018  34.0512
 VFA  C2   C  CR6   0   0.117  47.4437  71.2578  34.2395
 VFA  C3   C  CR6   0   0.397  48.0121  73.5997  34.4387
 VFA  C4   C  CR16  0  -0.326  48.6543  70.9140  34.8217
 VFA  C5   C  CH2   0  -0.339  46.4682  70.2136  33.7454
 VFA  C6   C  CR16  0  -0.354  49.2301  73.2498  35.0269
 VFA  C7   C  CR16  0  -0.228  49.5373  71.9154  35.2138
 VFA  C8   C  CH3   0  -0.437  46.5638  75.3310  33.7006
 VFA  C9   C  CR16  0  -0.060  47.6694  61.2609  38.0785
 VFA  C10  C  CR16  0  -0.404  47.4236  62.4002  37.3296
 VFA  C11  C  CR66  0   0.287  46.9354  63.5306  37.9763
 VFA  C12  C  CR66  0  -0.114  46.7332  63.4559  39.3539
 VFA  C13  C  CR16  0  -0.091  47.0306  62.2727  40.0091
 VFA  C14  C  CR66  0  -0.017  46.6631  64.8104  37.3213
 VFA  C15  C  CR66  0   0.367  46.5734  65.9491  38.1324
 VFA  C16  C  C     0  -0.241  46.1687  64.6577  40.0428
 VFA  O1   O  O2    0  -0.473  47.7795  74.9185  34.2915
 VFA  C17  C  CR16  0  -0.314  46.5473  64.9668  35.9424
 VFA  C18  C  CR16  0  -0.292  46.3836  66.2184  35.3782
 VFA  O2   O  O     0  -0.475  46.6809  65.8569  39.4750
 VFA  N1   N  NH1   0  -0.652  46.5851  68.9311  34.3915
 VFA  C19  C  CR6   0  -0.039  46.3352  67.3489  36.1937
 VFA  O3   O  O     0  -0.474  45.6252  69.6105  36.3108
 VFA  C20  C  CR16  0  -0.373  46.4124  67.2075  37.5734
 VFA  C21  C  C     0   0.543  46.1471  68.7284  35.6454
 VFA  N2   N  N     0  -0.406  47.4829  61.1879  39.3917
 VFA  H1   H  HCR6  0   0.272  46.1690  72.8523  33.6042
 VFA  H2   H  HCR6  0   0.241  48.9161  69.8756  34.9781
 VFA  H3   H  HCH2  0   0.260  45.4476  70.5847  33.8535
 VFA  H4   H  HCH2  0   0.281  46.6272  70.0483  32.6786
 VFA  H5   H  HCR6  0   0.259  49.9201  74.0262  35.3337
 VFA  H6   H  HCR6  0   0.255  50.4806  71.6476  35.6726
 VFA  H7   H  HCH3  0   0.260  46.5864  76.4176  33.6735
 VFA  H8   H  HCH3  0   0.228  46.4567  74.9564  32.6790
 VFA  H9   H  HCH3  0   0.228  45.6957  75.0133  34.2845
 VFA  H11  H  HCR6  0   0.270  47.6243  62.3926  36.2669
 VFA  H12  H  HCR6  0   0.268  46.8913  62.1991  41.0834
 VFA  H13  H  H     0   0.250  45.0743  64.6580  39.9673
 VFA  H14  H  H     0   0.269  46.4308  64.6762  41.0994
 VFA  H15  H  HCR6  0   0.269  46.5773  64.0993  35.2965
 VFA  H16  H  HCR6  0   0.265  46.2747  66.2969  34.3048
 VFA  H17  H  HNH1  0   0.414  47.1177  68.2163  33.9248
 VFA  H18  H  HCR6  0   0.273  46.3556  68.0733  38.2206
 VFA  H10  H  HCR6  0   0.270  48.0440  60.3678  37.5917

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
 VFA  C5   C2   single    1.512  0.020  1.512
 VFA  C5   N1   single    1.441  0.020  1.441
 VFA  C8   O1   single    1.413  0.020  1.413
 VFA  C1   C2   aromatic  1.394  0.020  1.394
 VFA  C1   C3   aromatic  1.391  0.020  1.391
 VFA  C2   C4   aromatic  1.387  0.020  1.387
 VFA  O1   C3   single    1.347  0.020  1.347
 VFA  C3   C6   aromatic  1.397  0.020  1.397
 VFA  N1   C21  single    1.344  0.020  1.344
 VFA  C4   C7   aromatic  1.392  0.020  1.392
 VFA  C6   C7   aromatic  1.382  0.020  1.382
 VFA  C18  C17  aromatic  1.383  0.020  1.383
 VFA  C18  C19  aromatic  1.395  0.020  1.395
 VFA  C21  C19  single    1.496  0.020  1.496
 VFA  C21  O3   double    1.222  0.020  1.222
 VFA  C17  C14  aromatic  1.393  0.020  1.393
 VFA  C19  C20  aromatic  1.389  0.020  1.389
 VFA  C14  C11  aromatic  1.463  0.020  1.463
 VFA  C14  C15  aromatic  1.401  0.020  1.401
 VFA  C10  C11  aromatic  1.391  0.020  1.391
 VFA  C10  C9   aromatic  1.385  0.020  1.385
 VFA  C20  C15  aromatic  1.386  0.020  1.386
 VFA  C11  C12  aromatic  1.394  0.020  1.394
 VFA  C9   N2   aromatic  1.328  0.020  1.328
 VFA  C15  O2   single    1.350  0.020  1.350
 VFA  N2   C13  aromatic  1.328  0.020  1.328
 VFA  C12  C13  aromatic  1.385  0.020  1.385
 VFA  C12  C16  single    1.496  0.020  1.496
 VFA  O2   C16  single    1.422  0.020  1.422
 VFA  C1   H1   single    0.930  0.020  1.080
 VFA  C4   H2   single    0.930  0.020  1.080
 VFA  C5   H3   single    0.970  0.020  1.090
 VFA  C5   H4   single    0.970  0.020  1.090
 VFA  C6   H5   single    0.930  0.020  1.080
 VFA  C7   H6   single    0.930  0.020  1.080
 VFA  C8   H7   single    0.970  0.020  1.090
 VFA  C8   H8   single    0.970  0.020  1.090
 VFA  C8   H9   single    0.970  0.020  1.090
 VFA  C9   H10  single    0.930  0.020  1.080
 VFA  C10  H11  single    0.930  0.020  1.080
 VFA  C13  H12  single    0.930  0.020  1.080
 VFA  C16  H13  single    0.970  0.020  1.090
 VFA  C16  H14  single    0.970  0.020  1.090
 VFA  C17  H15  single    0.930  0.020  1.080
 VFA  C18  H16  single    0.930  0.020  1.080
 VFA  N1   H17  single    0.860  0.020  1.020
 VFA  C20  H18  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
 VFA  H1   C1   C3   120.79  3.000
 VFA  H1   C1   C2   118.76  3.000
 VFA  C3   C1   C2   120.45  3.000
 VFA  C5   C2   C4   121.95  3.000
 VFA  C4   C2   C1   119.76  3.000
 VFA  C5   C2   C1   118.24  3.000
 VFA  O1   C3   C6   116.21  3.000
 VFA  C6   C3   C1   119.64  3.000
 VFA  O1   C3   C1   124.15  3.000
 VFA  H2   C4   C7   119.75  3.000
 VFA  H2   C4   C2   120.65  3.000
 VFA  C7   C4   C2   119.60  3.000
 VFA  H4   C5   H3   106.54  3.000
 VFA  H4   C5   N1   106.96  3.000
 VFA  H3   C5   N1   109.52  3.000
 VFA  H4   C5   C2   109.27  3.000
 VFA  H3   C5   C2   109.64  3.000
 VFA  N1   C5   C2   114.57  3.000
 VFA  H5   C6   C7   120.81  3.000
 VFA  H5   C6   C3   119.68  3.000
 VFA  C7   C6   C3   119.51  3.000
 VFA  H6   C7   C6   119.33  3.000
 VFA  H6   C7   C4   119.63  3.000
 VFA  C6   C7   C4   121.04  3.000
 VFA  H9   C8   H8   108.76  3.000
 VFA  H9   C8   H7   108.68  3.000
 VFA  H8   C8   H7   108.73  3.000
 VFA  H9   C8   O1   112.02  3.000
 VFA  H8   C8   O1   112.02  3.000
 VFA  H7   C8   O1   106.52  3.000
 VFA  H10  C9   N2   116.57  3.000
 VFA  H10  C9   C10  119.75  3.000
 VFA  N2   C9   C10  123.68  3.000
 VFA  H11  C10  C11  121.85  3.000
 VFA  H11  C10  C9   119.50  3.000
 VFA  C11  C10  C9   118.64  3.000
 VFA  C14  C11  C12  117.52  3.000
 VFA  C12  C11  C10  117.82  3.000
 VFA  C14  C11  C10  124.62  3.000
 VFA  C16  C12  C13  123.34  3.000
 VFA  C16  C12  C11  117.82  3.000
 VFA  C13  C12  C11  118.82  3.000
 VFA  H12  C13  N2   116.65  3.000
 VFA  H12  C13  C12  119.90  3.000
 VFA  N2   C13  C12  123.45  3.000
 VFA  C17  C14  C15  118.47  3.000
 VFA  C15  C14  C11  117.63  3.000
 VFA  C17  C14  C11  123.84  3.000
 VFA  C20  C15  O2   118.18  3.000
 VFA  O2   C15  C14  121.00  3.000
 VFA  C20  C15  C14  120.78  3.000
 VFA  H14  C16  H13  107.87  3.000
 VFA  H14  C16  O2   106.64  3.000
 VFA  H13  C16  O2   109.37  3.000
 VFA  H14  C16  C12  111.70  3.000
 VFA  H13  C16  C12  110.18  3.000
 VFA  O2   C16  C12  110.96  3.000
 VFA  C8   O1   C3   118.68  3.000
 VFA  H15  C17  C18  119.04  3.000
 VFA  H15  C17  C14  119.92  3.000
 VFA  C18  C17  C14  121.04  3.000
 VFA  H16  C18  C19  121.19  3.000
 VFA  H16  C18  C17  118.85  3.000
 VFA  C19  C18  C17  119.95  3.000
 VFA  C16  O2   C15  115.21  3.000
 VFA  H17  N1   C21  119.88  3.000
 VFA  H17  N1   C5   117.86  3.000
 VFA  C21  N1   C5   121.76  3.000
 VFA  C21  C19  C20  117.70  3.000
 VFA  C20  C19  C18  119.75  3.000
 VFA  C21  C19  C18  122.51  3.000
 VFA  H18  C20  C19  120.63  3.000
 VFA  H18  C20  C15  119.41  3.000
 VFA  C19  C20  C15  119.96  3.000
 VFA  O3   C21  C19  121.31  3.000
 VFA  O3   C21  N1   122.58  3.000
 VFA  C19  C21  N1   116.11  3.000
 VFA  C13  N2   C9   117.56  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
 VFA  CONST_01  C7   C4   C2   C1      0.00   0.0  0
 VFA  CONST_02  C7   C6   C3   C1      0.00   0.0  0
 VFA  CONST_03  C6   C3   C1   C2      0.00   0.0  0
 VFA  CONST_04  C6   C7   C4   C2      0.00   0.0  0
 VFA  CONST_05  C4   C2   C1   C3      0.00   0.0  0
 VFA  CONST_06  C4   C7   C6   C3      0.00   0.0  0
 VFA  CONST_07  C14  C11  C10  C9    180.00   0.0  0
 VFA  CONST_08  C12  C11  C10  C9      0.00   0.0  0
 VFA  CONST_09  C12  C13  N2   C9      0.00   0.0  0
 VFA  CONST_12  C13  C12  C11  C10     0.00   0.0  0
 VFA  CONST_13  C13  N2   C9   C10     0.00   0.0  0
 VFA  CONST_14  C18  C17  C14  C11   180.00   0.0  0
 VFA  CONST_15  C20  C15  C14  C11   180.00   0.0  0
 VFA  CONST_16  N2   C9   C10  C11     0.00   0.0  0
 VFA  CONST_17  N2   C13  C12  C11     0.00   0.0  0
 VFA  CONST_18  C17  C14  C11  C12   180.00   0.0  0
 VFA  CONST_20  C14  C11  C12  C13   180.00   0.0  0
 VFA  CONST_21  C19  C18  C17  C14     0.00   0.0  0
 VFA  CONST_22  C19  C20  C15  C14     0.00   0.0  0
 VFA  CONST_23  C18  C17  C14  C15     0.00   0.0  0
 VFA  CONST_24  C18  C19  C20  C15     0.00   0.0  0
 VFA  CONST_25  C20  C19  C18  C17     0.00   0.0  0
 VFA  CONST_26  C20  C15  C14  C17     0.00   0.0  0
 VFA  CONST_27  O1   C3   C1   C2    180.00   0.0  0
 VFA  CONST_28  C5   C2   C1   C3    180.00   0.0  0
 VFA  CONST_29  C7   C4   C2   C5    180.00   0.0  0
 VFA  CONST_30  O1   C3   C6   C7    180.00   0.0  0
 VFA  CONST_31  C21  C19  C20  C15   180.00   0.0  0
 VFA  CONST_32  C21  C19  C18  C17   180.00   0.0  0
 VFA  CONST_33  H2   C4   C2   C1    180.00   0.0  0
 VFA  CONST_34  H5   C6   C3   C1    180.00   0.0  0
 VFA  CONST_35  H6   C7   C4   C2    180.00   0.0  0
 VFA  CONST_36  H1   C1   C2   C4    180.00   0.0  0
 VFA  CONST_37  H12  C13  N2   C9    180.00   0.0  0
 VFA  CONST_38  H15  C17  C14  C11     0.00   0.0  0
 VFA  CONST_39  H10  C9   C10  C11   180.00   0.0  0
 VFA  CONST_40  H11  C10  C11  C12   180.00   0.0  0
 VFA  CONST_41  H16  C18  C17  C14   180.00   0.0  0
 VFA  CONST_42  H18  C20  C15  C14   180.00   0.0  0
 VFA  CONST_43  C19  C21  N1   C5    180.00   0.0  0
 VFA  CONST_44  H17  N1   C21  C19     0.00   0.0  0
 VFA  CONST_45  O3   C21  N1   C5      0.00   0.0  0
 VFA  Var_01    O2   C16  C12  C11   -37.10  30.0  1
 VFA  Var_02    C20  C15  O2   C16   148.97  30.0  1
 VFA  Var_03    N1   C5   C2   C1   -157.53  30.0  1
 VFA  Var_04    N1   C21  C19  C18   -27.59  30.0  2
 VFA  Var_05    C21  N1   C5   C2     74.29  30.0  3
 VFA  Var_06    H7   C8   O1   C3   -179.61  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
 VFA  plan-1  C1   0.020
 VFA  plan-1  C2   0.020
 VFA  plan-1  C3   0.020
 VFA  plan-1  C4   0.020
 VFA  plan-1  C5   0.020
 VFA  plan-1  C6   0.020
 VFA  plan-1  C7   0.020
 VFA  plan-1  O1   0.020
 VFA  plan-1  H1   0.020
 VFA  plan-1  H2   0.020
 VFA  plan-1  H5   0.020
 VFA  plan-1  H6   0.020
 VFA  plan-2  C9   0.020
 VFA  plan-2  C10  0.020
 VFA  plan-2  C11  0.020
 VFA  plan-2  C12  0.020
 VFA  plan-2  C13  0.020
 VFA  plan-2  C14  0.020
 VFA  plan-2  C16  0.020
 VFA  plan-2  N2   0.020
 VFA  plan-2  H11  0.020
 VFA  plan-2  H12  0.020
 VFA  plan-2  H10  0.020
 VFA  plan-3  C11  0.020
 VFA  plan-3  C14  0.020
 VFA  plan-3  C15  0.020
 VFA  plan-3  C17  0.020
 VFA  plan-3  C18  0.020
 VFA  plan-3  O2   0.020
 VFA  plan-3  C19  0.020
 VFA  plan-3  C20  0.020
 VFA  plan-3  C21  0.020
 VFA  plan-3  H15  0.020
 VFA  plan-3  H16  0.020
 VFA  plan-3  H18  0.020
 VFA  plan-4  C5   0.020
 VFA  plan-4  N1   0.020
 VFA  plan-4  C19  0.020
 VFA  plan-4  O3   0.020
 VFA  plan-4  C21  0.020
 VFA  plan-4  H17  0.020

