# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 07:40:27 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: N-(pyridin-4-ylmethyl)-2,3-dihydro-1,4-benzodioxin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1COc2cc(NCc3ccncc3)ccc2O1
#
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
 F91  F91  N-(pyridin-4-ylmethyl)-2,3-dihydro-1,4-benzodioxin-6-amine  ligand  32  18  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F91
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
 F91  C1    C  CR6   0   0.337   2.7046   0.6061   0.1186
 F91  O2    O  O2    0  -0.484   3.5601   1.6527   0.1973
 F91  C3    C  CH2   0  -0.222   4.9003   1.3000   0.5066
 F91  C4    C  CH2   0  -0.227   5.3181   0.0818  -0.2820
 F91  O5    O  O2    0  -0.486   4.4889  -1.0192   0.0457
 F91  C6    C  CR6   0   0.281   3.1611  -0.7148   0.0470
 F91  C7    C  CR16  0  -0.354   2.2290  -1.7341  -0.0345
 F91  C8    C  CR16  0  -0.357   0.8657  -1.4702  -0.0452
 F91  C9    C  CR6   0   0.371   0.4034  -0.1528   0.0235
 F91  N10   N  NH1   0  -0.701  -0.9448   0.1688   0.0545
 F91  C11   C  CH2   0  -0.320  -1.9336  -0.8085  -0.3273
 F91  C12   C  CR6   0   0.167  -3.3266  -0.2723  -0.1530
 F91  C13   C  CR16  0  -0.467   1.3459   0.8767   0.1068
 F91  C14   C  CR16  0  -0.363  -3.6779   0.5250   0.9319
 F91  C15   C  CR16  0  -0.057  -4.9902   0.9537   1.0536
 F91  N16   N  N     0  -0.410  -5.9503   0.6475   0.1873
 F91  C17   C  CR16  0  -0.060  -5.6127  -0.1124  -0.8476
 F91  C18   C  CR16  0  -0.374  -4.3284  -0.5898  -1.0618
 F91  H3    H  HCH2  0   0.258   5.5246   2.1546   0.2486
 F91  H3A   H  HCH2  0   0.241   5.0013   1.1110   1.5808
 F91  H4    H  HCH2  0   0.237   5.2674   0.2905  -1.3569
 F91  H4A   H  HCH2  0   0.258   6.3418  -0.1961  -0.0343
 F91  H7    H  HCR6  0   0.262   2.5758  -2.7585  -0.0983
 F91  H8    H  HCR6  0   0.266   0.1796  -2.3020  -0.1198
 F91  HN10  H  HNH1  0   0.378  -1.1426   1.0940  -0.2967
 F91  H11   H  HCH2  0   0.240  -1.8051  -1.1676  -1.3572
 F91  H11A  H  HCH2  0   0.263  -1.8355  -1.6873   0.3177
 F91  H13   H  HCR6  0   0.265   1.0201   1.9093   0.1707
 F91  H14   H  HCR6  0   0.267  -2.9460   0.8118   1.6751
 F91  H15   H  HCR6  0   0.263  -5.2779   1.5745   1.8952
 F91  H17   H  HCR6  0   0.264  -6.4023  -0.3538  -1.5508
 F91  H18   H  HCR6  0   0.267  -4.1174  -1.1990  -1.9316

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
 F91  O2   C1    single    1.354  0.020  1.354
 F91  C6   C1    aromatic  1.399  0.020  1.399
 F91  C1   C13   aromatic  1.385  0.020  1.385
 F91  C3   O2    single    1.420  0.020  1.420
 F91  C3   C4    single    1.510  0.020  1.510
 F91  C3   H3    single    0.970  0.020  1.090
 F91  C3   H3A   single    0.970  0.020  1.090
 F91  C4   O5    single    1.417  0.020  1.417
 F91  C4   H4    single    0.970  0.020  1.090
 F91  C4   H4A   single    0.970  0.020  1.090
 F91  O5   C6    single    1.362  0.020  1.362
 F91  C6   C7    aromatic  1.384  0.020  1.384
 F91  C7   C8    aromatic  1.389  0.020  1.389
 F91  C7   H7    single    0.930  0.020  1.080
 F91  C8   C9    aromatic  1.398  0.020  1.398
 F91  C8   H8    single    0.930  0.020  1.080
 F91  C13  C9    aromatic  1.398  0.020  1.398
 F91  C9   N10   single    1.386  0.020  1.386
 F91  N10  C11   single    1.442  0.020  1.442
 F91  N10  HN10  single    0.890  0.020  1.040
 F91  C12  C11   single    1.503  0.020  1.503
 F91  C11  H11   single    0.970  0.020  1.090
 F91  C11  H11A  single    0.970  0.020  1.090
 F91  C14  C12   aromatic  1.391  0.020  1.391
 F91  C12  C18   aromatic  1.389  0.020  1.389
 F91  C13  H13   single    0.930  0.020  1.080
 F91  C15  C14   aromatic  1.386  0.020  1.386
 F91  C14  H14   single    0.930  0.020  1.080
 F91  C15  N16   aromatic  1.329  0.020  1.329
 F91  C15  H15   single    0.930  0.020  1.080
 F91  N16  C17   aromatic  1.328  0.020  1.328
 F91  C17  C18   aromatic  1.387  0.020  1.387
 F91  C17  H17   single    0.930  0.020  1.080
 F91  C18  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
 F91  C13   C1   C6   120.25  3.000
 F91  C13   C1   O2   117.98  3.000
 F91  C6    C1   O2   121.77  3.000
 F91  C3    O2   C1   114.64  3.000
 F91  H3A   C3   H3   108.35  3.000
 F91  H3A   C3   C4   110.34  3.000
 F91  H3    C3   C4   110.53  3.000
 F91  H3A   C3   O2   110.09  3.000
 F91  H3    C3   O2   107.12  3.000
 F91  C4    C3   O2   110.35  3.000
 F91  H4A   C4   H4   108.37  3.000
 F91  H4A   C4   O5   107.41  3.000
 F91  H4    C4   O5   110.35  3.000
 F91  H4A   C4   C3   110.31  3.000
 F91  H4    C4   C3   110.23  3.000
 F91  O5    C4   C3   110.13  3.000
 F91  C6    O5   C4   113.39  3.000
 F91  C7    C6   O5   119.47  3.000
 F91  C7    C6   C1   118.60  3.000
 F91  O5    C6   C1   121.93  3.000
 F91  H7    C7   C8   119.58  3.000
 F91  H7    C7   C6   118.97  3.000
 F91  C8    C7   C6   121.45  3.000
 F91  H8    C8   C9   121.24  3.000
 F91  H8    C8   C7   118.52  3.000
 F91  C9    C8   C7   120.23  3.000
 F91  C13   C9   N10  118.91  3.000
 F91  N10   C9   C8   122.78  3.000
 F91  C13   C9   C8   118.28  3.000
 F91  HN10  N10  C11  113.26  3.000
 F91  HN10  N10  C9   113.30  3.000
 F91  C11   N10  C9   120.25  3.000
 F91  H11A  C11  H11  106.23  3.000
 F91  H11A  C11  C12  107.53  3.000
 F91  H11   C11  C12  109.51  3.000
 F91  H11A  C11  N10  109.07  3.000
 F91  H11   C11  N10  112.94  3.000
 F91  C12   C11  N10  111.30  3.000
 F91  C18   C12  C14  117.32  3.000
 F91  C18   C12  C11  120.73  3.000
 F91  C14   C12  C11  121.93  3.000
 F91  H13   C13  C9   120.13  3.000
 F91  H13   C13  C1   118.68  3.000
 F91  C9    C13  C1   121.19  3.000
 F91  H14   C14  C15  119.88  3.000
 F91  H14   C14  C12  121.12  3.000
 F91  C15   C14  C12  119.00  3.000
 F91  H15   C15  N16  116.49  3.000
 F91  H15   C15  C14  119.76  3.000
 F91  N16   C15  C14  123.75  3.000
 F91  C17   N16  C15  117.15  3.000
 F91  H17   C17  C18  119.83  3.000
 F91  H17   C17  N16  116.60  3.000
 F91  C18   C17  N16  123.57  3.000
 F91  H18   C18  C17  119.89  3.000
 F91  H18   C18  C12  120.90  3.000
 F91  C17   C18  C12  119.21  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
 F91  CONST_01  C8   C7   C6   C1     0.00   0.0  0
 F91  CONST_02  C8   C9   C13  C1     0.00   0.0  0
 F91  CONST_03  C9   C13  C1   C6     0.00   0.0  0
 F91  CONST_04  C9   C8   C7   C6     0.00   0.0  0
 F91  CONST_05  C13  C1   C6   C7     0.00   0.0  0
 F91  CONST_06  C13  C9   C8   C7     0.00   0.0  0
 F91  CONST_07  N16  C15  C14  C12    0.00   0.0  0
 F91  CONST_08  N16  C17  C18  C12    0.00   0.0  0
 F91  CONST_09  C17  C18  C12  C14    0.00   0.0  0
 F91  CONST_10  C17  N16  C15  C14    0.00   0.0  0
 F91  CONST_11  C18  C12  C14  C15    0.00   0.0  0
 F91  CONST_12  C18  C17  N16  C15    0.00   0.0  0
 F91  CONST_13  N10  C9   C13  C1   180.00   0.0  0
 F91  CONST_14  N10  C9   C8   C7   180.00   0.0  0
 F91  CONST_15  C15  C14  C12  C11  180.00   0.0  0
 F91  CONST_16  C17  C18  C12  C11  180.00   0.0  0
 F91  CONST_17  H7   C7   C6   C1   180.00   0.0  0
 F91  CONST_18  H13  C13  C1   O2     0.00   0.0  0
 F91  CONST_19  H8   C8   C7   C6   180.00   0.0  0
 F91  CONST_20  H15  C15  C14  C12  180.00   0.0  0
 F91  CONST_21  H17  C17  C18  C12  180.00   0.0  0
 F91  CONST_22  H18  C18  C12  C14  180.00   0.0  0
 F91  CONST_23  H14  C14  C15  N16  180.00   0.0  0
 F91  CONST_25  C13  C9   N10  C11  180.00   0.0  0
 F91  Var_01    C4   C3   O2   C1    42.92  30.0  1
 F91  Var_02    O5   C4   C3   O2   -60.86  30.0  1
 F91  Var_03    C6   C1   O2   C3   -13.72  30.0  1
 F91  Var_04    C7   C6   O5   C4   161.52  30.0  1
 F91  Var_05    C12  C11  N10  C9   177.11  30.0  3
 F91  Var_06    C14  C12  C11  N10  -39.07  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
 F91  plan-1  C11   0.020
 F91  plan-1  C12   0.020
 F91  plan-1  C14   0.020
 F91  plan-1  C15   0.020
 F91  plan-1  N16   0.020
 F91  plan-1  C17   0.020
 F91  plan-1  C18   0.020
 F91  plan-1  H14   0.020
 F91  plan-1  H15   0.020
 F91  plan-1  H17   0.020
 F91  plan-1  H18   0.020
 F91  plan-2  C1    0.020
 F91  plan-2  O2    0.020
 F91  plan-2  O5    0.020
 F91  plan-2  C6    0.020
 F91  plan-2  C7    0.020
 F91  plan-2  C8    0.020
 F91  plan-2  C9    0.020
 F91  plan-2  N10   0.020
 F91  plan-2  C13   0.020
 F91  plan-2  H7    0.020
 F91  plan-2  H8    0.020
 F91  plan-2  H13   0.020
 F91  plan-3  C9    0.020
 F91  plan-3  N10   0.020
 F91  plan-3  C11   0.020
 F91  plan-3  HN10  0.020

