# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 17:53:40 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 10-[(4-fluorophenyl)methyl]-2,3,4,10-tetrahydropyrimido[1,2-a]benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(CN2c3ccccc3N4CCCN=C24)cc1
#
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
 FVV  FVV  10-[(4-fluorophenyl)methyl]-2,3,4,10-tetrahydropyrimido[1,2-a]benzimidazole  ligand  37  21  .  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_FVV
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
 FVV  C10  C  CR6   0   0.516  -4.1774  -0.3515  -0.6088
 FVV  C13  C  CR16  0  -0.324   0.6968  -2.3875   0.4193
 FVV  C15  C  CR16  0  -0.298  -2.7544  -1.0757   1.1542
 FVV  C17  C  CR16  0  -0.397  -3.3382   0.7124  -0.8881
 FVV  C20  C  CR16  0  -0.278   1.4594  -3.3268  -0.2809
 FVV  C21  C  CR16  0  -0.277   2.5607  -2.9428  -1.0332
 FVV  C01  C  CR5   0   0.712   1.2968   1.1754   0.4987
 FVV  N02  N  NR5   0  -0.596   0.5629   0.0795   0.9077
 FVV  N03  N  NR5   0  -0.611   2.3019   0.6884  -0.3053
 FVV  C04  C  CR56  0   0.327   1.0799  -1.0644   0.3367
 FVV  C05  C  CR56  0   0.332   2.1915  -0.6776  -0.4271
 FVV  N06  N  N     0  -0.523   1.0594   2.3852   0.8183
 FVV  C08  C  CH2   0  -0.279   3.2937   1.5682  -0.8820
 FVV  C09  C  CR6   0   0.112  -1.8866  -0.0211   0.9024
 FVV  F11  F  F     0  -0.316  -5.2890  -0.5112  -1.3459
 FVV  C12  C  CH2   0  -0.314   1.9738   3.3650   0.2622
 FVV  C14  C  CR16  0  -0.338   2.9458  -1.6021  -1.1194
 FVV  C16  C  CR16  0  -0.268  -2.1930   0.8706  -0.1242
 FVV  C18  C  CR16  0  -0.398  -3.9102  -1.2508   0.4025
 FVV  C19  C  CH2   0  -0.508   3.3720   2.8171  -0.0160
 FVV  H2   H  HCR6  0   0.265  -2.5375  -1.7779   1.9504
 FVV  H3   H  HCR6  0   0.280  -3.5763   1.4072  -1.6828
 FVV  H4   H  HCR6  0   0.252   1.1793  -4.3707  -0.2343
 FVV  H5   H  HCR6  0   0.252   3.1324  -3.6901  -1.5672
 FVV  H9   H  HCH2  0   0.262   4.2532   1.0502  -0.9141
 FVV  H10  H  HCH2  0   0.249   3.0191   1.8217  -1.9096
 FVV  H11  H  HCH2  0   0.216   1.5590   3.7780  -0.6661
 FVV  H12  H  HCH2  0   0.228   2.0482   4.2061   0.9552
 FVV  H13  H  HCR6  0   0.267   3.8038  -1.3066  -1.7093
 FVV  H14  H  HCR6  0   0.265  -1.5318   1.7051  -0.3253
 FVV  H15  H  HCR6  0   0.281  -4.5848  -2.0734   0.6009
 FVV  H16  H  HCH2  0   0.242   3.8665   2.5713   0.9272
 FVV  H17  H  HCH2  0   0.253   3.9820   3.5692  -0.5169
 FVV  C07  C  CH2   0  -0.409  -0.6288   0.1602   1.7133
 FVV  H1   H  HCR6  0   0.259  -0.1631  -2.6982   0.9976
 FVV  H7   H  HCH2  0   0.278  -0.5772  -0.5877   2.5081
 FVV  H8   H  HCH2  0   0.287  -0.6211   1.1381   2.1953

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
 FVV  F11  C10  single    1.343  0.020  1.343
 FVV  C17  C10  aromatic  1.384  0.020  1.384
 FVV  C17  C16  aromatic  1.386  0.020  1.386
 FVV  C10  C18  aromatic  1.379  0.020  1.379
 FVV  C16  C09  aromatic  1.394  0.020  1.394
 FVV  C20  C13  aromatic  1.398  0.020  1.398
 FVV  C20  C21  aromatic  1.388  0.020  1.388
 FVV  C18  C15  aromatic  1.390  0.020  1.390
 FVV  C13  C04  aromatic  1.380  0.020  1.380
 FVV  C09  C15  aromatic  1.389  0.020  1.389
 FVV  C09  C07  single    1.507  0.020  1.507
 FVV  C21  C14  aromatic  1.398  0.020  1.398
 FVV  C07  N02  single    1.441  0.020  1.441
 FVV  C04  N02  single    1.379  0.020  1.379
 FVV  C04  C05  aromatic  1.403  0.020  1.403
 FVV  N02  C01  single    1.381  0.020  1.381
 FVV  C14  C05  aromatic  1.379  0.020  1.379
 FVV  C05  N03  single    1.376  0.020  1.376
 FVV  C01  N03  single    1.376  0.020  1.376
 FVV  C01  N06  double    1.274  0.020  1.274
 FVV  N03  C08  single    1.446  0.020  1.446
 FVV  N06  C12  single    1.451  0.020  1.451
 FVV  C08  C19  single    1.522  0.020  1.522
 FVV  C12  C19  single    1.527  0.020  1.527
 FVV  C13  H1   single    0.930  0.020  1.080
 FVV  C15  H2   single    0.930  0.020  1.080
 FVV  C17  H3   single    0.930  0.020  1.080
 FVV  C20  H4   single    0.930  0.020  1.080
 FVV  C21  H5   single    0.930  0.020  1.080
 FVV  C07  H7   single    0.970  0.020  1.090
 FVV  C07  H8   single    0.970  0.020  1.090
 FVV  C08  H9   single    0.970  0.020  1.090
 FVV  C08  H10  single    0.970  0.020  1.090
 FVV  C12  H11  single    0.970  0.020  1.090
 FVV  C12  H12  single    0.970  0.020  1.090
 FVV  C14  H13  single    0.930  0.020  1.080
 FVV  C16  H14  single    0.930  0.020  1.080
 FVV  C18  H15  single    0.930  0.020  1.080
 FVV  C19  H16  single    0.970  0.020  1.090
 FVV  C19  H17  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
 FVV  C18  C10  F11  119.02  3.000
 FVV  C18  C10  C17  122.13  3.000
 FVV  F11  C10  C17  118.86  3.000
 FVV  H1   C13  C04  121.87  3.000
 FVV  H1   C13  C20  120.56  3.000
 FVV  C04  C13  C20  117.57  3.000
 FVV  H2   C15  C18  118.83  3.000
 FVV  H2   C15  C09  120.02  3.000
 FVV  C18  C15  C09  121.15  3.000
 FVV  H3   C17  C16  120.89  3.000
 FVV  H3   C17  C10  120.56  3.000
 FVV  C16  C17  C10  118.54  3.000
 FVV  H4   C20  C21  119.72  3.000
 FVV  H4   C20  C13  119.05  3.000
 FVV  C21  C20  C13  121.23  3.000
 FVV  H5   C21  C14  119.12  3.000
 FVV  H5   C21  C20  119.72  3.000
 FVV  C14  C21  C20  121.16  3.000
 FVV  N06  C01  N03  128.24  3.000
 FVV  N06  C01  N02  125.49  3.000
 FVV  N03  C01  N02  106.28  3.000
 FVV  C07  N02  C04  126.02  3.000
 FVV  C04  N02  C01  109.66  3.000
 FVV  C07  N02  C01  124.11  3.000
 FVV  C08  N03  C05  128.60  3.000
 FVV  C08  N03  C01  121.24  3.000
 FVV  C05  N03  C01  110.15  3.000
 FVV  C05  C04  N02  107.08  3.000
 FVV  C05  C04  C13  121.13  3.000
 FVV  N02  C04  C13  131.79  3.000
 FVV  C14  C05  C04  121.44  3.000
 FVV  C14  C05  N03  131.75  3.000
 FVV  C04  C05  N03  106.81  3.000
 FVV  C12  N06  C01  115.33  3.000
 FVV  H10  C08  H9   107.66  3.000
 FVV  H10  C08  C19  110.95  3.000
 FVV  H9   C08  C19  111.17  3.000
 FVV  H10  C08  N03  110.10  3.000
 FVV  H9   C08  N03  109.04  3.000
 FVV  C19  C08  N03  107.92  3.000
 FVV  C16  C09  C07  120.18  3.000
 FVV  C07  C09  C15  121.01  3.000
 FVV  C16  C09  C15  118.81  3.000
 FVV  H12  C12  H11  105.82  3.000
 FVV  H12  C12  C19  109.24  3.000
 FVV  H11  C12  C19  109.09  3.000
 FVV  H12  C12  N06  108.65  3.000
 FVV  H11  C12  N06  109.88  3.000
 FVV  C19  C12  N06  113.86  3.000
 FVV  H13  C14  C05  121.60  3.000
 FVV  H13  C14  C21  120.93  3.000
 FVV  C05  C14  C21  117.47  3.000
 FVV  H14  C16  C09  119.68  3.000
 FVV  H14  C16  C17  119.34  3.000
 FVV  C09  C16  C17  120.98  3.000
 FVV  H15  C18  C15  121.00  3.000
 FVV  H15  C18  C10  120.61  3.000
 FVV  C15  C18  C10  118.39  3.000
 FVV  H17  C19  H16  107.37  3.000
 FVV  H17  C19  C12  110.39  3.000
 FVV  H16  C19  C12  109.74  3.000
 FVV  H17  C19  C08  109.48  3.000
 FVV  H16  C19  C08  109.26  3.000
 FVV  C12  C19  C08  110.55  3.000
 FVV  H8   C07  H7   106.98  3.000
 FVV  H8   C07  C09  110.59  3.000
 FVV  H7   C07  C09  110.39  3.000
 FVV  H8   C07  N02  106.95  3.000
 FVV  H7   C07  N02  109.23  3.000
 FVV  C09  C07  N02  112.50  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
 FVV  CONST_01  C09  C16  C17  C10    0.00   0.0  0
 FVV  CONST_02  C09  C15  C18  C10    0.00   0.0  0
 FVV  CONST_03  C14  C21  C20  C13    0.00   0.0  0
 FVV  CONST_04  C14  C05  C04  C13    0.00   0.0  0
 FVV  CONST_05  C17  C10  C18  C15    0.00   0.0  0
 FVV  CONST_06  C17  C16  C09  C15    0.00   0.0  0
 FVV  CONST_07  C05  C04  C13  C20    0.00   0.0  0
 FVV  CONST_08  C05  C14  C21  C20    0.00   0.0  0
 FVV  CONST_09  C04  C13  C20  C21    0.00   0.0  0
 FVV  CONST_10  C04  C05  C14  C21    0.00   0.0  0
 FVV  CONST_11  C18  C10  C17  C16    0.00   0.0  0
 FVV  CONST_12  C18  C15  C09  C16    0.00   0.0  0
 FVV  CONST_13  C05  C04  N02  C01    0.00   0.0  0
 FVV  CONST_14  C04  C05  N03  C01    0.00   0.0  0
 FVV  CONST_15  N03  C05  C04  N02    0.00   0.0  0
 FVV  CONST_16  C05  N03  C01  N02    0.00   0.0  0
 FVV  CONST_17  C08  N03  C01  N02  180.00   0.0  0
 FVV  CONST_18  C12  N06  C01  N02  180.00   0.0  0
 FVV  CONST_19  C04  N02  C01  N03    0.00   0.0  0
 FVV  CONST_20  C12  N06  C01  N03    0.00   0.0  0
 FVV  CONST_21  N06  C01  N02  C04  180.00   0.0  0
 FVV  CONST_22  C08  N03  C05  C04  180.00   0.0  0
 FVV  CONST_23  N06  C01  N03  C05  180.00   0.0  0
 FVV  CONST_24  C08  N03  C01  N06    0.00   0.0  0
 FVV  CONST_25  F11  C10  C18  C15  180.00   0.0  0
 FVV  CONST_26  C07  C09  C16  C17  180.00   0.0  0
 FVV  CONST_27  C18  C15  C09  C07  180.00   0.0  0
 FVV  CONST_28  C16  C17  C10  F11  180.00   0.0  0
 FVV  CONST_29  C07  N02  C01  N03  180.00   0.0  0
 FVV  CONST_30  C07  N02  C04  C05  180.00   0.0  0
 FVV  CONST_31  C07  N02  C01  N06    0.00   0.0  0
 FVV  CONST_32  H14  C16  C17  C10  180.00   0.0  0
 FVV  CONST_33  H2   C15  C18  C10  180.00   0.0  0
 FVV  CONST_34  H5   C21  C20  C13  180.00   0.0  0
 FVV  CONST_35  H15  C18  C10  C17  180.00   0.0  0
 FVV  CONST_36  H13  C14  C21  C20  180.00   0.0  0
 FVV  CONST_37  H1   C13  C20  C21  180.00   0.0  0
 FVV  CONST_38  H4   C20  C13  C04  180.00   0.0  0
 FVV  CONST_39  H3   C17  C16  C09  180.00   0.0  0
 FVV  Var_01    C19  C08  N03  C01   23.69  30.0  1
 FVV  Var_02    C19  C12  N06  C01  -27.96  30.0  1
 FVV  Var_03    C12  C19  C08  N03  -48.50  30.0  1
 FVV  Var_04    C08  C19  C12  N06   53.41  30.0  1
 FVV  Var_05    N02  C07  C09  C15  118.56  30.0  2
 FVV  Var_06    C09  C07  N02  C01  102.45  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
 FVV  plan-1  C10  0.020
 FVV  plan-1  C15  0.020
 FVV  plan-1  C17  0.020
 FVV  plan-1  C09  0.020
 FVV  plan-1  F11  0.020
 FVV  plan-1  C16  0.020
 FVV  plan-1  C18  0.020
 FVV  plan-1  H2   0.020
 FVV  plan-1  H3   0.020
 FVV  plan-1  H14  0.020
 FVV  plan-1  H15  0.020
 FVV  plan-1  C07  0.020
 FVV  plan-2  C13  0.020
 FVV  plan-2  C20  0.020
 FVV  plan-2  C21  0.020
 FVV  plan-2  C01  0.020
 FVV  plan-2  N02  0.020
 FVV  plan-2  N03  0.020
 FVV  plan-2  C04  0.020
 FVV  plan-2  C05  0.020
 FVV  plan-2  N06  0.020
 FVV  plan-2  C08  0.020
 FVV  plan-2  C12  0.020
 FVV  plan-2  C14  0.020
 FVV  plan-2  H4   0.020
 FVV  plan-2  H5   0.020
 FVV  plan-2  H13  0.020
 FVV  plan-2  C07  0.020
 FVV  plan-2  H1   0.020

