# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 06:42:55 2022
#   Inital geometry file: a 65 line input string
#   Ligand name: 1-(3,4-dihydro-2H-1,5-benzodioxepin-6-yl)methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1cccc2OCCCOc12
#
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
 VXU  VXU  1-(3,4-dihydro-2H-1,5-benzodioxepin-6-yl)methanamine  ligand  26  13  .  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_VXU
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
 VXU  C2    C  CR16  0  -0.252  -1.3153   2.4534   0.2887
 VXU  C3    C  CR16  0  -0.321  -2.1145   1.3376   0.0827
 VXU  C1    C  CR16  0  -0.369   0.0621   2.3439   0.1864
 VXU  C4    C  CR6   0  -0.008  -1.5542   0.1051  -0.2346
 VXU  C11   C  CR6   0   0.319   0.6422   1.1244  -0.1429
 VXU  C5    C  CR6   0   0.295  -0.1671   0.0048  -0.3612
 VXU  C8    C  CH2   0  -0.472   2.6212  -1.2628   0.1746
 VXU  C9    C  CH2   0  -0.199   2.6909   0.1905   0.5962
 VXU  C7    C  CH2   0  -0.192   1.2174  -1.8325   0.1827
 VXU  C12   C  CH2   0  -0.344  -2.4219  -1.1126  -0.4012
 VXU  N13   N  NH2   0  -0.779  -2.2752  -1.9977   0.7479
 VXU  O10   O  O2    0  -0.498   1.9923   1.0653  -0.2877
 VXU  O6    O  O2    0  -0.488   0.3682  -1.1775  -0.7543
 VXU  H2    H  HCR6  0   0.254  -1.7631   3.4057   0.5404
 VXU  H3    H  HCR6  0   0.249  -3.1909   1.4203   0.1749
 VXU  H1    H  HCR6  0   0.263   0.7004   3.2030   0.3514
 VXU  H121  H  HCH2  0   0.213  -3.4541  -0.7800  -0.5709
 VXU  H122  H  HCH2  0   0.233  -2.1264  -1.6640  -1.2951
 VXU  H81C  H  HCH2  0   0.239   3.0664  -1.3871  -0.8160
 VXU  H82C  H  HCH2  0   0.243   3.2326  -1.8443   0.8700
 VXU  H91C  H  HCH2  0   0.219   2.3117   0.3123   1.6174
 VXU  H92C  H  HCH2  0   0.248   3.7268   0.5301   0.5867
 VXU  H71C  H  HCH2  0   0.243   1.2396  -2.8807  -0.1161
 VXU  H72C  H  HCH2  0   0.217   0.7758  -1.7842   1.1833
 VXU  H131  H  HNH2  0   0.339  -2.6859  -1.5549   1.5607
 VXU  H132  H  HNH2  0   0.348  -2.8175  -2.8379   0.5888

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
 VXU  C2   C3    aromatic  1.388  0.020  1.388
 VXU  C2   C1    aromatic  1.386  0.020  1.386
 VXU  C3   C4    aromatic  1.391  0.020  1.391
 VXU  C1   C11   aromatic  1.390  0.020  1.390
 VXU  C4   C5    aromatic  1.396  0.020  1.396
 VXU  C4   C12   single    1.504  0.020  1.504
 VXU  C11  C5    aromatic  1.399  0.020  1.399
 VXU  C11  O10   single    1.359  0.020  1.359
 VXU  C5   O6    single    1.356  0.020  1.356
 VXU  C8   C9    single    1.515  0.020  1.515
 VXU  C8   C7    single    1.515  0.020  1.515
 VXU  C9   O10   single    1.426  0.020  1.426
 VXU  C7   O6    single    1.424  0.020  1.424
 VXU  C12  N13   single    1.458  0.020  1.458
 VXU  C2   H2    single    0.930  0.020  1.080
 VXU  C3   H3    single    0.930  0.020  1.080
 VXU  C1   H1    single    0.930  0.020  1.080
 VXU  C12  H121  single    0.970  0.020  1.090
 VXU  C12  H122  single    0.970  0.020  1.090
 VXU  C8   H81C  single    0.970  0.020  1.090
 VXU  C8   H82C  single    0.970  0.020  1.090
 VXU  C9   H91C  single    0.970  0.020  1.090
 VXU  C9   H92C  single    0.970  0.020  1.090
 VXU  C7   H71C  single    0.970  0.020  1.090
 VXU  C7   H72C  single    0.970  0.020  1.090
 VXU  N13  H131  single    0.890  0.020  1.040
 VXU  N13  H132  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
 VXU  H2    C2   C1    119.88  3.000
 VXU  H2    C2   C3    120.26  3.000
 VXU  C1    C2   C3    119.86  3.000
 VXU  H3    C3   C4    119.16  3.000
 VXU  H3    C3   C2    119.87  3.000
 VXU  C4    C3   C2    120.97  3.000
 VXU  H1    C1   C11   119.08  3.000
 VXU  H1    C1   C2    120.80  3.000
 VXU  C11   C1   C2    120.12  3.000
 VXU  C12   C4   C5    120.32  3.000
 VXU  C12   C4   C3    120.68  3.000
 VXU  C5    C4   C3    118.98  3.000
 VXU  O10   C11  C5    121.56  3.000
 VXU  O10   C11  C1    118.56  3.000
 VXU  C5    C11  C1    119.85  3.000
 VXU  O6    C5   C11   120.98  3.000
 VXU  O6    C5   C4    118.75  3.000
 VXU  C11   C5   C4    120.21  3.000
 VXU  H82C  C8   H81C  106.74  3.000
 VXU  H82C  C8   C7    108.34  3.000
 VXU  H81C  C8   C7    109.85  3.000
 VXU  H82C  C8   C9    107.91  3.000
 VXU  H81C  C8   C9    110.04  3.000
 VXU  C7    C8   C9    113.69  3.000
 VXU  H92C  C9   H91C  107.59  3.000
 VXU  H92C  C9   O10   105.61  3.000
 VXU  H91C  C9   O10   109.87  3.000
 VXU  H92C  C9   C8    109.88  3.000
 VXU  H91C  C9   C8    110.48  3.000
 VXU  O10   C9   C8    113.16  3.000
 VXU  H72C  C7   H71C  107.53  3.000
 VXU  H72C  C7   O6    109.91  3.000
 VXU  H71C  C7   O6    105.90  3.000
 VXU  H72C  C7   C8    111.23  3.000
 VXU  H71C  C7   C8    109.95  3.000
 VXU  O6    C7   C8    112.09  3.000
 VXU  H122  C12  H121  106.33  3.000
 VXU  H122  C12  N13   108.16  3.000
 VXU  H121  C12  N13   113.61  3.000
 VXU  H122  C12  C4    110.09  3.000
 VXU  H121  C12  C4    108.32  3.000
 VXU  N13   C12  C4    110.25  3.000
 VXU  H132  N13  H131  105.76  3.000
 VXU  H132  N13  C12   109.03  3.000
 VXU  H131  N13  C12   109.05  3.000
 VXU  C9    O10  C11   116.56  3.000
 VXU  C7    O6   C5    116.46  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
 VXU  CONST_01  C5    C4   C3   C2      0.00   0.0  0
 VXU  CONST_02  C5    C11  C1   C2      0.00   0.0  0
 VXU  CONST_03  C11   C1   C2   C3      0.00   0.0  0
 VXU  CONST_04  C11   C5   C4   C3      0.00   0.0  0
 VXU  CONST_05  C4    C3   C2   C1      0.00   0.0  0
 VXU  CONST_06  C4    C5   C11  C1      0.00   0.0  0
 VXU  CONST_07  C12   C4   C3   C2    180.00   0.0  0
 VXU  CONST_08  C12   C4   C5   C11   180.00   0.0  0
 VXU  CONST_09  O6    C5   C4   C12     0.00   0.0  0
 VXU  CONST_10  H1    C1   C2   C3    180.00   0.0  0
 VXU  CONST_11  H3    C3   C2   C1    180.00   0.0  0
 VXU  CONST_12  H2    C2   C3   C4    180.00   0.0  0
 VXU  Var_01    C8    C9   O10  C11    79.48  30.0  1
 VXU  Var_02    C8    C7   O6   C5    -81.12  30.0  1
 VXU  Var_03    O6    C7   C8   C9     63.26  30.0  1
 VXU  Var_04    O10   C9   C8   C7    -63.32  30.0  1
 VXU  Var_05    N13   C12  C4   C3   -105.99  30.0  2
 VXU  Var_06    H131  N13  C12  C4     68.73  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
 VXU  plan-1  C2   0.020
 VXU  plan-1  C3   0.020
 VXU  plan-1  C1   0.020
 VXU  plan-1  C4   0.020
 VXU  plan-1  C11  0.020
 VXU  plan-1  C5   0.020
 VXU  plan-1  C12  0.020
 VXU  plan-1  O10  0.020
 VXU  plan-1  O6   0.020
 VXU  plan-1  H2   0.020
 VXU  plan-1  H3   0.020
 VXU  plan-1  H1   0.020

