# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 19:46:18 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: (1R,4S)-1,2,3,4-tetrahydro-1,4-methanonaphthalene-5,8-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(O)c2[C@H]3CC[C@H](C3)c12
#
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
 7SI  7SI  (1R,4S)-1,2,3,4-tetrahydro-1,4-methanonaphthalene-5,8-diol  ligand  25  13  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7SI
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
 7SI  C    C  CH2   0  -0.430   2.1255   0.8106   0.9861
 7SI  O    O  OH1   0  -0.636  -1.0483  -2.7500  -0.1440
 7SI  C1   C  CH2   0  -0.430   2.1312  -0.7407   0.9923
 7SI  O1   O  OH1   0  -0.636  -1.0675   2.7876  -0.1662
 7SI  C2   C  CH1   0  -0.339   1.5073  -1.1020  -0.3803
 7SI  C3   C  CH2   0  -0.406   2.0816   0.0256  -1.2546
 7SI  C4   C  CH1   0  -0.339   1.4992   1.1561  -0.3894
 7SI  C5   C  CR6   0   0.086   0.0592   0.7185  -0.3153
 7SI  C6   C  CR6   0   0.223  -1.1192   1.4327  -0.1800
 7SI  C7   C  CR16  0  -0.388  -2.3066   0.7103  -0.0715
 7SI  C8   C  CR16  0  -0.388  -2.3015  -0.6807  -0.0658
 7SI  C9   C  CR6   0   0.223  -1.1091  -1.3956  -0.1687
 7SI  C10  C  CR6   0   0.086   0.0642  -0.6741  -0.3098
 7SI  H    H  HCH2  0   0.236   1.5571   1.2370   1.8130
 7SI  HA   H  HCH2  0   0.240   3.1402   1.2081   1.0495
 7SI  HO   H  HOH1  0   0.469  -1.9329  -3.1164  -0.0407
 7SI  H1   H  HCH2  0   0.240   3.1489  -1.1300   1.0584
 7SI  H1A  H  HCH2  0   0.236   1.5662  -1.1647   1.8227
 7SI  HO1  H  HOH1  0   0.469  -1.9541   3.1490  -0.0629
 7SI  H2   H  HCH1  0   0.239   1.6918  -2.1249  -0.7032
 7SI  H3   H  HCH2  0   0.233   3.1739   0.0293  -1.2865
 7SI  H3A  H  HCH2  0   0.242   1.6947   0.0202  -2.2752
 7SI  H4   H  HCH1  0   0.239   1.6763   2.1776  -0.7209
 7SI  H7   H  HCR6  0   0.265  -3.2543   1.2315   0.0134
 7SI  H8   H  HCR6  0   0.265  -3.2452  -1.2080   0.0236

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
 7SI  C   C1   single    1.551  0.020  1.551
 7SI  C   C4   single    1.550  0.020  1.550
 7SI  O   C9   single    1.356  0.020  1.356
 7SI  C1  C2   single    1.550  0.020  1.550
 7SI  O1  C6   single    1.356  0.020  1.356
 7SI  C2  C3   single    1.538  0.020  1.538
 7SI  C2  C10  single    1.507  0.020  1.507
 7SI  C3  C4   single    1.538  0.020  1.538
 7SI  C4  C5   single    1.507  0.020  1.507
 7SI  C5  C6   aromatic  1.385  0.020  1.385
 7SI  C5  C10  aromatic  1.393  0.020  1.393
 7SI  C6  C7   aromatic  1.394  0.020  1.394
 7SI  C7  C8   aromatic  1.391  0.020  1.391
 7SI  C8  C9   aromatic  1.394  0.020  1.394
 7SI  C9  C10  aromatic  1.385  0.020  1.385
 7SI  C   H    single    0.970  0.020  1.090
 7SI  C   HA   single    0.970  0.020  1.090
 7SI  O   HO   single    0.850  0.020  0.980
 7SI  C1  H1   single    0.970  0.020  1.090
 7SI  C1  H1A  single    0.970  0.020  1.090
 7SI  O1  HO1  single    0.850  0.020  0.980
 7SI  C2  H2   single    0.970  0.020  1.090
 7SI  C3  H3   single    0.970  0.020  1.090
 7SI  C3  H3A  single    0.970  0.020  1.090
 7SI  C4  H4   single    0.970  0.020  1.090
 7SI  C7  H7   single    0.930  0.020  1.080
 7SI  C8  H8   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
 7SI  HA   C    H    107.35  3.000
 7SI  HA   C    C4   110.24  3.000
 7SI  H    C    C4   112.03  3.000
 7SI  HA   C    C1   111.13  3.000
 7SI  H    C    C1   112.95  3.000
 7SI  C4   C    C1   103.17  3.000
 7SI  HO   O    C9   109.93  3.000
 7SI  H1A  C1   H1   107.36  3.000
 7SI  H1A  C1   C2   112.03  3.000
 7SI  H1   C1   C2   110.22  3.000
 7SI  H1A  C1   C    112.96  3.000
 7SI  H1   C1   C    111.12  3.000
 7SI  C2   C1   C    103.18  3.000
 7SI  HO1  O1   C6   109.93  3.000
 7SI  H2   C2   C10  116.30  3.000
 7SI  H2   C2   C3   117.20  3.000
 7SI  C10  C2   C3   100.14  3.000
 7SI  H2   C2   C1   114.42  3.000
 7SI  C10  C2   C1   106.13  3.000
 7SI  C3   C2   C1   100.49  3.000
 7SI  H3A  C3   H3   109.09  3.000
 7SI  H3A  C3   C4   113.28  3.000
 7SI  H3   C3   C4   113.11  3.000
 7SI  H3A  C3   C2   113.30  3.000
 7SI  H3   C3   C2   113.10  3.000
 7SI  C4   C3   C2    94.46  3.000
 7SI  H4   C4   C5   116.30  3.000
 7SI  H4   C4   C3   117.18  3.000
 7SI  C5   C4   C3   100.14  3.000
 7SI  H4   C4   C    114.43  3.000
 7SI  C5   C4   C    106.12  3.000
 7SI  C3   C4   C    100.50  3.000
 7SI  C10  C5   C6   121.23  3.000
 7SI  C10  C5   C4   106.69  3.000
 7SI  C6   C5   C4   131.94  3.000
 7SI  C7   C6   C5   117.72  3.000
 7SI  C7   C6   O1   123.33  3.000
 7SI  C5   C6   O1   118.94  3.000
 7SI  H7   C7   C8   118.90  3.000
 7SI  H7   C7   C6   120.08  3.000
 7SI  C8   C7   C6   121.02  3.000
 7SI  H8   C8   C9   120.06  3.000
 7SI  H8   C8   C7   118.90  3.000
 7SI  C9   C8   C7   121.04  3.000
 7SI  C10  C9   C8   117.72  3.000
 7SI  C10  C9   O    118.97  3.000
 7SI  C8   C9   O    123.31  3.000
 7SI  C9   C10  C5   121.23  3.000
 7SI  C9   C10  C2   131.94  3.000
 7SI  C5   C10  C2   106.69  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
 7SI  CONST_01  C8   C7   C6   C5    0.00   0.0  0
 7SI  CONST_02  C8   C9   C10  C5    0.00   0.0  0
 7SI  CONST_03  C9   C10  C5   C6    0.00   0.0  0
 7SI  CONST_04  C9   C8   C7   C6    0.00   0.0  0
 7SI  CONST_05  C10  C5   C6   C7    0.00   0.0  0
 7SI  CONST_06  C10  C9   C8   C7    0.00   0.0  0
 7SI  CONST_07  C7   C8   C9   O   180.00   0.0  0
 7SI  CONST_08  C2   C10  C9   O     0.00   0.0  0
 7SI  CONST_09  C5   C10  C9   O   180.00   0.0  0
 7SI  CONST_10  C4   C5   C6   O1    0.00   0.0  0
 7SI  CONST_11  C10  C5   C6   O1  180.00   0.0  0
 7SI  CONST_12  C8   C7   C6   O1  180.00   0.0  0
 7SI  CONST_13  H7   C7   C6   C5  180.00   0.0  0
 7SI  CONST_14  H8   C8   C7   C6  180.00   0.0  0
 7SI  Var_01    C4   C    C1   C2   -0.01  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 7SI  chir_01  C2  C1  C3  C10  positiv
 7SI  chir_02  C4  C5  C3  C    positiv

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
 7SI  plan-1  O    0.020
 7SI  plan-1  O1   0.020
 7SI  plan-1  C2   0.020
 7SI  plan-1  C4   0.020
 7SI  plan-1  C5   0.020
 7SI  plan-1  C6   0.020
 7SI  plan-1  C7   0.020
 7SI  plan-1  C8   0.020
 7SI  plan-1  C9   0.020
 7SI  plan-1  C10  0.020
 7SI  plan-1  H7   0.020
 7SI  plan-1  H8   0.020

