# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 13:08:59 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: (3s,5s,7s)-N-[(5-bromothiophen-2-yl)methyl]tricyclo[3.3.1.1~3,7~]decan-1-aminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Brc1sc(C[NH2+]C23CC4CC(CC(C4)C2)C3)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
 3LW  3LW  (3s,5s,7s)-N-[(5-bromothiophen-2-yl)methyl]tricyclo[3.3.1.1~3,7~]decan-1-aminium  ligand  39  18  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3LW
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
 3LW  S     S   S2    0   0.308  -2.0665  -0.7900  -0.1888
 3LW  BR    BR  BR    0   0.037  -5.0035  -0.5331   0.7556
 3LW  C1    C   CR5   0  -0.342  -3.3739   0.2163   0.2778
 3LW  C2    C   CR15  0  -0.142  -3.0606   1.5396   0.2318
 3LW  N2    N   NT2   1  -0.685   1.2290   0.2191   0.3578
 3LW  C3    C   CR15  0  -0.184  -1.7196   1.7431  -0.1834
 3LW  C5    C   CH2   0  -0.393   0.3682   0.4319  -0.8493
 3LW  C10   C   C     0   0.065   2.7201   0.0687   0.1558
 3LW  C12   C   CR5   0  -0.198  -1.0542   0.5832  -0.4458
 3LW  C61   C   C     0  -0.430   3.3133  -0.1752   1.5443
 3LW  C62   C   C     0  -0.432   3.3029   1.3490  -0.4383
 3LW  C63   C   C     0  -0.437   3.0112  -1.1202  -0.7563
 3LW  C71   C   C     0  -0.258   4.8289  -0.3430   1.4211
 3LW  C72   C   C     0  -0.257   4.8234   1.1808  -0.5553
 3LW  C73   C   C     0  -0.256   4.5322  -1.2836  -0.8698
 3LW  C81   C   C     0  -0.423   5.4272   0.9328   0.8273
 3LW  C82   C   C     0  -0.425   5.1305  -0.0085  -1.4683
 3LW  C83   C   C     0  -0.423   5.1324  -1.5351   0.5132
 3LW  H2    H   HCR5  0   0.295  -3.7493   2.3341   0.4781
 3LW  H3    H   HCR5  0   0.288  -1.2680   2.7199  -0.2899
 3LW  H5    H   HCH2  0   0.332   0.7134   1.3358  -1.3441
 3LW  H61   H   H     0   0.257   3.0823   0.6671   2.2052
 3LW  H81   H   H     0   0.234   5.2317   1.7834   1.4872
 3LW  H62   H   H     0   0.260   2.8846   1.5479  -1.4290
 3LW  H82   H   H     0   0.235   4.7242   0.1668  -2.4692
 3LW  HN2   H   HNT2  0   0.466   1.0690   0.9951   1.0056
 3LW  H63   H   H     0   0.257   2.5543  -2.0319  -0.3579
 3LW  H83   H   H     0   0.237   6.2133  -1.6801   0.4315
 3LW  H5A   H   HCH2  0   0.329   0.5202  -0.4097  -1.5204
 3LW  H61A  H   H     0   0.257   2.8682  -1.0696   1.9933
 3LW  H62A  H   H     0   0.256   3.0604   2.2063   0.1980
 3LW  H63A  H   H     0   0.261   2.5962  -0.9577  -1.7547
 3LW  H71   H   H     0   0.247   5.2403  -0.5193   2.4179
 3LW  H72   H   H     0   0.247   5.2388   2.0954  -0.9850
 3LW  H73   H   H     0   0.247   4.7378  -2.1327  -1.5257
 3LW  H81A  H   H     0   0.237   6.5137   0.8365   0.7479
 3LW  H82A  H   H     0   0.238   6.2124  -0.1205  -1.5828
 3LW  H83A  H   H     0   0.234   4.7232  -2.4537   0.9451
 3LW  HN2A  H   HNT2  0   0.458   0.8932  -0.6062   0.8595

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
 3LW  S    C1    aromatic  1.715  0.020  1.715
 3LW  S    C12   aromatic  1.725  0.020  1.725
 3LW  BR   C1    single    1.856  0.020  1.856
 3LW  C1   C2    aromatic  1.361  0.020  1.361
 3LW  C2   C3    aromatic  1.418  0.020  1.418
 3LW  C2   H2    single    0.930  0.020  1.080
 3LW  N2   C5    single    1.498  0.020  1.498
 3LW  N2   C10   single    1.512  0.020  1.512
 3LW  N2   HN2   single    0.890  0.020  1.040
 3LW  N2   HN2A  single    0.890  0.020  1.040
 3LW  C3   C12   aromatic  1.363  0.020  1.363
 3LW  C3   H3    single    0.930  0.020  1.080
 3LW  C5   C12   single    1.486  0.020  1.486
 3LW  C5   H5    single    0.970  0.020  1.090
 3LW  C5   H5A   single    0.970  0.020  1.090
 3LW  C10  C61   single    1.529  0.020  1.529
 3LW  C10  C62   single    1.527  0.020  1.527
 3LW  C10  C63   single    1.526  0.020  1.526
 3LW  C61  C71   single    1.530  0.020  1.530
 3LW  C61  H61   single    0.970  0.020  1.090
 3LW  C61  H61A  single    0.970  0.020  1.090
 3LW  C62  C72   single    1.534  0.020  1.534
 3LW  C62  H62   single    0.970  0.020  1.090
 3LW  C62  H62A  single    0.970  0.020  1.090
 3LW  C63  C73   single    1.534  0.020  1.534
 3LW  C63  H63   single    0.970  0.020  1.090
 3LW  C63  H63A  single    0.970  0.020  1.090
 3LW  C71  C81   single    1.529  0.020  1.529
 3LW  C71  C83   single    1.529  0.020  1.529
 3LW  C71  H71   single    0.970  0.020  1.090
 3LW  C72  C81   single    1.529  0.020  1.529
 3LW  C72  C82   single    1.530  0.020  1.530
 3LW  C72  H72   single    0.970  0.020  1.090
 3LW  C73  C82   single    1.530  0.020  1.530
 3LW  C73  C83   single    1.528  0.020  1.528
 3LW  C73  H73   single    0.970  0.020  1.090
 3LW  C81  H81   single    0.970  0.020  1.090
 3LW  C81  H81A  single    0.970  0.020  1.090
 3LW  C82  H82   single    0.970  0.020  1.090
 3LW  C82  H82A  single    0.970  0.020  1.090
 3LW  C83  H83   single    0.970  0.020  1.090
 3LW  C83  H83A  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
 3LW  C12   S    C1    91.19  3.000
 3LW  C2    C1   BR   127.12  3.000
 3LW  C2    C1   S    112.71  3.000
 3LW  BR    C1   S    120.17  3.000
 3LW  H2    C2   C3   124.34  3.000
 3LW  H2    C2   C1   124.12  3.000
 3LW  C3    C2   C1   111.54  3.000
 3LW  HN2A  N2   HN2  104.48  3.000
 3LW  HN2A  N2   C10  108.00  3.000
 3LW  HN2   N2   C10  108.30  3.000
 3LW  HN2A  N2   C5   108.75  3.000
 3LW  HN2   N2   C5   108.22  3.000
 3LW  C10   N2   C5   118.24  3.000
 3LW  H3    C3   C12  123.09  3.000
 3LW  H3    C3   C2   123.58  3.000
 3LW  C12   C3   C2   113.32  3.000
 3LW  H5A   C5   H5   108.57  3.000
 3LW  H5A   C5   C12  112.35  3.000
 3LW  H5    C5   C12  110.05  3.000
 3LW  H5A   C5   N2   107.89  3.000
 3LW  H5    C5   N2   107.61  3.000
 3LW  C12   C5   N2   110.23  3.000
 3LW  C63   C10  C62  110.35  3.000
 3LW  C63   C10  C61  110.14  3.000
 3LW  C62   C10  C61  109.81  3.000
 3LW  C63   C10  N2   110.20  3.000
 3LW  C62   C10  N2   110.18  3.000
 3LW  C61   C10  N2   106.08  3.000
 3LW  C5    C12  C3   127.32  3.000
 3LW  C5    C12  S    121.40  3.000
 3LW  C3    C12  S    111.24  3.000
 3LW  H61A  C61  H61  107.15  3.000
 3LW  H61A  C61  C71  110.24  3.000
 3LW  H61   C61  C71  109.98  3.000
 3LW  H61A  C61  C10  110.17  3.000
 3LW  H61   C61  C10  110.08  3.000
 3LW  C71   C61  C10  109.19  3.000
 3LW  H62A  C62  H62  107.42  3.000
 3LW  H62A  C62  C72  110.46  3.000
 3LW  H62   C62  C72  109.26  3.000
 3LW  H62A  C62  C10  110.24  3.000
 3LW  H62   C62  C10  111.04  3.000
 3LW  C72   C62  C10  108.42  3.000
 3LW  H63A  C63  H63  107.31  3.000
 3LW  H63A  C63  C73  108.94  3.000
 3LW  H63   C63  C73  110.61  3.000
 3LW  H63A  C63  C10  110.95  3.000
 3LW  H63   C63  C10  110.58  3.000
 3LW  C73   C63  C10  108.44  3.000
 3LW  H71   C71  C83  109.95  3.000
 3LW  H71   C71  C81  109.98  3.000
 3LW  C83   C71  C81  110.01  3.000
 3LW  H71   C71  C61  108.50  3.000
 3LW  C83   C71  C61  109.27  3.000
 3LW  C81   C71  C61  109.11  3.000
 3LW  H72   C72  C82  109.85  3.000
 3LW  H72   C72  C81  109.96  3.000
 3LW  C82   C72  C81  109.52  3.000
 3LW  H72   C72  C62  108.37  3.000
 3LW  C82   C72  C62  109.24  3.000
 3LW  C81   C72  C62  109.89  3.000
 3LW  H73   C73  C83  109.97  3.000
 3LW  H73   C73  C82  109.83  3.000
 3LW  C83   C73  C82  109.72  3.000
 3LW  H73   C73  C63  108.29  3.000
 3LW  C83   C73  C63  109.87  3.000
 3LW  C82   C73  C63  109.13  3.000
 3LW  H81A  C81  H81  106.84  3.000
 3LW  H81A  C81  C72  109.94  3.000
 3LW  H81   C81  C72  110.41  3.000
 3LW  H81A  C81  C71  110.09  3.000
 3LW  H81   C81  C71  110.15  3.000
 3LW  C72   C81  C71  109.39  3.000
 3LW  H82A  C82  H82  106.73  3.000
 3LW  H82A  C82  C73  110.02  3.000
 3LW  H82   C82  C73  110.24  3.000
 3LW  H82A  C82  C72  109.91  3.000
 3LW  H82   C82  C72  110.28  3.000
 3LW  C73   C82  C72  109.62  3.000
 3LW  H83A  C83  H83  106.73  3.000
 3LW  H83A  C83  C73  110.39  3.000
 3LW  H83   C83  C73  110.02  3.000
 3LW  H83A  C83  C71  110.23  3.000
 3LW  H83   C83  C71  110.11  3.000
 3LW  C73   C83  C71  109.34  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
 3LW  CONST_01  C3   C2   C1   S       0.00   0.0  0
 3LW  CONST_02  C2   C3   C12  S       0.00   0.0  0
 3LW  CONST_03  C3   C12  S    C1      0.00   0.0  0
 3LW  CONST_04  C12  C3   C2   C1      0.00   0.0  0
 3LW  CONST_05  C12  S    C1   C2      0.00   0.0  0
 3LW  CONST_06  C12  S    C1   BR    180.00   0.0  0
 3LW  CONST_07  C3   C2   C1   BR    180.00   0.0  0
 3LW  CONST_08  C5   C12  S    C1    180.00   0.0  0
 3LW  CONST_09  C5   C12  C3   C2    180.00   0.0  0
 3LW  CONST_10  H2   C2   C1   S     180.00   0.0  0
 3LW  CONST_11  H3   C3   C12  S     180.00   0.0  0
 3LW  Var_01    N2   C5   C12  S     -84.56  30.0  1
 3LW  Var_02    C12  C5   N2   C10  -178.87  30.0  3

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
 3LW  chir_01  C10  C61  C62  C63  negativ
 3LW  chir_02  C71  C61  C81  C83  positiv
 3LW  chir_03  C72  C62  C81  C82  negativ
 3LW  chir_04  C73  C63  C82  C83  negativ

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
 3LW  plan-1  S    0.020
 3LW  plan-1  BR   0.020
 3LW  plan-1  C1   0.020
 3LW  plan-1  C2   0.020
 3LW  plan-1  C3   0.020
 3LW  plan-1  C5   0.020
 3LW  plan-1  C12  0.020
 3LW  plan-1  H2   0.020
 3LW  plan-1  H3   0.020

