# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 09:00:10 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: (1S,2R)-1-amino-2,3-dihydro-1H-inden-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1[C@H](O)Cc2ccccc12
#
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
 00X  00X  (1S,2R)-1-amino-2,3-dihydro-1H-inden-2-ol  ligand  22  11  .  2021-07-27  2021-07-27  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_00X
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
 00X  N30   N  NH2   0  -0.796  -1.7689   1.9381   0.0587
 00X  O30   O  OH1   0  -0.664  -2.1753  -0.5236   1.1629
 00X  C31   C  CR15  0  -0.144  -1.2125   0.7717  -0.5963
 00X  C32   C  CR56  0   0.123   0.2284   0.4951  -0.2476
 00X  C33   C  CR16  0  -0.338   1.2544   1.3826   0.0244
 00X  C34   C  CR16  0  -0.261   2.5240   0.8781   0.2994
 00X  C35   C  CR15  0   0.005  -1.8955  -0.5524  -0.2165
 00X  C36   C  CR56  0   0.107   0.4562  -0.8789  -0.2444
 00X  C37   C  CR16  0  -0.338   1.7163  -1.3828   0.0285
 00X  C38   C  CR16  0  -0.261   2.7531  -0.4925   0.3005
 00X  C39   C  CH2   0  -0.525  -0.8240  -1.6019  -0.5576
 00X  HN30  H  HNH2  0   0.349  -1.3868   2.7691  -0.3754
 00X  HN3A  H  HNH2  0   0.348  -2.7640   1.9818  -0.1271
 00X  HO30  H  HOH1  0   0.449  -2.5891  -1.3598   1.3969
 00X  H31   H  HCR5  0   0.232  -1.2755   0.8335  -1.6963
 00X  H33   H  HCR6  0   0.242   1.0863   2.4531   0.0302
 00X  H34   H  HCR6  0   0.250   3.3368   1.5585   0.5194
 00X  H35   H  HCR5  0   0.219  -2.8114  -0.7078  -0.8005
 00X  H37   H  HCR6  0   0.245   1.8962  -2.4512   0.0435
 00X  H38   H  HCR6  0   0.250   3.7424  -0.8713   0.5240
 00X  H39   H  HCH2  0   0.257  -0.9569  -2.5362  -0.0078
 00X  H39A  H  HCH2  0   0.251  -0.8727  -1.8519  -1.6225

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
 00X  N30  C31   single    1.449  0.020  1.449
 00X  N30  HN30  single    0.890  0.020  1.040
 00X  N30  HN3A  single    0.890  0.020  1.040
 00X  C35  O30   single    1.408  0.020  1.408
 00X  O30  HO30  single    0.850  0.020  0.980
 00X  C32  C31   single    1.508  0.020  1.508
 00X  C31  C35   single    1.538  0.020  1.538
 00X  C31  H31   single    0.970  0.020  1.090
 00X  C33  C32   aromatic  1.384  0.020  1.384
 00X  C32  C36   aromatic  1.393  0.020  1.393
 00X  C34  C33   aromatic  1.394  0.020  1.394
 00X  C33  H33   single    0.930  0.020  1.080
 00X  C34  C38   aromatic  1.390  0.020  1.390
 00X  C34  H34   single    0.930  0.020  1.080
 00X  C39  C35   single    1.538  0.020  1.538
 00X  C35  H35   single    0.970  0.020  1.090
 00X  C37  C36   aromatic  1.384  0.020  1.384
 00X  C36  C39   single    1.503  0.020  1.503
 00X  C38  C37   aromatic  1.393  0.020  1.393
 00X  C37  H37   single    0.930  0.020  1.080
 00X  C38  H38   single    0.930  0.020  1.080
 00X  C39  H39   single    0.970  0.020  1.090
 00X  C39  H39A  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
 00X  HN3A  N30  HN30  104.87  3.000
 00X  HN3A  N30  C31   109.20  3.000
 00X  HN30  N30  C31   108.79  3.000
 00X  HO30  O30  C35   107.82  3.000
 00X  H31   C31  C35   105.61  3.000
 00X  H31   C31  C32   107.17  3.000
 00X  C35   C31  C32   102.09  3.000
 00X  H31   C31  N30   112.56  3.000
 00X  C35   C31  N30   114.27  3.000
 00X  C32   C31  N30   114.21  3.000
 00X  C36   C32  C33   120.73  3.000
 00X  C36   C32  C31   109.74  3.000
 00X  C33   C32  C31   129.52  3.000
 00X  H33   C33  C34   119.86  3.000
 00X  H33   C33  C32   121.31  3.000
 00X  C34   C33  C32   118.83  3.000
 00X  H34   C34  C38   119.73  3.000
 00X  H34   C34  C33   119.78  3.000
 00X  C38   C34  C33   120.49  3.000
 00X  H35   C35  C39   111.52  3.000
 00X  H35   C35  C31   111.18  3.000
 00X  C39   C35  C31   102.91  3.000
 00X  H35   C35  O30   111.01  3.000
 00X  C39   C35  O30   111.70  3.000
 00X  C31   C35  O30   108.22  3.000
 00X  C39   C36  C37   129.89  3.000
 00X  C39   C36  C32   109.55  3.000
 00X  C37   C36  C32   120.56  3.000
 00X  H37   C37  C38   120.25  3.000
 00X  H37   C37  C36   120.85  3.000
 00X  C38   C37  C36   118.90  3.000
 00X  H38   C38  C37   119.78  3.000
 00X  H38   C38  C34   119.73  3.000
 00X  C37   C38  C34   120.49  3.000
 00X  H39A  C39  H39   106.79  3.000
 00X  H39A  C39  C36   110.51  3.000
 00X  H39   C39  C36   114.21  3.000
 00X  H39A  C39  C35   109.90  3.000
 00X  H39   C39  C35   112.79  3.000
 00X  C36   C39  C35   102.65  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
 00X  CONST_01  C38  C34  C33  C32    0.00   0.0  0
 00X  CONST_02  C38  C37  C36  C32    0.00   0.0  0
 00X  CONST_03  C37  C36  C32  C33    0.00   0.0  0
 00X  CONST_04  C37  C38  C34  C33    0.00   0.0  0
 00X  CONST_05  C36  C32  C33  C34    0.00   0.0  0
 00X  CONST_06  C36  C37  C38  C34    0.00   0.0  0
 00X  CONST_07  H33  C33  C32  C31    0.00   0.0  0
 00X  CONST_08  H34  C34  C33  C32  180.00   0.0  0
 00X  CONST_09  H37  C37  C36  C32  180.00   0.0  0
 00X  CONST_10  H38  C38  C34  C33  180.00   0.0  0
 00X  Var_01    C35  C39  C36  C32  -20.75  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
 00X  chir_01  C31  N30  C32  C35  negativ
 00X  chir_02  C35  O30  C31  C39  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
 00X  plan-1  C31  0.020
 00X  plan-1  C32  0.020
 00X  plan-1  C33  0.020
 00X  plan-1  C34  0.020
 00X  plan-1  C36  0.020
 00X  plan-1  C37  0.020
 00X  plan-1  C38  0.020
 00X  plan-1  C39  0.020
 00X  plan-1  H33  0.020
 00X  plan-1  H34  0.020
 00X  plan-1  H37  0.020
 00X  plan-1  H38  0.020

