# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 15:55:40 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: 3-(thiophen-2-yl)-6,7-dihydro-5H-pyrrolo[1,2-a]imidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1Cn2c(C1)ncc2c3sccc3
#
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
 556  556  3-(thiophen-2-yl)-6,7-dihydro-5H-pyrrolo[1,2-a]imidazole  ligand  23  13  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_556
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
 556  CAF  C  CH2   0  -0.545   3.5764  -0.2471  -0.1411
 556  CAE  C  CH2   0  -0.485   2.9585  -1.5772   0.3358
 556  CAG  C  CH2   0  -0.286   1.4594  -1.5020  -0.0148
 556  NAM  N  N     0  -0.502   1.2516  -0.0684  -0.0977
 556  CAK  C  CR55  0   0.449   2.3866   0.6482  -0.1595
 556  NAH  N  N     0  -0.465   2.1584   1.9338  -0.2502
 556  CAD  C  CR15  0  -0.271   0.7969   2.0426  -0.2539
 556  CAL  C  CR5   0   0.349   0.1980   0.8045  -0.1608
 556  CAJ  C  CR5   0  -0.248  -1.1983   0.4396  -0.1183
 556  SAI  S  S2    0   0.213  -1.7714  -1.0761  -0.7223
 556  CAB  C  CR15  0  -0.469  -3.4002  -0.6759  -0.3720
 556  CAA  C  CR15  0  -0.174  -3.5018   0.5685   0.1701
 556  CAC  C  CR15  0  -0.251  -2.2439   1.2067   0.3211
 556  H1   H  HCH2  0   0.273   4.3656   0.1086   0.5200
 556  H2   H  HCH2  0   0.267   4.0048  -0.3350  -1.1431
 556  H3   H  HCH2  0   0.264   3.4294  -2.4458  -0.1189
 556  H4   H  HCH2  0   0.261   3.0711  -1.6657   1.4162
 556  H5   H  HCH2  0   0.263   1.2326  -1.9737  -0.9727
 556  H6   H  HCH2  0   0.271   0.8279  -1.9516   0.7499
 556  H7   H  HCR5  0   0.256   0.3007   2.9989  -0.3295
 556  H8   H  HCR5  0   0.298  -4.1894  -1.3819  -0.5786
 556  H9   H  HCR5  0   0.270  -4.4411   1.0134   0.4650
 556  H10  H  HCR5  0   0.261  -2.1121   2.1898   0.7509

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
 556  CAE  CAG  single    1.541  0.020  1.541
 556  CAE  CAF  single    1.542  0.020  1.542
 556  CAG  NAM  single    1.451  0.020  1.451
 556  CAF  CAK  single    1.489  0.020  1.489
 556  NAM  CAK  aromatic  1.344  0.020  1.344
 556  NAM  CAL  aromatic  1.370  0.020  1.370
 556  CAC  CAA  aromatic  1.419  0.020  1.419
 556  CAC  CAJ  aromatic  1.369  0.020  1.369
 556  CAK  NAH  aromatic  1.309  0.020  1.309
 556  CAA  CAB  aromatic  1.361  0.020  1.361
 556  CAL  CAJ  single    1.444  0.020  1.444
 556  CAL  CAD  aromatic  1.379  0.020  1.379
 556  CAJ  SAI  aromatic  1.729  0.020  1.729
 556  NAH  CAD  aromatic  1.366  0.020  1.366
 556  CAB  SAI  aromatic  1.714  0.020  1.714
 556  CAF  H1   single    0.970  0.020  1.090
 556  CAF  H2   single    0.970  0.020  1.090
 556  CAE  H3   single    0.970  0.020  1.090
 556  CAE  H4   single    0.970  0.020  1.090
 556  CAG  H5   single    0.970  0.020  1.090
 556  CAG  H6   single    0.970  0.020  1.090
 556  CAD  H7   single    0.930  0.020  1.080
 556  CAB  H8   single    0.930  0.020  1.080
 556  CAA  H9   single    0.930  0.020  1.080
 556  CAC  H10  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
 556  H2   CAF  H1   107.37  3.000
 556  H2   CAF  CAK  110.49  3.000
 556  H1   CAF  CAK  112.96  3.000
 556  H2   CAF  CAE  111.78  3.000
 556  H1   CAF  CAE  112.60  3.000
 556  CAK  CAF  CAE  101.67  3.000
 556  H4   CAE  H3   107.75  3.000
 556  H4   CAE  CAG  109.26  3.000
 556  H3   CAE  CAG  111.41  3.000
 556  H4   CAE  CAF  109.58  3.000
 556  H3   CAE  CAF  112.71  3.000
 556  CAG  CAE  CAF  106.09  3.000
 556  H6   CAG  H5   108.50  3.000
 556  H6   CAG  NAM  111.41  3.000
 556  H5   CAG  NAM  110.31  3.000
 556  H6   CAG  CAE  112.59  3.000
 556  H5   CAG  CAE  112.37  3.000
 556  NAM  CAG  CAE  101.57  3.000
 556  CAL  NAM  CAK  107.93  3.000
 556  CAL  NAM  CAG  137.94  3.000
 556  CAK  NAM  CAG  114.11  3.000
 556  NAH  CAK  NAM  112.32  3.000
 556  NAH  CAK  CAF  136.95  3.000
 556  NAM  CAK  CAF  110.71  3.000
 556  CAD  NAH  CAK  104.61  3.000
 556  H7   CAD  CAL  126.90  3.000
 556  H7   CAD  NAH  121.92  3.000
 556  CAL  CAD  NAH  111.18  3.000
 556  CAJ  CAL  CAD  130.48  3.000
 556  CAD  CAL  NAM  103.96  3.000
 556  CAJ  CAL  NAM  125.56  3.000
 556  CAC  CAJ  SAI  110.49  3.000
 556  SAI  CAJ  CAL  122.12  3.000
 556  CAC  CAJ  CAL  127.33  3.000
 556  CAB  SAI  CAJ   92.23  3.000
 556  H8   CAB  CAA  128.31  3.000
 556  H8   CAB  SAI  120.22  3.000
 556  CAA  CAB  SAI  111.46  3.000
 556  H9   CAA  CAC  123.83  3.000
 556  H9   CAA  CAB  123.37  3.000
 556  CAC  CAA  CAB  112.80  3.000
 556  H10  CAC  CAA  124.03  3.000
 556  H10  CAC  CAJ  122.96  3.000
 556  CAA  CAC  CAJ  113.01  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
 556  CONST_01  CAD  NAH  CAK  NAM    0.00   0.0  0
 556  CONST_04  NAH  CAD  CAL  NAM    0.00   0.0  0
 556  CONST_05  CAJ  CAL  NAM  CAK  180.00   0.0  0
 556  CONST_06  CAD  CAL  NAM  CAK    0.00   0.0  0
 556  CONST_07  CAL  CAD  NAH  CAK    0.00   0.0  0
 556  CONST_08  CAL  NAM  CAK  NAH    0.00   0.0  0
 556  CONST_09  CAJ  CAL  CAD  NAH  180.00   0.0  0
 556  CONST_12  CAA  CAC  CAJ  CAL  180.00   0.0  0
 556  CONST_13  CAB  SAI  CAJ  CAL  180.00   0.0  0
 556  CONST_14  CAB  CAA  CAC  CAJ    0.00   0.0  0
 556  CONST_15  CAA  CAB  SAI  CAJ    0.00   0.0  0
 556  CONST_16  CAA  CAC  CAJ  SAI    0.00   0.0  0
 556  CONST_17  CAC  CAA  CAB  SAI    0.00   0.0  0
 556  CONST_18  CAC  CAJ  SAI  CAB    0.00   0.0  0
 556  CONST_19  CAJ  CAL  NAM  CAG    0.00   0.0  0
 556  CONST_20  H7   CAD  CAL  NAM  180.00   0.0  0
 556  CONST_21  H10  CAC  CAJ  CAL    0.00   0.0  0
 556  CONST_22  H9   CAA  CAC  CAJ  180.00   0.0  0
 556  CONST_23  H8   CAB  SAI  CAJ  180.00   0.0  0
 556  Var_01    NAM  CAG  CAE  CAF  -22.76  30.0  1
 556  Var_02    CAK  NAM  CAG  CAE   14.19  30.0  1
 556  Var_03    NAM  CAK  CAF  CAE  -15.17  30.0  1
 556  Var_04    CAK  CAF  CAE  CAG   23.13  30.0  1

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
 556  plan-1  CAL  0.020
 556  plan-1  CAJ  0.020
 556  plan-1  SAI  0.020
 556  plan-1  CAB  0.020
 556  plan-1  CAA  0.020
 556  plan-1  CAC  0.020
 556  plan-1  H8   0.020
 556  plan-1  H9   0.020
 556  plan-1  H10  0.020
 556  plan-2  CAF  0.020
 556  plan-2  CAG  0.020
 556  plan-2  NAM  0.020
 556  plan-2  CAK  0.020
 556  plan-2  NAH  0.020
 556  plan-2  CAD  0.020
 556  plan-2  CAL  0.020
 556  plan-2  CAJ  0.020
 556  plan-2  H7   0.020

