# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 13:24:48 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: (2S,3S,4R,5S)-2-(1H-benzimidazol-2-yl)-5-methylpyrrolidine-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1N[C@H]([C@H](O)[C@@H]1O)c2[nH]c3ccccc3n2
#
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
 EAT  EAT  (2S,3S,4R,5S)-2-(1H-benzimidazol-2-yl)-5-methylpyrrolidine-3,4-diol  ligand  32  17  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EAT
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
 EAT  OAD  O  OH1   0  -0.662  -1.8035   2.1290  -0.7326
 EAT  CAG  C  CH1   0  -0.004  -1.8443   0.7276  -0.7242
 EAT  CAA  C  CH1   0  -0.012  -3.2407   0.1266  -0.5681
 EAT  OAC  O  OH1   0  -0.674  -3.9717   0.8073   0.4217
 EAT  CAF  C  CH1   0  -0.071  -2.9026  -1.2834  -0.1053
 EAT  CAB  C  CH3   0  -0.660  -4.0362  -2.0361   0.5652
 EAT  NAH  N  NH1   0  -0.625  -1.7600  -1.0942   0.8016
 EAT  CAE  C  CH1   0  -0.158  -1.1186   0.1846   0.5173
 EAT  CAP  C  CR5   0   0.447   0.3526   0.0621   0.3022
 EAT  NAQ  N  NR15  0  -0.704   1.2420   0.8477   0.9582
 EAT  CAM  C  CR56  0   0.328   2.4954   0.4909   0.5393
 EAT  CAN  C  CR16  0  -0.307   3.7667   0.9460   0.8689
 EAT  CAI  C  CR16  0  -0.280   4.8306   0.3283   0.2346
 EAT  CAJ  C  CR16  0  -0.271   4.6306  -0.7059  -0.6929
 EAT  CAK  C  CR16  0  -0.339   3.3615  -1.1532  -1.0142
 EAT  CAL  C  CR56  0   0.139   2.2750  -0.5448  -0.3853
 EAT  NAO  N  N     0  -0.468   0.9272  -0.7840  -0.5094
 EAT  H1   H  HOH1  0   0.463  -2.0705   2.4396  -1.6039
 EAT  H2   H  HCH1  0   0.238  -1.3838   0.3047  -1.6260
 EAT  H3   H  HCH1  0   0.230  -3.7861   0.1064  -1.5222
 EAT  H4   H  HOH1  0   0.444  -3.7944   1.7495   0.3165
 EAT  H5   H  HCH1  0   0.224  -2.6040  -1.8400  -1.0044
 EAT  H6   H  HCH3  0   0.221  -4.8929  -2.1308  -0.1037
 EAT  H7   H  HCH3  0   0.229  -3.7158  -3.0435   0.8342
 EAT  H8   H  HCH3  0   0.224  -4.3596  -1.5315   1.4743
 EAT  H9   H  HNH1  0   0.357  -1.1078  -1.8614   0.7231
 EAT  H11  H  HCH1  0   0.248  -1.2772   0.8913   1.3423
 EAT  H12  H  HNR5  0   0.420   1.0131   1.5639   1.6297
 EAT  H13  H  HCR6  0   0.266   3.9190   1.7460   1.5817
 EAT  H14  H  HCR6  0   0.255   5.8395   0.6494   0.4579
 EAT  H15  H  HCR6  0   0.252   5.4910  -1.1599  -1.1673
 EAT  H16  H  HCR6  0   0.253   3.2142  -1.9527  -1.7289

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
 EAT  OAC  CAA  single    1.406  0.020  1.406
 EAT  OAD  CAG  single    1.402  0.020  1.402
 EAT  CAA  CAG  single    1.528  0.020  1.528
 EAT  CAA  CAF  single    1.522  0.020  1.522
 EAT  CAE  CAG  single    1.537  0.020  1.537
 EAT  CAE  NAH  single    1.459  0.020  1.459
 EAT  CAE  CAP  single    1.492  0.020  1.492
 EAT  CAB  CAF  single    1.517  0.020  1.517
 EAT  NAH  CAF  single    1.471  0.020  1.471
 EAT  NAQ  CAP  aromatic  1.356  0.020  1.356
 EAT  NAQ  CAM  aromatic  1.369  0.020  1.369
 EAT  CAP  NAO  aromatic  1.306  0.020  1.306
 EAT  CAM  CAN  aromatic  1.390  0.020  1.390
 EAT  CAM  CAL  aromatic  1.406  0.020  1.406
 EAT  CAN  CAI  aromatic  1.384  0.020  1.384
 EAT  NAO  CAL  aromatic  1.374  0.020  1.374
 EAT  CAL  CAK  aromatic  1.395  0.020  1.395
 EAT  CAI  CAJ  aromatic  1.404  0.020  1.404
 EAT  CAK  CAJ  aromatic  1.383  0.020  1.383
 EAT  OAD  H1   single    0.850  0.020  0.980
 EAT  CAG  H2   single    0.970  0.020  1.090
 EAT  CAA  H3   single    0.970  0.020  1.090
 EAT  OAC  H4   single    0.850  0.020  0.980
 EAT  CAF  H5   single    0.970  0.020  1.090
 EAT  CAB  H6   single    0.970  0.020  1.090
 EAT  CAB  H7   single    0.970  0.020  1.090
 EAT  CAB  H8   single    0.970  0.020  1.090
 EAT  NAH  H9   single    0.890  0.020  1.040
 EAT  CAE  H11  single    0.970  0.020  1.090
 EAT  NAQ  H12  single    0.860  0.020  1.020
 EAT  CAN  H13  single    0.930  0.020  1.080
 EAT  CAI  H14  single    0.930  0.020  1.080
 EAT  CAJ  H15  single    0.930  0.020  1.080
 EAT  CAK  H16  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
 EAT  H1   OAD  CAG  108.65  3.000
 EAT  H2   CAG  CAE  109.23  3.000
 EAT  H2   CAG  CAA  108.41  3.000
 EAT  CAE  CAG  CAA  102.12  3.000
 EAT  H2   CAG  OAD  111.60  3.000
 EAT  CAE  CAG  OAD  110.13  3.000
 EAT  CAA  CAG  OAD  114.86  3.000
 EAT  H3   CAA  CAF  110.93  3.000
 EAT  H3   CAA  OAC  111.22  3.000
 EAT  CAF  CAA  OAC  110.48  3.000
 EAT  H3   CAA  CAG  111.84  3.000
 EAT  CAF  CAA  CAG  101.10  3.000
 EAT  OAC  CAA  CAG  110.88  3.000
 EAT  H4   OAC  CAA  107.49  3.000
 EAT  H5   CAF  NAH  111.01  3.000
 EAT  H5   CAF  CAB  108.26  3.000
 EAT  NAH  CAF  CAB  111.83  3.000
 EAT  H5   CAF  CAA  106.31  3.000
 EAT  NAH  CAF  CAA  103.94  3.000
 EAT  CAB  CAF  CAA  115.35  3.000
 EAT  H8   CAB  H7   108.02  3.000
 EAT  H8   CAB  H6   108.60  3.000
 EAT  H7   CAB  H6   107.56  3.000
 EAT  H8   CAB  CAF  111.16  3.000
 EAT  H7   CAB  CAF  110.35  3.000
 EAT  H6   CAB  CAF  111.02  3.000
 EAT  H9   NAH  CAE  111.52  3.000
 EAT  H9   NAH  CAF  110.85  3.000
 EAT  CAE  NAH  CAF  109.52  3.000
 EAT  H11  CAE  CAP  107.68  3.000
 EAT  H11  CAE  NAH  110.75  3.000
 EAT  CAP  CAE  NAH  112.94  3.000
 EAT  H11  CAE  CAG  108.14  3.000
 EAT  CAP  CAE  CAG  112.22  3.000
 EAT  NAH  CAE  CAG  105.04  3.000
 EAT  NAO  CAP  NAQ  112.80  3.000
 EAT  NAO  CAP  CAE  125.22  3.000
 EAT  NAQ  CAP  CAE  121.98  3.000
 EAT  H12  NAQ  CAM  126.65  3.000
 EAT  H12  NAQ  CAP  125.80  3.000
 EAT  CAM  NAQ  CAP  107.55  3.000
 EAT  CAL  CAM  CAN  122.73  3.000
 EAT  CAL  CAM  NAQ  104.46  3.000
 EAT  CAN  CAM  NAQ  132.81  3.000
 EAT  H13  CAN  CAI  121.57  3.000
 EAT  H13  CAN  CAM  121.80  3.000
 EAT  CAI  CAN  CAM  116.63  3.000
 EAT  H14  CAI  CAJ  119.20  3.000
 EAT  H14  CAI  CAN  119.32  3.000
 EAT  CAJ  CAI  CAN  121.48  3.000
 EAT  H15  CAJ  CAK  119.46  3.000
 EAT  H15  CAJ  CAI  119.04  3.000
 EAT  CAK  CAJ  CAI  121.49  3.000
 EAT  H16  CAK  CAL  120.92  3.000
 EAT  H16  CAK  CAJ  121.13  3.000
 EAT  CAL  CAK  CAJ  117.95  3.000
 EAT  NAO  CAL  CAK  130.32  3.000
 EAT  CAK  CAL  CAM  119.72  3.000
 EAT  NAO  CAL  CAM  109.96  3.000
 EAT  CAL  NAO  CAP  105.23  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
 EAT  CONST_01  CAN  CAM  NAQ  CAP  180.00  0.0  0
 EAT  CONST_02  CAL  CAM  NAQ  CAP    0.00  0.0  0
 EAT  CONST_03  CAM  CAL  NAO  CAP    0.00  0.0  0
 EAT  CONST_04  CAK  CAL  NAO  CAP  180.00  0.0  0
 EAT  CONST_05  CAL  NAO  CAP  NAQ    0.00  0.0  0
 EAT  CONST_06  CAI  CAN  CAM  NAQ  180.00  0.0  0
 EAT  CONST_07  NAO  CAL  CAM  NAQ    0.00  0.0  0
 EAT  CONST_08  CAK  CAL  CAM  NAQ  180.00  0.0  0
 EAT  CONST_09  NAO  CAP  NAQ  CAM    0.00  0.0  0
 EAT  CONST_10  CAJ  CAI  CAN  CAM    0.00  0.0  0
 EAT  CONST_11  CAJ  CAK  CAL  CAM    0.00  0.0  0
 EAT  CONST_12  NAO  CAL  CAM  CAN  180.00  0.0  0
 EAT  CONST_13  CAK  CAL  CAM  CAN    0.00  0.0  0
 EAT  CONST_14  CAK  CAJ  CAI  CAN    0.00  0.0  0
 EAT  CONST_15  CAL  CAM  CAN  CAI    0.00  0.0  0
 EAT  CONST_16  CAL  CAK  CAJ  CAI    0.00  0.0  0
 EAT  CONST_17  NAO  CAL  CAK  CAJ  180.00  0.0  0
 EAT  CONST_18  CAM  NAQ  CAP  CAE  180.00  0.0  0
 EAT  CONST_19  CAL  NAO  CAP  CAE  180.00  0.0  0
 EAT  CONST_20  H12  NAQ  CAP  CAE    0.00  0.0  0
 EAT  CONST_21  H13  CAN  CAM  NAQ    0.00  0.0  0
 EAT  CONST_22  H14  CAI  CAN  CAM  180.00  0.0  0
 EAT  CONST_23  H16  CAK  CAL  CAM  180.00  0.0  0
 EAT  CONST_24  H15  CAJ  CAI  CAN  180.00  0.0  0

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
 EAT  chir_01  CAG  OAD  CAA  CAE  positiv
 EAT  chir_02  CAA  OAC  CAG  CAF  negativ
 EAT  chir_03  CAF  NAH  CAA  CAB  positiv
 EAT  chir_04  CAE  NAH  CAP  CAG  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
 EAT  plan-1  CAE  0.020
 EAT  plan-1  CAP  0.020
 EAT  plan-1  NAQ  0.020
 EAT  plan-1  CAM  0.020
 EAT  plan-1  CAN  0.020
 EAT  plan-1  CAI  0.020
 EAT  plan-1  CAJ  0.020
 EAT  plan-1  CAK  0.020
 EAT  plan-1  CAL  0.020
 EAT  plan-1  NAO  0.020
 EAT  plan-1  H12  0.020
 EAT  plan-1  H13  0.020
 EAT  plan-1  H14  0.020
 EAT  plan-1  H15  0.020
 EAT  plan-1  H16  0.020

