# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 12:03:16 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: dimethyl (1S,2S,4S,5S)-4,5-dihydroxycyclohexane-1,2-dicarboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@H]1C[C@H](O)[C@@H](O)C[C@@H]1C(=O)OC
#
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
 07B  07B  'dimethyl (1S,2S,4S,5S)-4,5-dihydroxycyclohexane-1,2-dicarboxylate'  ligand  32  16  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_07B
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
 07B  CBK   C  CH1   0  -0.002   2.6100  -0.7377   0.1554
 07B  CAR   C  CH2   0  -0.447   1.3498  -1.4207  -0.3502
 07B  CBO   C  CH1   0  -0.373   0.0815  -0.7388   0.1884
 07B  CBA   C  C     0   0.617  -1.1328  -1.4604  -0.3411
 07B  OAE   O  O     0  -0.452  -1.7779  -1.1122  -1.2996
 07B  OAT   O  O2    0  -0.452  -1.3871  -2.5609   0.3512
 07B  CAB   C  CH3   0  -0.426  -2.4707  -3.3828  -0.0832
 07B  CBN   C  CH1   0  -0.381   0.0723   0.7322  -0.2127
 07B  CAZ   C  C     0   0.625  -1.1625   1.4280   0.3059
 07B  OAD   O  O     0  -0.449  -1.9048   0.9811   1.1458
 07B  OAS   O  O2    0  -0.453  -1.3290   2.6131  -0.2609
 07B  CAA   C  CH3   0  -0.425  -2.4426   3.4015   0.1606
 07B  CAQ   C  CH2   0  -0.447   1.3333   1.4299   0.3217
 07B  CBJ   C  CH1   0  -0.002   2.6007   0.7599  -0.1841
 07B  OAV   O  OH1   0  -0.670   2.6692   0.9593  -1.5791
 07B  OX0   O  OH1   0  -0.670   2.6820  -0.9373   1.5500
 07B  HBK   H  HCH1  0   0.230   3.4759  -1.1998  -0.3432
 07B  HAR1  H  HCH2  0   0.247   1.3507  -1.3881  -1.4419
 07B  HAR2  H  HCH2  0   0.262   1.3696  -2.4743  -0.0647
 07B  HBJ   H  HCH1  0   0.231   3.4613   1.2331   0.3131
 07B  HX0   H  HOH1  0   0.453   3.4834  -0.5191   1.8812
 07B  HBO   H  HCH1  0   0.277   0.0802  -0.8220   1.2785
 07B  HBN   H  HCH1  0   0.281   0.0681   0.8153  -1.3035
 07B  HAB1  H  HCH3  0   0.239  -3.4153  -2.8400  -0.0642
 07B  HAB2  H  HCH3  0   0.239  -2.2989  -3.7702  -1.0872
 07B  HAB3  H  HCH3  0   0.252  -2.5177  -4.2103   0.6183
 07B  HAQ1  H  HCH2  0   0.263   1.3424   2.4823   0.0333
 07B  HAQ2  H  HCH2  0   0.247   1.3363   1.4006   1.4137
 07B  HAA1  H  HCH3  0   0.252  -2.3929   4.3201  -0.4166
 07B  HAA2  H  HCH3  0   0.239  -3.3864   2.8967  -0.0444
 07B  HAA3  H  HCH3  0   0.239  -2.3840   3.6386   1.2225
 07B  HAV   H  HOH1  0   0.453   3.4797   0.5574  -1.9085

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
 07B  CBK  CAR   single  1.520  0.020  1.520
 07B  CBK  CBJ   single  1.536  0.020  1.536
 07B  CBK  OX0   single  1.411  0.020  1.411
 07B  CAR  CBO   single  1.537  0.020  1.537
 07B  CBO  CBA   single  1.508  0.020  1.508
 07B  CBO  CBN   single  1.525  0.020  1.525
 07B  CBA  OAE   double  1.207  0.020  1.207
 07B  CBA  OAT   single  1.325  0.020  1.325
 07B  OAT  CAB   single  1.428  0.020  1.428
 07B  CBN  CAZ   single  1.509  0.020  1.509
 07B  CBN  CAQ   single  1.537  0.020  1.537
 07B  CAZ  OAD   double  1.207  0.020  1.207
 07B  CAZ  OAS   single  1.324  0.020  1.324
 07B  OAS  CAA   single  1.428  0.020  1.428
 07B  CAQ  CBJ   single  1.520  0.020  1.520
 07B  CBJ  OAV   single  1.411  0.020  1.411
 07B  CBK  HBK   single  0.970  0.020  1.090
 07B  CAR  HAR1  single  0.970  0.020  1.090
 07B  CAR  HAR2  single  0.970  0.020  1.090
 07B  CBJ  HBJ   single  0.970  0.020  1.090
 07B  OX0  HX0   single  0.850  0.020  0.980
 07B  CBO  HBO   single  0.970  0.020  1.090
 07B  CBN  HBN   single  0.970  0.020  1.090
 07B  CAB  HAB1  single  0.970  0.020  1.090
 07B  CAB  HAB2  single  0.970  0.020  1.090
 07B  CAB  HAB3  single  0.970  0.020  1.090
 07B  CAQ  HAQ1  single  0.970  0.020  1.090
 07B  CAQ  HAQ2  single  0.970  0.020  1.090
 07B  CAA  HAA1  single  0.970  0.020  1.090
 07B  CAA  HAA2  single  0.970  0.020  1.090
 07B  CAA  HAA3  single  0.970  0.020  1.090
 07B  OAV  HAV   single  0.850  0.020  0.980

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
 07B  HBK   CBK  OX0   110.38  3.000
 07B  HBK   CBK  CBJ   108.30  3.000
 07B  OX0   CBK  CBJ   110.91  3.000
 07B  HBK   CBK  CAR   108.23  3.000
 07B  OX0   CBK  CAR   107.91  3.000
 07B  CBJ   CBK  CAR   111.08  3.000
 07B  HAR2  CAR  HAR1  106.87  3.000
 07B  HAR2  CAR  CBO   110.57  3.000
 07B  HAR1  CAR  CBO   109.73  3.000
 07B  HAR2  CAR  CBK   109.37  3.000
 07B  HAR1  CAR  CBK   108.57  3.000
 07B  CBO   CAR  CBK   111.60  3.000
 07B  HBO   CBO  CBN   109.62  3.000
 07B  HBO   CBO  CBA   108.22  3.000
 07B  CBN   CBO  CBA   111.36  3.000
 07B  HBO   CBO  CAR   108.45  3.000
 07B  CBN   CBO  CAR   109.92  3.000
 07B  CBA   CBO  CAR   109.20  3.000
 07B  OAT   CBA  OAE   123.52  3.000
 07B  OAT   CBA  CBO   111.62  3.000
 07B  OAE   CBA  CBO   124.83  3.000
 07B  CAB   OAT  CBA   117.71  3.000
 07B  HAB3  CAB  HAB2  109.33  3.000
 07B  HAB3  CAB  HAB1  109.32  3.000
 07B  HAB2  CAB  HAB1  109.26  3.000
 07B  HAB3  CAB  OAT   105.97  3.000
 07B  HAB2  CAB  OAT   111.42  3.000
 07B  HAB1  CAB  OAT   111.46  3.000
 07B  HBN   CBN  CAQ   108.39  3.000
 07B  HBN   CBN  CAZ   107.72  3.000
 07B  CAQ   CBN  CAZ   110.03  3.000
 07B  HBN   CBN  CBO   109.61  3.000
 07B  CAQ   CBN  CBO   109.97  3.000
 07B  CAZ   CBN  CBO   111.05  3.000
 07B  OAS   CAZ  OAD   123.50  3.000
 07B  OAS   CAZ  CBN   111.62  3.000
 07B  OAD   CAZ  CBN   124.87  3.000
 07B  CAA   OAS  CAZ   117.76  3.000
 07B  HAA3  CAA  HAA2  109.31  3.000
 07B  HAA3  CAA  HAA1  109.35  3.000
 07B  HAA2  CAA  HAA1  109.36  3.000
 07B  HAA3  CAA  OAS   111.46  3.000
 07B  HAA2  CAA  OAS   111.36  3.000
 07B  HAA1  CAA  OAS   105.92  3.000
 07B  HAQ2  CAQ  HAQ1  106.86  3.000
 07B  HAQ2  CAQ  CBJ   108.57  3.000
 07B  HAQ1  CAQ  CBJ   109.28  3.000
 07B  HAQ2  CAQ  CBN   109.74  3.000
 07B  HAQ1  CAQ  CBN   110.66  3.000
 07B  CBJ   CAQ  CBN   111.61  3.000
 07B  HBJ   CBJ  OAV   110.36  3.000
 07B  HBJ   CBJ  CAQ   108.19  3.000
 07B  OAV   CBJ  CAQ   107.89  3.000
 07B  HBJ   CBJ  CBK   108.34  3.000
 07B  OAV   CBJ  CBK   110.86  3.000
 07B  CAQ   CBJ  CBK   111.18  3.000
 07B  HAV   OAV  CBJ   108.67  3.000
 07B  HX0   OX0  CBK   108.73  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
 07B  Var_01  HAB1  CAB  OAT  CBA  -60.28  30.0  3
 07B  Var_02  HAA1  CAA  OAS  CAZ  179.82  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
 07B  chir_01  CBK  CAR  CBJ  OX0  negativ
 07B  chir_02  CBO  CAR  CBA  CBN  positiv
 07B  chir_03  CBN  CAQ  CAZ  CBO  positiv
 07B  chir_04  CBJ  OAV  CBK  CAQ  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
 07B  plan-1  CBO  0.020
 07B  plan-1  CBA  0.020
 07B  plan-1  OAE  0.020
 07B  plan-1  OAT  0.020
 07B  plan-2  CBN  0.020
 07B  plan-2  CAZ  0.020
 07B  plan-2  OAD  0.020
 07B  plan-2  OAS  0.020

