# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 17:02:26 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: dimethyl (1S,2S,4S,5S)-4-(2-aminoethoxy)-5-hydroxycyclohexane-1,2-dicarboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@H]1C[C@H](O)[C@H](C[C@@H]1C(=O)OC)OCCN
#
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
 M5C  M5C  'dimethyl (1S,2S,4S,5S)-4-(2-aminoethoxy)-5-hydroxycyclohexane-1,2-dicarboxylate'  ligand  40  19  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M5C
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
 M5C  OAD   O  O     0  -0.451  -2.6166   1.4264   0.8769
 M5C  CAT   C  C     0   0.618  -1.5745   1.6240   0.3015
 M5C  OAO   O  O2    0  -0.453  -1.2535   2.7856  -0.2488
 M5C  CAA   C  CH3   0  -0.425  -2.1971   3.8518  -0.1381
 M5C  CBC   C  CH1   0  -0.376  -0.4636   0.6119   0.1621
 M5C  CBD   C  CH1   0  -0.371  -0.9946  -0.8077   0.3248
 M5C  CAU   C  C     0   0.625  -2.0422  -1.1143  -0.7175
 M5C  OAP   O  O2    0  -0.454  -2.7083  -2.2234  -0.4336
 M5C  CAB   C  CH3   0  -0.426  -3.6945  -2.6618  -1.3686
 M5C  OAE   O  O     0  -0.449  -2.2430  -0.4535  -1.7073
 M5C  CAM   C  CH2   0  -0.449   0.6191   0.8991   1.2152
 M5C  CAZ   C  CH1   0   0.030   1.7600  -0.1056   1.1370
 M5C  OAQ   O  O2    0  -0.491   2.4148   0.0822  -0.0938
 M5C  CAL   C  CH2   0  -0.151   3.7461  -0.3747  -0.1395
 M5C  CAJ   C  CH2   0  -0.316   4.3815   0.0325  -1.4513
 M5C  NAC   N  NH2   0  -0.795   4.4632   1.4770  -1.5913
 M5C  CBA   C  CH1   0   0.012   1.2374  -1.5406   1.2657
 M5C  CAN   C  CH2   0  -0.472   0.1547  -1.8210   0.2281
 M5C  OX0   O  OH1   0  -0.672   0.7544  -1.6702   2.5860
 M5C  HBC   H  HCH1  0   0.277  -0.0193   0.7272  -0.8303
 M5C  HAA1  H  HCH3  0   0.239  -2.3805   4.1158   0.9031
 M5C  HAA2  H  HCH3  0   0.252  -1.7524   4.6991  -0.6512
 M5C  HAA3  H  HCH3  0   0.239  -3.1426   3.5964  -0.6157
 M5C  HBD   H  HCH1  0   0.278  -1.4563  -0.9152   1.3110
 M5C  HAM1  H  HCH2  0   0.260   1.0220   1.9043   1.0800
 M5C  HAM2  H  HCH2  0   0.248   0.1804   0.8637   2.2153
 M5C  HAN1  H  HCH2  0   0.261  -0.2222  -2.8376   0.3644
 M5C  HAN2  H  HCH2  0   0.246   0.6033  -1.7865  -0.7684
 M5C  HAB1  H  HCH3  0   0.240  -4.4950  -1.9301  -1.4744
 M5C  HAB2  H  HCH3  0   0.239  -3.2567  -2.8596  -2.3466
 M5C  HAB3  H  HCH3  0   0.252  -4.1004  -3.5838  -0.9635
 M5C  HAZ   H  HCH1  0   0.235   2.4544   0.0885   1.9687
 M5C  HBA   H  HCH1  0   0.234   2.0633  -2.2449   1.0947
 M5C  HAL1  H  HCH2  0   0.198   4.3217   0.0421   0.7006
 M5C  HAL2  H  HCH2  0   0.205   3.8064  -1.4670  -0.0500
 M5C  HAJ1  H  HCH2  0   0.201   5.3540  -0.4770  -1.5050
 M5C  HAJ2  H  HCH2  0   0.224   3.7833  -0.3659  -2.2750
 M5C  HAC1  H  HNH2  0   0.337   5.1483   1.8382  -0.9388
 M5C  HAC2  H  HNH2  0   0.348   4.8192   1.7031  -2.5108
 M5C  HX0   H  HOH1  0   0.454   0.4549  -2.5761   2.7116

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
 M5C  OAD  CAT   double  1.207  0.020  1.207
 M5C  CAT  OAO   single  1.325  0.020  1.325
 M5C  CAT  CBC   single  1.509  0.020  1.509
 M5C  OAO  CAA   single  1.428  0.020  1.428
 M5C  CBC  CBD   single  1.524  0.020  1.524
 M5C  CBC  CAM   single  1.537  0.020  1.537
 M5C  CBD  CAU   single  1.509  0.020  1.509
 M5C  CBD  CAN   single  1.535  0.020  1.535
 M5C  CAU  OAP   single  1.325  0.020  1.325
 M5C  CAU  OAE   double  1.207  0.020  1.207
 M5C  OAP  CAB   single  1.428  0.020  1.428
 M5C  CAM  CAZ   single  1.522  0.020  1.522
 M5C  CAZ  OAQ   single  1.407  0.020  1.407
 M5C  CAZ  CBA   single  1.533  0.020  1.533
 M5C  OAQ  CAL   single  1.408  0.020  1.408
 M5C  CAL  CAJ   single  1.513  0.020  1.513
 M5C  CAJ  NAC   single  1.454  0.020  1.454
 M5C  CBA  CAN   single  1.526  0.020  1.526
 M5C  CBA  OX0   single  1.412  0.020  1.412
 M5C  CBC  HBC   single  0.970  0.020  1.090
 M5C  CAA  HAA1  single  0.970  0.020  1.090
 M5C  CAA  HAA2  single  0.970  0.020  1.090
 M5C  CAA  HAA3  single  0.970  0.020  1.090
 M5C  CBD  HBD   single  0.970  0.020  1.090
 M5C  CAM  HAM1  single  0.970  0.020  1.090
 M5C  CAM  HAM2  single  0.970  0.020  1.090
 M5C  CAN  HAN1  single  0.970  0.020  1.090
 M5C  CAN  HAN2  single  0.970  0.020  1.090
 M5C  CAB  HAB1  single  0.970  0.020  1.090
 M5C  CAB  HAB2  single  0.970  0.020  1.090
 M5C  CAB  HAB3  single  0.970  0.020  1.090
 M5C  CAZ  HAZ   single  0.970  0.020  1.090
 M5C  CBA  HBA   single  0.970  0.020  1.090
 M5C  CAL  HAL1  single  0.970  0.020  1.090
 M5C  CAL  HAL2  single  0.970  0.020  1.090
 M5C  CAJ  HAJ1  single  0.970  0.020  1.090
 M5C  CAJ  HAJ2  single  0.970  0.020  1.090
 M5C  NAC  HAC1  single  0.890  0.020  1.040
 M5C  NAC  HAC2  single  0.890  0.020  1.040
 M5C  OX0  HX0   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
 M5C  CBC   CAT  OAO   111.80  3.000
 M5C  CBC   CAT  OAD   124.74  3.000
 M5C  OAO   CAT  OAD   123.43  3.000
 M5C  CAA   OAO  CAT   117.54  3.000
 M5C  HAA3  CAA  HAA2  109.34  3.000
 M5C  HAA3  CAA  HAA1  109.24  3.000
 M5C  HAA2  CAA  HAA1  109.35  3.000
 M5C  HAA3  CAA  OAO   111.37  3.000
 M5C  HAA2  CAA  OAO   105.99  3.000
 M5C  HAA1  CAA  OAO   111.48  3.000
 M5C  HBC   CBC  CAM   108.41  3.000
 M5C  HBC   CBC  CBD   109.67  3.000
 M5C  CAM   CBC  CBD   110.25  3.000
 M5C  HBC   CBC  CAT   108.20  3.000
 M5C  CAM   CBC  CAT   109.26  3.000
 M5C  CBD   CBC  CAT   110.99  3.000
 M5C  HBD   CBD  CAN   107.93  3.000
 M5C  HBD   CBD  CAU   108.04  3.000
 M5C  CAN   CBD  CAU   110.00  3.000
 M5C  HBD   CBD  CBC   109.55  3.000
 M5C  CAN   CBD  CBC   110.31  3.000
 M5C  CAU   CBD  CBC   110.93  3.000
 M5C  OAE   CAU  OAP   123.41  3.000
 M5C  OAE   CAU  CBD   124.79  3.000
 M5C  OAP   CAU  CBD   111.79  3.000
 M5C  CAB   OAP  CAU   117.65  3.000
 M5C  HAB3  CAB  HAB2  109.33  3.000
 M5C  HAB3  CAB  HAB1  109.38  3.000
 M5C  HAB2  CAB  HAB1  109.27  3.000
 M5C  HAB3  CAB  OAP   105.94  3.000
 M5C  HAB2  CAB  OAP   111.46  3.000
 M5C  HAB1  CAB  OAP   111.39  3.000
 M5C  HAM2  CAM  HAM1  106.94  3.000
 M5C  HAM2  CAM  CAZ   109.06  3.000
 M5C  HAM1  CAM  CAZ   108.95  3.000
 M5C  HAM2  CAM  CBC   109.77  3.000
 M5C  HAM1  CAM  CBC   110.31  3.000
 M5C  CAZ   CAM  CBC   111.67  3.000
 M5C  HAZ   CAZ  CBA   108.47  3.000
 M5C  HAZ   CAZ  OAQ   110.12  3.000
 M5C  CBA   CAZ  OAQ   110.93  3.000
 M5C  HAZ   CAZ  CAM   108.51  3.000
 M5C  CBA   CAZ  CAM   110.98  3.000
 M5C  OAQ   CAZ  CAM   107.80  3.000
 M5C  CAL   OAQ  CAZ   115.16  3.000
 M5C  HAL2  CAL  HAL1  106.61  3.000
 M5C  HAL2  CAL  CAJ   108.38  3.000
 M5C  HAL1  CAL  CAJ   109.89  3.000
 M5C  HAL2  CAL  OAQ   111.85  3.000
 M5C  HAL1  CAL  OAQ   110.30  3.000
 M5C  CAJ   CAL  OAQ   109.74  3.000
 M5C  HAJ2  CAJ  HAJ1  106.17  3.000
 M5C  HAJ2  CAJ  NAC   108.68  3.000
 M5C  HAJ1  CAJ  NAC   113.97  3.000
 M5C  HAJ2  CAJ  CAL   108.98  3.000
 M5C  HAJ1  CAJ  CAL   106.80  3.000
 M5C  NAC   CAJ  CAL   111.99  3.000
 M5C  HAC2  NAC  HAC1  105.54  3.000
 M5C  HAC2  NAC  CAJ   109.24  3.000
 M5C  HAC1  NAC  CAJ   109.29  3.000
 M5C  HBA   CBA  OX0   110.11  3.000
 M5C  HBA   CBA  CAN   108.05  3.000
 M5C  OX0   CBA  CAN   112.11  3.000
 M5C  HBA   CBA  CAZ   109.31  3.000
 M5C  OX0   CBA  CAZ   106.33  3.000
 M5C  CAN   CBA  CAZ   110.91  3.000
 M5C  HAN2  CAN  HAN1  106.54  3.000
 M5C  HAN2  CAN  CBA   108.84  3.000
 M5C  HAN1  CAN  CBA   109.32  3.000
 M5C  HAN2  CAN  CBD   110.10  3.000
 M5C  HAN1  CAN  CBD   110.36  3.000
 M5C  CBA   CAN  CBD   111.54  3.000
 M5C  HX0   OX0  CBA   108.36  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
 M5C  Var_01  CBC   CAT  OAO  CAA  -177.45  30.0  1
 M5C  Var_02  CAJ   CAL  OAQ  CAZ  -173.31  30.0  3
 M5C  Var_03  NAC   CAJ  CAL  OAQ    63.26  30.0  3
 M5C  Var_04  HAA1  CAA  OAO  CAT    61.44  30.0  3
 M5C  Var_05  HAB1  CAB  OAP  CAU   -62.33  30.0  3
 M5C  Var_06  HAC1  NAC  CAJ  CAL    69.80  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
 M5C  chir_01  CBC  CAT  CBD  CAM  positiv
 M5C  chir_02  CBD  CBC  CAU  CAN  negativ
 M5C  chir_03  CAZ  OAQ  CBA  CAM  positiv
 M5C  chir_04  CBA  OX0  CAN  CAZ  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
 M5C  plan-1  OAD  0.020
 M5C  plan-1  CAT  0.020
 M5C  plan-1  OAO  0.020
 M5C  plan-1  CBC  0.020
 M5C  plan-2  CBD  0.020
 M5C  plan-2  CAU  0.020
 M5C  plan-2  OAP  0.020
 M5C  plan-2  OAE  0.020

