# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 25 09:34:37 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: (2S,3R)-1-[7-(2-carboxyethyl)phenanthrene-2-carbonyl]piperazine-2,3-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCc1ccc2c(ccc3cc(ccc23)C(=O)N4CCN[C@H]([C@H]4C(O)=O)C(O)=O)c1
#
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
 QM4  QM4  '(2S,3R)-1-[7-(2-carboxyethyl)phenanthrene-2-carbonyl]piperazine-2,3-dicarboxylic acid'  ligand  55  33  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_QM4
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
 QM4  N    N  NH1   0  -0.576    5.2589  -2.0264   1.0268
 QM4  CA   C  CH1   0  -0.228    5.6801  -0.6511   1.0107
 QM4  C    C  C     0   0.552    7.1899  -0.5435   0.9214
 QM4  O    O  O     0  -0.427    7.9398  -1.4826   0.9211
 QM4  CB   C  CH1   0  -0.253    4.9168   0.2174  -0.0114
 QM4  CG   C  C     0   0.576    5.2068  -0.0911  -1.4767
 QM4  OD1  O  O     0  -0.419    4.3878  -0.0020  -2.3519
 QM4  OD2  O  OH1   0  -0.588    6.4710  -0.4253  -1.6690
 QM4  OXT  O  OH1   0  -0.592    7.5827   0.7220   0.9111
 QM4  CAB  C  CR66  0   0.108   -3.0005   0.8204  -0.0117
 QM4  CAF  C  CR66  0   0.131   -1.5602   0.9161   0.0898
 QM4  CAK  C  CR16  0  -0.352   -0.9096   1.5220   1.1809
 QM4  CAL  C  CH2   0  -0.314    3.8278  -2.1130   1.2472
 QM4  CAM  C  CR16  0  -0.255    0.4596   1.5945   1.2473
 QM4  CAP  C  CR16  0  -0.326   -1.3797  -0.2341  -2.0783
 QM4  CAQ  C  CR6   0   0.127   -5.8106   0.5687  -0.2738
 QM4  CAS  C  CH2   0  -0.512   -7.2998   0.3941  -0.3666
 QM4  CAT  C  CR16  0  -0.339   -3.8736   1.3191   0.9729
 QM4  CAV  C  CR16  0  -0.311    0.6393   0.4402  -0.8478
 QM4  CAW  C  CR16  0  -0.382   -4.9695   0.0846  -1.2486
 QM4  CAX  C  CR66  0   0.109   -3.5714   0.1977  -1.1427
 QM4  CAY  C  CH2   0  -0.577   -7.7575  -0.7818   0.4903
 QM4  CAZ  C  CR6   0  -0.091    1.2496   1.0304   0.2342
 QM4  CBA  C  CR66  0   0.095   -0.7611   0.3788  -0.9439
 QM4  CBC  C  CR16  0  -0.282   -5.2353   1.1964   0.8453
 QM4  CBD  C  CR16  0  -0.326   -2.7246  -0.3198  -2.1727
 QM4  CBE  C  C     0   0.553   -9.2420  -1.0163   0.4389
 QM4  CBG  C  CH2   0  -0.323    3.0018  -1.2919   0.2637
 QM4  NAI  N  NT    0  -0.452    3.4952   0.0794   0.2145
 QM4  OAO  O  O     0  -0.444  -10.0220  -0.3888  -0.2331
 QM4  OAU  O  O     0  -0.475    3.2084   2.3176   0.3709
 QM4  OBB  O  OH1   0  -0.596   -9.6080  -2.0189   1.2310
 QM4  H1   H  HNH1  0   0.355    5.5225  -2.5051   0.1729
 QM4  H3   H  HCH1  0   0.312    5.4201  -0.2221   1.9881
 QM4  H4   H  HCH1  0   0.336    5.1846   1.2667   0.1395
 QM4  H5   H  HOH1  0   0.494    6.6486  -0.5824  -2.6099
 QM4  H6   H  HOH1  0   0.488    8.5496   0.7734   0.8765
 QM4  H7   H  HCR6  0   0.259   -1.4825   1.9483   1.9924
 QM4  H8   H  HCH2  0   0.262    3.5172  -3.1563   1.1866
 QM4  H9   H  HCH2  0   0.239    3.6190  -1.7682   2.2639
 QM4  H10  H  HCR6  0   0.266    0.9301   2.0727   2.0963
 QM4  H11  H  HCR6  0   0.258   -0.7483  -0.6337  -2.8622
 QM4  H12  H  HCH2  0   0.257   -7.8017   1.3069  -0.0383
 QM4  H13  H  HCH2  0   0.257   -7.5882   0.2279  -1.4057
 QM4  H14  H  HCR6  0   0.256   -3.4838   1.8093   1.8546
 QM4  H15  H  HCR6  0   0.265    1.2333   0.0163  -1.6503
 QM4  H16  H  HCR6  0   0.251   -5.3840  -0.3992  -2.1265
 QM4  H17  H  HCH2  0   0.291   -7.2565  -1.7014   0.1725
 QM4  H18  H  HCH2  0   0.286   -7.4675  -0.6360   1.5351
 QM4  H19  H  HCR6  0   0.255   -5.8762   1.5945   1.6231
 QM4  H20  H  HCR6  0   0.258   -3.1847  -0.7868  -3.0346
 QM4  H21  H  HCH2  0   0.250    3.0453  -1.7425  -0.7328
 QM4  H22  H  HCH2  0   0.281    1.9618  -1.2985   0.5778
 QM4  H23  H  HOH1  0   0.479  -10.5648  -2.1577   1.1701
 QM4  CAC  C  C     0   0.536    2.7328   1.1951   0.2838

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
 QM4  OAU  CAC  double    1.222  0.020  1.222
 QM4  O    C    double    1.202  0.020  1.202
 QM4  CAC  CAZ  single    1.493  0.020  1.493
 QM4  CAC  NAI  single    1.353  0.020  1.353
 QM4  CAM  CAK  aromatic  1.373  0.020  1.373
 QM4  CAM  CAZ  aromatic  1.403  0.020  1.403
 QM4  OD1  CG   double    1.202  0.020  1.202
 QM4  C    CA   single    1.516  0.020  1.516
 QM4  C    OXT  single    1.325  0.020  1.325
 QM4  CB   CG   single    1.525  0.020  1.525
 QM4  CB   CA   single    1.543  0.020  1.543
 QM4  CB   NAI  single    1.446  0.020  1.446
 QM4  CAK  CAF  aromatic  1.407  0.020  1.407
 QM4  CAZ  CAV  aromatic  1.375  0.020  1.375
 QM4  CG   OD2  single    1.322  0.020  1.322
 QM4  CA   N    single    1.438  0.020  1.438
 QM4  NAI  CBG  single    1.458  0.020  1.458
 QM4  CAV  CBA  aromatic  1.405  0.020  1.405
 QM4  CAF  CBA  aromatic  1.413  0.020  1.413
 QM4  CAF  CAB  aromatic  1.447  0.020  1.447
 QM4  CAT  CAB  aromatic  1.407  0.020  1.407
 QM4  CAT  CBC  aromatic  1.373  0.020  1.373
 QM4  CBA  CAP  aromatic  1.430  0.020  1.430
 QM4  CAB  CAX  aromatic  1.412  0.020  1.412
 QM4  CBC  CAQ  aromatic  1.406  0.020  1.406
 QM4  N    CAL  single    1.451  0.020  1.451
 QM4  CBG  CAL  single    1.524  0.020  1.524
 QM4  OAO  CBE  double    1.206  0.020  1.206
 QM4  CAP  CBD  aromatic  1.351  0.020  1.351
 QM4  CAX  CBD  aromatic  1.430  0.020  1.430
 QM4  CAX  CAW  aromatic  1.407  0.020  1.407
 QM4  CAQ  CAW  aromatic  1.376  0.020  1.376
 QM4  CAQ  CAS  single    1.502  0.020  1.502
 QM4  CAY  CAS  single    1.525  0.020  1.525
 QM4  CAY  CBE  single    1.504  0.020  1.504
 QM4  CBE  OBB  single    1.329  0.020  1.329
 QM4  N    H1   single    0.890  0.020  1.040
 QM4  CA   H3   single    0.970  0.020  1.090
 QM4  CB   H4   single    0.970  0.020  1.090
 QM4  OD2  H5   single    0.850  0.020  0.980
 QM4  OXT  H6   single    0.850  0.020  0.980
 QM4  CAK  H7   single    0.930  0.020  1.080
 QM4  CAL  H8   single    0.970  0.020  1.090
 QM4  CAL  H9   single    0.970  0.020  1.090
 QM4  CAM  H10  single    0.930  0.020  1.080
 QM4  CAP  H11  single    0.930  0.020  1.080
 QM4  CAS  H12  single    0.970  0.020  1.090
 QM4  CAS  H13  single    0.970  0.020  1.090
 QM4  CAT  H14  single    0.930  0.020  1.080
 QM4  CAV  H15  single    0.930  0.020  1.080
 QM4  CAW  H16  single    0.930  0.020  1.080
 QM4  CAY  H17  single    0.970  0.020  1.090
 QM4  CAY  H18  single    0.970  0.020  1.090
 QM4  CBC  H19  single    0.930  0.020  1.080
 QM4  CBD  H20  single    0.930  0.020  1.080
 QM4  CBG  H21  single    0.970  0.020  1.090
 QM4  CBG  H22  single    0.970  0.020  1.090
 QM4  OBB  H23  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
 QM4  H1   N    CAL  110.88  3.000
 QM4  H1   N    CA   111.46  3.000
 QM4  CAL  N    CA   110.35  3.000
 QM4  H3   CA   CB   104.62  3.000
 QM4  H3   CA   C    105.09  3.000
 QM4  CB   CA   C    114.43  3.000
 QM4  H3   CA   N    107.10  3.000
 QM4  CB   CA   N    113.62  3.000
 QM4  C    CA   N    111.11  3.000
 QM4  OXT  C    O    124.14  3.000
 QM4  OXT  C    CA   111.31  3.000
 QM4  O    C    CA   124.47  3.000
 QM4  H4   CB   NAI  108.11  3.000
 QM4  H4   CB   CG   106.27  3.000
 QM4  NAI  CB   CG   108.52  3.000
 QM4  H4   CB   CA   109.12  3.000
 QM4  NAI  CB   CA   109.21  3.000
 QM4  CG   CB   CA   115.36  3.000
 QM4  OD2  CG   OD1  124.37  3.000
 QM4  OD2  CG   CB   111.89  3.000
 QM4  OD1  CG   CB   123.71  3.000
 QM4  H5   OD2  CG   110.92  3.000
 QM4  H6   OXT  C    110.29  3.000
 QM4  CAX  CAB  CAT  117.77  3.000
 QM4  CAX  CAB  CAF  119.20  3.000
 QM4  CAT  CAB  CAF  123.03  3.000
 QM4  CBA  CAF  CAK  118.01  3.000
 QM4  CBA  CAF  CAB  119.11  3.000
 QM4  CAK  CAF  CAB  122.88  3.000
 QM4  H7   CAK  CAM  118.13  3.000
 QM4  H7   CAK  CAF  120.45  3.000
 QM4  CAM  CAK  CAF  121.42  3.000
 QM4  H9   CAL  H8   107.40  3.000
 QM4  H9   CAL  CBG  109.06  3.000
 QM4  H8   CAL  CBG  108.98  3.000
 QM4  H9   CAL  N    108.11  3.000
 QM4  H8   CAL  N    109.26  3.000
 QM4  CBG  CAL  N    113.85  3.000
 QM4  H10  CAM  CAZ  119.96  3.000
 QM4  H10  CAM  CAK  119.67  3.000
 QM4  CAZ  CAM  CAK  120.36  3.000
 QM4  H11  CAP  CBD  120.42  3.000
 QM4  H11  CAP  CBA  118.69  3.000
 QM4  CBD  CAP  CBA  120.88  3.000
 QM4  CBC  CAQ  CAW  118.09  3.000
 QM4  CAW  CAQ  CAS  121.43  3.000
 QM4  CBC  CAQ  CAS  120.44  3.000
 QM4  H13  CAS  H12  106.98  3.000
 QM4  H13  CAS  CAY  109.77  3.000
 QM4  H12  CAS  CAY  109.72  3.000
 QM4  H13  CAS  CAQ  109.79  3.000
 QM4  H12  CAS  CAQ  109.87  3.000
 QM4  CAY  CAS  CAQ  110.63  3.000
 QM4  H14  CAT  CBC  118.27  3.000
 QM4  H14  CAT  CAB  120.49  3.000
 QM4  CBC  CAT  CAB  121.24  3.000
 QM4  H15  CAV  CBA  118.56  3.000
 QM4  H15  CAV  CAZ  120.45  3.000
 QM4  CBA  CAV  CAZ  120.99  3.000
 QM4  H16  CAW  CAX  118.46  3.000
 QM4  H16  CAW  CAQ  119.80  3.000
 QM4  CAX  CAW  CAQ  121.74  3.000
 QM4  CBD  CAX  CAW  120.34  3.000
 QM4  CAW  CAX  CAB  119.85  3.000
 QM4  CBD  CAX  CAB  119.81  3.000
 QM4  H18  CAY  H17  105.54  3.000
 QM4  H18  CAY  CBE  108.37  3.000
 QM4  H17  CAY  CBE  108.12  3.000
 QM4  H18  CAY  CAS  110.74  3.000
 QM4  H17  CAY  CAS  110.32  3.000
 QM4  CBE  CAY  CAS  113.40  3.000
 QM4  CAV  CAZ  CAM  119.39  3.000
 QM4  CAV  CAZ  CAC  120.95  3.000
 QM4  CAM  CAZ  CAC  119.40  3.000
 QM4  CAV  CBA  CAP  120.27  3.000
 QM4  CAP  CBA  CAF  119.91  3.000
 QM4  CAV  CBA  CAF  119.81  3.000
 QM4  H19  CBC  CAT  119.15  3.000
 QM4  H19  CBC  CAQ  119.55  3.000
 QM4  CAT  CBC  CAQ  121.30  3.000
 QM4  H20  CBD  CAX  118.53  3.000
 QM4  H20  CBD  CAP  120.40  3.000
 QM4  CAX  CBD  CAP  121.07  3.000
 QM4  OBB  CBE  OAO  123.14  3.000
 QM4  OBB  CBE  CAY  111.66  3.000
 QM4  OAO  CBE  CAY  125.21  3.000
 QM4  H22  CBG  H21  107.39  3.000
 QM4  H22  CBG  NAI  109.84  3.000
 QM4  H21  CBG  NAI  110.05  3.000
 QM4  H22  CBG  CAL  109.21  3.000
 QM4  H21  CBG  CAL  110.13  3.000
 QM4  NAI  CBG  CAL  110.18  3.000
 QM4  CBG  NAI  CAC  125.67  3.000
 QM4  CBG  NAI  CB   115.32  3.000
 QM4  CAC  NAI  CB   118.89  3.000
 QM4  H23  OBB  CBE  110.03  3.000
 QM4  OAU  CAC  NAI  122.80  3.000
 QM4  NAI  CAC  CAZ  117.84  3.000
 QM4  OAU  CAC  CAZ  119.36  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
 QM4  CONST_01  CAM  CAK  CAF  CAB   180.00   0.0  0
 QM4  CONST_02  CAV  CBA  CAF  CAB   180.00   0.0  0
 QM4  CONST_03  CAP  CBA  CAF  CAB     0.00   0.0  0
 QM4  CONST_04  CAQ  CBC  CAT  CAB     0.00   0.0  0
 QM4  CONST_05  CAP  CBD  CAX  CAB     0.00   0.0  0
 QM4  CONST_06  CAQ  CAW  CAX  CAB     0.00   0.0  0
 QM4  CONST_07  CAZ  CAM  CAK  CAF     0.00   0.0  0
 QM4  CONST_08  CAZ  CAV  CBA  CAF     0.00   0.0  0
 QM4  CONST_09  CBD  CAP  CBA  CAF     0.00   0.0  0
 QM4  CONST_10  CBC  CAT  CAB  CAF   180.00   0.0  0
 QM4  CONST_11  CBD  CAX  CAB  CAF     0.00   0.0  0
 QM4  CONST_12  CAW  CAX  CAB  CAF   180.00   0.0  0
 QM4  CONST_13  CAV  CAZ  CAM  CAK     0.00   0.0  0
 QM4  CONST_14  CAV  CBA  CAF  CAK     0.00   0.0  0
 QM4  CONST_15  CAP  CBA  CAF  CAK   180.00   0.0  0
 QM4  CONST_16  CAT  CAB  CAF  CAK     0.00   0.0  0
 QM4  CONST_17  CAX  CAB  CAF  CAK   180.00   0.0  0
 QM4  CONST_18  CBA  CAF  CAK  CAM     0.00   0.0  0
 QM4  CONST_19  CBA  CAV  CAZ  CAM     0.00   0.0  0
 QM4  CONST_20  CAZ  CAV  CBA  CAP   180.00   0.0  0
 QM4  CONST_21  CAW  CAX  CBD  CAP   180.00   0.0  0
 QM4  CONST_22  CBD  CAX  CAW  CAQ   180.00   0.0  0
 QM4  CONST_23  CBA  CAF  CAB  CAT   180.00   0.0  0
 QM4  CONST_24  CBD  CAX  CAB  CAT   180.00   0.0  0
 QM4  CONST_25  CAW  CAX  CAB  CAT     0.00   0.0  0
 QM4  CONST_26  CAW  CAQ  CBC  CAT     0.00   0.0  0
 QM4  CONST_27  CBD  CAP  CBA  CAV   180.00   0.0  0
 QM4  CONST_28  CBA  CAF  CAB  CAX     0.00   0.0  0
 QM4  CONST_29  CBC  CAT  CAB  CAX     0.00   0.0  0
 QM4  CONST_30  CBA  CAP  CBD  CAX     0.00   0.0  0
 QM4  CONST_31  CBC  CAQ  CAW  CAX     0.00   0.0  0
 QM4  CONST_32  CAK  CAM  CAZ  CAC   180.00   0.0  0
 QM4  CONST_33  CBA  CAV  CAZ  CAC   180.00   0.0  0
 QM4  CONST_34  CAT  CBC  CAQ  CAS   180.00   0.0  0
 QM4  CONST_35  CAX  CAW  CAQ  CAS   180.00   0.0  0
 QM4  CONST_36  CAZ  CAC  NAI  CB    180.00   0.0  0
 QM4  CONST_37  CBG  NAI  CAC  CAZ     0.00   0.0  0
 QM4  CONST_38  H7   CAK  CAF  CAB     0.00   0.0  0
 QM4  CONST_39  H19  CBC  CAT  CAB   180.00   0.0  0
 QM4  CONST_40  H20  CBD  CAX  CAB   180.00   0.0  0
 QM4  CONST_41  H16  CAW  CAX  CAB   180.00   0.0  0
 QM4  CONST_42  H10  CAM  CAK  CAF   180.00   0.0  0
 QM4  CONST_43  H15  CAV  CBA  CAF   180.00   0.0  0
 QM4  CONST_44  H11  CAP  CBA  CAF   180.00   0.0  0
 QM4  CONST_45  H14  CAT  CAB  CAF     0.00   0.0  0
 QM4  CONST_46  OAU  CAC  NAI  CB      0.00   0.0  0
 QM4  CONST_47  OAU  CAC  NAI  CBG   180.00   0.0  0
 QM4  CONST_48  H6   OXT  C    CA    180.00   0.0  0
 QM4  CONST_49  H5   OD2  CG   CB    180.00   0.0  0
 QM4  CONST_50  H23  OBB  CBE  CAY   180.00   0.0  0
 QM4  Var_01    NAI  CBG  CAL  N     -51.48  30.0  1
 QM4  Var_02    CBG  CAL  N    CA     53.99  30.0  1
 QM4  Var_03    CAL  CBG  NAI  CB     51.51  30.0  1
 QM4  Var_04    NAI  CAC  CAZ  CAM   126.34  30.0  3
 QM4  Var_05    CAY  CAS  CAQ  CAW    99.12  30.0  2
 QM4  Var_06    CBE  CAY  CAS  CAQ  -179.79  30.0  1
 QM4  Var_07    OAO  CBE  CAY  CAS     2.32  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
 QM4  chir_01  CA  C    CB  N   negativ
 QM4  chir_02  CB  NAI  CA  CG  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
 QM4  plan-1  CAB  0.020
 QM4  plan-1  CAF  0.020
 QM4  plan-1  CAK  0.020
 QM4  plan-1  CAM  0.020
 QM4  plan-1  CAP  0.020
 QM4  plan-1  CAQ  0.020
 QM4  plan-1  CAS  0.020
 QM4  plan-1  CAT  0.020
 QM4  plan-1  CAV  0.020
 QM4  plan-1  CAW  0.020
 QM4  plan-1  CAX  0.020
 QM4  plan-1  CAZ  0.020
 QM4  plan-1  CBA  0.020
 QM4  plan-1  CBC  0.020
 QM4  plan-1  CBD  0.020
 QM4  plan-1  H7   0.020
 QM4  plan-1  H10  0.020
 QM4  plan-1  H11  0.020
 QM4  plan-1  H14  0.020
 QM4  plan-1  H15  0.020
 QM4  plan-1  H16  0.020
 QM4  plan-1  H19  0.020
 QM4  plan-1  H20  0.020
 QM4  plan-1  CAC  0.020
 QM4  plan-2  CB   0.020
 QM4  plan-2  CAZ  0.020
 QM4  plan-2  CBG  0.020
 QM4  plan-2  NAI  0.020
 QM4  plan-2  OAU  0.020
 QM4  plan-2  CAC  0.020
 QM4  plan-3  CA   0.020
 QM4  plan-3  C    0.020
 QM4  plan-3  O    0.020
 QM4  plan-3  OXT  0.020
 QM4  plan-3  H6   0.020
 QM4  plan-4  CB   0.020
 QM4  plan-4  CG   0.020
 QM4  plan-4  OD1  0.020
 QM4  plan-4  OD2  0.020
 QM4  plan-4  H5   0.020
 QM4  plan-5  CAY  0.020
 QM4  plan-5  CBE  0.020
 QM4  plan-5  OAO  0.020
 QM4  plan-5  OBB  0.020
 QM4  plan-5  H23  0.020

