# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 15:46:21 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (2S,3R)-1-(phenanthren-2-ylcarbonyl)piperazine-2,3-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1NCCN([C@@H]1C(O)=O)C(=O)c2ccc3c(ccc4ccccc34)c2
#
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
 2JL  2JL  '(2S,3R)-1-(phenanthren-2-ylcarbonyl)piperazine-2,3-dicarboxylic acid'  ligand  44  28  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2JL
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
 2JL  N    N  NH1    0  -0.578   3.8625  -0.5469   1.9177
 2JL  CA   C  CH1    0  -0.231   4.1435   0.3458   0.8098
 2JL  CAF  C  CR16   0  -0.263  -7.5066  -0.1180   0.2887
 2JL  CAG  C  CR16   0  -0.242  -6.9616   1.1354   0.5969
 2JL  CAH  C  C1     0  -0.260  -1.3174   1.9035   0.0465
 2JL  CAI  C  CR16   0  -0.307  -6.6800  -1.1340  -0.1234
 2JL  CAJ  C  CR16   0  -0.352  -5.6080   1.3523   0.4877
 2JL  CAK  C  C1     0  -0.350  -2.6737   1.7507   0.1978
 2JL  CAL  C  C1     0  -0.323  -4.4403  -1.9994  -0.6696
 2JL  CAM  C  C1     0  -0.326  -3.1063  -1.8222  -0.7866
 2JL  CAN  C  C1     0  -0.314  -1.1132  -0.3914  -0.6133
 2JL  CAO  C  CH2    0  -0.306   2.4729  -0.4491   2.3153
 2JL  CAP  C  CH2    0  -0.311   1.4646  -0.6110   1.1791
 2JL  CAU  C  C      0  -0.092  -0.5184   0.8190  -0.3450
 2JL  CAV  C  CR6    0   0.079  -5.2921  -0.9330  -0.2414
 2JL  CAW  C  C      0   0.099  -2.5031  -0.5598  -0.4891
 2JL  CAX  C  CR6    0   0.125  -4.7372   0.3301   0.0658
 2JL  CAY  C  C      0   0.120  -3.3076   0.5223  -0.0674
 2JL  C    C  C      0   0.422   5.6203   0.3402   0.3699
 2JL  O    O  O      0  -0.611   6.4365  -0.2921   1.0625
 2JL  NAZ  N  NT     0  -0.421   1.8118   0.2778   0.0844
 2JL  OAC  O  O      0  -0.506   1.2687   1.8450  -1.4589
 2JL  CB   C  CH1    0  -0.238   3.1898   0.1428  -0.3688
 2JL  CG   C  C      0   0.422   3.3357  -1.2240  -1.0968
 2JL  OD1  O  O      0  -0.598   2.3607  -1.5832  -1.7841
 2JL  OD2  O  OC    -1  -0.584   4.4148  -1.8275  -0.9557
 2JL  OXT  O  OC    -1  -0.630   5.8806   1.0475  -0.6273
 2JL  H1   H  HNH1   0   0.328   4.0837  -1.4951   1.6371
 2JL  H3   H  HCH1   0   0.220   3.9527   1.3658   1.1786
 2JL  H6   H  H      0   0.261  -0.8629   2.8655   0.2462
 2JL  H7   H  HCR6   0   0.258  -7.0892  -2.1077  -0.3652
 2JL  H8   H  HCR6   0   0.256  -5.2233   2.3314   0.7377
 2JL  H9   H  H      0   0.256  -3.2496   2.6077   0.5183
 2JL  H10  H  H      0   0.257  -4.8877  -2.9585  -0.9003
 2JL  H11  H  H      0   0.256  -2.4705  -2.6377  -1.1087
 2JL  H12  H  H      0   0.261  -0.5093  -1.2321  -0.9385
 2JL  H13  H  HCH2   0   0.235   2.2583  -1.1958   3.0830
 2JL  H14  H  HCH2   0   0.212   2.3184   0.5344   2.7726
 2JL  H15  H  HCH2   0   0.228   1.4538  -1.6487   0.8275
 2JL  H16  H  HCH2   0   0.259   0.4686  -0.3825   1.5526
 2JL  H17  H  HCH1   0   0.256   3.3797   0.9273  -1.1011
 2JL  CAT  C  C      0   0.510   0.9405   1.0201  -0.6097
 2JL  H4   H  HCR6   0   0.260  -8.5726  -0.2824   0.3760
 2JL  H5   H  HCR6   0   0.261  -7.6077   1.9400   0.9230

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
 2JL  OAC  CAT  double    1.229  0.020  1.229
 2JL  O    C    deloc     1.243  0.020  1.243
 2JL  CAT  CAU  single    1.496  0.020  1.496
 2JL  CAT  NAZ  single    1.339  0.020  1.339
 2JL  CAH  CAK  aromatic  1.373  0.020  1.373
 2JL  CAH  CAU  aromatic  1.403  0.020  1.403
 2JL  C    CA   single    1.541  0.020  1.541
 2JL  C    OXT  deloc     1.250  0.020  1.250
 2JL  CB   CG   single    1.555  0.020  1.555
 2JL  CB   CA   single    1.530  0.020  1.530
 2JL  CB   NAZ  single    1.457  0.020  1.457
 2JL  OD1  CG   deloc     1.246  0.020  1.246
 2JL  CAK  CAY  aromatic  1.408  0.020  1.408
 2JL  CAU  CAN  aromatic  1.375  0.020  1.375
 2JL  CG   OD2  deloc     1.244  0.020  1.244
 2JL  CA   N    single    1.450  0.020  1.450
 2JL  NAZ  CAP  single    1.452  0.020  1.452
 2JL  CAN  CAW  aromatic  1.406  0.020  1.406
 2JL  CAY  CAW  aromatic  1.413  0.020  1.413
 2JL  CAY  CAX  aromatic  1.449  0.020  1.449
 2JL  CAJ  CAX  aromatic  1.408  0.020  1.408
 2JL  CAJ  CAG  aromatic  1.375  0.020  1.375
 2JL  CAW  CAM  aromatic  1.430  0.020  1.430
 2JL  CAX  CAV  aromatic  1.413  0.020  1.413
 2JL  CAG  CAF  aromatic  1.401  0.020  1.401
 2JL  CAP  CAO  single    1.528  0.020  1.528
 2JL  N    CAO  single    1.449  0.020  1.449
 2JL  CAM  CAL  aromatic  1.351  0.020  1.351
 2JL  CAV  CAL  aromatic  1.430  0.020  1.430
 2JL  CAV  CAI  aromatic  1.407  0.020  1.407
 2JL  CAF  CAI  aromatic  1.373  0.020  1.373
 2JL  N    H1   single    0.890  0.020  1.040
 2JL  CA   H3   single    0.970  0.020  1.090
 2JL  CAF  H4   single    0.930  0.020  1.080
 2JL  CAG  H5   single    0.930  0.020  1.080
 2JL  CAH  H6   single    0.930  0.020  1.080
 2JL  CAI  H7   single    0.930  0.020  1.080
 2JL  CAJ  H8   single    0.930  0.020  1.080
 2JL  CAK  H9   single    0.930  0.020  1.080
 2JL  CAL  H10  single    0.930  0.020  1.080
 2JL  CAM  H11  single    0.930  0.020  1.080
 2JL  CAN  H12  single    0.930  0.020  1.080
 2JL  CAO  H13  single    0.970  0.020  1.090
 2JL  CAO  H14  single    0.970  0.020  1.090
 2JL  CAP  H15  single    0.970  0.020  1.090
 2JL  CAP  H16  single    0.970  0.020  1.090
 2JL  CB   H17  single    0.970  0.020  1.090

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
 2JL  H1   N    CAO  110.39  3.000
 2JL  H1   N    CA   108.79  3.000
 2JL  CAO  N    CA   110.73  3.000
 2JL  H3   CA   CB   105.84  3.000
 2JL  H3   CA   C    105.37  3.000
 2JL  CB   CA   C    112.16  3.000
 2JL  H3   CA   N    106.30  3.000
 2JL  CB   CA   N    112.71  3.000
 2JL  C    CA   N    113.67  3.000
 2JL  H4   CAF  CAI  120.32  3.000
 2JL  H4   CAF  CAG  120.09  3.000
 2JL  CAI  CAF  CAG  119.59  3.000
 2JL  H5   CAG  CAJ  119.62  3.000
 2JL  H5   CAG  CAF  119.94  3.000
 2JL  CAJ  CAG  CAF  120.43  3.000
 2JL  H6   CAH  CAU  119.96  3.000
 2JL  H6   CAH  CAK  119.55  3.000
 2JL  CAU  CAH  CAK  120.49  3.000
 2JL  H7   CAI  CAV  118.82  3.000
 2JL  H7   CAI  CAF  120.30  3.000
 2JL  CAV  CAI  CAF  120.88  3.000
 2JL  H8   CAJ  CAX  120.45  3.000
 2JL  H8   CAJ  CAG  118.34  3.000
 2JL  CAX  CAJ  CAG  121.21  3.000
 2JL  H9   CAK  CAY  120.52  3.000
 2JL  H9   CAK  CAH  118.07  3.000
 2JL  CAY  CAK  CAH  121.40  3.000
 2JL  H10  CAL  CAV  118.55  3.000
 2JL  H10  CAL  CAM  120.37  3.000
 2JL  CAV  CAL  CAM  121.08  3.000
 2JL  H11  CAM  CAW  118.61  3.000
 2JL  H11  CAM  CAL  120.44  3.000
 2JL  CAW  CAM  CAL  120.95  3.000
 2JL  H12  CAN  CAW  118.96  3.000
 2JL  H12  CAN  CAU  119.98  3.000
 2JL  CAW  CAN  CAU  121.06  3.000
 2JL  H14  CAO  H13  107.02  3.000
 2JL  H14  CAO  CAP  108.21  3.000
 2JL  H13  CAO  CAP  108.70  3.000
 2JL  H14  CAO  N    108.08  3.000
 2JL  H13  CAO  N    109.59  3.000
 2JL  CAP  CAO  N    114.95  3.000
 2JL  H16  CAP  H15  107.46  3.000
 2JL  H16  CAP  NAZ  110.43  3.000
 2JL  H15  CAP  NAZ  109.88  3.000
 2JL  H16  CAP  CAO  109.06  3.000
 2JL  H15  CAP  CAO  110.22  3.000
 2JL  NAZ  CAP  CAO  109.75  3.000
 2JL  CAT  CAU  CAN  120.36  3.000
 2JL  CAN  CAU  CAH  119.25  3.000
 2JL  CAT  CAU  CAH  120.05  3.000
 2JL  CAX  CAV  CAL  119.83  3.000
 2JL  CAL  CAV  CAI  120.39  3.000
 2JL  CAX  CAV  CAI  119.78  3.000
 2JL  CAY  CAW  CAN  119.85  3.000
 2JL  CAY  CAW  CAM  119.86  3.000
 2JL  CAN  CAW  CAM  120.29  3.000
 2JL  CAY  CAX  CAV  119.08  3.000
 2JL  CAV  CAX  CAJ  118.11  3.000
 2JL  CAY  CAX  CAJ  122.81  3.000
 2JL  CAX  CAY  CAW  119.19  3.000
 2JL  CAX  CAY  CAK  122.88  3.000
 2JL  CAW  CAY  CAK  117.92  3.000
 2JL  OXT  C    O    126.55  3.000
 2JL  OXT  C    CA   115.16  3.000
 2JL  O    C    CA   118.17  3.000
 2JL  CB   NAZ  CAT  120.38  3.000
 2JL  CB   NAZ  CAP  113.82  3.000
 2JL  CAT  NAZ  CAP  125.08  3.000
 2JL  H17  CB   CG   107.56  3.000
 2JL  H17  CB   NAZ  107.89  3.000
 2JL  CG   CB   NAZ  108.40  3.000
 2JL  H17  CB   CA   108.27  3.000
 2JL  NAZ  CB   CA   109.74  3.000
 2JL  CG   CB   CA   114.75  3.000
 2JL  OD2  CG   OD1  126.97  3.000
 2JL  OD2  CG   CB   117.03  3.000
 2JL  OD1  CG   CB   115.98  3.000
 2JL  OAC  CAT  NAZ  123.84  3.000
 2JL  NAZ  CAT  CAU  117.93  3.000
 2JL  OAC  CAT  CAU  118.23  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
 2JL  CONST_01  CAX  CAJ  CAG  CAF    0.00   0.0  0
 2JL  CONST_02  CAX  CAV  CAI  CAF    0.00   0.0  0
 2JL  CONST_03  CAL  CAV  CAI  CAF  180.00   0.0  0
 2JL  CONST_04  CAY  CAX  CAJ  CAG  180.00   0.0  0
 2JL  CONST_05  CAV  CAX  CAJ  CAG    0.00   0.0  0
 2JL  CONST_06  CAV  CAI  CAF  CAG    0.00   0.0  0
 2JL  CONST_07  CAW  CAY  CAK  CAH    0.00   0.0  0
 2JL  CONST_08  CAX  CAY  CAK  CAH  180.00   0.0  0
 2JL  CONST_09  CAW  CAN  CAU  CAH    0.00   0.0  0
 2JL  CONST_10  CAY  CAX  CAV  CAI  180.00   0.0  0
 2JL  CONST_11  CAJ  CAX  CAV  CAI    0.00   0.0  0
 2JL  CONST_12  CAM  CAL  CAV  CAI  180.00   0.0  0
 2JL  CONST_13  CAJ  CAG  CAF  CAI    0.00   0.0  0
 2JL  CONST_14  CAK  CAY  CAX  CAJ    0.00   0.0  0
 2JL  CONST_15  CAW  CAY  CAX  CAJ  180.00   0.0  0
 2JL  CONST_16  CAL  CAV  CAX  CAJ  180.00   0.0  0
 2JL  CONST_17  CAN  CAU  CAH  CAK    0.00   0.0  0
 2JL  CONST_18  CAN  CAW  CAY  CAK    0.00   0.0  0
 2JL  CONST_19  CAM  CAW  CAY  CAK  180.00   0.0  0
 2JL  CONST_20  CAV  CAX  CAY  CAK  180.00   0.0  0
 2JL  CONST_21  CAN  CAW  CAM  CAL  180.00   0.0  0
 2JL  CONST_22  CAY  CAW  CAM  CAL    0.00   0.0  0
 2JL  CONST_23  CAY  CAX  CAV  CAL    0.00   0.0  0
 2JL  CONST_24  CAU  CAN  CAW  CAM  180.00   0.0  0
 2JL  CONST_25  CAX  CAY  CAW  CAM    0.00   0.0  0
 2JL  CONST_26  CAX  CAV  CAL  CAM    0.00   0.0  0
 2JL  CONST_27  CAX  CAY  CAW  CAN  180.00   0.0  0
 2JL  CONST_28  CAY  CAK  CAH  CAU    0.00   0.0  0
 2JL  CONST_29  CAY  CAW  CAN  CAU    0.00   0.0  0
 2JL  CONST_30  CAW  CAY  CAX  CAV    0.00   0.0  0
 2JL  CONST_31  CAW  CAM  CAL  CAV    0.00   0.0  0
 2JL  CONST_32  CAT  CAU  CAH  CAK  180.00   0.0  0
 2JL  CONST_33  CAW  CAN  CAU  CAT  180.00   0.0  0
 2JL  CONST_34  CAU  CAT  NAZ  CAP    0.00   0.0  0
 2JL  CONST_36  H8   CAJ  CAG  CAF  180.00   0.0  0
 2JL  CONST_37  H7   CAI  CAF  CAG  180.00   0.0  0
 2JL  CONST_38  H12  CAN  CAU  CAH  180.00   0.0  0
 2JL  CONST_39  H10  CAL  CAV  CAI    0.00   0.0  0
 2JL  CONST_40  H5   CAG  CAF  CAI  180.00   0.0  0
 2JL  CONST_41  H4   CAF  CAG  CAJ  180.00   0.0  0
 2JL  CONST_42  H6   CAH  CAU  CAN  180.00   0.0  0
 2JL  CONST_43  H11  CAM  CAW  CAN    0.00   0.0  0
 2JL  CONST_44  H9   CAK  CAH  CAU  180.00   0.0  0
 2JL  CONST_45  OAC  CAT  NAZ  CAP  180.00   0.0  0
 2JL  Var_01    NAZ  CAP  CAO  N    -50.96  30.0  1
 2JL  Var_02    CAP  CAO  N    CA    51.80  30.0  1
 2JL  Var_03    CB   NAZ  CAP  CAO   52.88  30.0  1
 2JL  Var_04    NAZ  CAT  CAU  CAH  123.32  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
 2JL  chir_01  CA  C    CB  N   negativ
 2JL  chir_02  CB  NAZ  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
 2JL  plan-1  CAF  0.020
 2JL  plan-1  CAG  0.020
 2JL  plan-1  CAH  0.020
 2JL  plan-1  CAI  0.020
 2JL  plan-1  CAJ  0.020
 2JL  plan-1  CAK  0.020
 2JL  plan-1  CAL  0.020
 2JL  plan-1  CAM  0.020
 2JL  plan-1  CAN  0.020
 2JL  plan-1  CAU  0.020
 2JL  plan-1  CAV  0.020
 2JL  plan-1  CAW  0.020
 2JL  plan-1  CAX  0.020
 2JL  plan-1  CAY  0.020
 2JL  plan-1  H6   0.020
 2JL  plan-1  H7   0.020
 2JL  plan-1  H8   0.020
 2JL  plan-1  H9   0.020
 2JL  plan-1  H10  0.020
 2JL  plan-1  H11  0.020
 2JL  plan-1  H12  0.020
 2JL  plan-1  CAT  0.020
 2JL  plan-1  H4   0.020
 2JL  plan-1  H5   0.020
 2JL  plan-2  CAP  0.020
 2JL  plan-2  CAU  0.020
 2JL  plan-2  NAZ  0.020
 2JL  plan-2  OAC  0.020
 2JL  plan-2  CB   0.020
 2JL  plan-2  CAT  0.020
 2JL  plan-3  CA   0.020
 2JL  plan-3  C    0.020
 2JL  plan-3  O    0.020
 2JL  plan-3  OXT  0.020
 2JL  plan-4  CB   0.020
 2JL  plan-4  CG   0.020
 2JL  plan-4  OD1  0.020
 2JL  plan-4  OD2  0.020

