# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 11:42:02 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: (2R)-6-bromo-9-(2-{[(1R)-1-carboxy-2-phenylethyl]amino}-2-oxoethyl)-2,3,4,9-tetrahydro-1H-carbazole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1CCc2c(C1)n(CC(=O)N[C@H](Cc3ccccc3)C(O)=O)c4ccc(Br)cc24
#
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
 2VD  2VD  '(2R)-6-bromo-9-(2-{[(1R)-1-carboxy-2-phenylethyl]amino}-2-oxoethyl)-2,3,4,9-tetrahydro-1H-carbazole-2-carboxylic acid'  ligand  53  32  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2VD
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
 2VD  CAM  C   CH2    0  -0.510   3.2701  -2.7559  -0.2570
 2VD  CAL  C   CH2    0  -0.442   2.5542  -3.9875   0.2979
 2VD  CAK  C   CH1    0  -0.389   1.0441  -3.9475   0.0330
 2VD  CBD  C   C      0   0.435   0.3836  -5.2993   0.3801
 2VD  OBF  O   OC    -1  -0.622   0.8424  -6.2966  -0.2157
 2VD  OBE  O   O      0  -0.596  -0.5430  -5.3040   1.2133
 2VD  CAJ  C   CH2    0  -0.531   0.3917  -2.7587   0.7399
 2VD  CAH  C   CR5    0   0.351   1.2309  -1.5433   0.5614
 2VD  CAI  C   CR5    0  -0.039   2.5201  -1.5201   0.1124
 2VD  CAE  C   CR56   0   0.048   2.9238  -0.1510   0.0944
 2VD  CAF  C   CR16   0  -0.358   4.1081   0.4986  -0.2627
 2VD  CAA  C   CR6    0  -0.124   4.1473   1.8750  -0.1581
 2VD  BR   BR  BR     0  -0.080   5.7384   2.7908  -0.6373
 2VD  CAB  C   CR16   0  -0.263   3.0530   2.6275   0.2864
 2VD  CAC  C   CR16   0  -0.312   1.8757   1.9938   0.6436
 2VD  CAD  C   CR56   0   0.366   1.8208   0.6080   0.5503
 2VD  NAG  N   NR5    0  -0.585   0.8130  -0.2646   0.8540
 2VD  CAO  C   CH2    0  -0.477  -0.5245   0.0951   1.2161
 2VD  CAP  C   C      0   0.549  -1.4363   0.1392  -0.0075
 2VD  OAQ  O   O      0  -0.489  -0.9920   0.4310  -1.1065
 2VD  N    N   NH1    0  -0.611  -2.7230  -0.1072   0.2504
 2VD  CA   C   CH1    0  -0.198  -3.7184  -0.2383  -0.7842
 2VD  C    C   C      0   0.419  -3.7429  -1.6600  -1.4147
 2VD  OXT  O   OC    -1  -0.613  -4.6069  -1.8220  -2.2990
 2VD  O    O   O      0  -0.571  -2.9148  -2.4893  -1.0058
 2VD  CB   C   CH2    0  -0.553  -5.0947   0.1598  -0.2416
 2VD  CG   C   CR6    0   0.167  -5.1417   1.5845   0.2328
 2VD  CD1  C   CR16   0  -0.309  -5.2770   2.6269  -0.6831
 2VD  CE1  C   CR16   0  -0.241  -5.2925   3.9496  -0.2635
 2VD  CZ   C   CR16   0  -0.276  -5.1733   4.2548   1.0871
 2VD  CE2  C   CR16   0  -0.241  -5.0411   3.2262   2.0098
 2VD  CD2  C   CR16   0  -0.322  -5.0246   1.9041   1.5829
 2VD  H1   H   HCH2   0   0.232   4.2966  -2.7143   0.1189
 2VD  H2   H   HCH2   0   0.226   3.3541  -2.8397  -1.3467
 2VD  H3   H   HCH2   0   0.230   2.9748  -4.8889  -0.1475
 2VD  H4   H   HCH2   0   0.214   2.7278  -4.0547   1.3778
 2VD  H5   H   HCH1   0   0.224   0.9157  -3.8033  -1.0486
 2VD  H7   H   HCH2   0   0.270  -0.6182  -2.6036   0.3469
 2VD  H8   H   HCH2   0   0.239   0.2709  -2.9732   1.8071
 2VD  H9   H   HCR6   0   0.261   4.9627  -0.0662  -0.6131
 2VD  H10  H   HCR6   0   0.269   3.1163   3.7052   0.3505
 2VD  H11  H   HCR6   0   0.267   1.0299   2.5797   0.9801
 2VD  H12  H   HCH2   0   0.290  -0.9021  -0.5895   1.9775
 2VD  H13  H   HCH2   0   0.307  -0.5154   1.0843   1.6790
 2VD  H14  H   HNH1   0   0.388  -2.9568  -0.4756   1.1589
 2VD  H15  H   HCH1   0   0.251  -3.4551   0.4628  -1.5810
 2VD  H17  H   HCH2   0   0.260  -5.8202   0.0078  -1.0404
 2VD  H18  H   HCH2   0   0.247  -5.3777  -0.5157   0.5724
 2VD  H19  H   HCR6   0   0.245  -5.3759   2.4015  -1.7392
 2VD  H20  H   HCR6   0   0.252  -5.4019   4.7435  -0.9914
 2VD  H21  H   HCR6   0   0.251  -5.1880   5.2860   1.4163
 2VD  H22  H   HCR6   0   0.251  -4.9528   3.4504   3.0654
 2VD  H23  H   HCR6   0   0.242  -4.9297   1.1092   2.3134

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
 2VD  CZ   CE1  aromatic  1.390  0.020  1.390
 2VD  CZ   CE2  aromatic  1.388  0.020  1.388
 2VD  CE1  CD1  aromatic  1.388  0.020  1.388
 2VD  CE2  CD2  aromatic  1.389  0.020  1.389
 2VD  OAQ  CAP  double    1.221  0.020  1.221
 2VD  CD1  CG   aromatic  1.394  0.020  1.394
 2VD  CAO  CAP  single    1.527  0.020  1.527
 2VD  CAO  NAG  single    1.432  0.020  1.432
 2VD  CD2  CG   aromatic  1.392  0.020  1.392
 2VD  CAP  N    single    1.335  0.020  1.335
 2VD  CAC  CAB  aromatic  1.384  0.020  1.384
 2VD  CAC  CAD  aromatic  1.390  0.020  1.390
 2VD  CG   CB   single    1.502  0.020  1.502
 2VD  NAG  CAD  aromatic  1.367  0.020  1.367
 2VD  NAG  CAH  aromatic  1.377  0.020  1.377
 2VD  CAB  CAA  aromatic  1.400  0.020  1.400
 2VD  CAD  CAE  aromatic  1.414  0.020  1.414
 2VD  N    CA   single    1.442  0.020  1.442
 2VD  CAH  CAJ  single    1.488  0.020  1.488
 2VD  CAH  CAI  aromatic  1.365  0.020  1.365
 2VD  CAJ  CAK  single    1.529  0.020  1.529
 2VD  CA   CB   single    1.532  0.020  1.532
 2VD  CA   C    single    1.555  0.020  1.555
 2VD  CAA  CAF  aromatic  1.381  0.020  1.381
 2VD  CAA  BR   single    1.897  0.020  1.897
 2VD  CAE  CAI  aromatic  1.427  0.020  1.427
 2VD  CAE  CAF  aromatic  1.397  0.020  1.397
 2VD  CAI  CAM  single    1.492  0.020  1.492
 2VD  CAK  CBD  single    1.544  0.020  1.544
 2VD  CAK  CAL  single    1.534  0.020  1.534
 2VD  OBE  CBD  deloc     1.246  0.020  1.246
 2VD  CBD  OBF  deloc     1.249  0.020  1.249
 2VD  C    O    deloc     1.241  0.020  1.241
 2VD  C    OXT  deloc     1.247  0.020  1.247
 2VD  CAM  CAL  single    1.529  0.020  1.529
 2VD  CAM  H1   single    0.970  0.020  1.090
 2VD  CAM  H2   single    0.970  0.020  1.090
 2VD  CAL  H3   single    0.970  0.020  1.090
 2VD  CAL  H4   single    0.970  0.020  1.090
 2VD  CAK  H5   single    0.970  0.020  1.090
 2VD  CAJ  H7   single    0.970  0.020  1.090
 2VD  CAJ  H8   single    0.970  0.020  1.090
 2VD  CAF  H9   single    0.930  0.020  1.080
 2VD  CAB  H10  single    0.930  0.020  1.080
 2VD  CAC  H11  single    0.930  0.020  1.080
 2VD  CAO  H12  single    0.970  0.020  1.090
 2VD  CAO  H13  single    0.970  0.020  1.090
 2VD  N    H14  single    0.860  0.020  1.020
 2VD  CA   H15  single    0.970  0.020  1.090
 2VD  CB   H17  single    0.970  0.020  1.090
 2VD  CB   H18  single    0.970  0.020  1.090
 2VD  CD1  H19  single    0.930  0.020  1.080
 2VD  CE1  H20  single    0.930  0.020  1.080
 2VD  CZ   H21  single    0.930  0.020  1.080
 2VD  CE2  H22  single    0.930  0.020  1.080
 2VD  CD2  H23  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
 2VD  H2   CAM  H1   105.81  3.000
 2VD  H2   CAM  CAI  110.36  3.000
 2VD  H1   CAM  CAI  110.80  3.000
 2VD  H2   CAM  CAL  109.58  3.000
 2VD  H1   CAM  CAL  110.20  3.000
 2VD  CAI  CAM  CAL  110.00  3.000
 2VD  H4   CAL  H3   106.91  3.000
 2VD  H4   CAL  CAK  109.13  3.000
 2VD  H3   CAL  CAK  109.33  3.000
 2VD  H4   CAL  CAM  109.44  3.000
 2VD  H3   CAL  CAM  109.71  3.000
 2VD  CAK  CAL  CAM  112.17  3.000
 2VD  H5   CAK  CAJ  107.65  3.000
 2VD  H5   CAK  CBD  106.63  3.000
 2VD  CAJ  CAK  CBD  113.22  3.000
 2VD  H5   CAK  CAL  106.77  3.000
 2VD  CBD  CAK  CAL  111.07  3.000
 2VD  CAJ  CAK  CAL  111.13  3.000
 2VD  OBE  CBD  OBF  126.09  3.000
 2VD  OBF  CBD  CAK  115.77  3.000
 2VD  OBE  CBD  CAK  118.14  3.000
 2VD  H8   CAJ  H7   106.01  3.000
 2VD  H8   CAJ  CAH  109.82  3.000
 2VD  H7   CAJ  CAH  111.19  3.000
 2VD  H8   CAJ  CAK  110.20  3.000
 2VD  H7   CAJ  CAK  109.74  3.000
 2VD  CAH  CAJ  CAK  109.81  3.000
 2VD  NAG  CAH  CAI  109.92  3.000
 2VD  CAI  CAH  CAJ  125.87  3.000
 2VD  NAG  CAH  CAJ  124.20  3.000
 2VD  CAE  CAI  CAH  106.71  3.000
 2VD  CAE  CAI  CAM  130.48  3.000
 2VD  CAH  CAI  CAM  122.81  3.000
 2VD  CAD  CAE  CAF  119.60  3.000
 2VD  CAF  CAE  CAI  133.54  3.000
 2VD  CAD  CAE  CAI  106.86  3.000
 2VD  H9   CAF  CAA  121.47  3.000
 2VD  H9   CAF  CAE  120.62  3.000
 2VD  CAA  CAF  CAE  117.91  3.000
 2VD  CAB  CAA  BR   118.43  3.000
 2VD  BR   CAA  CAF  119.06  3.000
 2VD  CAB  CAA  CAF  122.50  3.000
 2VD  H10  CAB  CAC  119.39  3.000
 2VD  H10  CAB  CAA  120.57  3.000
 2VD  CAC  CAB  CAA  120.04  3.000
 2VD  H11  CAC  CAD  121.98  3.000
 2VD  H11  CAC  CAB  119.80  3.000
 2VD  CAD  CAC  CAB  118.22  3.000
 2VD  NAG  CAD  CAC  130.58  3.000
 2VD  NAG  CAD  CAE  107.70  3.000
 2VD  CAC  CAD  CAE  121.72  3.000
 2VD  CAO  NAG  CAD  125.77  3.000
 2VD  CAD  NAG  CAH  108.77  3.000
 2VD  CAO  NAG  CAH  124.80  3.000
 2VD  H13  CAO  H12  105.98  3.000
 2VD  H13  CAO  CAP  108.57  3.000
 2VD  H12  CAO  CAP  111.76  3.000
 2VD  H13  CAO  NAG  109.08  3.000
 2VD  H12  CAO  NAG  110.01  3.000
 2VD  CAP  CAO  NAG  111.26  3.000
 2VD  N    CAP  OAQ  124.66  3.000
 2VD  N    CAP  CAO  114.54  3.000
 2VD  OAQ  CAP  CAO  120.74  3.000
 2VD  H14  N    CA   116.97  3.000
 2VD  H14  N    CAP  117.72  3.000
 2VD  CA   N    CAP  122.93  3.000
 2VD  H15  CA   CB   107.93  3.000
 2VD  H15  CA   C    107.13  3.000
 2VD  CB   CA   C    111.52  3.000
 2VD  H15  CA   N    107.36  3.000
 2VD  C    CA   N    112.63  3.000
 2VD  CB   CA   N    110.03  3.000
 2VD  O    C    OXT  127.53  3.000
 2VD  OXT  C    CA   114.65  3.000
 2VD  O    C    CA   117.82  3.000
 2VD  H18  CB   H17  106.67  3.000
 2VD  H18  CB   CG   110.01  3.000
 2VD  H17  CB   CG   110.05  3.000
 2VD  H18  CB   CA   109.59  3.000
 2VD  H17  CB   CA   107.59  3.000
 2VD  CG   CB   CA   112.73  3.000
 2VD  CD2  CG   CD1  118.26  3.000
 2VD  CD2  CG   CB   121.41  3.000
 2VD  CD1  CG   CB   120.31  3.000
 2VD  H19  CD1  CE1  119.44  3.000
 2VD  H19  CD1  CG   119.55  3.000
 2VD  CE1  CD1  CG   121.01  3.000
 2VD  H20  CE1  CZ   120.06  3.000
 2VD  H20  CE1  CD1  119.80  3.000
 2VD  CZ   CE1  CD1  120.15  3.000
 2VD  H21  CZ   CE2  120.33  3.000
 2VD  H21  CZ   CE1  120.24  3.000
 2VD  CE2  CZ   CE1  119.43  3.000
 2VD  H22  CE2  CD2  119.72  3.000
 2VD  H22  CE2  CZ   120.15  3.000
 2VD  CD2  CE2  CZ   120.13  3.000
 2VD  H23  CD2  CE2  119.46  3.000
 2VD  H23  CD2  CG   119.52  3.000
 2VD  CE2  CD2  CG   121.02  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
 2VD  CONST_01  CAC  CAD  NAG  CAH  180.00   0.0  0
 2VD  CONST_02  CAE  CAD  NAG  CAH    0.00   0.0  0
 2VD  CONST_03  CAD  CAE  CAI  CAH    0.00   0.0  0
 2VD  CONST_04  CAF  CAE  CAI  CAH  180.00   0.0  0
 2VD  CONST_05  CAD  NAG  CAH  CAI    0.00   0.0  0
 2VD  CONST_06  CAC  CAD  CAE  CAI  180.00   0.0  0
 2VD  CONST_07  NAG  CAD  CAE  CAI    0.00   0.0  0
 2VD  CONST_08  CAA  CAF  CAE  CAI  180.00   0.0  0
 2VD  CONST_09  CAB  CAC  CAD  CAE    0.00   0.0  0
 2VD  CONST_10  NAG  CAH  CAI  CAE    0.00   0.0  0
 2VD  CONST_11  CAB  CAA  CAF  CAE    0.00   0.0  0
 2VD  CONST_12  CAC  CAB  CAA  CAF    0.00   0.0  0
 2VD  CONST_13  CAC  CAD  CAE  CAF    0.00   0.0  0
 2VD  CONST_14  NAG  CAD  CAE  CAF  180.00   0.0  0
 2VD  CONST_15  CAD  CAC  CAB  CAA    0.00   0.0  0
 2VD  CONST_16  CAD  CAE  CAF  CAA    0.00   0.0  0
 2VD  CONST_17  NAG  CAD  CAC  CAB  180.00   0.0  0
 2VD  CONST_18  CZ   CE1  CD1  CG     0.00   0.0  0
 2VD  CONST_19  CZ   CE2  CD2  CG     0.00   0.0  0
 2VD  CONST_20  CE2  CZ   CE1  CD1    0.00   0.0  0
 2VD  CONST_21  CE2  CD2  CG   CD1    0.00   0.0  0
 2VD  CONST_22  CD2  CE2  CZ   CE1    0.00   0.0  0
 2VD  CONST_23  CD2  CG   CD1  CE1    0.00   0.0  0
 2VD  CONST_24  CAO  NAG  CAH  CAJ    0.00   0.0  0
 2VD  CONST_25  CAO  NAG  CAH  CAI  180.00   0.0  0
 2VD  CONST_26  CAO  NAG  CAD  CAE  180.00   0.0  0
 2VD  CONST_27  BR   CAA  CAF  CAE  180.00   0.0  0
 2VD  CONST_28  CAC  CAB  CAA  BR   180.00   0.0  0
 2VD  CONST_29  CAO  NAG  CAD  CAC    0.00   0.0  0
 2VD  CONST_30  CE1  CD1  CG   CB   180.00   0.0  0
 2VD  CONST_31  CE2  CD2  CG   CB   180.00   0.0  0
 2VD  CONST_32  H9   CAF  CAE  CAI    0.00   0.0  0
 2VD  CONST_33  H11  CAC  CAD  CAE  180.00   0.0  0
 2VD  CONST_34  H10  CAB  CAA  CAF  180.00   0.0  0
 2VD  CONST_35  H20  CE1  CD1  CG   180.00   0.0  0
 2VD  CONST_36  H22  CE2  CD2  CG   180.00   0.0  0
 2VD  CONST_37  H21  CZ   CE1  CD1  180.00   0.0  0
 2VD  CONST_38  H23  CD2  CG   CD1  180.00   0.0  0
 2VD  CONST_39  H19  CD1  CE1  CZ   180.00   0.0  0
 2VD  CONST_40  CA   N    CAP  CAO  180.00   0.0  0
 2VD  CONST_41  CA   N    CAP  OAQ    0.00   0.0  0
 2VD  CONST_42  H14  N    CAP  CAO    0.00   0.0  0
 2VD  Var_01    CAH  CAI  CAM  CAL  -15.61  30.0  1
 2VD  Var_02    NAG  CAH  CAJ  CAK  167.36  30.0  1
 2VD  Var_03    CAI  CAM  CAL  CAK   46.15  30.0  1
 2VD  Var_04    CAP  CAO  NAG  CAH  -77.23  30.0  2
 2VD  Var_05    CD1  CG   CB   CA    79.42  30.0  2
 2VD  Var_06    OAQ  CAP  CAO  NAG  -30.11  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
 2VD  chir_01  CAK  CAJ  CBD  CAL  positiv
 2VD  chir_02  CA   N    CB   C    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
 2VD  plan-1  CB   0.020
 2VD  plan-1  CG   0.020
 2VD  plan-1  CD1  0.020
 2VD  plan-1  CE1  0.020
 2VD  plan-1  CZ   0.020
 2VD  plan-1  CE2  0.020
 2VD  plan-1  CD2  0.020
 2VD  plan-1  H19  0.020
 2VD  plan-1  H20  0.020
 2VD  plan-1  H21  0.020
 2VD  plan-1  H22  0.020
 2VD  plan-1  H23  0.020
 2VD  plan-2  CAM  0.020
 2VD  plan-2  CAJ  0.020
 2VD  plan-2  CAH  0.020
 2VD  plan-2  CAI  0.020
 2VD  plan-2  CAE  0.020
 2VD  plan-2  CAF  0.020
 2VD  plan-2  CAA  0.020
 2VD  plan-2  BR   0.020
 2VD  plan-2  CAB  0.020
 2VD  plan-2  CAC  0.020
 2VD  plan-2  CAD  0.020
 2VD  plan-2  NAG  0.020
 2VD  plan-2  CAO  0.020
 2VD  plan-2  H9   0.020
 2VD  plan-2  H10  0.020
 2VD  plan-2  H11  0.020
 2VD  plan-3  CAO  0.020
 2VD  plan-3  CAP  0.020
 2VD  plan-3  OAQ  0.020
 2VD  plan-3  N    0.020
 2VD  plan-3  CA   0.020
 2VD  plan-3  H14  0.020
 2VD  plan-4  CAK  0.020
 2VD  plan-4  CBD  0.020
 2VD  plan-4  OBF  0.020
 2VD  plan-4  OBE  0.020
 2VD  plan-5  CA   0.020
 2VD  plan-5  C    0.020
 2VD  plan-5  OXT  0.020
 2VD  plan-5  O    0.020

