# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 13:08:11 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: (2-{2-[(2S)-3-methylbutan-2-yl]-5-phenyl-1H-indol-3-yl}ethane-1,1-diyl)bis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](C)c1[nH]c2ccc(cc2c1CC([P](O)(O)=O)[P](O)(O)=O)c3ccccc3
#
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
 WC1  WC1  '(2-{2-[(2S)-3-methylbutan-2-yl]-5-phenyl-1H-indol-3-yl}ethane-1,1-diyl)bis(phosphonic acid)'  ligand  53  30  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WC1
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
 WC1  OAE  O  O      0  -0.937   0.8193  -2.4610   1.2475
 WC1  PAD  P  P      0   1.223   0.0819  -2.4827  -0.1128
 WC1  OAF  O  OP    -1  -0.868   0.9484  -1.9231  -1.2661
 WC1  OAG  O  OP    -1  -0.976  -0.4461  -3.8864  -0.4448
 WC1  CAC  C  CH1    0  -0.755  -1.3770  -1.2980   0.0387
 WC1  PAH  P  P      0   1.169  -3.0711  -2.0593   0.0942
 WC1  OAI  O  OP    -1  -0.904  -4.0572  -0.8674   0.2281
 WC1  OAK  O  O      0  -0.918  -3.2964  -2.8039  -1.2325
 WC1  OAJ  O  OP    -1  -0.970  -3.1180  -2.9578   1.3436
 WC1  CAB  C  CH2    0  -0.516  -1.2202  -0.3086   1.2175
 WC1  CAA  C  CR5    0  -0.100  -0.6946   1.0396   0.8419
 WC1  CAO  C  CR5    0   0.342  -1.4176   2.1867   0.6501
 WC1  CAT  C  CH1    0  -0.292  -2.8934   2.4013   0.7288
 WC1  CAU  C  CH3    0  -0.649  -3.2429   3.3861   1.8490
 WC1  CAV  C  CH1    0  -0.225  -3.4812   2.8216  -0.6366
 WC1  CAX  C  CH3    0  -0.673  -3.0497   1.8486  -1.7301
 WC1  CAW  C  CH3    0  -0.663  -5.0057   2.8761  -0.5822
 WC1  NAN  N  NR15   0  -0.619  -0.5641   3.2172   0.3007
 WC1  CAM  C  CR56   0   0.202   0.7124   2.7484   0.2255
 WC1  CAS  C  CR16   0  -0.328   1.9066   3.3796  -0.1188
 WC1  CAR  C  CR16   0  -0.382   3.0539   2.6083  -0.1518
 WC1  CAL  C  CR56   0   0.231   0.6702   1.3777   0.5625
 WC1  CAP  C  CR16   0  -0.538   1.8410   0.6234   0.5235
 WC1  CAQ  C  CR6    0   0.178   3.0360   1.2305   0.1566
 WC1  CAY  C  CR6    0   0.004   4.2592   0.4128   0.0311
 WC1  CAZ  C  CR16   0  -0.307   5.5254   0.9343   0.3084
 WC1  CBA  C  CR16   0  -0.255   6.6658   0.1542   0.1739
 WC1  CBB  C  CR16   0  -0.253   6.5645  -1.1684  -0.2370
 WC1  CBC  C  CR16   0  -0.269   5.3100  -1.6995  -0.5141
 WC1  CBD  C  CR16   0  -0.229   4.1681  -0.9214  -0.3855
 WC1  H3   H  HCH1   0   0.188  -1.3684  -0.7030  -0.8824
 WC1  H6   H  HCH2   0   0.203  -2.1849  -0.1602   1.7066
 WC1  H7   H  HCH2   0   0.211  -0.5553  -0.7536   1.9604
 WC1  H8   H  HCH1   0   0.261  -3.3284   1.4230   0.9529
 WC1  H9   H  HCH3   0   0.190  -2.9101   4.4007   1.6152
 WC1  H10  H  HCH3   0   0.240  -4.3175   3.4293   2.0260
 WC1  H11  H  HCH3   0   0.221  -2.7718   3.0893   2.7870
 WC1  H12  H  HCH1   0   0.225  -3.1134   3.8270  -0.8839
 WC1  H13  H  HCH3   0   0.205  -3.3420   0.8362  -1.4431
 WC1  H14  H  HCH3   0   0.239  -3.5166   2.1042  -2.6843
 WC1  H15  H  HCH3   0   0.234  -1.9686   1.8508  -1.8752
 WC1  H16  H  HCH3   0   0.185  -5.4070   1.8985  -0.3027
 WC1  H17  H  HCH3   0   0.251  -5.3782   3.6120   0.1310
 WC1  H18  H  HCH3   0   0.244  -5.4180   3.1356  -1.5594
 WC1  H19  H  HNR5   0   0.374  -0.8502   4.1557   0.0794
 WC1  H20  H  HCR6   0   0.228   1.9383   4.4307  -0.3783
 WC1  H21  H  HCR6   0   0.178   3.9832   3.0740  -0.4568
 WC1  H22  H  HCR6   0   0.256   1.7944  -0.4305   0.7736
 WC1  H23  H  HCR6   0   0.228   5.6247   1.9584   0.6485
 WC1  H24  H  HCR6   0   0.222   7.6354   0.5808   0.3980
 WC1  H25  H  HCR6   0   0.240   7.4531  -1.7773  -0.3437
 WC1  H26  H  HCR6   0   0.217   5.2208  -2.7273  -0.8442
 WC1  H27  H  HCR6   0   0.240   3.1939  -1.3370  -0.6358

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
 WC1  OAE  PAD  deloc     1.547  0.020  1.547
 WC1  OAG  PAD  deloc     1.536  0.020  1.536
 WC1  PAD  OAF  deloc     1.547  0.020  1.547
 WC1  PAD  CAC  single    1.885  0.020  1.885
 WC1  OAK  PAH  deloc     1.538  0.020  1.538
 WC1  CAB  CAC  single    1.547  0.020  1.547
 WC1  CAB  CAA  single    1.495  0.020  1.495
 WC1  CAC  PAH  single    1.858  0.020  1.858
 WC1  CBB  CBC  aromatic  1.390  0.020  1.390
 WC1  CBB  CBA  aromatic  1.389  0.020  1.389
 WC1  CAX  CAV  single    1.526  0.020  1.526
 WC1  CBC  CBD  aromatic  1.388  0.020  1.388
 WC1  CBA  CAZ  aromatic  1.388  0.020  1.388
 WC1  PAH  OAJ  deloc     1.540  0.020  1.540
 WC1  PAH  OAI  deloc     1.553  0.020  1.553
 WC1  CBD  CAY  aromatic  1.401  0.020  1.401
 WC1  CAZ  CAY  aromatic  1.397  0.020  1.397
 WC1  CAP  CAL  aromatic  1.393  0.020  1.393
 WC1  CAP  CAQ  aromatic  1.390  0.020  1.390
 WC1  CAY  CAQ  single    1.477  0.020  1.477
 WC1  CAA  CAL  aromatic  1.433  0.020  1.433
 WC1  CAA  CAO  aromatic  1.369  0.020  1.369
 WC1  CAL  CAM  aromatic  1.412  0.020  1.412
 WC1  CAQ  CAR  aromatic  1.412  0.020  1.412
 WC1  CAV  CAT  single    1.545  0.020  1.545
 WC1  CAV  CAW  single    1.526  0.020  1.526
 WC1  CAO  CAT  single    1.493  0.020  1.493
 WC1  CAO  NAN  aromatic  1.383  0.020  1.383
 WC1  CAT  CAU  single    1.532  0.020  1.532
 WC1  CAM  NAN  aromatic  1.362  0.020  1.362
 WC1  CAM  CAS  aromatic  1.394  0.020  1.394
 WC1  CAR  CAS  aromatic  1.383  0.020  1.383
 WC1  CAC  H3   single    0.970  0.020  1.090
 WC1  CAB  H6   single    0.970  0.020  1.090
 WC1  CAB  H7   single    0.970  0.020  1.090
 WC1  CAT  H8   single    0.970  0.020  1.090
 WC1  CAU  H9   single    0.970  0.020  1.090
 WC1  CAU  H10  single    0.970  0.020  1.090
 WC1  CAU  H11  single    0.970  0.020  1.090
 WC1  CAV  H12  single    0.970  0.020  1.090
 WC1  CAX  H13  single    0.970  0.020  1.090
 WC1  CAX  H14  single    0.970  0.020  1.090
 WC1  CAX  H15  single    0.970  0.020  1.090
 WC1  CAW  H16  single    0.970  0.020  1.090
 WC1  CAW  H17  single    0.970  0.020  1.090
 WC1  CAW  H18  single    0.970  0.020  1.090
 WC1  NAN  H19  single    0.860  0.020  1.020
 WC1  CAS  H20  single    0.930  0.020  1.080
 WC1  CAR  H21  single    0.930  0.020  1.080
 WC1  CAP  H22  single    0.930  0.020  1.080
 WC1  CAZ  H23  single    0.930  0.020  1.080
 WC1  CBA  H24  single    0.930  0.020  1.080
 WC1  CBB  H25  single    0.930  0.020  1.080
 WC1  CBC  H26  single    0.930  0.020  1.080
 WC1  CBD  H27  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
 WC1  CAC  PAD  OAG  109.00  3.000
 WC1  CAC  PAD  OAF  105.42  3.000
 WC1  OAG  PAD  OAF  111.22  3.000
 WC1  CAC  PAD  OAE  106.81  3.000
 WC1  OAF  PAD  OAE  112.54  3.000
 WC1  OAG  PAD  OAE  111.50  3.000
 WC1  H3   CAC  CAB  107.00  3.000
 WC1  H3   CAC  PAH  104.75  3.000
 WC1  CAB  CAC  PAH  109.37  3.000
 WC1  H3   CAC  PAD  105.51  3.000
 WC1  PAH  CAC  PAD  116.77  3.000
 WC1  CAB  CAC  PAD  112.62  3.000
 WC1  OAJ  PAH  OAK  114.39  3.000
 WC1  OAJ  PAH  OAI  111.02  3.000
 WC1  OAK  PAH  OAI  110.67  3.000
 WC1  OAI  PAH  CAC  105.49  3.000
 WC1  OAJ  PAH  CAC  106.93  3.000
 WC1  OAK  PAH  CAC  107.83  3.000
 WC1  H7   CAB  H6   106.78  3.000
 WC1  H7   CAB  CAA  108.93  3.000
 WC1  H6   CAB  CAA  107.49  3.000
 WC1  H7   CAB  CAC  108.64  3.000
 WC1  H6   CAB  CAC  109.80  3.000
 WC1  CAA  CAB  CAC  114.89  3.000
 WC1  CAL  CAA  CAO  106.12  3.000
 WC1  CAO  CAA  CAB  127.23  3.000
 WC1  CAL  CAA  CAB  126.61  3.000
 WC1  NAN  CAO  CAT  121.07  3.000
 WC1  NAN  CAO  CAA  109.50  3.000
 WC1  CAT  CAO  CAA  129.40  3.000
 WC1  H8   CAT  CAV  105.84  3.000
 WC1  H8   CAT  CAU  109.54  3.000
 WC1  CAV  CAT  CAU  112.62  3.000
 WC1  H8   CAT  CAO  105.98  3.000
 WC1  CAU  CAT  CAO  110.88  3.000
 WC1  CAV  CAT  CAO  111.63  3.000
 WC1  H11  CAU  H10  107.27  3.000
 WC1  H11  CAU  H9   107.76  3.000
 WC1  H10  CAU  H9   107.34  3.000
 WC1  H11  CAU  CAT  110.82  3.000
 WC1  H10  CAU  CAT  111.67  3.000
 WC1  H9   CAU  CAT  111.77  3.000
 WC1  H12  CAV  CAW  108.04  3.000
 WC1  H12  CAV  CAX  109.12  3.000
 WC1  CAW  CAV  CAX  109.31  3.000
 WC1  H12  CAV  CAT  108.69  3.000
 WC1  CAW  CAV  CAT  110.99  3.000
 WC1  CAX  CAV  CAT  110.63  3.000
 WC1  H15  CAX  H14  107.87  3.000
 WC1  H15  CAX  H13  107.58  3.000
 WC1  H14  CAX  H13  109.39  3.000
 WC1  H15  CAX  CAV  111.98  3.000
 WC1  H14  CAX  CAV  110.84  3.000
 WC1  H13  CAX  CAV  109.09  3.000
 WC1  H18  CAW  H17  107.21  3.000
 WC1  H18  CAW  H16  107.63  3.000
 WC1  H17  CAW  H16  108.12  3.000
 WC1  H18  CAW  CAV  110.71  3.000
 WC1  H17  CAW  CAV  112.86  3.000
 WC1  H16  CAW  CAV  110.11  3.000
 WC1  H19  NAN  CAM  125.15  3.000
 WC1  H19  NAN  CAO  125.13  3.000
 WC1  CAM  NAN  CAO  109.62  3.000
 WC1  CAL  CAM  CAS  121.61  3.000
 WC1  CAS  CAM  NAN  131.35  3.000
 WC1  CAL  CAM  NAN  107.03  3.000
 WC1  H20  CAS  CAR  120.75  3.000
 WC1  H20  CAS  CAM  121.58  3.000
 WC1  CAR  CAS  CAM  117.65  3.000
 WC1  H21  CAR  CAQ  119.46  3.000
 WC1  H21  CAR  CAS  118.60  3.000
 WC1  CAQ  CAR  CAS  121.91  3.000
 WC1  CAP  CAL  CAM  119.58  3.000
 WC1  CAM  CAL  CAA  107.69  3.000
 WC1  CAP  CAL  CAA  132.67  3.000
 WC1  H22  CAP  CAQ  121.51  3.000
 WC1  H22  CAP  CAL  118.92  3.000
 WC1  CAQ  CAP  CAL  119.57  3.000
 WC1  CAY  CAQ  CAP  119.53  3.000
 WC1  CAY  CAQ  CAR  120.75  3.000
 WC1  CAP  CAQ  CAR  119.65  3.000
 WC1  CBD  CAY  CAZ  118.26  3.000
 WC1  CAZ  CAY  CAQ  121.81  3.000
 WC1  CBD  CAY  CAQ  119.93  3.000
 WC1  H23  CAZ  CBA  119.09  3.000
 WC1  H23  CAZ  CAY  119.87  3.000
 WC1  CBA  CAZ  CAY  121.03  3.000
 WC1  H24  CBA  CBB  120.12  3.000
 WC1  H24  CBA  CAZ  119.62  3.000
 WC1  CBB  CBA  CAZ  120.26  3.000
 WC1  H25  CBB  CBC  120.41  3.000
 WC1  H25  CBB  CBA  120.34  3.000
 WC1  CBC  CBB  CBA  119.25  3.000
 WC1  H26  CBC  CBD  119.50  3.000
 WC1  H26  CBC  CBB  119.84  3.000
 WC1  CBD  CBC  CBB  120.66  3.000
 WC1  H27  CBD  CBC  120.08  3.000
 WC1  H27  CBD  CAY  119.36  3.000
 WC1  CBC  CBD  CAY  120.54  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
 WC1  CONST_01  CAQ  CAP  CAL  CAA  180.00   0.0  0
 WC1  CONST_02  NAN  CAM  CAL  CAA    0.00   0.0  0
 WC1  CONST_03  CAS  CAM  CAL  CAA  180.00   0.0  0
 WC1  CONST_04  CAM  NAN  CAO  CAA    0.00   0.0  0
 WC1  CONST_05  CAP  CAL  CAA  CAO  180.00   0.0  0
 WC1  CONST_06  CAM  CAL  CAA  CAO    0.00   0.0  0
 WC1  CONST_07  CAL  CAM  NAN  CAO    0.00   0.0  0
 WC1  CONST_08  CAS  CAM  NAN  CAO  180.00   0.0  0
 WC1  CONST_09  CAL  CAA  CAO  NAN    0.00   0.0  0
 WC1  CONST_10  CAP  CAL  CAM  NAN  180.00   0.0  0
 WC1  CONST_11  CAR  CAS  CAM  NAN  180.00   0.0  0
 WC1  CONST_12  CAQ  CAP  CAL  CAM    0.00   0.0  0
 WC1  CONST_13  CAQ  CAR  CAS  CAM    0.00   0.0  0
 WC1  CONST_14  CAP  CAL  CAM  CAS    0.00   0.0  0
 WC1  CONST_15  CAP  CAQ  CAR  CAS    0.00   0.0  0
 WC1  CONST_16  CAY  CAQ  CAR  CAS  180.00   0.0  0
 WC1  CONST_17  CAL  CAP  CAQ  CAR    0.00   0.0  0
 WC1  CONST_20  CAL  CAM  CAS  CAR    0.00   0.0  0
 WC1  CONST_21  CAY  CAQ  CAP  CAL  180.00   0.0  0
 WC1  CONST_24  CBC  CBD  CAY  CAQ  180.00   0.0  0
 WC1  CONST_25  CBA  CAZ  CAY  CAQ  180.00   0.0  0
 WC1  CONST_26  CBB  CBC  CBD  CAY    0.00   0.0  0
 WC1  CONST_27  CBB  CBA  CAZ  CAY    0.00   0.0  0
 WC1  CONST_28  CBC  CBB  CBA  CAZ    0.00   0.0  0
 WC1  CONST_29  CBC  CBD  CAY  CAZ    0.00   0.0  0
 WC1  CONST_30  CBD  CBC  CBB  CBA    0.00   0.0  0
 WC1  CONST_31  CBD  CAY  CAZ  CBA    0.00   0.0  0
 WC1  CONST_32  CAP  CAL  CAA  CAB    0.00   0.0  0
 WC1  CONST_33  CAM  CAL  CAA  CAB  180.00   0.0  0
 WC1  CONST_34  NAN  CAO  CAA  CAB  180.00   0.0  0
 WC1  CONST_35  CAL  CAA  CAO  CAT  180.00   0.0  0
 WC1  CONST_36  CAM  NAN  CAO  CAT  180.00   0.0  0
 WC1  CONST_37  H22  CAP  CAL  CAA    0.00   0.0  0
 WC1  CONST_38  H19  NAN  CAO  CAA  180.00   0.0  0
 WC1  CONST_39  H20  CAS  CAM  NAN    0.00   0.0  0
 WC1  CONST_40  H21  CAR  CAS  CAM  180.00   0.0  0
 WC1  CONST_41  H27  CBD  CAY  CAQ    0.00   0.0  0
 WC1  CONST_42  H23  CAZ  CAY  CAQ    0.00   0.0  0
 WC1  CONST_43  H26  CBC  CBD  CAY  180.00   0.0  0
 WC1  CONST_44  H24  CBA  CAZ  CAY  180.00   0.0  0
 WC1  CONST_45  H25  CBB  CBA  CAZ  180.00   0.0  0
 WC1  Var_01    CAL  CAA  CAB  CAC  -77.93  30.0  2
 WC1  Var_02    CAA  CAB  CAC  PAD   97.72  30.0  2
 WC1  Var_03    CAB  CAC  PAD  OAE   18.41  30.0  3
 WC1  Var_04    OAK  PAH  CAC  PAD  -62.07  30.0  3
 WC1  Var_05    H13  CAX  CAV  CAT   55.74  30.0  3
 WC1  Var_06    H16  CAW  CAV  CAT  -58.90  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
 WC1  chir_01  CAT  CAV  CAO  CAU  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
 WC1  plan-1  CAQ  0.020
 WC1  plan-1  CAY  0.020
 WC1  plan-1  CAZ  0.020
 WC1  plan-1  CBA  0.020
 WC1  plan-1  CBB  0.020
 WC1  plan-1  CBC  0.020
 WC1  plan-1  CBD  0.020
 WC1  plan-1  H23  0.020
 WC1  plan-1  H24  0.020
 WC1  plan-1  H25  0.020
 WC1  plan-1  H26  0.020
 WC1  plan-1  H27  0.020
 WC1  plan-2  CAB  0.020
 WC1  plan-2  CAA  0.020
 WC1  plan-2  CAO  0.020
 WC1  plan-2  CAT  0.020
 WC1  plan-2  NAN  0.020
 WC1  plan-2  CAM  0.020
 WC1  plan-2  CAS  0.020
 WC1  plan-2  CAR  0.020
 WC1  plan-2  CAL  0.020
 WC1  plan-2  CAP  0.020
 WC1  plan-2  CAQ  0.020
 WC1  plan-2  CAY  0.020
 WC1  plan-2  H19  0.020
 WC1  plan-2  H20  0.020
 WC1  plan-2  H21  0.020
 WC1  plan-2  H22  0.020

