# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  2 16:05:54 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  57  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 OK
;

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  -0.689   0.6678  -2.4176  -0.5298
 WC1  PAD  P  P     0   1.373  -0.4636  -1.7324  -1.2006
 WC1  OAF  O  OH1   0  -0.731  -0.0793  -0.4561  -2.0885
 WC1  OAG  O  OH1   0  -0.757  -1.2578  -2.5422  -2.3193
 WC1  CAC  C  CH1   0  -0.840  -1.7403  -1.2036   0.0039
 WC1  PAH  P  P     0   1.413  -2.6274  -2.6736   0.5965
 WC1  OAI  O  OH1   0  -0.728  -3.9424  -2.0153   1.2143
 WC1  OAK  O  O     0  -0.714  -2.8161  -3.6940  -0.4763
 WC1  OAJ  O  OH1   0  -0.731  -1.8049  -3.3291   1.7985
 WC1  CAB  C  CH2   0  -0.610  -1.1776  -0.3483   1.1609
 WC1  CAA  C  CR5   0  -0.069  -0.6315   0.9712   0.7212
 WC1  CAO  C  CR5   0   0.388  -1.3468   2.1152   0.4766
 WC1  CAT  C  CH1   0  -0.316  -2.8105   2.3826   0.6301
 WC1  CAU  C  CH3   0  -0.660  -3.0400   3.3715   1.7791
 WC1  CAV  C  CH1   0  -0.219  -3.4452   2.8480  -0.6977
 WC1  CAX  C  CH3   0  -0.668  -3.2102   1.8299  -1.8087
 WC1  CAW  C  CH3   0  -0.665  -4.9412   3.1058  -0.5467
 WC1  NAN  N  NR15  0  -0.743  -0.4868   3.1010   0.0668
 WC1  CAM  C  CR56  0   0.329   0.7892   2.6235   0.0307
 WC1  CAS  C  CR16  0  -0.297   1.9857   3.2391  -0.3233
 WC1  CAR  C  CR16  0  -0.335   3.1396   2.4831  -0.2631
 WC1  CAL  C  CR56  0   0.026   0.7417   1.2754   0.4443
 WC1  CAP  C  CR16  0  -0.434   1.9275   0.5384   0.5061
 WC1  CAQ  C  CR6   0   0.085   3.1299   1.1336   0.1475
 WC1  CAY  C  CR6   0   0.093   4.3829   0.3521   0.1855
 WC1  CAZ  C  CR16  0  -0.318   5.5935   0.9441   0.5522
 WC1  CBA  C  CR16  0  -0.240   6.7667   0.2043   0.5902
 WC1  CBB  C  CR16  0  -0.270   6.7541  -1.1458   0.2654
 WC1  CBC  C  CR16  0  -0.241   5.5567  -1.7477  -0.0996
 WC1  CBD  C  CR16  0  -0.319   4.3850  -1.0067  -0.1422
 WC1  H1   H  HOH1  0   0.500   0.5881   0.1129  -1.6782
 WC1  H2   H  HOH1  0   0.492  -1.8981  -3.1639  -1.9012
 WC1  H3   H  HCH1  0   0.343  -2.4837  -0.6249  -0.5563
 WC1  H4   H  HOH1  0   0.506  -4.5586  -2.6342   1.6329
 WC1  H5   H  HOH1  0   0.501  -1.7784  -2.8390   2.6312
 WC1  H6   H  HCH2  0   0.287  -1.9734  -0.1843   1.8917
 WC1  H7   H  HCH2  0   0.282  -0.3992  -0.9083   1.6836
 WC1  H8   H  HCH1  0   0.233  -3.2823   1.4317   0.9055
 WC1  H9   H  HCH3  0   0.222  -2.6849   4.3721   1.5234
 WC1  H10  H  HCH3  0   0.244  -4.0968   3.4511   2.0286
 WC1  H11  H  HCH3  0   0.243  -2.5155   3.0478   2.6781
 WC1  H12  H  HCH1  0   0.216  -2.9695   3.7931  -0.9879
 WC1  H13  H  HCH3  0   0.215  -3.6999   0.8829  -1.5649
 WC1  H14  H  HCH3  0   0.240  -3.6346   2.1796  -2.7505
 WC1  H15  H  HCH3  0   0.237  -2.1519   1.6267  -1.9776
 WC1  H16  H  HCH3  0   0.217  -5.4588   2.2054  -0.2059
 WC1  H17  H  HCH3  0   0.235  -5.1603   3.9042   0.1610
 WC1  H18  H  HCH3  0   0.234  -5.3770   3.3916  -1.5052
 WC1  H19  H  HNR5  0   0.405  -0.7563   4.0388  -0.1813
 WC1  H20  H  HCR6  0   0.263   2.0154   4.2714  -0.6478
 WC1  H21  H  HCR6  0   0.251   4.0741   2.9390  -0.5637
 WC1  H22  H  HCR6  0   0.255   1.9081  -0.4893   0.8457
 WC1  H23  H  HCR6  0   0.250   5.6202   1.9905   0.8300
 WC1  H24  H  HCR6  0   0.256   7.6920   0.6838   0.8825
 WC1  H25  H  HCR6  0   0.255   7.6687  -1.7238   0.2945
 WC1  H26  H  HCR6  0   0.256   5.5354  -2.7978  -0.3615
 WC1  H27  H  HCR6  0   0.250   3.4634  -1.4871  -0.4500

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  double    1.483  0.020  1.483
 WC1  OAG  PAD  single    1.593  0.020  1.593
 WC1  PAD  OAF  single    1.602  0.020  1.602
 WC1  PAD  CAC  single    1.833  0.020  1.833
 WC1  OAK  PAH  double    1.493  0.020  1.493
 WC1  CAB  CAC  single    1.545  0.020  1.545
 WC1  CAB  CAA  single    1.494  0.020  1.494
 WC1  CAC  PAH  single    1.816  0.020  1.816
 WC1  CBB  CBC  aromatic  1.389  0.020  1.389
 WC1  CBB  CBA  aromatic  1.389  0.020  1.389
 WC1  CAX  CAV  single    1.525  0.020  1.525
 WC1  CBC  CBD  aromatic  1.387  0.020  1.387
 WC1  CBA  CAZ  aromatic  1.387  0.020  1.387
 WC1  PAH  OAJ  single    1.597  0.020  1.597
 WC1  PAH  OAI  single    1.595  0.020  1.595
 WC1  CBD  CAY  aromatic  1.398  0.020  1.398
 WC1  CAZ  CAY  aromatic  1.397  0.020  1.397
 WC1  CAP  CAL  aromatic  1.398  0.020  1.398
 WC1  CAP  CAQ  aromatic  1.389  0.020  1.389
 WC1  CAY  CAQ  single    1.477  0.020  1.477
 WC1  CAA  CAL  aromatic  1.433  0.020  1.433
 WC1  CAA  CAO  aromatic  1.371  0.020  1.371
 WC1  CAL  CAM  aromatic  1.411  0.020  1.411
 WC1  CAQ  CAR  aromatic  1.411  0.020  1.411
 WC1  CAV  CAT  single    1.544  0.020  1.544
 WC1  CAV  CAW  single    1.526  0.020  1.526
 WC1  CAO  CAT  single    1.496  0.020  1.496
 WC1  CAO  NAN  aromatic  1.371  0.020  1.371
 WC1  CAT  CAU  single    1.533  0.020  1.533
 WC1  CAM  NAN  aromatic  1.363  0.020  1.363
 WC1  CAM  CAS  aromatic  1.391  0.020  1.391
 WC1  CAR  CAS  aromatic  1.381  0.020  1.381
 WC1  OAF  H1   single    0.850  0.020  0.980
 WC1  OAG  H2   single    0.850  0.020  0.980
 WC1  CAC  H3   single    0.970  0.020  1.090
 WC1  OAI  H4   single    0.850  0.020  0.980
 WC1  OAJ  H5   single    0.850  0.020  0.980
 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  105.12  3.000
 WC1  CAC  PAD  OAF  107.55  3.000
 WC1  OAG  PAD  OAF   97.78  3.000
 WC1  CAC  PAD  OAE  111.56  3.000
 WC1  OAF  PAD  OAE  115.84  3.000
 WC1  OAG  PAD  OAE  117.58  3.000
 WC1  H1   OAF  PAD  113.50  3.000
 WC1  H2   OAG  PAD  110.28  3.000
 WC1  H3   CAC  CAB  109.73  3.000
 WC1  H3   CAC  PAH  105.24  3.000
 WC1  CAB  CAC  PAH  112.44  3.000
 WC1  H3   CAC  PAD  106.79  3.000
 WC1  PAH  CAC  PAD  108.72  3.000
 WC1  CAB  CAC  PAD  113.46  3.000
 WC1  OAJ  PAH  OAK  108.99  3.000
 WC1  OAJ  PAH  OAI  107.60  3.000
 WC1  OAK  PAH  OAI  117.15  3.000
 WC1  OAI  PAH  CAC  101.24  3.000
 WC1  OAJ  PAH  CAC  109.04  3.000
 WC1  OAK  PAH  CAC  112.37  3.000
 WC1  H4   OAI  PAH  115.36  3.000
 WC1  H5   OAJ  PAH  117.03  3.000
 WC1  H7   CAB  H6   106.02  3.000
 WC1  H7   CAB  CAA  109.46  3.000
 WC1  H6   CAB  CAA  109.29  3.000
 WC1  H7   CAB  CAC  109.52  3.000
 WC1  H6   CAB  CAC  108.58  3.000
 WC1  CAA  CAB  CAC  113.68  3.000
 WC1  CAL  CAA  CAO  106.75  3.000
 WC1  CAO  CAA  CAB  126.77  3.000
 WC1  CAL  CAA  CAB  126.47  3.000
 WC1  NAN  CAO  CAT  121.06  3.000
 WC1  NAN  CAO  CAA  109.03  3.000
 WC1  CAT  CAO  CAA  129.89  3.000
 WC1  H8   CAT  CAV  107.49  3.000
 WC1  H8   CAT  CAU  107.86  3.000
 WC1  CAV  CAT  CAU  112.87  3.000
 WC1  H8   CAT  CAO  106.96  3.000
 WC1  CAU  CAT  CAO  109.80  3.000
 WC1  CAV  CAT  CAO  111.59  3.000
 WC1  H11  CAU  H10  107.45  3.000
 WC1  H11  CAU  H9   107.98  3.000
 WC1  H10  CAU  H9   107.60  3.000
 WC1  H11  CAU  CAT  110.77  3.000
 WC1  H10  CAU  CAT  111.36  3.000
 WC1  H9   CAU  CAT  111.52  3.000
 WC1  H12  CAV  CAW  107.81  3.000
 WC1  H12  CAV  CAX  108.40  3.000
 WC1  CAW  CAV  CAX  109.63  3.000
 WC1  H12  CAV  CAT  108.00  3.000
 WC1  CAW  CAV  CAT  111.65  3.000
 WC1  CAX  CAV  CAT  111.22  3.000
 WC1  H15  CAX  H14  107.68  3.000
 WC1  H15  CAX  H13  107.92  3.000
 WC1  H14  CAX  H13  107.21  3.000
 WC1  H15  CAX  CAV  112.74  3.000
 WC1  H14  CAX  CAV  110.80  3.000
 WC1  H13  CAX  CAV  110.28  3.000
 WC1  H18  CAW  H17  107.37  3.000
 WC1  H18  CAW  H16  107.50  3.000
 WC1  H17  CAW  H16  107.81  3.000
 WC1  H18  CAW  CAV  110.42  3.000
 WC1  H17  CAW  CAV  112.67  3.000
 WC1  H16  CAW  CAV  110.86  3.000
 WC1  H19  NAN  CAM  124.78  3.000
 WC1  H19  NAN  CAO  125.14  3.000
 WC1  CAM  NAN  CAO  110.07  3.000
 WC1  CAL  CAM  CAS  121.75  3.000
 WC1  CAS  CAM  NAN  131.06  3.000
 WC1  CAL  CAM  NAN  107.19  3.000
 WC1  H20  CAS  CAR  120.82  3.000
 WC1  H20  CAS  CAM  121.45  3.000
 WC1  CAR  CAS  CAM  117.72  3.000
 WC1  H21  CAR  CAQ  119.32  3.000
 WC1  H21  CAR  CAS  118.60  3.000
 WC1  CAQ  CAR  CAS  122.06  3.000
 WC1  CAP  CAL  CAM  119.23  3.000
 WC1  CAM  CAL  CAA  106.95  3.000
 WC1  CAP  CAL  CAA  133.82  3.000
 WC1  H22  CAP  CAQ  120.23  3.000
 WC1  H22  CAP  CAL  119.95  3.000
 WC1  CAQ  CAP  CAL  119.81  3.000
 WC1  CAY  CAQ  CAP  120.07  3.000
 WC1  CAY  CAQ  CAR  120.52  3.000
 WC1  CAP  CAQ  CAR  119.41  3.000
 WC1  CBD  CAY  CAZ  118.18  3.000
 WC1  CAZ  CAY  CAQ  121.18  3.000
 WC1  CBD  CAY  CAQ  120.63  3.000
 WC1  H23  CAZ  CBA  119.17  3.000
 WC1  H23  CAZ  CAY  119.88  3.000
 WC1  CBA  CAZ  CAY  120.94  3.000
 WC1  H24  CBA  CBB  120.10  3.000
 WC1  H24  CBA  CAZ  119.60  3.000
 WC1  CBB  CBA  CAZ  120.29  3.000
 WC1  H25  CBB  CBC  120.27  3.000
 WC1  H25  CBB  CBA  120.35  3.000
 WC1  CBC  CBB  CBA  119.38  3.000
 WC1  H26  CBC  CBD  119.62  3.000
 WC1  H26  CBC  CBB  120.06  3.000
 WC1  CBD  CBC  CBB  120.32  3.000
 WC1  H27  CBD  CBC  119.35  3.000
 WC1  H27  CBD  CAY  119.74  3.000
 WC1  CBC  CBD  CAY  120.90  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  -96.47  30.0  2
 WC1  Var_02    CAA  CAB  CAC  PAD   65.15  30.0  2
 WC1  Var_03    CAB  CAC  PAD  OAE   53.53  30.0  3
 WC1  Var_04    OAK  PAH  CAC  PAD  -36.54  30.0  3
 WC1  Var_05    H13  CAX  CAV  CAT   63.20  30.0  3
 WC1  Var_06    H16  CAW  CAV  CAT  -58.54  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

