# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 03:07:20 2021
#   Inital geometry file: a 143 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-5-[2-chloranyl-6-[methyl-(phenylmethyl)amino]purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(Cc1ccccc1)c2nc(Cl)nc3n(cnc23)[C@@H]4O[C@H](CO[P](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]4O
#
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
 KYW  KYW  '[[(2~{R},3~{S},4~{R},5~{R})-5-[2-chloranyl-6-[methyl-(phenylmethyl)amino]purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid'  ligand  60  36  .  2022-03-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KYW
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
 KYW  N1    N   N     0  -0.472  -13.1599  23.3129  -37.0227
 KYW  N3    N   N     0  -0.433  -14.6452  21.4626  -37.1330
 KYW  C4    C   CR56  0   0.500  -14.7381  21.5941  -35.8080
 KYW  C5    C   CR56  0   0.016  -14.1070  22.5422  -35.0110
 KYW  C6    C   CR6   0   0.532  -13.2571  23.4539  -35.6893
 KYW  C8    C   CR15  0   0.088  -15.2817  21.3437  -33.7091
 KYW  C20   C   CH3   0  -0.525  -11.6633  25.2412  -35.9623
 KYW  C21   C   CH2   0  -0.435  -12.5677  24.7458  -33.7129
 KYW  C22   C   CR16  0  -0.267   -8.9383  23.5793  -31.7209
 KYW  C24   C   CR16  0  -0.314  -10.4847  25.2893  -32.4055
 KYW  C26   C   CR16  0  -0.289  -10.9129  22.9979  -32.9694
 KYW  PB    P   P     0   1.382  -16.5374  20.4968  -29.2917
 KYW  O1B   O   OH1   0  -0.735  -15.3425  20.9781  -28.3466
 KYW  O2B   O   O     0  -0.684  -16.5553  21.0261  -30.6760
 KYW  O3B   O   OH1   0  -0.740  -17.8192  20.8772  -28.4047
 KYW  PA    P   P     0   1.383  -17.5084  17.6921  -30.1091
 KYW  O1A   O   O     0  -0.691  -17.3319  16.2374  -29.9007
 KYW  O2A   O   OH1   0  -0.737  -18.9129  18.3275  -29.6935
 KYW  C3A   C   CH2   0  -1.050  -16.3436  18.7032  -29.1713
 KYW  C5'   C   CH2   0  -0.174  -16.1973  17.9253  -32.3790
 KYW  C4'   C   CH1   0   0.006  -16.5098  17.9709  -33.8533
 KYW  O4'   O   O2    0  -0.491  -17.0190  19.2477  -34.2299
 KYW  C3'   C   CH1   0  -0.045  -15.2607  17.7603  -34.7081
 KYW  O3'   O   OH1   0  -0.654  -15.0662  16.3963  -34.9474
 KYW  C2'   C   CH1   0  -0.044  -15.5969  18.5692  -35.9646
 KYW  O2'   O   OH1   0  -0.663  -16.4821  17.8681  -36.7922
 KYW  C1'   C   CH1   0   0.176  -16.3690  19.7392  -35.3603
 KYW  N9    N   NR5   0  -0.549  -15.4737  20.8257  -34.9598
 KYW  N7    N   N     0  -0.464  -14.4670  22.3582  -33.7008
 KYW  N6    N   NT    0  -0.455  -12.5427  24.4360  -35.1328
 KYW  C2    C   CR6   0   0.270  -13.8380  22.3652  -37.6272
 KYW  C23   C   CR16  0  -0.240   -9.3121  24.9146  -31.7593
 KYW  C25   C   CR6   0   0.132  -11.2948  24.3379  -33.0147
 KYW  C27   C   CR16  0  -0.241   -9.7431  22.6209  -32.3281
 KYW  CL2   CL  CL    0  -0.114  -13.6285  22.3052  -39.3519
 KYW  H8    H   HCR5  0   0.319  -15.7798  20.9542  -32.8339
 KYW  H1    H   HCH3  0   0.253  -11.0879  25.8965  -35.3140
 KYW  H2    H   HCH3  0   0.251  -10.9677  24.6231  -36.5272
 KYW  H3    H   HCH3  0   0.252  -12.2264  25.8567  -36.6641
 KYW  H5    H   HCH2  0   0.282  -12.7237  25.8211  -33.6018
 KYW  H4    H   HCH2  0   0.300  -13.4182  24.2514  -33.2512
 KYW  H21   H   HCR6  0   0.257   -8.0246  23.2838  -31.2219
 KYW  H23   H   HCR6  0   0.255  -10.7722  26.3340  -32.4363
 KYW  H25   H   HCR6  0   0.252  -11.5355  22.2416  -33.4325
 KYW  H6    H   HOH1  0   0.501  -15.1315  21.9194  -28.4238
 KYW  H7    H   HOH1  0   0.494  -18.6616  20.8245  -28.8751
 KYW  H9    H   HOH1  0   0.506  -19.6848  17.7840  -29.9074
 KYW  H3A2  H   HCH2  0   0.345  -16.3991  18.3925  -28.1249
 KYW  H3A1  H   HCH2  0   0.337  -15.3381  18.4452  -29.5169
 KYW  H5'2  H   HCH2  0   0.258  -15.7798  16.9396  -32.1521
 KYW  H5'1  H   HCH2  0   0.235  -15.4481  18.6792  -32.1206
 KYW  H4'   H   HCH1  0   0.261  -17.2589  17.2055  -34.0867
 KYW  H3'   H   HCH1  0   0.253  -14.3880  18.2106  -34.2166
 KYW  HO3'  H   HOH1  0   0.471  -14.1467  16.2491  -35.1916
 KYW  H2'   H   HCH1  0   0.268  -14.6998  18.8931  -36.5035
 KYW  HO2'  H   HOH1  0   0.453  -16.2216  16.9386  -36.7823
 KYW  H1'   H   HCH1  0   0.293  -17.0979  20.1532  -36.0617
 KYW  H22   H   HCR6  0   0.256   -8.6906  25.6674  -31.2917
 KYW  H26   H   HCR6  0   0.256   -9.4582  21.5771  -32.2979
 KYW  O5'   O   O2    0  -0.584  -17.3921  18.1637  -31.6397

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
 KYW  CL2  C2    single    1.738  0.020  1.738
 KYW  C2   N3    aromatic  1.308  0.020  1.308
 KYW  C2   N1    aromatic  1.313  0.020  1.313
 KYW  N3   C4    aromatic  1.335  0.020  1.335
 KYW  N1   C6    aromatic  1.344  0.020  1.344
 KYW  O2'  C2'   single    1.400  0.020  1.400
 KYW  C20  N6    single    1.452  0.020  1.452
 KYW  C4   C5    aromatic  1.390  0.020  1.390
 KYW  C4   N9    aromatic  1.361  0.020  1.361
 KYW  C6   N6    single    1.336  0.020  1.336
 KYW  C6   C5    aromatic  1.419  0.020  1.419
 KYW  C2'  C1'   single    1.526  0.020  1.526
 KYW  C2'  C3'   single    1.532  0.020  1.532
 KYW  C1'  N9    single    1.464  0.020  1.464
 KYW  C1'  O4'   single    1.394  0.020  1.394
 KYW  N6   C21   single    1.454  0.020  1.454
 KYW  C5   N7    aromatic  1.371  0.020  1.371
 KYW  N9   C8    aromatic  1.367  0.020  1.367
 KYW  O3'  C3'   single    1.398  0.020  1.398
 KYW  C3'  C4'   single    1.528  0.020  1.528
 KYW  O4'  C4'   single    1.425  0.020  1.425
 KYW  C26  C27   aromatic  1.386  0.020  1.386
 KYW  C26  C25   aromatic  1.394  0.020  1.394
 KYW  C27  C22   aromatic  1.391  0.020  1.391
 KYW  C4'  C5'   single    1.508  0.020  1.508
 KYW  C21  C25   single    1.508  0.020  1.508
 KYW  C8   N7    aromatic  1.301  0.020  1.301
 KYW  C25  C24   aromatic  1.390  0.020  1.390
 KYW  C22  C23   aromatic  1.387  0.020  1.387
 KYW  C24  C23   aromatic  1.390  0.020  1.390
 KYW  C5'  O5'   single    1.425  0.020  1.425
 KYW  O5'  PA    single    1.606  0.020  1.606
 KYW  O1A  PA    double    1.480  0.020  1.480
 KYW  PA   O2A   single    1.597  0.020  1.597
 KYW  PA   C3A   single    1.805  0.020  1.805
 KYW  O2B  PB    double    1.482  0.020  1.482
 KYW  C3A  PB    single    1.808  0.020  1.808
 KYW  PB   O3B   single    1.604  0.020  1.604
 KYW  PB   O1B   single    1.598  0.020  1.598
 KYW  C8   H8    single    0.930  0.020  1.080
 KYW  C20  H1    single    0.970  0.020  1.090
 KYW  C20  H2    single    0.970  0.020  1.090
 KYW  C20  H3    single    0.970  0.020  1.090
 KYW  C21  H5    single    0.970  0.020  1.090
 KYW  C21  H4    single    0.970  0.020  1.090
 KYW  C22  H21   single    0.930  0.020  1.080
 KYW  C24  H23   single    0.930  0.020  1.080
 KYW  C26  H25   single    0.930  0.020  1.080
 KYW  O1B  H6    single    0.850  0.020  0.980
 KYW  O3B  H7    single    0.850  0.020  0.980
 KYW  O2A  H9    single    0.850  0.020  0.980
 KYW  C3A  H3A2  single    0.970  0.020  1.090
 KYW  C3A  H3A1  single    0.970  0.020  1.090
 KYW  C5'  H5'2  single    0.970  0.020  1.090
 KYW  C5'  H5'1  single    0.970  0.020  1.090
 KYW  C4'  H4'   single    0.970  0.020  1.090
 KYW  C3'  H3'   single    0.970  0.020  1.090
 KYW  O3'  HO3'  single    0.850  0.020  0.980
 KYW  C2'  H2'   single    0.970  0.020  1.090
 KYW  O2'  HO2'  single    0.850  0.020  0.980
 KYW  C1'  H1'   single    0.970  0.020  1.090
 KYW  C23  H22   single    0.930  0.020  1.080
 KYW  C27  H26   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
 KYW  C2    N1   C6    119.68  3.000
 KYW  C2    N3   C4    110.49  3.000
 KYW  N9    C4   C5    105.85  3.000
 KYW  N9    C4   N3    126.93  3.000
 KYW  C5    C4   N3    127.21  3.000
 KYW  N7    C5   C6    134.44  3.000
 KYW  N7    C5   C4    109.71  3.000
 KYW  C6    C5   C4    115.85  3.000
 KYW  N6    C6   C5    126.41  3.000
 KYW  C5    C6   N1    116.74  3.000
 KYW  N6    C6   N1    116.85  3.000
 KYW  H8    C8   N7    124.40  3.000
 KYW  H8    C8   N9    122.69  3.000
 KYW  N7    C8   N9    112.90  3.000
 KYW  H3    C20  H2    108.45  3.000
 KYW  H3    C20  H1    108.49  3.000
 KYW  H2    C20  H1    108.28  3.000
 KYW  H3    C20  N6    111.59  3.000
 KYW  H2    C20  N6    111.63  3.000
 KYW  H1    C20  N6    108.31  3.000
 KYW  H4    C21  H5    107.04  3.000
 KYW  H4    C21  C25   109.92  3.000
 KYW  H5    C21  C25   109.86  3.000
 KYW  H4    C21  N6    109.36  3.000
 KYW  H5    C21  N6    108.16  3.000
 KYW  C25   C21  N6    112.34  3.000
 KYW  H21   C22  C27   120.11  3.000
 KYW  H21   C22  C23   120.20  3.000
 KYW  C27   C22  C23   119.69  3.000
 KYW  H23   C24  C25   119.51  3.000
 KYW  H23   C24  C23   119.78  3.000
 KYW  C25   C24  C23   120.71  3.000
 KYW  H25   C26  C27   119.52  3.000
 KYW  H25   C26  C25   119.97  3.000
 KYW  C27   C26  C25   120.50  3.000
 KYW  C3A   PB   O3B   106.50  3.000
 KYW  O3B   PB   O2B   114.96  3.000
 KYW  C3A   PB   O2B   114.69  3.000
 KYW  O3B   PB   O1B   101.48  3.000
 KYW  C3A   PB   O1B   100.33  3.000
 KYW  O2B   PB   O1B   116.99  3.000
 KYW  H6    O1B  PB    114.14  3.000
 KYW  H7    O3B  PB    114.48  3.000
 KYW  O5'   PA   C3A   106.50  3.000
 KYW  C3A   PA   O2A   102.10  3.000
 KYW  O5'   PA   O2A   101.24  3.000
 KYW  C3A   PA   O1A   113.60  3.000
 KYW  O2A   PA   O1A   117.35  3.000
 KYW  O5'   PA   O1A   114.46  3.000
 KYW  H9    O2A  PA    114.86  3.000
 KYW  H3A1  C3A  H3A2  106.39  3.000
 KYW  H3A1  C3A  PA    107.27  3.000
 KYW  H3A2  C3A  PA    107.78  3.000
 KYW  H3A1  C3A  PB    108.15  3.000
 KYW  H3A2  C3A  PB    109.90  3.000
 KYW  PA    C3A  PB    116.86  3.000
 KYW  H5'1  C5'  H5'2  108.09  3.000
 KYW  H5'1  C5'  C4'   110.62  3.000
 KYW  H5'2  C5'  C4'   108.01  3.000
 KYW  H5'1  C5'  O5'   109.65  3.000
 KYW  H5'2  C5'  O5'   111.28  3.000
 KYW  C4'   C5'  O5'   109.17  3.000
 KYW  H4'   C4'  C3'   110.07  3.000
 KYW  H4'   C4'  O4'   108.98  3.000
 KYW  C3'   C4'  O4'   105.52  3.000
 KYW  H4'   C4'  C5'   109.19  3.000
 KYW  O4'   C4'  C5'   111.07  3.000
 KYW  C3'   C4'  C5'   111.92  3.000
 KYW  C1'   O4'  C4'   111.33  3.000
 KYW  H3'   C3'  C2'   108.97  3.000
 KYW  H3'   C3'  O3'   111.47  3.000
 KYW  C2'   C3'  O3'   113.90  3.000
 KYW  H3'   C3'  C4'   110.04  3.000
 KYW  O3'   C3'  C4'   110.11  3.000
 KYW  C2'   C3'  C4'   101.93  3.000
 KYW  HO3'  O3'  C3'   108.99  3.000
 KYW  H2'   C2'  C1'   112.48  3.000
 KYW  H2'   C2'  O2'   112.03  3.000
 KYW  C1'   C2'  O2'   107.34  3.000
 KYW  H2'   C2'  C3'   112.33  3.000
 KYW  C1'   C2'  C3'   101.01  3.000
 KYW  O2'   C2'  C3'   111.06  3.000
 KYW  HO2'  O2'  C2'   107.78  3.000
 KYW  H1'   C1'  N9    107.60  3.000
 KYW  H1'   C1'  C2'   111.94  3.000
 KYW  N9    C1'  C2'   111.59  3.000
 KYW  H1'   C1'  O4'   110.07  3.000
 KYW  N9    C1'  O4'   108.97  3.000
 KYW  C2'   C1'  O4'   106.66  3.000
 KYW  C1'   N9   C8    128.13  3.000
 KYW  C8    N9   C4    106.28  3.000
 KYW  C1'   N9   C4    125.40  3.000
 KYW  C8    N7   C5    105.24  3.000
 KYW  C21   N6   C20   116.75  3.000
 KYW  C21   N6   C6    123.67  3.000
 KYW  C20   N6   C6    119.57  3.000
 KYW  CL2   C2   N3    115.18  3.000
 KYW  N3    C2   N1    130.02  3.000
 KYW  CL2   C2   N1    114.80  3.000
 KYW  H22   C23  C24   119.84  3.000
 KYW  H22   C23  C22   120.18  3.000
 KYW  C24   C23  C22   119.97  3.000
 KYW  C26   C25  C24   118.95  3.000
 KYW  C24   C25  C21   120.64  3.000
 KYW  C26   C25  C21   120.42  3.000
 KYW  H26   C27  C26   119.82  3.000
 KYW  H26   C27  C22   120.00  3.000
 KYW  C26   C27  C22   120.18  3.000
 KYW  C5'   O5'  PA    120.41  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
 KYW  CONST_01  C4   N3   C2   N1      0.00   0.0  0
 KYW  CONST_02  C4   C5   C6   N1      0.00   0.0  0
 KYW  CONST_03  N7   C5   C6   N1    180.00   0.0  0
 KYW  CONST_04  C6   N1   C2   N3      0.00   0.0  0
 KYW  CONST_05  C6   C5   C4   N3      0.00   0.0  0
 KYW  CONST_06  N7   C5   C4   N3    180.00   0.0  0
 KYW  CONST_07  C8   N9   C4   N3    180.00   0.0  0
 KYW  CONST_08  C8   N7   C5   C4      0.00   0.0  0
 KYW  CONST_09  N7   C8   N9   C4      0.00   0.0  0
 KYW  CONST_10  C2   N3   C4   C5      0.00   0.0  0
 KYW  CONST_11  C8   N9   C4   C5      0.00   0.0  0
 KYW  CONST_12  C2   N1   C6   C5      0.00   0.0  0
 KYW  CONST_13  N9   C8   N7   C5      0.00   0.0  0
 KYW  CONST_14  N9   C4   C5   C6    180.00   0.0  0
 KYW  CONST_15  C8   N7   C5   C6    180.00   0.0  0
 KYW  CONST_16  C25  C26  C27  C22     0.00   0.0  0
 KYW  CONST_17  C25  C24  C23  C22     0.00   0.0  0
 KYW  CONST_18  C27  C26  C25  C24     0.00   0.0  0
 KYW  CONST_19  C27  C22  C23  C24     0.00   0.0  0
 KYW  CONST_20  C23  C22  C27  C26     0.00   0.0  0
 KYW  CONST_21  C23  C24  C25  C26     0.00   0.0  0
 KYW  CONST_22  C2   N3   C4   N9    180.00   0.0  0
 KYW  CONST_23  N7   C5   C4   N9      0.00   0.0  0
 KYW  CONST_24  C1'  N9   C4   N3      0.00   0.0  0
 KYW  CONST_25  C1'  N9   C4   C5    180.00   0.0  0
 KYW  CONST_26  N7   C8   N9   C1'   180.00   0.0  0
 KYW  CONST_27  CL2  C2   N3   C4    180.00   0.0  0
 KYW  CONST_28  N6   C6   C5   C4    180.00   0.0  0
 KYW  CONST_29  CL2  C2   N1   C6    180.00   0.0  0
 KYW  CONST_30  C27  C26  C25  C21   180.00   0.0  0
 KYW  CONST_31  C23  C24  C25  C21   180.00   0.0  0
 KYW  CONST_32  N6   C6   C5   N7      0.00   0.0  0
 KYW  CONST_33  C2   N1   C6   N6    180.00   0.0  0
 KYW  CONST_34  H8   C8   N9   C4    180.00   0.0  0
 KYW  CONST_35  H25  C26  C27  C22   180.00   0.0  0
 KYW  CONST_36  H23  C24  C23  C22   180.00   0.0  0
 KYW  CONST_37  H21  C22  C23  C24   180.00   0.0  0
 KYW  CONST_38  H26  C27  C22  C23   180.00   0.0  0
 KYW  CONST_39  H22  C23  C24  C25   180.00   0.0  0
 KYW  CONST_40  C20  N6   C6   N1      0.00   0.0  0
 KYW  CONST_41  C21  N6   C6   N1    180.00   0.0  0
 KYW  CONST_42  C20  N6   C6   C5    180.00   0.0  0
 KYW  CONST_43  C21  N6   C6   C5      0.00   0.0  0
 KYW  Var_01    C25  C21  N6   C6    107.74  30.0  3
 KYW  Var_02    N6   C21  C25  C24   117.72  30.0  3
 KYW  Var_03    C4'  C5'  O5'  PA    158.83  30.0  2
 KYW  Var_04    H1   C20  N6   C6   -173.25  30.0  3
 KYW  Var_05    O5'  PA   C3A  PB     56.25  30.0  1
 KYW  Var_06    PA   C3A  PB   O1B  -179.80  30.0  1

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
 KYW  chir_02  C4'  C3'  O4'  C5'  positiv
 KYW  chir_03  C3'  O3'  C2'  C4'  negativ
 KYW  chir_04  C2'  O2'  C1'  C3'  negativ
 KYW  chir_05  C1'  O4'  N9   C2'  negativ
 KYW  chir_06  PA   O1A  O2A  C3A  both

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
 KYW  plan-1  C21  0.020
 KYW  plan-1  C22  0.020
 KYW  plan-1  C24  0.020
 KYW  plan-1  C26  0.020
 KYW  plan-1  C23  0.020
 KYW  plan-1  C25  0.020
 KYW  plan-1  C27  0.020
 KYW  plan-1  H21  0.020
 KYW  plan-1  H23  0.020
 KYW  plan-1  H25  0.020
 KYW  plan-1  H22  0.020
 KYW  plan-1  H26  0.020
 KYW  plan-2  N1   0.020
 KYW  plan-2  N3   0.020
 KYW  plan-2  C4   0.020
 KYW  plan-2  C5   0.020
 KYW  plan-2  C6   0.020
 KYW  plan-2  C8   0.020
 KYW  plan-2  C1'  0.020
 KYW  plan-2  N9   0.020
 KYW  plan-2  N7   0.020
 KYW  plan-2  N6   0.020
 KYW  plan-2  C2   0.020
 KYW  plan-2  CL2  0.020
 KYW  plan-2  H8   0.020
 KYW  plan-3  C6   0.020
 KYW  plan-3  C20  0.020
 KYW  plan-3  C21  0.020
 KYW  plan-3  N6   0.020

