# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 03:16:16 2022
#   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  57  36  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.471  -13.3314  23.5308  -36.9530
 KYW  N3    N   N      0  -0.433  -14.6699  21.5697  -37.0372
 KYW  C4    C   CR56   0   0.490  -14.6858  21.6526  -35.7046
 KYW  C5    C   CR56   0   0.020  -14.0729  22.6184  -34.9154
 KYW  C6    C   CR6    0   0.521  -13.3531  23.6205  -35.6116
 KYW  C8    C   CR15   0   0.053  -15.0567  21.2788  -33.5799
 KYW  C22   C   CR16   0  -0.266   -8.6489  23.5797  -32.2514
 KYW  C24   C   CR16   0  -0.312  -10.3099  25.2940  -32.5480
 KYW  C26   C   CR16   0  -0.294  -10.7561  23.0603  -33.2943
 KYW  O1B   O   OP    -1  -0.899  -15.5314  20.9130  -28.2487
 KYW  O2B   O   O      0  -0.842  -15.5248  20.5380  -30.7788
 KYW  O3B   O   OP    -1  -0.892  -17.6775  21.3276  -29.6076
 KYW  PA    P   P      0   1.243  -18.0635  17.8171  -30.1226
 KYW  O1A   O   O      0  -0.829  -17.8171  16.3380  -29.9253
 KYW  O2A   O   OP    -1  -0.812  -19.4571  18.3532  -29.9171
 KYW  C3A   C   CH2    0  -1.014  -16.8217  18.7473  -29.1615
 KYW  C5'   C   CH2    0  -0.151  -16.4713  17.8340  -32.2409
 KYW  C4'   C   CH1    0  -0.013  -16.4994  17.9278  -33.7469
 KYW  O4'   O   O2     0  -0.490  -16.8829  19.2399  -34.1656
 KYW  C3'   C   CH1    0  -0.015  -15.1271  17.7069  -34.3898
 KYW  O3'   O   OH1    0  -0.660  -14.7986  16.3741  -34.6541
 KYW  C2'   C   CH1    0  -0.047  -15.2717  18.4773  -35.6987
 KYW  O2'   O   OH1    0  -0.661  -16.0326  17.7645  -36.6368
 KYW  C1'   C   CH1    0   0.183  -16.1222  19.6662  -35.2480
 KYW  N9    N   NR5    0  -0.542  -15.3056  20.8060  -34.8408
 KYW  N7    N   N      0  -0.478  -14.3205  22.3564  -33.5929
 KYW  N6    N   NT     0  -0.455  -12.6998  24.6514  -35.0607
 KYW  C2    C   CR6    0   0.266  -13.9715  22.5504  -37.5481
 KYW  C23   C   CR16   0  -0.238   -9.0553  24.8970  -32.0996
 KYW  C25   C   CR6    0   0.137  -11.1726  24.3827  -33.1469
 KYW  C27   C   CR16   0  -0.237   -9.5041  22.6617  -32.8514
 KYW  CL2   CL  CL     0  -0.119  -13.8650  22.5596  -39.2847
 KYW  H8    H   HCR5   0   0.344  -15.4301  20.8256  -32.6574
 KYW  H1    H   HCH3   0   0.253  -11.5684  26.3684  -35.2919
 KYW  H2    H   HCH3   0   0.243  -11.0997  25.0647  -36.3863
 KYW  H3    H   HCH3   0   0.254  -12.5782  25.9842  -36.6869
 KYW  H5    H   HCH2   0   0.279  -12.6958  25.8680  -33.3852
 KYW  H4    H   HCH2   0   0.300  -13.3095  24.2489  -33.1102
 KYW  H23   H   HCR6   0   0.252  -10.6206  26.3258  -32.4304
 KYW  H25   H   HCR6   0   0.254  -11.4147  22.3311  -33.7509
 KYW  H3A2  H   HCH2   0   0.212  -17.1787  18.6828  -28.1262
 KYW  H3A1  H   HCH2   0   0.204  -15.8931  18.1662  -29.1736
 KYW  H5'2  H   HCH2   0   0.188  -16.1882  16.8021  -31.9899
 KYW  H5'1  H   HCH2   0   0.219  -15.7027  18.5023  -31.8396
 KYW  H4'   H   HCH1   0   0.227  -17.2158  17.2024  -34.1528
 KYW  H3'   H   HCH1   0   0.231  -14.3557  18.1964  -33.7771
 KYW  HO3'  H   HOH1   0   0.464  -14.6829  15.9021  -33.8235
 KYW  H2'   H   HCH1   0   0.258  -14.3058  18.7924  -36.1116
 KYW  HO2'  H   HOH1   0   0.454  -15.6965  16.8622  -36.6782
 KYW  H1'   H   HCH1   0   0.275  -16.7643  20.0137  -36.0633
 KYW  H22   H   HCR6   0   0.253   -8.3962  25.6197  -31.6358
 KYW  H26   H   HCR6   0   0.254   -9.1953  21.6309  -32.9692
 KYW  O5'   O   O2     0  -0.629  -17.7320  18.1688  -31.7196
 KYW  C20   C   CH3    0  -0.526  -11.9478  25.5578  -35.9090
 KYW  C21   C   CH2    0  -0.439  -12.5373  24.8150  -33.6259
 KYW  H21   H   HCR6   0   0.254   -7.6723  23.2674  -31.9045
 KYW  PB    P   P      0   1.182  -16.3676  20.5466  -29.4805

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    1.740  0.020  1.740
 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  1.345  0.020  1.345
 KYW  O2'  C2'   single    1.402  0.020  1.402
 KYW  C20  N6    single    1.452  0.020  1.452
 KYW  C4   C5    aromatic  1.390  0.020  1.390
 KYW  C4   N9    aromatic  1.359  0.020  1.359
 KYW  C6   N6    single    1.339  0.020  1.339
 KYW  C6   C5    aromatic  1.417  0.020  1.417
 KYW  C2'  C1'   single    1.530  0.020  1.530
 KYW  C2'  C3'   single    1.526  0.020  1.526
 KYW  C1'  N9    single    1.460  0.020  1.460
 KYW  C1'  O4'   single    1.390  0.020  1.390
 KYW  N6   C21   single    1.453  0.020  1.453
 KYW  C5   N7    aromatic  1.371  0.020  1.371
 KYW  N9   C8    aromatic  1.369  0.020  1.369
 KYW  O3'  C3'   single    1.398  0.020  1.398
 KYW  C3'  C4'   single    1.532  0.020  1.532
 KYW  O4'  C4'   single    1.430  0.020  1.430
 KYW  C26  C27   aromatic  1.387  0.020  1.387
 KYW  C26  C25   aromatic  1.394  0.020  1.394
 KYW  C27  C22   aromatic  1.391  0.020  1.391
 KYW  C4'  C5'   single    1.509  0.020  1.509
 KYW  C21  C25   single    1.510  0.020  1.510
 KYW  C8   N7    aromatic  1.305  0.020  1.305
 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    1.405  0.020  1.405
 KYW  O5'  PA    single    1.668  0.020  1.668
 KYW  O1A  PA    deloc     1.512  0.020  1.512
 KYW  PA   O2A   deloc     1.507  0.020  1.507
 KYW  PA   C3A   single    1.825  0.020  1.825
 KYW  O2B  PB    deloc     1.548  0.020  1.548
 KYW  C3A  PB    single    1.883  0.020  1.883
 KYW  PB   O3B   deloc     1.530  0.020  1.530
 KYW  PB   O1B   deloc     1.533  0.020  1.533
 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  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    119.60  3.000
 KYW  C2    N3   C4    110.46  3.000
 KYW  N9    C4   C5    105.85  3.000
 KYW  N9    C4   N3    126.94  3.000
 KYW  C5    C4   N3    127.21  3.000
 KYW  N7    C5   C6    134.52  3.000
 KYW  N7    C5   C4    109.60  3.000
 KYW  C6    C5   C4    115.89  3.000
 KYW  N6    C6   C5    126.17  3.000
 KYW  C5    C6   N1    116.83  3.000
 KYW  N6    C6   N1    117.00  3.000
 KYW  H8    C8   N7    122.91  3.000
 KYW  H8    C8   N9    124.85  3.000
 KYW  N7    C8   N9    112.24  3.000
 KYW  H21   C22  C27   120.18  3.000
 KYW  H21   C22  C23   120.22  3.000
 KYW  C27   C22  C23   119.61  3.000
 KYW  H23   C24  C25   119.52  3.000
 KYW  H23   C24  C23   119.71  3.000
 KYW  C25   C24  C23   120.78  3.000
 KYW  H25   C26  C27   119.34  3.000
 KYW  H25   C26  C25   120.09  3.000
 KYW  C27   C26  C25   120.57  3.000
 KYW  O5'   PA   C3A   105.16  3.000
 KYW  C3A   PA   O2A   112.09  3.000
 KYW  O5'   PA   O2A   103.84  3.000
 KYW  C3A   PA   O1A   108.59  3.000
 KYW  O2A   PA   O1A   118.73  3.000
 KYW  O5'   PA   O1A   107.38  3.000
 KYW  H3A1  C3A  H3A2  104.78  3.000
 KYW  H3A1  C3A  PA    107.49  3.000
 KYW  H3A2  C3A  PA    104.22  3.000
 KYW  H3A1  C3A  PB    107.49  3.000
 KYW  H3A2  C3A  PB    107.13  3.000
 KYW  PA    C3A  PB    124.19  3.000
 KYW  H5'1  C5'  H5'2  107.97  3.000
 KYW  H5'1  C5'  C4'   109.94  3.000
 KYW  H5'2  C5'  C4'   106.92  3.000
 KYW  H5'1  C5'  O5'   110.40  3.000
 KYW  H5'2  C5'  O5'   111.72  3.000
 KYW  C4'   C5'  O5'   109.81  3.000
 KYW  H4'   C4'  C3'   109.53  3.000
 KYW  H4'   C4'  O4'   108.86  3.000
 KYW  C3'   C4'  O4'   104.47  3.000
 KYW  H4'   C4'  C5'   109.89  3.000
 KYW  O4'   C4'  C5'   110.75  3.000
 KYW  C3'   C4'  C5'   113.16  3.000
 KYW  C1'   O4'  C4'   111.27  3.000
 KYW  H3'   C3'  C2'   108.64  3.000
 KYW  H3'   C3'  O3'   111.40  3.000
 KYW  C2'   C3'  O3'   109.97  3.000
 KYW  H3'   C3'  C4'   109.29  3.000
 KYW  O3'   C3'  C4'   115.31  3.000
 KYW  C2'   C3'  C4'   101.67  3.000
 KYW  HO3'  O3'  C3'   109.43  3.000
 KYW  H2'   C2'  C1'   112.16  3.000
 KYW  H2'   C2'  O2'   111.85  3.000
 KYW  C1'   C2'  O2'   106.88  3.000
 KYW  H2'   C2'  C3'   112.62  3.000
 KYW  C1'   C2'  C3'   101.09  3.000
 KYW  O2'   C2'  C3'   111.63  3.000
 KYW  HO2'  O2'  C2'   108.38  3.000
 KYW  H1'   C1'  N9    106.74  3.000
 KYW  H1'   C1'  C2'   110.70  3.000
 KYW  N9    C1'  C2'   112.21  3.000
 KYW  H1'   C1'  O4'   110.88  3.000
 KYW  N9    C1'  O4'   109.17  3.000
 KYW  C2'   C1'  O4'   107.18  3.000
 KYW  C1'   N9   C8    128.90  3.000
 KYW  C8    N9   C4    106.69  3.000
 KYW  C1'   N9   C4    124.34  3.000
 KYW  C8    N7   C5    105.62  3.000
 KYW  C21   N6   C20   116.67  3.000
 KYW  C21   N6   C6    123.19  3.000
 KYW  C20   N6   C6    119.54  3.000
 KYW  CL2   C2   N3    115.25  3.000
 KYW  N3    C2   N1    130.02  3.000
 KYW  CL2   C2   N1    114.74  3.000
 KYW  H22   C23  C24   119.80  3.000
 KYW  H22   C23  C22   120.17  3.000
 KYW  C24   C23  C22   120.02  3.000
 KYW  C26   C25  C24   118.80  3.000
 KYW  C24   C25  C21   120.66  3.000
 KYW  C26   C25  C21   120.53  3.000
 KYW  H26   C27  C26   119.77  3.000
 KYW  H26   C27  C22   120.01  3.000
 KYW  C26   C27  C22   120.22  3.000
 KYW  C5'   O5'  PA    118.90  3.000
 KYW  H3    C20  H2    108.34  3.000
 KYW  H3    C20  H1    108.41  3.000
 KYW  H2    C20  H1    108.30  3.000
 KYW  H3    C20  N6    111.24  3.000
 KYW  H2    C20  N6    112.10  3.000
 KYW  H1    C20  N6    108.34  3.000
 KYW  H4    C21  H5    107.12  3.000
 KYW  H4    C21  C25   110.02  3.000
 KYW  H5    C21  C25   109.72  3.000
 KYW  H4    C21  N6    109.28  3.000
 KYW  H5    C21  N6    108.06  3.000
 KYW  C25   C21  N6    112.47  3.000
 KYW  C3A   PB   O3B   107.17  3.000
 KYW  O3B   PB   O2B   113.53  3.000
 KYW  C3A   PB   O2B   105.55  3.000
 KYW  O3B   PB   O1B   114.31  3.000
 KYW  C3A   PB   O1B   102.93  3.000
 KYW  O2B   PB   O1B   112.22  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   100.58  30.0  3
 KYW  Var_02    N6   C21  C25  C24  118.02  30.0  2
 KYW  Var_03    C4'  C5'  O5'  PA   166.45  30.0  2
 KYW  Var_04    H1   C20  N6   C6   175.04  30.0  3
 KYW  Var_05    O5'  PA   C3A  PB    45.63  30.0  1
 KYW  Var_06    PA   C3A  PB   O1B  168.56  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
 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

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  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  H23  0.020
 KYW  plan-1  H25  0.020
 KYW  plan-1  H22  0.020
 KYW  plan-1  H26  0.020
 KYW  plan-1  C21  0.020
 KYW  plan-1  H21  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  N6   0.020
 KYW  plan-3  C20  0.020
 KYW  plan-3  C21  0.020

