# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 05:22:27 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: [(2~{R},3~{S},5~{R})-5-[2-[(3-acetamidonaphthalen-2-yl)amino]-6-oxidanylidene-1~{H}-purin-9-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphite
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1cc2ccccc2cc1NC3=Nc4n(cnc4C(=O)N3)[C@H]5C[C@H](O)[C@@H](COP(O)O)O5
#
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
 6TW  6TW  '[(2~{R},3~{S},5~{R})-5-[2-[(3-acetamidonaphthalen-2-yl)amino]-6-oxidanylidene-1~{H}-purin-9-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphite'  ligand  59  36  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_6TW
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
 6TW  C2   C  CR6   0   0.768   1.6584   1.5807  -0.2070
 6TW  C1'  C  CH1   0   0.233  -1.9909   0.1292   1.4804
 6TW  C2'  C  CH2   0  -0.571  -2.7341  -0.0138   2.8017
 6TW  C3'  C  CH1   0  -0.003  -3.6503  -1.1991   2.5286
 6TW  C4'  C  CH1   0  -0.020  -4.0129  -0.9746   1.0642
 6TW  O3'  O  OH1   0  -0.667  -2.9720  -2.4285   2.6185
 6TW  O4'  O  O2    0  -0.512  -2.8787  -0.3321   0.4811
 6TW  C5'  C  CH2   0  -0.178  -5.2451  -0.1022   0.8948
 6TW  C10  C  CR66  0   0.106   3.6977  -3.2038  -0.4253
 6TW  C11  C  CR16  0  -0.343   4.6905  -2.2068  -0.3231
 6TW  C12  C  CR6   0   0.278   4.3645  -0.8804  -0.3424
 6TW  C16  C  CR16  0  -0.317   1.3428  -3.8011  -0.6336
 6TW  C17  C  CR16  0  -0.256   1.6777  -5.1276  -0.6108
 6TW  C18  C  CR16  0  -0.261   3.0270  -5.5235  -0.4910
 6TW  C19  C  CR16  0  -0.310   4.0151  -4.5816  -0.4003
 6TW  C23  C  C     0   0.510   6.4172   0.2517  -1.0590
 6TW  C24  C  CH3   0  -0.783   7.3611   1.3694  -0.7029
 6TW  C3   C  CR6   0   0.341   3.0030  -0.4765  -0.4839
 6TW  C4   C  CR56  0   0.527  -0.3781   1.8180   0.6119
 6TW  C5   C  CR56  0  -0.090  -0.4332   3.1852   0.4411
 6TW  C6   C  CR6   0   0.506   0.6945   3.8496  -0.1263
 6TW  C7   C  CR16  0  -0.382   2.0202  -1.4304  -0.5721
 6TW  C8   C  CR15  0   0.105  -2.2838   2.6393   1.3013
 6TW  C9   C  CR66  0   0.137   2.3433  -2.8041  -0.5409
 6TW  N1   N  NR16  0  -0.754   1.7072   2.9283  -0.4256
 6TW  N2   N  NH1   0  -0.793   2.7729   0.8982  -0.5595
 6TW  N3   N  N     0  -0.512   0.6247   0.9819   0.3097
 6TW  N7   N  N     0  -0.440  -1.6349   3.6785   0.8783
 6TW  N9   N  NR5   0  -0.546  -1.5686   1.4721   1.1767
 6TW  O25  O  O     0  -0.469   6.5828  -0.4614  -2.0304
 6TW  O5'  O  O2    0  -0.604  -5.4953   0.1738  -0.4689
 6TW  O6   O  O     0  -0.466   0.8469   5.0357  -0.3565
 6TW  P    P  P     0   0.896  -4.6257   1.3834  -1.1989
 6TW  H1   H  HCH1  0   0.268  -1.0857  -0.4814   1.4704
 6TW  H2   H  HCH2  0   0.294  -2.0530  -0.1751   3.6369
 6TW  H3   H  HCH2  0   0.268  -3.3259   0.8721   3.0374
 6TW  H4   H  HCH1  0   0.256  -4.5384  -1.1793   3.1716
 6TW  H5   H  HCH1  0   0.268  -4.1717  -1.9265   0.5487
 6TW  H6   H  HOH1  0   0.457  -2.6575  -2.5352   3.5220
 6TW  H7   H  HCH2  0   0.255  -6.1149  -0.6331   1.2866
 6TW  H8   H  HCH2  0   0.219  -5.1472   0.8253   1.4752
 6TW  H9   H  HCR6  0   0.268   5.7248  -2.5015  -0.2004
 6TW  H10  H  HCR6  0   0.254   0.3058  -3.5014  -0.7251
 6TW  H11  H  HCR6  0   0.261   0.9049  -5.8814  -0.6832
 6TW  H12  H  HCR6  0   0.259   3.2754  -6.5765  -0.4714
 6TW  H13  H  HCR6  0   0.258   5.0521  -4.8813  -0.3068
 6TW  H14  H  HCH3  0   0.272   8.3773   0.9804  -0.6536
 6TW  H15  H  HCH3  0   0.275   7.3380   2.1218  -1.4913
 6TW  H16  H  HCH3  0   0.254   7.1282   1.8538   0.2431
 6TW  H17  H  HCR6  0   0.275   0.9864  -1.1403  -0.6814
 6TW  H18  H  HCR5  0   0.291  -3.2797   2.6579   1.7148
 6TW  H19  H  HNR6  0   0.429   2.5435   3.3259  -0.8347
 6TW  H20  H  HNH1  0   0.415   3.5669   1.4462  -0.8570
 6TW  H21  H  HNH1  0   0.415   5.2967   0.7343   0.5775
 6TW  H22  H  HOH1  0   0.472  -2.9343   0.1447  -1.7793
 6TW  H23  H  HOH1  0   0.486  -6.1159   2.6356  -2.1620
 6TW  N22  N  NH1   0  -0.758   5.3535   0.1171  -0.2194
 6TW  OP1  O  OH1   0  -0.778  -3.6944   0.5225  -2.2394
 6TW  OP2  O  OH1   0  -0.761  -5.7168   1.7787  -2.3500

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
 6TW  C18  C19  aromatic  1.368  0.020  1.368
 6TW  C18  C17  aromatic  1.411  0.020  1.411
 6TW  C19  C10  aromatic  1.414  0.020  1.414
 6TW  C17  C16  aromatic  1.368  0.020  1.368
 6TW  C10  C11  aromatic  1.411  0.020  1.411
 6TW  C10  C9   aromatic  1.417  0.020  1.417
 6TW  C11  C12  aromatic  1.366  0.020  1.366
 6TW  C16  C9   aromatic  1.416  0.020  1.416
 6TW  C9   C7   aromatic  1.411  0.020  1.411
 6TW  C12  N22  single    1.410  0.020  1.410
 6TW  C12  C3   aromatic  1.427  0.020  1.427
 6TW  C7   C3   aromatic  1.372  0.020  1.372
 6TW  N22  C23  single    1.362  0.020  1.362
 6TW  C3   N2   single    1.396  0.020  1.396
 6TW  C23  O25  double    1.216  0.020  1.216
 6TW  C23  C24  single    1.506  0.020  1.506
 6TW  N2   C2   single    1.354  0.020  1.354
 6TW  O6   C6   double    1.218  0.020  1.218
 6TW  N1   C2   single    1.366  0.020  1.366
 6TW  N1   C6   single    1.401  0.020  1.401
 6TW  C2   N3   double    1.302  0.020  1.302
 6TW  C6   C5   single    1.427  0.020  1.427
 6TW  N3   C4   single    1.340  0.020  1.340
 6TW  C5   C4   aromatic  1.379  0.020  1.379
 6TW  C5   N7   aromatic  1.371  0.020  1.371
 6TW  C4   N9   aromatic  1.362  0.020  1.362
 6TW  N7   C8   aromatic  1.296  0.020  1.296
 6TW  N9   C8   aromatic  1.375  0.020  1.375
 6TW  N9   C1'  single    1.440  0.020  1.440
 6TW  C1'  O4'  single    1.414  0.020  1.414
 6TW  C1'  C2'  single    1.523  0.020  1.523
 6TW  O4'  C4'  single    1.428  0.020  1.428
 6TW  C2'  C3'  single    1.523  0.020  1.523
 6TW  C4'  C3'  single    1.525  0.020  1.525
 6TW  C4'  C5'  single    1.519  0.020  1.519
 6TW  O3'  C3'  single    1.407  0.020  1.407
 6TW  O5'  C5'  single    1.414  0.020  1.414
 6TW  O5'  P    single    1.659  0.020  1.659
 6TW  P    OP1  single    1.640  0.020  1.640
 6TW  P    OP2  single    1.635  0.020  1.635
 6TW  C1'  H1   single    0.970  0.020  1.090
 6TW  C2'  H2   single    0.970  0.020  1.090
 6TW  C2'  H3   single    0.970  0.020  1.090
 6TW  C3'  H4   single    0.970  0.020  1.090
 6TW  C4'  H5   single    0.970  0.020  1.090
 6TW  O3'  H6   single    0.850  0.020  0.980
 6TW  C5'  H7   single    0.970  0.020  1.090
 6TW  C5'  H8   single    0.970  0.020  1.090
 6TW  C11  H9   single    0.930  0.020  1.080
 6TW  C16  H10  single    0.930  0.020  1.080
 6TW  C17  H11  single    0.930  0.020  1.080
 6TW  C18  H12  single    0.930  0.020  1.080
 6TW  C19  H13  single    0.930  0.020  1.080
 6TW  C24  H14  single    0.970  0.020  1.090
 6TW  C24  H15  single    0.970  0.020  1.090
 6TW  C24  H16  single    0.970  0.020  1.090
 6TW  C7   H17  single    0.930  0.020  1.080
 6TW  C8   H18  single    0.930  0.020  1.080
 6TW  N1   H19  single    0.860  0.020  1.020
 6TW  N2   H20  single    0.860  0.020  1.020
 6TW  N22  H21  single    0.860  0.020  1.020
 6TW  OP1  H22  single    0.850  0.020  0.980
 6TW  OP2  H23  single    0.850  0.020  0.980

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
 6TW  N3   C2   N2   121.69  3.000
 6TW  N3   C2   N1   123.07  3.000
 6TW  N2   C2   N1   115.24  3.000
 6TW  H1   C1'  N9   106.05  3.000
 6TW  H1   C1'  O4'  109.36  3.000
 6TW  N9   C1'  O4'  109.83  3.000
 6TW  H1   C1'  C2'  111.10  3.000
 6TW  O4'  C1'  C2'  106.03  3.000
 6TW  N9   C1'  C2'  114.44  3.000
 6TW  H3   C2'  H2   107.07  3.000
 6TW  H3   C2'  C3'  110.14  3.000
 6TW  H2   C2'  C3'  113.47  3.000
 6TW  H3   C2'  C1'  112.08  3.000
 6TW  H2   C2'  C1'  111.96  3.000
 6TW  C3'  C2'  C1'  102.19  3.000
 6TW  H4   C3'  O3'  111.64  3.000
 6TW  H4   C3'  C4'  111.58  3.000
 6TW  O3'  C3'  C4'  107.73  3.000
 6TW  H4   C3'  C2'  111.59  3.000
 6TW  O3'  C3'  C2'  112.25  3.000
 6TW  C4'  C3'  C2'  101.57  3.000
 6TW  H5   C4'  C5'  109.23  3.000
 6TW  H5   C4'  O4'  108.32  3.000
 6TW  C5'  C4'  O4'  109.90  3.000
 6TW  H5   C4'  C3'  111.02  3.000
 6TW  C5'  C4'  C3'  112.61  3.000
 6TW  O4'  C4'  C3'  105.63  3.000
 6TW  H6   O3'  C3'  108.32  3.000
 6TW  C4'  O4'  C1'  110.91  3.000
 6TW  H8   C5'  H7   106.98  3.000
 6TW  H8   C5'  O5'  111.14  3.000
 6TW  H7   C5'  O5'  107.47  3.000
 6TW  H8   C5'  C4'  110.71  3.000
 6TW  H7   C5'  C4'  109.08  3.000
 6TW  O5'  C5'  C4'  111.30  3.000
 6TW  C9   C10  C19  119.40  3.000
 6TW  C9   C10  C11  118.63  3.000
 6TW  C19  C10  C11  121.96  3.000
 6TW  H9   C11  C12  119.61  3.000
 6TW  H9   C11  C10  119.22  3.000
 6TW  C12  C11  C10  121.15  3.000
 6TW  N22  C12  C3   118.53  3.000
 6TW  C3   C12  C11  120.26  3.000
 6TW  N22  C12  C11  121.22  3.000
 6TW  H10  C16  C9   119.16  3.000
 6TW  H10  C16  C17  120.26  3.000
 6TW  C9   C16  C17  120.58  3.000
 6TW  H11  C17  C18  119.54  3.000
 6TW  H11  C17  C16  119.97  3.000
 6TW  C18  C17  C16  120.49  3.000
 6TW  H12  C18  C19  120.20  3.000
 6TW  H12  C18  C17  119.60  3.000
 6TW  C19  C18  C17  120.20  3.000
 6TW  H13  C19  C18  120.43  3.000
 6TW  H13  C19  C10  119.07  3.000
 6TW  C18  C19  C10  120.50  3.000
 6TW  O25  C23  N22  122.73  3.000
 6TW  O25  C23  C24  122.60  3.000
 6TW  N22  C23  C24  114.66  3.000
 6TW  H16  C24  H15  108.48  3.000
 6TW  H16  C24  H14  108.62  3.000
 6TW  H15  C24  H14  107.40  3.000
 6TW  H16  C24  C23  113.70  3.000
 6TW  H15  C24  C23  109.15  3.000
 6TW  H14  C24  C23  109.29  3.000
 6TW  N2   C3   C7   124.27  3.000
 6TW  N2   C3   C12  116.19  3.000
 6TW  C7   C3   C12  119.52  3.000
 6TW  N9   C4   N3   126.09  3.000
 6TW  N9   C4   C5   105.56  3.000
 6TW  N3   C4   C5   128.35  3.000
 6TW  N7   C5   C6   130.71  3.000
 6TW  N7   C5   C4   110.63  3.000
 6TW  C6   C5   C4   118.65  3.000
 6TW  O6   C6   N1   120.63  3.000
 6TW  N1   C6   C5   110.48  3.000
 6TW  O6   C6   C5   128.88  3.000
 6TW  H17  C7   C9   118.89  3.000
 6TW  H17  C7   C3   120.37  3.000
 6TW  C9   C7   C3   120.74  3.000
 6TW  H18  C8   N9   122.00  3.000
 6TW  H18  C8   N7   125.00  3.000
 6TW  N9   C8   N7   113.00  3.000
 6TW  C7   C9   C16  121.48  3.000
 6TW  C7   C9   C10  119.68  3.000
 6TW  C16  C9   C10  118.84  3.000
 6TW  H19  N1   C6   115.16  3.000
 6TW  H19  N1   C2   118.79  3.000
 6TW  C6   N1   C2   126.06  3.000
 6TW  H20  N2   C3   114.90  3.000
 6TW  H20  N2   C2   116.78  3.000
 6TW  C3   N2   C2   128.19  3.000
 6TW  C4   N3   C2   113.38  3.000
 6TW  C8   N7   C5   104.74  3.000
 6TW  C8   N9   C4   106.06  3.000
 6TW  C8   N9   C1'  128.32  3.000
 6TW  C4   N9   C1'  125.48  3.000
 6TW  P    O5'  C5'  118.30  3.000
 6TW  OP2  P    OP1   93.39  3.000
 6TW  OP2  P    O5'   97.83  3.000
 6TW  OP1  P    O5'  101.19  3.000
 6TW  H21  N22  C23  118.04  3.000
 6TW  H21  N22  C12  117.51  3.000
 6TW  C23  N22  C12  124.33  3.000
 6TW  H22  OP1  P    110.49  3.000
 6TW  H23  OP2  P    110.74  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
 6TW  CONST_01  C17  C18  C19  C10    0.00   0.0  0
 6TW  CONST_02  C3   C12  C11  C10    0.00   0.0  0
 6TW  CONST_03  C17  C16  C9   C10    0.00   0.0  0
 6TW  CONST_04  C3   C7   C9   C10    0.00   0.0  0
 6TW  CONST_05  C18  C19  C10  C11  180.00   0.0  0
 6TW  CONST_06  C16  C9   C10  C11  180.00   0.0  0
 6TW  CONST_07  C7   C9   C10  C11    0.00   0.0  0
 6TW  CONST_08  C7   C3   C12  C11    0.00   0.0  0
 6TW  CONST_09  C19  C10  C11  C12  180.00   0.0  0
 6TW  CONST_10  C9   C10  C11  C12    0.00   0.0  0
 6TW  CONST_11  C9   C7   C3   C12    0.00   0.0  0
 6TW  CONST_12  C19  C18  C17  C16    0.00   0.0  0
 6TW  CONST_13  C19  C10  C9   C16    0.00   0.0  0
 6TW  CONST_14  C3   C7   C9   C16  180.00   0.0  0
 6TW  CONST_15  C7   C9   C16  C17  180.00   0.0  0
 6TW  CONST_16  C9   C10  C19  C18    0.00   0.0  0
 6TW  CONST_17  C9   C16  C17  C18    0.00   0.0  0
 6TW  CONST_18  C7   C9   C10  C19  180.00   0.0  0
 6TW  CONST_19  C8   N7   C5   C4     0.00   0.0  0
 6TW  CONST_20  N7   C8   N9   C4     0.00   0.0  0
 6TW  CONST_21  C8   N9   C4   C5     0.00   0.0  0
 6TW  CONST_22  N9   C8   N7   C5     0.00   0.0  0
 6TW  CONST_23  N9   C4   C5   N7     0.00   0.0  0
 6TW  CONST_24  N3   C4   N9   C1'    0.00   0.0  0
 6TW  CONST_25  C5   C4   N9   C1'  180.00   0.0  0
 6TW  CONST_26  N7   C8   N9   C1'  180.00   0.0  0
 6TW  CONST_27  C5   C6   N1   C2     0.00   0.0  0
 6TW  CONST_28  N1   C2   N3   C4     0.00   0.0  0
 6TW  CONST_29  N3   C2   N1   C6     0.00   0.0  0
 6TW  CONST_30  N22  C12  C11  C10  180.00   0.0  0
 6TW  CONST_31  N2   C3   C12  C11  180.00   0.0  0
 6TW  CONST_32  N22  C12  C3   C7   180.00   0.0  0
 6TW  CONST_33  N2   C3   C7   C9   180.00   0.0  0
 6TW  CONST_36  N1   C2   N2   C3   180.00   0.0  0
 6TW  CONST_37  N3   C2   N2   C3     0.00   0.0  0
 6TW  CONST_38  O6   C6   N1   C2   180.00   0.0  0
 6TW  CONST_39  N2   C2   N3   C4   180.00   0.0  0
 6TW  CONST_40  N2   C2   N1   C6   180.00   0.0  0
 6TW  CONST_41  H18  C8   N9   C1'    0.00   0.0  0
 6TW  CONST_42  H12  C18  C19  C10  180.00   0.0  0
 6TW  CONST_43  H10  C16  C9   C10  180.00   0.0  0
 6TW  CONST_44  H17  C7   C9   C10  180.00   0.0  0
 6TW  CONST_45  H13  C19  C10  C11    0.00   0.0  0
 6TW  CONST_46  H11  C17  C18  C19  180.00   0.0  0
 6TW  CONST_47  H9   C11  C10  C19    0.00   0.0  0
 6TW  CONST_48  H19  N1   C6   C5   180.00   0.0  0
 6TW  CONST_53  O25  C23  N22  C12    0.00   0.0  0
 6TW  CONST_54  C24  C23  N22  C12  180.00   0.0  0
 6TW  Var_01    OP1  P    O5'  C5'  111.53  30.0  3
 6TW  Var_02    H14  C24  C23  N22  127.97  30.0  3
 6TW  Var_03    H7   C5'  O5'  P    159.72  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
 6TW  chir_01  C1'  N9   O4'  C2'  positiv
 6TW  chir_02  C3'  O3'  C4'  C2'  positiv
 6TW  chir_03  C4'  O4'  C3'  C5'  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
 6TW  plan-1  C10  0.020
 6TW  plan-1  C11  0.020
 6TW  plan-1  C12  0.020
 6TW  plan-1  C16  0.020
 6TW  plan-1  C17  0.020
 6TW  plan-1  C18  0.020
 6TW  plan-1  C19  0.020
 6TW  plan-1  C3   0.020
 6TW  plan-1  C7   0.020
 6TW  plan-1  C9   0.020
 6TW  plan-1  N2   0.020
 6TW  plan-1  H9   0.020
 6TW  plan-1  H10  0.020
 6TW  plan-1  H11  0.020
 6TW  plan-1  H12  0.020
 6TW  plan-1  H13  0.020
 6TW  plan-1  H17  0.020
 6TW  plan-1  N22  0.020
 6TW  plan-2  C2   0.020
 6TW  plan-2  C1'  0.020
 6TW  plan-2  C3   0.020
 6TW  plan-2  C4   0.020
 6TW  plan-2  C5   0.020
 6TW  plan-2  C6   0.020
 6TW  plan-2  C8   0.020
 6TW  plan-2  N1   0.020
 6TW  plan-2  N2   0.020
 6TW  plan-2  N3   0.020
 6TW  plan-2  N7   0.020
 6TW  plan-2  N9   0.020
 6TW  plan-2  O6   0.020
 6TW  plan-2  H18  0.020
 6TW  plan-2  H19  0.020
 6TW  plan-2  H20  0.020
 6TW  plan-3  C12  0.020
 6TW  plan-3  C23  0.020
 6TW  plan-3  C24  0.020
 6TW  plan-3  O25  0.020
 6TW  plan-3  H21  0.020
 6TW  plan-3  N22  0.020

