# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 07:27:53 2021
#   Inital geometry file: a 129 line input string
#   Ligand name: [(2S,4S,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxytetrahydrofuran-2-yl]methyl hydrogen (S)-[(2S,3R)-2,3-dihydroxy-4-methylpentanoyl]phosphoramidate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@@H](O)[C@H](O)C(=O)N[P](O)(=O)OC[C@@H]1C[C@H](O)[C@@H](O1)n2cnc3c(N)ncnc23
#
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
 84T  84T  '[(2S,4S,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxytetrahydrofuran-2-yl]methyl hydrogen (S)-[(2S,3R)-2,3-dihydroxy-4-methylpentanoyl]phosphoramidate (non-preferred name)'  ligand  56  31  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_84T
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
 84T  O1P   O  OH1   0  -0.746  -49.2826  33.2836  -40.5647
 84T  P     P  P     0   1.481  -49.2679  32.4399  -39.2098
 84T  O2P   O  O     0  -0.683  -48.6405  31.1080  -39.2454
 84T  N     N  NH1   0  -0.834  -48.5509  33.6155  -38.2367
 84T  C     C  C     0   0.556  -48.3629  33.4538  -36.8981
 84T  CA    C  CH1   0  -0.104  -47.7634  34.6611  -36.1783
 84T  CB    C  CH1   0   0.073  -48.8037  35.1899  -35.1906
 84T  CG    C  CH1   0  -0.259  -48.3386  36.4370  -34.4298
 84T  CD2   C  CH3   0  -0.680  -47.0082  36.1962  -33.7208
 84T  CD1   C  CH3   0  -0.675  -49.3966  36.8636  -33.4134
 84T  OHB   O  OH1   0  -0.674  -49.9799  35.4283  -35.9386
 84T  OH    O  OH1   0  -0.662  -47.3786  35.6739  -37.0706
 84T  O     O  O     0  -0.454  -48.6495  32.4328  -36.3088
 84T  O5'   O  O2    0  -0.585  -50.7798  32.3193  -38.7139
 84T  C5'   C  CH2   0  -0.210  -51.6209  33.4510  -38.4954
 84T  C4'   C  CH1   0   0.012  -52.6947  33.1084  -37.4958
 84T  C3'   C  CH2   0  -0.532  -52.2355  32.5307  -36.1698
 84T  C2'   C  CH1   0   0.015  -53.4950  31.8247  -35.7060
 84T  O2'   O  OH1   0  -0.648  -53.2242  30.8445  -34.7529
 84T  O4'   O  O2    0  -0.495  -53.5924  32.1319  -38.0413
 84T  C1'   C  CH1   0   0.152  -54.0632  31.2854  -37.0439
 84T  N9    N  NR5   0  -0.514  -53.6263  29.9254  -37.3075
 84T  C4    C  CR56  0   0.487  -54.2364  28.8082  -36.8230
 84T  N3    N  N     0  -0.465  -55.3445  28.7307  -36.0865
 84T  C2    C  CR16  0   0.038  -55.6590  27.4774  -35.8100
 84T  C8    C  CR15  0   0.093  -52.5245  29.4937  -37.9919
 84T  N7    N  N     0  -0.456  -52.3953  28.1973  -37.9951
 84T  C5    C  CR56  0  -0.004  -53.4624  27.7468  -37.2640
 84T  C6    C  CR6   0   0.453  -53.9051  26.4616  -36.9010
 84T  N1    N  N     0  -0.475  -55.0196  26.3660  -36.1666
 84T  N6    N  NH2   0  -0.817  -53.2564  25.3496  -37.2513
 84T  H1P   H  HOH1  0   0.505  -49.3809  32.7476  -41.3640
 84T  H     H  HNH1  0   0.433  -48.2676  34.5049  -38.6308
 84T  HA    H  HCH1  0   0.284  -46.9105  34.2829  -35.6047
 84T  HB    H  HCH1  0   0.222  -48.9661  34.3894  -34.4544
 84T  HH    H  HOH1  0   0.472  -46.4513  35.5559  -37.2980
 84T  HG    H  HCH1  0   0.232  -48.2078  37.2480  -35.1521
 84T  HHB   H  HOH1  0   0.459  -50.7187  35.5328  -35.3329
 84T  HD21  H  HCH3  0   0.238  -46.7556  37.0476  -33.0876
 84T  HD22  H  HCH3  0   0.222  -47.0562  35.3140  -33.0778
 84T  HD23  H  HCH3  0   0.234  -46.1823  36.0581  -34.4192
 84T  HD11  H  HCH3  0   0.239  -49.0779  37.7664  -32.8910
 84T  HD12  H  HCH3  0   0.225  -50.3600  37.0917  -33.8721
 84T  HD13  H  HCH3  0   0.221  -49.5544  36.0867  -32.6610
 84T  H5'1  H  HCH2  0   0.249  -51.0542  34.2929  -38.0920
 84T  H5'2  H  HCH2  0   0.264  -52.0689  33.7615  -39.4422
 84T  H4'   H  HCH1  0   0.252  -53.2503  34.0389  -37.3222
 84T  H3'1  H  HCH2  0   0.262  -51.4219  31.8140  -36.3025
 84T  H3'2  H  HCH2  0   0.268  -51.8986  33.3059  -35.4838
 84T  H2'   H  HCH1  0   0.243  -54.2100  32.5662  -35.3275
 84T  HC    H  HOH1  0   0.459  -54.0545  30.5454  -34.3675
 84T  H8    H  HCR5  0   0.297  -51.8557  30.1781  -38.4889
 84T  H2    H  HCR6  0   0.251  -56.5536  27.3291  -35.2144
 84T  HN61  H  HNH2  0   0.402  -53.6400  24.4479  -37.0279
 84T  HN62  H  HNH2  0   0.410  -52.4480  25.3876  -37.8469
 84T  HC1'  H  HCH1  0   0.271  -55.1564  31.2638  -37.0396

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
 84T  O1P  P     single    1.596  0.020  1.596
 84T  P    O2P   double    1.473  0.020  1.473
 84T  P    N     single    1.686  0.020  1.686
 84T  P    O5'   single    1.596  0.020  1.596
 84T  N    C     single    1.361  0.020  1.361
 84T  C    CA    single    1.528  0.020  1.528
 84T  C    O     double    1.213  0.020  1.213
 84T  CA   CB    single    1.529  0.020  1.529
 84T  CA   OH    single    1.404  0.020  1.404
 84T  CB   CG    single    1.533  0.020  1.533
 84T  CB   OHB   single    1.414  0.020  1.414
 84T  CG   CD2   single    1.527  0.020  1.527
 84T  CG   CD1   single    1.528  0.020  1.528
 84T  O5'  C5'   single    1.427  0.020  1.427
 84T  C5'  C4'   single    1.507  0.020  1.507
 84T  C4'  C3'   single    1.518  0.020  1.518
 84T  C4'  O4'   single    1.434  0.020  1.434
 84T  C3'  C2'   single    1.517  0.020  1.517
 84T  C2'  O2'   single    1.394  0.020  1.394
 84T  C2'  C1'   single    1.550  0.020  1.550
 84T  O4'  C1'   single    1.390  0.020  1.390
 84T  C1'  N9    single    1.453  0.020  1.453
 84T  N9   C4    aromatic  1.362  0.020  1.362
 84T  N9   C8    aromatic  1.367  0.020  1.367
 84T  C4   N3    aromatic  1.333  0.020  1.333
 84T  C4   C5    aromatic  1.386  0.020  1.386
 84T  N3   C2    aromatic  1.321  0.020  1.321
 84T  C2   N1    aromatic  1.331  0.020  1.331
 84T  C8   N7    aromatic  1.303  0.020  1.303
 84T  N7   C5    aromatic  1.370  0.020  1.370
 84T  C5   C6    aromatic  1.407  0.020  1.407
 84T  C6   N1    aromatic  1.338  0.020  1.338
 84T  C1'  HC1'  single    0.970  0.020  1.090
 84T  O1P  H1P   single    0.850  0.020  0.980
 84T  N    H     single    0.860  0.020  1.020
 84T  CA   HA    single    0.970  0.020  1.090
 84T  CB   HB    single    0.970  0.020  1.090
 84T  OH   HH    single    0.850  0.020  0.980
 84T  CG   HG    single    0.970  0.020  1.090
 84T  OHB  HHB   single    0.850  0.020  0.980
 84T  CD2  HD21  single    0.970  0.020  1.090
 84T  CD2  HD22  single    0.970  0.020  1.090
 84T  CD2  HD23  single    0.970  0.020  1.090
 84T  CD1  HD11  single    0.970  0.020  1.090
 84T  CD1  HD12  single    0.970  0.020  1.090
 84T  CD1  HD13  single    0.970  0.020  1.090
 84T  C5'  H5'1  single    0.970  0.020  1.090
 84T  C5'  H5'2  single    0.970  0.020  1.090
 84T  C4'  H4'   single    0.970  0.020  1.090
 84T  C3'  H3'1  single    0.970  0.020  1.090
 84T  C3'  H3'2  single    0.970  0.020  1.090
 84T  C2'  H2'   single    0.970  0.020  1.090
 84T  O2'  HC    single    0.850  0.020  0.980
 84T  C8   H8    single    0.930  0.020  1.080
 84T  C2   H2    single    0.930  0.020  1.080
 84T  C6   N6    single    1.334  0.020  1.334
 84T  N6   HN61  single    0.860  0.020  1.020
 84T  N6   HN62  single    0.860  0.020  1.020

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
 84T  H1P   O1P  P     114.17  3.000
 84T  O5'   P    N     106.03  3.000
 84T  O5'   P    O2P   110.05  3.000
 84T  N     P    O2P   117.60  3.000
 84T  O5'   P    O1P   107.16  3.000
 84T  N     P    O1P    97.20  3.000
 84T  O2P   P    O1P   117.48  3.000
 84T  H     N    C     116.62  3.000
 84T  H     N    P     120.43  3.000
 84T  C     N    P     122.92  3.000
 84T  O     C    CA    121.92  3.000
 84T  O     C    N     123.02  3.000
 84T  CA    C    N     115.06  3.000
 84T  HA    CA   OH    111.63  3.000
 84T  HA    CA   CB    108.12  3.000
 84T  OH    CA   CB    110.35  3.000
 84T  HA    CA   C     106.22  3.000
 84T  OH    CA   C     112.22  3.000
 84T  CB    CA   C     108.10  3.000
 84T  HB    CB   OHB   110.73  3.000
 84T  HB    CB   CG    107.74  3.000
 84T  OHB   CB   CG    112.19  3.000
 84T  HB    CB   CA    106.34  3.000
 84T  OHB   CB   CA    106.42  3.000
 84T  CG    CB   CA    113.30  3.000
 84T  HG    CG   CD1   108.36  3.000
 84T  HG    CG   CD2   108.63  3.000
 84T  CD1   CG   CD2   109.79  3.000
 84T  HG    CG   CB    108.16  3.000
 84T  CD1   CG   CB    110.31  3.000
 84T  CD2   CG   CB    111.51  3.000
 84T  HD23  CD2  HD22  107.93  3.000
 84T  HD23  CD2  HD21  107.18  3.000
 84T  HD22  CD2  HD21  107.39  3.000
 84T  HD23  CD2  CG    112.49  3.000
 84T  HD22  CD2  CG    111.24  3.000
 84T  HD21  CD2  CG    110.39  3.000
 84T  HD13  CD1  HD12  108.09  3.000
 84T  HD13  CD1  HD11  107.50  3.000
 84T  HD12  CD1  HD11  106.64  3.000
 84T  HD13  CD1  CG    111.07  3.000
 84T  HD12  CD1  CG    112.97  3.000
 84T  HD11  CD1  CG    110.33  3.000
 84T  HHB   OHB  CB    108.93  3.000
 84T  HH    OH   CA    109.03  3.000
 84T  C5'   O5'  P     123.10  3.000
 84T  H5'2  C5'  H5'1  108.29  3.000
 84T  H5'2  C5'  C4'   110.32  3.000
 84T  H5'1  C5'  C4'   107.46  3.000
 84T  H5'2  C5'  O5'   109.54  3.000
 84T  H5'1  C5'  O5'   111.23  3.000
 84T  C4'   C5'  O5'   109.96  3.000
 84T  H4'   C4'  O4'   108.69  3.000
 84T  H4'   C4'  C3'   109.74  3.000
 84T  O4'   C4'  C3'   105.22  3.000
 84T  H4'   C4'  C5'   105.84  3.000
 84T  O4'   C4'  C5'   110.40  3.000
 84T  C3'   C4'  C5'   116.79  3.000
 84T  H3'2  C3'  H3'1  108.26  3.000
 84T  H3'2  C3'  C2'   113.32  3.000
 84T  H3'1  C3'  C2'   110.50  3.000
 84T  H3'2  C3'  C4'   111.91  3.000
 84T  H3'1  C3'  C4'   111.65  3.000
 84T  C2'   C3'  C4'   101.14  3.000
 84T  H2'   C2'  C1'   107.09  3.000
 84T  H2'   C2'  O2'   111.46  3.000
 84T  C1'   C2'  O2'   114.63  3.000
 84T  H2'   C2'  C3'   109.39  3.000
 84T  C1'   C2'  C3'   101.68  3.000
 84T  O2'   C2'  C3'   112.03  3.000
 84T  HC    O2'  C2'   108.94  3.000
 84T  C1'   O4'  C4'   110.71  3.000
 84T  HC1'  C1'  N9    106.43  3.000
 84T  HC1'  C1'  O4'   110.70  3.000
 84T  N9    C1'  O4'   109.76  3.000
 84T  HC1'  C1'  C2'   111.71  3.000
 84T  N9    C1'  C2'   111.84  3.000
 84T  O4'   C1'  C2'   106.45  3.000
 84T  C8    N9   C4    106.27  3.000
 84T  C8    N9   C1'   128.97  3.000
 84T  C4    N9   C1'   124.66  3.000
 84T  C5    C4   N3    126.56  3.000
 84T  C5    C4   N9    105.36  3.000
 84T  N3    C4   N9    128.08  3.000
 84T  C2    N3   C4    111.64  3.000
 84T  H2    C2   N1    115.41  3.000
 84T  H2    C2   N3    116.16  3.000
 84T  N1    C2   N3    128.43  3.000
 84T  H8    C8   N7    124.68  3.000
 84T  H8    C8   N9    122.02  3.000
 84T  N7    C8   N9    113.29  3.000
 84T  C5    N7   C8    104.40  3.000
 84T  C6    C5   N7    133.10  3.000
 84T  C6    C5   C4    116.22  3.000
 84T  N7    C5   C4    110.68  3.000
 84T  N6    C6   N1    119.31  3.000
 84T  N6    C6   C5    122.72  3.000
 84T  N1    C6   C5    117.97  3.000
 84T  C6    N1   C2    119.18  3.000
 84T  HN62  N6   HN61  118.21  3.000
 84T  HN62  N6   C6    121.02  3.000
 84T  HN61  N6   C6    120.25  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
 84T  CONST_01  C2    N3   C4   N9    180.00   0.0  0
 84T  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 84T  CONST_03  C6    C5   C4   N9    180.00   0.0  0
 84T  CONST_04  C5    N7   C8   N9      0.00   0.0  0
 84T  CONST_05  N7    C8   N9   C4      0.00   0.0  0
 84T  CONST_06  N1    C2   N3   C4      0.00   0.0  0
 84T  CONST_07  C8    N7   C5   C4      0.00   0.0  0
 84T  CONST_08  N1    C6   C5   C4      0.00   0.0  0
 84T  CONST_09  C8    N9   C4   N3    180.00   0.0  0
 84T  CONST_10  N7    C5   C4   N3    180.00   0.0  0
 84T  CONST_11  C6    C5   C4   N3      0.00   0.0  0
 84T  CONST_12  C6    N1   C2   N3      0.00   0.0  0
 84T  CONST_13  C5    C4   N3   C2      0.00   0.0  0
 84T  CONST_14  C5    C6   N1   C2      0.00   0.0  0
 84T  CONST_15  C5    C4   N9   C8      0.00   0.0  0
 84T  CONST_16  C6    C5   N7   C8    180.00   0.0  0
 84T  CONST_17  N1    C6   C5   N7    180.00   0.0  0
 84T  CONST_18  N3    C4   N9   C1'     0.00   0.0  0
 84T  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 84T  CONST_20  N7    C8   N9   C1'   180.00   0.0  0
 84T  CONST_21  N6    C6   C5   C4    180.00   0.0  0
 84T  CONST_22  N6    C6   N1   C2    180.00   0.0  0
 84T  CONST_23  N6    C6   C5   N7      0.00   0.0  0
 84T  CONST_24  H8    C8   N9   C1'     0.00   0.0  0
 84T  CONST_25  H2    C2   N3   C4    180.00   0.0  0
 84T  CONST_26  HN61  N6   C6   C5    180.00   0.0  0
 84T  CONST_27  HN62  N6   C6   C5      0.00   0.0  0
 84T  CONST_28  CA    C    N    P     180.00   0.0  0
 84T  CONST_29  O     C    N    P       0.00   0.0  0
 84T  CONST_30  H     N    C    CA      0.00   0.0  0
 84T  Var_01    C4'   C5'  O5'  P    -154.77  30.0  3
 84T  Var_02    C     N    P    O1P   175.78  30.0  3
 84T  Var_03    HD21  CD2  CG   CB   -173.01  30.0  3
 84T  Var_04    HD11  CD1  CG   CB   -178.47  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
 84T  chir_02  CA   C    CB   OH   positiv
 84T  chir_03  CB   OHB  CA   CG   negativ
 84T  chir_04  C4'  C5'  C3'  O4'  positiv
 84T  chir_05  C2'  O2'  C1'  C3'  positiv
 84T  chir_06  C1'  O4'  N9   C2'  negativ
 84T  chir_07  P    O2P  N    O5'  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
 84T  plan-1  C1'   0.020
 84T  plan-1  N9    0.020
 84T  plan-1  C4    0.020
 84T  plan-1  N3    0.020
 84T  plan-1  C2    0.020
 84T  plan-1  C8    0.020
 84T  plan-1  N7    0.020
 84T  plan-1  C5    0.020
 84T  plan-1  C6    0.020
 84T  plan-1  N1    0.020
 84T  plan-1  N6    0.020
 84T  plan-1  H8    0.020
 84T  plan-1  H2    0.020
 84T  plan-2  C6    0.020
 84T  plan-2  N6    0.020
 84T  plan-2  HN61  0.020
 84T  plan-2  HN62  0.020
 84T  plan-3  P     0.020
 84T  plan-3  N     0.020
 84T  plan-3  C     0.020
 84T  plan-3  CA    0.020
 84T  plan-3  O     0.020
 84T  plan-3  H     0.020

