# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Nov 23 22:54:43 2022
#   Inital geometry file: a 118 line input string
#   Ligand name: 1-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-L-erythro-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@@H]2C[C@@H](O)[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
#
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
 XRF  XRF  "1-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-L-erythro-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione"  ligand  46  29  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_XRF
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
 XRF  N    N  NR6   0  -0.570  -0.1351  -45.4438  132.0707
 XRF  C    C  CH3   0  -0.709  -2.5052  -42.5717  132.6874
 XRF  O    O  O     0  -0.477  -0.3534  -47.6751  132.4964
 XRF  C1   C  CR6   0  -0.183  -1.9192  -43.9440  132.6251
 XRF  C2   C  CR16  0   0.055  -0.6847  -44.1916  132.1533
 XRF  C3   C  CR6   0   0.729  -0.8196  -46.5538  132.5084
 XRF  C4   C  CR6   0   0.556  -2.7175  -45.0682  133.0730
 XRF  C5   C  CH1   0   0.229   1.2175  -45.6371  131.5449
 XRF  C6   C  CH2   0  -0.549   2.3280  -45.3792  132.5534
 XRF  C7   C  CH1   0  -0.009   3.4796  -44.9640  131.6453
 XRF  C8   C  CH1   0  -0.025   2.7350  -44.1678  130.5737
 XRF  C9   C  CH2   0  -0.213   2.6762  -42.6967  130.9548
 XRF  N1   N  NR16  0  -0.734  -2.0827  -46.2937  132.9707
 XRF  O1   O  O     0  -0.446  -3.8509  -44.9938  133.5095
 XRF  O10  O  OH1   0  -0.698  -0.7718  -37.5796  126.0716
 XRF  O11  O  O     0  -0.705   1.2305  -38.2825  127.5668
 XRF  O12  O  OH1   0  -0.707  -0.7641  -36.8243  128.4358
 XRF  O13  O  OH1   0  -0.662   4.0927  -46.0611  131.0151
 XRF  O2   O  O2    0  -0.494   1.4315  -44.7322  130.4943
 XRF  O3   O  O2    0  -0.589   1.6746  -41.9837  130.2266
 XRF  O4   O  O     0  -0.662   2.3945  -42.4639  127.7691
 XRF  O5   O  OH1   0  -0.766   2.5630  -40.0946  128.8210
 XRF  O6   O  O2    0  -0.693   0.2947  -41.1497  128.3603
 XRF  O7   O  OH1   0  -0.736  -0.1893  -39.6132  130.2571
 XRF  O8   O  O     0  -0.630  -2.1141  -41.1262  129.2950
 XRF  O9   O  O2    0  -0.674  -1.1747  -39.1832  127.9512
 XRF  P    P  P     0   1.486   1.8477  -41.4909  128.7262
 XRF  P1   P  P     0   1.511  -0.9022  -40.3448  129.0486
 XRF  P2   P  P     0   1.502  -0.2169  -37.9652  127.4965
 XRF  H1   H  HCH3  0   0.245  -3.4064  -42.4965  132.0773
 XRF  H2   H  HCH3  0   0.244  -2.7827  -42.3048  133.7077
 XRF  H3   H  HCH3  0   0.247  -1.7956  -41.8294  132.3261
 XRF  H4   H  HCR6  0   0.318  -0.0661  -43.3837  131.7911
 XRF  H5   H  HCH1  0   0.268   1.2564  -46.6615  131.1724
 XRF  H6   H  HCH2  0   0.269   2.0612  -44.5652  133.2322
 XRF  H7   H  HCH2  0   0.285   2.5503  -46.2547  133.1635
 XRF  H8   H  HCH1  0   0.254   4.2118  -44.3412  132.1749
 XRF  H9   H  HCH1  0   0.270   3.2146  -44.2783  129.5986
 XRF  H10  H  HCH2  0   0.273   3.6632  -42.2479  130.8156
 XRF  H11  H  HCH2  0   0.266   2.4028  -42.5676  132.0030
 XRF  H12  H  HNR6  0   0.423  -2.6013  -47.1035  133.2895
 XRF  H13  H  HOH1  0   0.514  -0.4103  -38.0872  125.3295
 XRF  H14  H  HOH1  0   0.515  -0.2199  -36.0245  128.4870
 XRF  H15  H  HOH1  0   0.455   4.4838  -46.6222  131.6929
 XRF  H16  H  HOH1  0   0.500   2.1334  -39.3437  128.3165
 XRF  H17  H  HOH1  0   0.518  -0.7663  -39.3765  130.9997

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
 XRF  O11  P2   double  1.483  0.020  1.483
 XRF  O10  P2   single  1.577  0.020  1.577
 XRF  P2   O12  single  1.576  0.020  1.576
 XRF  P2   O9   single  1.615  0.020  1.615
 XRF  O4   P    double  1.470  0.020  1.470
 XRF  O9   P1   single  1.621  0.020  1.621
 XRF  O6   P    single  1.632  0.020  1.632
 XRF  O6   P1   single  1.598  0.020  1.598
 XRF  P    O5   single  1.572  0.020  1.572
 XRF  P    O3   single  1.589  0.020  1.589
 XRF  P1   O8   double  1.463  0.020  1.463
 XRF  P1   O7   single  1.582  0.020  1.582
 XRF  O3   C9   single  1.429  0.020  1.429
 XRF  O2   C8   single  1.423  0.020  1.423
 XRF  O2   C5   single  1.403  0.020  1.403
 XRF  C8   C9   single  1.521  0.020  1.521
 XRF  C8   C7   single  1.529  0.020  1.529
 XRF  O13  C7   single  1.406  0.020  1.406
 XRF  C5   N    single  1.464  0.020  1.464
 XRF  C5   C6   single  1.522  0.020  1.522
 XRF  C7   C6   single  1.524  0.020  1.524
 XRF  O    C3   double  1.214  0.020  1.214
 XRF  N    C3   single  1.376  0.020  1.376
 XRF  N    C2   single  1.370  0.020  1.370
 XRF  C3   N1   single  1.370  0.020  1.370
 XRF  C2   C1   double  1.345  0.020  1.345
 XRF  N1   C4   single  1.384  0.020  1.384
 XRF  C1   C4   single  1.450  0.020  1.450
 XRF  C1   C    single  1.494  0.020  1.494
 XRF  C4   O1   double  1.217  0.020  1.217
 XRF  C    H1   single  0.970  0.020  1.090
 XRF  C    H2   single  0.970  0.020  1.090
 XRF  C    H3   single  0.970  0.020  1.090
 XRF  C2   H4   single  0.930  0.020  1.080
 XRF  C5   H5   single  0.970  0.020  1.090
 XRF  C6   H6   single  0.970  0.020  1.090
 XRF  C6   H7   single  0.970  0.020  1.090
 XRF  C7   H8   single  0.970  0.020  1.090
 XRF  C8   H9   single  0.970  0.020  1.090
 XRF  C9   H10  single  0.970  0.020  1.090
 XRF  C9   H11  single  0.970  0.020  1.090
 XRF  N1   H12  single  0.860  0.020  1.020
 XRF  O10  H13  single  0.850  0.020  0.980
 XRF  O12  H14  single  0.850  0.020  0.980
 XRF  O13  H15  single  0.850  0.020  0.980
 XRF  O5   H16  single  0.850  0.020  0.980
 XRF  O7   H17  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
 XRF  C5   N    C3   117.87  3.000
 XRF  C3   N    C2   121.25  3.000
 XRF  C5   N    C2   120.86  3.000
 XRF  H3   C    H2   108.03  3.000
 XRF  H3   C    H1   107.82  3.000
 XRF  H2   C    H1   107.23  3.000
 XRF  H3   C    C1   110.91  3.000
 XRF  H2   C    C1   111.33  3.000
 XRF  H1   C    C1   111.36  3.000
 XRF  C4   C1   C2   118.11  3.000
 XRF  C4   C1   C    118.92  3.000
 XRF  C2   C1   C    122.96  3.000
 XRF  H4   C2   C1   120.39  3.000
 XRF  H4   C2   N    115.70  3.000
 XRF  C1   C2   N    123.90  3.000
 XRF  N1   C3   O    122.18  3.000
 XRF  N1   C3   N    114.39  3.000
 XRF  O    C3   N    123.43  3.000
 XRF  O1   C4   N1   120.52  3.000
 XRF  O1   C4   C1   125.19  3.000
 XRF  N1   C4   C1   114.29  3.000
 XRF  H5   C5   O2   110.16  3.000
 XRF  H5   C5   C6   111.07  3.000
 XRF  O2   C5   C6   105.99  3.000
 XRF  H5   C5   N    106.24  3.000
 XRF  C6   C5   N    114.44  3.000
 XRF  O2   C5   N    108.94  3.000
 XRF  H7   C6   H6   107.48  3.000
 XRF  H7   C6   C7   113.46  3.000
 XRF  H6   C6   C7   110.59  3.000
 XRF  H7   C6   C5   112.55  3.000
 XRF  H6   C6   C5   111.08  3.000
 XRF  C7   C6   C5   101.69  3.000
 XRF  H8   C7   O13  111.61  3.000
 XRF  H8   C7   C8   111.57  3.000
 XRF  O13  C7   C8   107.74  3.000
 XRF  H8   C7   C6   111.78  3.000
 XRF  O13  C7   C6   112.58  3.000
 XRF  C8   C7   C6   101.04  3.000
 XRF  H9   C8   O2   108.20  3.000
 XRF  H9   C8   C9   109.79  3.000
 XRF  O2   C8   C9   111.24  3.000
 XRF  H9   C8   C7   111.05  3.000
 XRF  C9   C8   C7   110.30  3.000
 XRF  O2   C8   C7   106.19  3.000
 XRF  H11  C9   H10  107.46  3.000
 XRF  H11  C9   O3   104.77  3.000
 XRF  H10  C9   O3   111.29  3.000
 XRF  H11  C9   C8   111.40  3.000
 XRF  H10  C9   C8   109.29  3.000
 XRF  O3   C9   C8   112.46  3.000
 XRF  H12  N1   C4   116.73  3.000
 XRF  H12  N1   C3   115.24  3.000
 XRF  C4   N1   C3   128.02  3.000
 XRF  H13  O10  P2   115.63  3.000
 XRF  H14  O12  P2   115.73  3.000
 XRF  H15  O13  C7   108.43  3.000
 XRF  C8   O2   C5   110.72  3.000
 XRF  P    O3   C9   124.04  3.000
 XRF  H16  O5   P    116.13  3.000
 XRF  P1   O6   P    136.18  3.000
 XRF  H17  O7   P1   115.44  3.000
 XRF  P2   O9   P1   129.15  3.000
 XRF  O6   P    O5   105.13  3.000
 XRF  O5   P    O4   117.25  3.000
 XRF  O6   P    O4   110.27  3.000
 XRF  O5   P    O3   105.56  3.000
 XRF  O6   P    O3    99.96  3.000
 XRF  O4   P    O3   116.74  3.000
 XRF  O9   P1   O8   110.95  3.000
 XRF  O8   P1   O7   119.44  3.000
 XRF  O9   P1   O7   105.16  3.000
 XRF  O7   P1   O6   102.97  3.000
 XRF  O8   P1   O6   115.08  3.000
 XRF  O9   P1   O6   101.26  3.000
 XRF  O9   P2   O12   99.92  3.000
 XRF  O9   P2   O11  113.83  3.000
 XRF  O12  P2   O11  117.74  3.000
 XRF  O9   P2   O10  103.31  3.000
 XRF  O12  P2   O10  103.85  3.000
 XRF  O11  P2   O10  116.00  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
 XRF  CONST_01  C4   N1  C3  N       0.00   0.0  0
 XRF  CONST_02  C3   N1  C4  C1      0.00   0.0  0
 XRF  CONST_03  N1   C3  N   C2      0.00   0.0  0
 XRF  CONST_04  N1   C3  N   C5    180.00   0.0  0
 XRF  CONST_05  C5   N   C3  O       0.00   0.0  0
 XRF  CONST_06  C2   N   C3  O     180.00   0.0  0
 XRF  CONST_07  C4   N1  C3  O     180.00   0.0  0
 XRF  CONST_08  O1   C4  N1  C3    180.00   0.0  0
 XRF  CONST_09  H12  N1  C3  N     180.00   0.0  0
 XRF  CONST_10  H12  N1  C4  C1    180.00   0.0  0
 XRF  CONST_11  H12  N1  C3  O       0.00   0.0  0
 XRF  CONST_12  H12  N1  C4  O1      0.00   0.0  0
 XRF  Var_01    C    C1  C2  N    -179.08  30.0  1
 XRF  Var_02    N1   C4  C1  C     179.86  30.0  1
 XRF  Var_03    H4   C2  N   C3    179.52  30.0  1
 XRF  Var_04    H4   C2  C1  C4    178.74  30.0  1
 XRF  Var_05    H4   C2  N   C5      1.18  30.0  1
 XRF  Var_06    O1   C4  C1  C      -0.17  30.0  1
 XRF  Var_07    H4   C2  C1  C      -0.32  30.0  1
 XRF  Var_08    H1   C   C1  C2    118.83  30.0  3
 XRF  Var_09    H2   C   C1  C2   -121.56  30.0  3
 XRF  Var_10    H3   C   C1  C2     -1.24  30.0  3
 XRF  Var_11    H1   C   C1  C4    -60.23  30.0  3
 XRF  Var_12    H2   C   C1  C4     59.38  30.0  3
 XRF  Var_13    H3   C   C1  C4    179.70  30.0  3
 XRF  Var_14    P    O3  C9  C8    -78.35  30.0  1
 XRF  Var_15    O4   P   O3  C9     46.33  30.0  2
 XRF  Var_16    O6   P   O3  C9    165.17  30.0  2
 XRF  Var_17    O5   P   O3  C9    -85.93  30.0  2
 XRF  Var_18    P1   O9  P2  O10   158.21  30.0  3
 XRF  Var_19    P1   O9  P2  O11    31.55  30.0  3
 XRF  Var_20    P1   O9  P2  O12   -94.87  30.0  3
 XRF  Var_21    P1   O6  P   O3     47.93  30.0  2
 XRF  Var_22    P1   O6  P   O4    171.43  30.0  2
 XRF  Var_23    P1   O6  P   O5    -61.31  30.0  2
 XRF  Var_24    P2   O9  P1  O6    -66.04  30.0  2
 XRF  Var_25    P2   O9  P1  O7     40.87  30.0  2
 XRF  Var_26    P    O6  P1  O7      9.57  30.0  1
 XRF  Var_27    P2   O9  P1  O8    171.34  30.0  2
 XRF  Var_28    P    O6  P1  O8   -122.09  30.0  1
 XRF  Var_29    P    O6  P1  O9    118.19  30.0  1
 XRF  Var_30    H10  C9  O3  P      44.65  30.0  3
 XRF  Var_31    H11  C9  O3  P     160.49  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
 XRF  chir_01  C5  O2   N   C6  positiv
 XRF  chir_02  C7  O13  C8  C6  negativ
 XRF  chir_03  C8  O2   C7  C9  positiv
 XRF  chir_04  P   O6   O5  O3  both
 XRF  chir_05  P1  O6   O8  O7  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
 XRF  plan-1  N    0.020
 XRF  plan-1  O    0.020
 XRF  plan-1  C1   0.020
 XRF  plan-1  C2   0.020
 XRF  plan-1  C3   0.020
 XRF  plan-1  C4   0.020
 XRF  plan-1  C5   0.020
 XRF  plan-1  N1   0.020
 XRF  plan-1  O1   0.020
 XRF  plan-1  H12  0.020

