# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 00:13:04 2021
#   Inital geometry file: a 158 line input string
#   Ligand name: a 2 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=C(C#Cc3ccc(cc3)C#C)C(=O)NC2=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
 0R5  0R5  '2'-deoxy-5-[(4-ethynylphenyl)ethynyl]uridine 5'-(tetrahydrogen triphosphate)'  ligand  57  38  .  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_0R5
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
 0R5  O2G  O  OH1   0  -0.590  18.0236  -13.3338  -13.3985
 0R5  PG   P  P     0   1.401  16.7369  -13.8872  -14.1140
 0R5  O1G  O  OH1   0  -0.730  15.7684  -12.6482  -13.9425
 0R5  O3G  O  O     0  -0.791  16.8556  -14.4871  -15.4505
 0R5  O3B  O  O2    0  -0.676  16.0801  -14.9340  -13.0171
 0R5  PB   P  P     0   1.457  16.6103  -16.3851  -12.6171
 0R5  O1B  O  OH1   0  -0.597  15.3055  -17.0376  -12.0461
 0R5  O2B  O  O     0  -0.619  17.4071  -17.0796  -13.6382
 0R5  O3A  O  O2    0  -0.737  17.4554  -16.0921  -11.2503
 0R5  PA   P  P     0   1.492  19.0421  -15.8152  -11.0990
 0R5  O1A  O  O     0  -0.714  19.5856  -15.1532  -12.3120
 0R5  O2A  O  OH1   0  -0.642  19.1649  -15.0641   -9.7225
 0R5  O5'  O  O2    0  -0.657  19.6722  -17.1921  -10.6650
 0R5  C5'  C  CH2   0  -0.222  19.5587  -18.4230  -11.4006
 0R5  C4'  C  CH1   0   0.019  18.8583  -19.4809  -10.5856
 0R5  C3'  C  CH1   0  -0.029  17.4748  -19.1596  -10.0126
 0R5  O3'  O  OH1   0  -0.670  16.4385  -19.1915  -10.9609
 0R5  C2'  C  CH2   0  -0.521  17.3806  -20.1906   -8.8968
 0R5  O4'  O  O2    0  -0.340  19.6359  -19.8212   -9.4445
 0R5  C1'  C  CH1   0   0.159  18.8205  -20.2507   -8.3942
 0R5  N1   N  NR6   0  -0.594  19.0501  -19.3673   -7.2242
 0R5  C2   C  CR6   0   0.718  18.6437  -19.8598   -5.9972
 0R5  O2   O  O     0  -0.527  18.1203  -20.9461   -5.8778
 0R5  N3   N  NR16  0  -0.622  18.8744  -19.0265   -4.9373
 0R5  C4   C  CR6   0   0.541  19.4347  -17.7622   -4.9519
 0R5  O4   O  O     0  -0.452  19.5753  -17.1245   -3.9299
 0R5  C6   C  CR16  0   0.026  19.6109  -18.1429   -7.3395
 0R5  C5   C  CR6   0  -0.396  19.8166  -17.3171   -6.2819
 0R5  C5M  C  CSP   0   0.166  20.3984  -16.0413   -6.4505
 0R5  C30  C  CSP   0   0.144  20.8800  -14.9475   -6.6211
 0R5  C31  C  CR6   0  -0.135  21.4353  -13.6607   -6.8453
 0R5  C36  C  CR16  0  -0.243  21.8442  -13.2822   -8.1293
 0R5  C35  C  CR16  0  -0.305  22.3769  -12.0278   -8.3530
 0R5  C34  C  CR6   0   0.014  22.5167  -11.1198   -7.2992
 0R5  C37  C  CSP   0   0.156  23.0679   -9.8261   -7.5321
 0R5  C38  C  CSP1  0  -0.536  23.5329   -8.7346   -7.7369
 0R5  C33  C  CR16  0  -0.202  22.1121  -11.4980   -6.0155
 0R5  C32  C  CR16  0  -0.346  21.5776  -12.7518   -5.7909
 0R5  H1   H  HOH1  0   0.554  18.7080  -13.9922  -13.1007
 0R5  H2   H  HOH1  0   0.508  15.0889  -12.5945  -14.6292
 0R5  H3   H  HOH1  0   0.502  15.5085  -17.9084  -11.6167
 0R5  H4   H  HOH1  0   0.519  19.0381  -14.1050   -9.7524
 0R5  H5   H  HCH2  0   0.306  19.0259  -18.2892  -12.3422
 0R5  H6   H  HCH2  0   0.291  20.5719  -18.7432  -11.6409
 0R5  H7   H  HCH1  0   0.257  18.7742  -20.3538  -11.2490
 0R5  H8   H  HCH1  0   0.252  17.4554  -18.1545   -9.5857
 0R5  H9   H  HOH1  0   0.446  16.3754  -20.0620  -11.3737
 0R5  H10  H  HCH2  0   0.287  16.6617  -19.9348   -8.1211
 0R5  H11  H  HCH2  0   0.236  17.1048  -21.1658   -9.3064
 0R5  H12  H  HCH1  0   0.269  19.1108  -21.2532   -8.0828
 0R5  H13  H  HNR6  0   0.469  18.5894  -19.3866   -4.0340
 0R5  H14  H  HCR6  0   0.337  19.9063  -17.8401   -8.3310
 0R5  H15  H  HCR6  0   0.254  21.7465  -13.9781   -8.9512
 0R5  H16  H  HCR6  0   0.269  22.6872  -11.7458   -9.3500
 0R5  H17  H  H     0   0.305  23.9458   -7.7678   -7.9141
 0R5  H18  H  HCR6  0   0.275  22.2181  -10.8039   -5.1927
 0R5  H19  H  HCR6  0   0.264  21.2681  -13.0342   -4.7938

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
 0R5  O3G  PG   double    1.470  0.020  1.470
 0R5  O2G  PG   single    1.573  0.020  1.573
 0R5  PG   O1G  single    1.582  0.020  1.582
 0R5  PG   O3B  single    1.652  0.020  1.652
 0R5  O2B  PB   double    1.470  0.020  1.470
 0R5  O1A  PA   double    1.485  0.020  1.485
 0R5  O3B  PB   single    1.596  0.020  1.596
 0R5  PB   O1B  single    1.567  0.020  1.567
 0R5  PB   O3A  single    1.634  0.020  1.634
 0R5  C5'  O5'  single    1.438  0.020  1.438
 0R5  C5'  C4'  single    1.508  0.020  1.508
 0R5  PA   O3A  single    1.618  0.020  1.618
 0R5  PA   O5'  single    1.575  0.020  1.575
 0R5  PA   O2A  single    1.573  0.020  1.573
 0R5  O3'  C3'  single    1.405  0.020  1.405
 0R5  C4'  C3'  single    1.532  0.020  1.532
 0R5  C4'  O4'  single    1.422  0.020  1.422
 0R5  C3'  C2'  single    1.522  0.020  1.522
 0R5  O4'  C1'  single    1.397  0.020  1.397
 0R5  C2'  C1'  single    1.526  0.020  1.526
 0R5  C35  C36  aromatic  1.381  0.020  1.381
 0R5  C35  C34  aromatic  1.398  0.020  1.398
 0R5  C1'  N1   single    1.484  0.020  1.484
 0R5  C36  C31  aromatic  1.400  0.020  1.400
 0R5  C38  C37  triple    1.204  0.020  1.204
 0R5  C37  C34  single    1.425  0.020  1.425
 0R5  C34  C33  aromatic  1.398  0.020  1.398
 0R5  C6   N1   single    1.352  0.020  1.352
 0R5  C6   C5   double    1.358  0.020  1.358
 0R5  N1   C2   single    1.383  0.020  1.383
 0R5  C31  C30  single    1.419  0.020  1.419
 0R5  C31  C32  aromatic  1.399  0.020  1.399
 0R5  C30  C5M  triple    1.207  0.020  1.207
 0R5  C5M  C5   single    1.412  0.020  1.412
 0R5  C5   C4   single    1.454  0.020  1.454
 0R5  C33  C32  aromatic  1.381  0.020  1.381
 0R5  C2   O2   double    1.212  0.020  1.212
 0R5  C2   N3   single    1.368  0.020  1.368
 0R5  C4   N3   single    1.383  0.020  1.383
 0R5  C4   O4   double    1.213  0.020  1.213
 0R5  O2G  H1   single    0.832  0.020  0.971
 0R5  O1G  H2   single    0.832  0.020  0.971
 0R5  O1B  H3   single    0.832  0.020  0.971
 0R5  O2A  H4   single    0.832  0.020  0.971
 0R5  C5'  H5   single    0.939  0.020  1.096
 0R5  C5'  H6   single    0.939  0.020  1.096
 0R5  C4'  H7   single    0.939  0.020  1.096
 0R5  C3'  H8   single    0.939  0.020  1.096
 0R5  O3'  H9   single    0.832  0.020  0.971
 0R5  C2'  H10  single    0.939  0.020  1.096
 0R5  C2'  H11  single    0.939  0.020  1.096
 0R5  C1'  H12  single    0.939  0.020  1.096
 0R5  N3   H13  single    0.868  0.020  1.013
 0R5  C6   H14  single    0.930  0.020  1.086
 0R5  C36  H15  single    0.929  0.020  1.085
 0R5  C35  H16  single    0.929  0.020  1.085
 0R5  C38  H17  single    0.913  0.020  1.066
 0R5  C33  H18  single    0.929  0.020  1.085
 0R5  C32  H19  single    0.929  0.020  1.085

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
 0R5  H1   O2G  PG   117.77  3.000
 0R5  O3B  PG   O3G  112.16  3.000
 0R5  O3B  PG   O1G  100.42  3.000
 0R5  O3G  PG   O1G  117.88  3.000
 0R5  O3B  PG   O2G  104.25  3.000
 0R5  O1G  PG   O2G  100.14  3.000
 0R5  O3G  PG   O2G  119.42  3.000
 0R5  H2   O1G  PG   113.36  3.000
 0R5  PB   O3B  PG   127.62  3.000
 0R5  O3A  PB   O2B  112.68  3.000
 0R5  O3A  PB   O1B  101.57  3.000
 0R5  O2B  PB   O1B  120.53  3.000
 0R5  O3A  PB   O3B  102.62  3.000
 0R5  O1B  PB   O3B  101.15  3.000
 0R5  O2B  PB   O3B  115.83  3.000
 0R5  H3   O1B  PB   110.67  3.000
 0R5  PA   O3A  PB   128.05  3.000
 0R5  O5'  PA   O2A   98.34  3.000
 0R5  O2A  PA   O1A  118.25  3.000
 0R5  O5'  PA   O1A  117.93  3.000
 0R5  O2A  PA   O3A  103.89  3.000
 0R5  O5'  PA   O3A  105.57  3.000
 0R5  O1A  PA   O3A  111.03  3.000
 0R5  H4   O2A  PA   115.85  3.000
 0R5  C5'  O5'  PA   125.14  3.000
 0R5  H6   C5'  H5   107.47  3.000
 0R5  H6   C5'  C4'  110.18  3.000
 0R5  H5   C5'  C4'  109.02  3.000
 0R5  H6   C5'  O5'  106.92  3.000
 0R5  H5   C5'  O5'  112.04  3.000
 0R5  C4'  C5'  O5'  111.13  3.000
 0R5  H7   C4'  O4'  109.63  3.000
 0R5  H7   C4'  C3'  108.85  3.000
 0R5  O4'  C4'  C3'  104.12  3.000
 0R5  H7   C4'  C5'  105.45  3.000
 0R5  O4'  C4'  C5'  110.34  3.000
 0R5  C3'  C4'  C5'  118.33  3.000
 0R5  H8   C3'  C2'  109.62  3.000
 0R5  H8   C3'  O3'  105.76  3.000
 0R5  C2'  C3'  O3'  115.70  3.000
 0R5  H8   C3'  C4'  110.81  3.000
 0R5  C2'  C3'  C4'  100.84  3.000
 0R5  O3'  C3'  C4'  114.14  3.000
 0R5  H9   O3'  C3'  110.93  3.000
 0R5  H11  C2'  H10  108.07  3.000
 0R5  H11  C2'  C1'  109.05  3.000
 0R5  H10  C2'  C1'  113.44  3.000
 0R5  H11  C2'  C3'  110.20  3.000
 0R5  H10  C2'  C3'  113.84  3.000
 0R5  C1'  C2'  C3'  102.10  3.000
 0R5  C1'  O4'  C4'  110.95  3.000
 0R5  H12  C1'  N1   106.33  3.000
 0R5  H12  C1'  O4'  110.02  3.000
 0R5  N1   C1'  O4'  108.63  3.000
 0R5  H12  C1'  C2'  112.45  3.000
 0R5  N1   C1'  C2'  112.47  3.000
 0R5  O4'  C1'  C2'  106.91  3.000
 0R5  C6   N1   C2   121.34  3.000
 0R5  C2   N1   C1'  116.23  3.000
 0R5  C6   N1   C1'  122.42  3.000
 0R5  N3   C2   O2   122.86  3.000
 0R5  N3   C2   N1   114.89  3.000
 0R5  O2   C2   N1   122.24  3.000
 0R5  H13  N3   C4   116.63  3.000
 0R5  H13  N3   C2   115.27  3.000
 0R5  C4   N3   C2   128.10  3.000
 0R5  C5   C4   O4   125.42  3.000
 0R5  O4   C4   N3   121.25  3.000
 0R5  C5   C4   N3   113.33  3.000
 0R5  H14  C6   C5   120.27  3.000
 0R5  H14  C6   N1   116.53  3.000
 0R5  C5   C6   N1   123.20  3.000
 0R5  C5M  C5   C6   121.26  3.000
 0R5  C5M  C5   C4   119.61  3.000
 0R5  C6   C5   C4   119.13  3.000
 0R5  C30  C5M  C5   180.00  3.000
 0R5  C31  C30  C5M  180.00  3.000
 0R5  C32  C31  C36  119.07  3.000
 0R5  C32  C31  C30  120.64  3.000
 0R5  C36  C31  C30  120.29  3.000
 0R5  H15  C36  C35  119.76  3.000
 0R5  H15  C36  C31  119.79  3.000
 0R5  C35  C36  C31  120.45  3.000
 0R5  H16  C35  C34  119.79  3.000
 0R5  H16  C35  C36  119.79  3.000
 0R5  C34  C35  C36  120.43  3.000
 0R5  C33  C34  C37  120.50  3.000
 0R5  C33  C34  C35  119.18  3.000
 0R5  C37  C34  C35  120.33  3.000
 0R5  C38  C37  C34  180.00  3.000
 0R5  H17  C38  C37  180.00  3.000
 0R5  H18  C33  C32  119.78  3.000
 0R5  H18  C33  C34  119.77  3.000
 0R5  C32  C33  C34  120.45  3.000
 0R5  H19  C32  C33  119.85  3.000
 0R5  H19  C32  C31  119.73  3.000
 0R5  C33  C32  C31  120.42  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
 0R5  CONST_01  C34  C35  C36  C31     0.00   0.0  0
 0R5  CONST_02  C34  C33  C32  C31     0.00   0.0  0
 0R5  CONST_03  C33  C34  C35  C36     0.00   0.0  0
 0R5  CONST_04  C33  C32  C31  C36     0.00   0.0  0
 0R5  CONST_05  C32  C31  C36  C35     0.00   0.0  0
 0R5  CONST_06  C32  C33  C34  C35     0.00   0.0  0
 0R5  CONST_07  N3   C2   N1   C1'   180.00   0.0  0
 0R5  CONST_08  C4   N3   C2   N1      0.00   0.0  0
 0R5  CONST_09  C5   C4   N3   C2      0.00   0.0  0
 0R5  CONST_10  C6   N1   C2   N3      0.00   0.0  0
 0R5  CONST_11  C35  C36  C31  C30   180.00   0.0  0
 0R5  CONST_12  C33  C32  C31  C30   180.00   0.0  0
 0R5  CONST_13  C37  C34  C35  C36   180.00   0.0  0
 0R5  CONST_14  C32  C33  C34  C37   180.00   0.0  0
 0R5  CONST_15  O2   C2   N1   C1'     0.00   0.0  0
 0R5  CONST_16  O4   C4   N3   C2    180.00   0.0  0
 0R5  CONST_17  C6   N1   C2   O2    180.00   0.0  0
 0R5  CONST_18  C4   N3   C2   O2    180.00   0.0  0
 0R5  CONST_19  H16  C35  C36  C31   180.00   0.0  0
 0R5  CONST_20  H18  C33  C32  C31   180.00   0.0  0
 0R5  CONST_21  H19  C32  C31  C36   180.00   0.0  0
 0R5  CONST_22  H15  C36  C35  C34   180.00   0.0  0
 0R5  CONST_23  H13  N3   C2   N1    180.00   0.0  0
 0R5  Var_01    C4'  C5'  O5'  PA   -118.92  30.0  1
 0R5  Var_02    O2B  PB   O3B  PG    -25.54  30.0  3
 0R5  Var_03    O1A  PA   O3A  PB     30.17  30.0  2

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
 0R5  chir_03  C4'  C5'  C3'  O4'  positiv
 0R5  chir_04  C3'  O3'  C2'  C4'  negativ
 0R5  chir_05  C1'  O4'  N1   C2'  negativ
 0R5  chir_06  PB   O3B  O1B  O3A  both
 0R5  chir_07  PA   O3A  O5'  O2A  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
 0R5  plan-1  C1'  0.020
 0R5  plan-1  N1   0.020
 0R5  plan-1  C2   0.020
 0R5  plan-1  O2   0.020
 0R5  plan-1  N3   0.020
 0R5  plan-1  C4   0.020
 0R5  plan-1  O4   0.020
 0R5  plan-1  C6   0.020
 0R5  plan-1  C5   0.020
 0R5  plan-1  C5M  0.020
 0R5  plan-1  C30  0.020
 0R5  plan-1  H13  0.020
 0R5  plan-1  H14  0.020
 0R5  plan-2  C5M  0.020
 0R5  plan-2  C30  0.020
 0R5  plan-2  C31  0.020
 0R5  plan-2  C36  0.020
 0R5  plan-2  C35  0.020
 0R5  plan-2  C34  0.020
 0R5  plan-2  C37  0.020
 0R5  plan-2  C38  0.020
 0R5  plan-2  C33  0.020
 0R5  plan-2  C32  0.020
 0R5  plan-2  H15  0.020
 0R5  plan-2  H16  0.020
 0R5  plan-2  H18  0.020
 0R5  plan-2  H19  0.020

