# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 00:45:26 2021
#   Inital geometry file: a 159 line input string
#   Ligand name: [[(2S,5R)-5-[4-azanyl-5-[2-(4-ethynylphenyl)ethynyl]-2-oxidanylidene-pyrimidin-1-yl]oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1C#Cc2ccc(cc2)C#C)[C@H]3CC[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
#
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
 0R7  0R7  '[[(2S,5R)-5-[4-azanyl-5-[2-(4-ethynylphenyl)ethynyl]-2-oxidanylidene-pyrimidin-1-yl]oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate'  ligand  57  37  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_0R7
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
 0R7  O5'  O  O2    0  -0.577  19.5971  -17.6918  -10.2233
 0R7  P1   P  P     0   1.490  19.1053  -16.2866  -10.7572
 0R7  O1   O  O2    0  -0.681  17.4737  -16.3714  -10.6444
 0R7  P2   P  P     0   1.494  16.4450  -16.6994  -11.8312
 0R7  O3   O  O2    0  -0.684  16.4826  -15.3254  -12.6693
 0R7  P3   P  P     0   1.464  16.5197  -15.1465  -14.2858
 0R7  O5   O  OH1   0  -0.717  16.4263  -13.5663  -14.3970
 0R7  O6   O  OH1   0  -0.732  15.0469  -15.6384  -14.6111
 0R7  O7   O  O     0  -0.675  17.6417  -15.7966  -14.9740
 0R7  O8   O  OH1   0  -0.702  15.1041  -16.6049  -11.0030
 0R7  O9   O  O     0  -0.668  16.7056  -17.9124  -12.6169
 0R7  O10  O  OH1   0  -0.696  19.4700  -15.4194   -9.4914
 0R7  O11  O  O     0  -0.671  19.5385  -15.8736  -12.0990
 0R7  C1'  C  CH1   0   0.211  19.0536  -20.9992   -8.3341
 0R7  N1   N  NR6   0  -0.550  18.9618  -20.1569   -7.1176
 0R7  C6   C  CR16  0   0.055  19.3869  -18.8897   -7.0891
 0R7  C5   C  CR6   0  -0.342  19.2950  -18.1292   -5.9598
 0R7  C1   C  CSP   0   0.133  19.7546  -16.7957   -5.9269
 0R7  C3   C  CSP   0   0.161  20.1481  -15.6538   -5.8782
 0R7  N2   N  N     0  -0.525  18.3150  -20.0245   -4.8460
 0R7  C4   C  CR6   0   0.480  18.7199  -18.7727   -4.8078
 0R7  C2   C  CR6   0   0.601  18.4132  -20.7597   -5.9682
 0R7  O2   O  O     0  -0.509  18.0478  -21.9243   -6.0398
 0R7  N3   N  NH2   0  -0.807  18.5942  -18.0960   -3.6713
 0R7  O4'  O  O2    0  -0.502  19.9040  -20.3934   -9.2575
 0R7  C4'  C  CH1   0   0.032  19.1990  -20.0661  -10.4612
 0R7  C3'  C  CH2   0  -0.503  17.7350  -20.0386  -10.0613
 0R7  C2'  C  CH2   0  -0.507  17.6973  -21.1520   -9.0253
 0R7  C5'  C  CH2   0  -0.211  19.7782  -18.8246  -11.0884
 0R7  C01  C  CR6   0  -0.106  20.6189  -14.3155   -5.8465
 0R7  C02  C  CR16  0  -0.295  21.3360  -13.7933   -6.9292
 0R7  C03  C  CR16  0  -0.264  21.7981  -12.4923   -6.9002
 0R7  C04  C  CR6   0  -0.062  21.5580  -11.6795   -5.7884
 0R7  C05  C  CR16  0  -0.267  20.8427  -12.2005   -4.7060
 0R7  C    C  CR16  0  -0.291  20.3783  -13.5012   -4.7342
 0R7  C7   C  CSP   0   0.308  22.0371  -10.3376   -5.7582
 0R7  C8   C  CSP1  0  -0.552  22.4439   -9.2048   -5.7323
 0R7  H1   H  HOH1  0   0.509  17.2607  -13.1336  -14.6246
 0R7  H2   H  HOH1  0   0.510  14.8663  -15.7871  -15.5499
 0R7  H3   H  HOH1  0   0.517  14.4027  -17.2026  -11.2983
 0R7  H4   H  HOH1  0   0.514  19.3173  -14.4690   -9.5904
 0R7  H5   H  HCH1  0   0.275  19.4736  -21.9526   -8.0143
 0R7  H6   H  HCR6  0   0.324  19.8128  -18.4841   -7.9927
 0R7  H7   H  HNH2  0   0.409  18.1918  -18.5410   -2.8638
 0R7  H8   H  HNH2  0   0.413  18.8803  -17.1354   -3.5894
 0R7  H9   H  HCH1  0   0.255  19.3613  -20.8676  -11.1938
 0R7  H10  H  HCH2  0   0.244  17.4565  -19.0822   -9.6137
 0R7  H11  H  HCH2  0   0.273  17.0768  -20.2159  -10.9093
 0R7  H12  H  HCH2  0   0.276  16.8574  -21.0867   -8.3382
 0R7  H13  H  HCH2  0   0.263  17.6564  -22.1284   -9.5114
 0R7  H14  H  HCH2  0   0.257  19.2972  -18.6750  -12.0567
 0R7  H15  H  HCH2  0   0.276  20.8481  -18.9435  -11.2616
 0R7  H16  H  HCR6  0   0.265  21.5323  -14.4147   -7.7920
 0R7  H17  H  HCR6  0   0.270  22.3515  -12.1004   -7.7428
 0R7  H18  H  HCR6  0   0.270  20.6503  -11.5803   -3.8408
 0R7  H19  H  HCR6  0   0.267  19.8259  -13.8926   -3.8905
 0R7  H20  H  H     0   0.285  22.8048   -8.2020   -5.7089

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
 0R7  O7   P3   double    1.468  0.020  1.468
 0R7  O6   P3   single    1.586  0.020  1.586
 0R7  P3   O5   single    1.587  0.020  1.587
 0R7  P3   O3   single    1.627  0.020  1.627
 0R7  O9   P2   double    1.468  0.020  1.468
 0R7  O11  P1   double    1.469  0.020  1.469
 0R7  O3   P2   single    1.610  0.020  1.610
 0R7  P2   O8   single    1.579  0.020  1.579
 0R7  P2   O1   single    1.604  0.020  1.604
 0R7  C5'  O5'  single    1.437  0.020  1.437
 0R7  C5'  C4'  single    1.507  0.020  1.507
 0R7  P1   O1   single    1.638  0.020  1.638
 0R7  P1   O5'  single    1.582  0.020  1.582
 0R7  P1   O10  single    1.577  0.020  1.577
 0R7  C4'  C3'  single    1.518  0.020  1.518
 0R7  C4'  O4'  single    1.433  0.020  1.433
 0R7  C3'  C2'  single    1.521  0.020  1.521
 0R7  O4'  C1'  single    1.394  0.020  1.394
 0R7  C2'  C1'  single    1.530  0.020  1.530
 0R7  C1'  N1   single    1.482  0.020  1.482
 0R7  C6   N1   single    1.337  0.020  1.337
 0R7  C6   C5   double    1.365  0.020  1.365
 0R7  N1   C2   single    1.409  0.020  1.409
 0R7  C02  C03  aromatic  1.381  0.020  1.381
 0R7  C02  C01  aromatic  1.400  0.020  1.400
 0R7  C03  C04  aromatic  1.398  0.020  1.398
 0R7  C1   C3   triple    1.209  0.020  1.209
 0R7  C1   C5   single    1.411  0.020  1.411
 0R7  C3   C01  single    1.419  0.020  1.419
 0R7  C5   C4   single    1.439  0.020  1.439
 0R7  C01  C    aromatic  1.399  0.020  1.399
 0R7  C04  C7   single    1.425  0.020  1.425
 0R7  C04  C05  aromatic  1.398  0.020  1.398
 0R7  C2   O2   double    1.223  0.020  1.223
 0R7  C2   N2   single    1.345  0.020  1.345
 0R7  C7   C8   triple    1.204  0.020  1.204
 0R7  C    C05  aromatic  1.381  0.020  1.381
 0R7  C4   N2   double    1.316  0.020  1.316
 0R7  C4   N3   single    1.329  0.020  1.329
 0R7  O5   H1   single    0.832  0.020  0.971
 0R7  O6   H2   single    0.832  0.020  0.971
 0R7  O8   H3   single    0.832  0.020  0.971
 0R7  O10  H4   single    0.832  0.020  0.971
 0R7  C1'  H5   single    0.939  0.020  1.096
 0R7  C6   H6   single    0.930  0.020  1.086
 0R7  N3   H7   single    0.868  0.020  1.013
 0R7  N3   H8   single    0.868  0.020  1.013
 0R7  C4'  H9   single    0.939  0.020  1.096
 0R7  C3'  H10  single    0.939  0.020  1.096
 0R7  C3'  H11  single    0.939  0.020  1.096
 0R7  C2'  H12  single    0.939  0.020  1.096
 0R7  C2'  H13  single    0.939  0.020  1.096
 0R7  C5'  H14  single    0.939  0.020  1.096
 0R7  C5'  H15  single    0.939  0.020  1.096
 0R7  C02  H16  single    0.929  0.020  1.085
 0R7  C03  H17  single    0.929  0.020  1.085
 0R7  C05  H18  single    0.929  0.020  1.085
 0R7  C    H19  single    0.929  0.020  1.085
 0R7  C8   H20  single    0.913  0.020  1.066

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
 0R7  C5'  O5'  P1   122.44  3.000
 0R7  O11  P1   O10  120.68  3.000
 0R7  O10  P1   O1   101.75  3.000
 0R7  O11  P1   O1   111.79  3.000
 0R7  O10  P1   O5'   98.38  3.000
 0R7  O1   P1   O5'  103.92  3.000
 0R7  O11  P1   O5'  117.80  3.000
 0R7  P2   O1   P1   126.76  3.000
 0R7  O9   P2   O8   118.74  3.000
 0R7  O8   P2   O3   103.99  3.000
 0R7  O9   P2   O3   114.98  3.000
 0R7  O8   P2   O1    98.30  3.000
 0R7  O3   P2   O1   101.28  3.000
 0R7  O9   P2   O1   116.80  3.000
 0R7  P3   O3   P2   127.71  3.000
 0R7  O7   P3   O6   118.43  3.000
 0R7  O6   P3   O5   103.87  3.000
 0R7  O7   P3   O5   116.94  3.000
 0R7  O5   P3   O3   100.24  3.000
 0R7  O6   P3   O3    98.54  3.000
 0R7  O7   P3   O3   115.76  3.000
 0R7  H1   O5   P3   114.28  3.000
 0R7  H2   O6   P3   114.82  3.000
 0R7  H3   O8   P2   114.74  3.000
 0R7  H4   O10  P1   114.93  3.000
 0R7  H5   C1'  C2'  112.76  3.000
 0R7  H5   C1'  O4'  109.85  3.000
 0R7  C2'  C1'  O4'  106.55  3.000
 0R7  H5   C1'  N1   106.27  3.000
 0R7  C2'  C1'  N1   111.87  3.000
 0R7  O4'  C1'  N1   109.54  3.000
 0R7  C2   N1   C6   120.79  3.000
 0R7  C2   N1   C1'  116.77  3.000
 0R7  C6   N1   C1'  122.44  3.000
 0R7  H6   C6   C5   120.70  3.000
 0R7  H6   C6   N1   117.67  3.000
 0R7  C5   C6   N1   121.63  3.000
 0R7  C4   C5   C1   122.28  3.000
 0R7  C4   C5   C6   116.11  3.000
 0R7  C1   C5   C6   121.61  3.000
 0R7  C3   C1   C5   180.00  3.000
 0R7  C01  C3   C1   180.00  3.000
 0R7  C2   N2   C4   121.43  3.000
 0R7  N3   C4   N2   118.69  3.000
 0R7  N3   C4   C5   119.65  3.000
 0R7  N2   C4   C5   121.66  3.000
 0R7  O2   C2   N2   123.20  3.000
 0R7  N2   C2   N1   118.37  3.000
 0R7  O2   C2   N1   118.43  3.000
 0R7  H8   N3   H7   118.10  3.000
 0R7  H8   N3   C4   121.95  3.000
 0R7  H7   N3   C4   119.95  3.000
 0R7  C4'  O4'  C1'  110.83  3.000
 0R7  H9   C4'  C5'  105.48  3.000
 0R7  H9   C4'  C3'  109.36  3.000
 0R7  C5'  C4'  C3'  117.74  3.000
 0R7  H9   C4'  O4'  108.73  3.000
 0R7  C3'  C4'  O4'  104.92  3.000
 0R7  C5'  C4'  O4'  110.41  3.000
 0R7  H11  C3'  H10  107.93  3.000
 0R7  H11  C3'  C2'  113.36  3.000
 0R7  H10  C3'  C2'  110.82  3.000
 0R7  H11  C3'  C4'  112.04  3.000
 0R7  H10  C3'  C4'  111.70  3.000
 0R7  C2'  C3'  C4'  100.96  3.000
 0R7  H13  C2'  H12  107.83  3.000
 0R7  H13  C2'  C3'  110.63  3.000
 0R7  H12  C2'  C3'  113.93  3.000
 0R7  H13  C2'  C1'  108.89  3.000
 0R7  H12  C2'  C1'  113.16  3.000
 0R7  C3'  C2'  C1'  102.28  3.000
 0R7  H15  C5'  H14  107.85  3.000
 0R7  H15  C5'  C4'  110.70  3.000
 0R7  H14  C5'  C4'  108.22  3.000
 0R7  H15  C5'  O5'  107.78  3.000
 0R7  H14  C5'  O5'  111.75  3.000
 0R7  C4'  C5'  O5'  110.52  3.000
 0R7  C    C01  C02  119.07  3.000
 0R7  C    C01  C3   120.63  3.000
 0R7  C02  C01  C3   120.30  3.000
 0R7  H16  C02  C03  119.83  3.000
 0R7  H16  C02  C01  119.73  3.000
 0R7  C03  C02  C01  120.44  3.000
 0R7  H17  C03  C04  119.79  3.000
 0R7  H17  C03  C02  119.75  3.000
 0R7  C04  C03  C02  120.46  3.000
 0R7  C7   C04  C05  120.43  3.000
 0R7  C05  C04  C03  119.14  3.000
 0R7  C7   C04  C03  120.43  3.000
 0R7  H18  C05  C    119.76  3.000
 0R7  H18  C05  C04  119.77  3.000
 0R7  C    C05  C04  120.47  3.000
 0R7  H19  C    C05  119.76  3.000
 0R7  H19  C    C01  119.82  3.000
 0R7  C05  C    C01  120.42  3.000
 0R7  C8   C7   C04  180.00  3.000
 0R7  H20  C8   C7   180.00  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
 0R7  CONST_01  C04  C03  C02  C01     0.00   0.0  0
 0R7  CONST_02  C04  C05  C    C01     0.00   0.0  0
 0R7  CONST_03  C05  C04  C03  C02     0.00   0.0  0
 0R7  CONST_04  C05  C    C01  C02     0.00   0.0  0
 0R7  CONST_05  C    C01  C02  C03     0.00   0.0  0
 0R7  CONST_06  C    C05  C04  C03     0.00   0.0  0
 0R7  CONST_07  N2   C2   N1   C1'   180.00   0.0  0
 0R7  CONST_08  C4   N2   C2   N1      0.00   0.0  0
 0R7  CONST_09  N2   C2   N1   C6      0.00   0.0  0
 0R7  CONST_10  C2   N2   C4   C5      0.00   0.0  0
 0R7  CONST_11  C03  C02  C01  C3    180.00   0.0  0
 0R7  CONST_12  C05  C    C01  C3    180.00   0.0  0
 0R7  CONST_13  C7   C04  C03  C02   180.00   0.0  0
 0R7  CONST_14  C7   C04  C05  C     180.00   0.0  0
 0R7  CONST_15  O2   C2   N1   C1'     0.00   0.0  0
 0R7  CONST_16  O2   C2   N1   C6    180.00   0.0  0
 0R7  CONST_17  O2   C2   N2   C4    180.00   0.0  0
 0R7  CONST_18  N3   C4   N2   C2    180.00   0.0  0
 0R7  CONST_19  H17  C03  C02  C01   180.00   0.0  0
 0R7  CONST_20  H18  C05  C    C01   180.00   0.0  0
 0R7  CONST_21  H19  C    C01  C02   180.00   0.0  0
 0R7  CONST_22  H16  C02  C03  C04   180.00   0.0  0
 0R7  CONST_23  H7   N3   C4   C5    180.00   0.0  0
 0R7  CONST_24  H8   N3   C4   C5      0.00   0.0  0
 0R7  Var_01    C4'  C3'  C2'  C1'    36.15  30.0  1
 0R7  Var_02    C4'  C5'  O5'  P1   -135.63  30.0  1
 0R7  Var_03    O9   P2   O1   P1     51.96  30.0  1
 0R7  Var_04    O7   P3   O3   P2    -57.59  30.0  1
 0R7  Var_05    O11  P1   O1   P2     28.92  30.0  1

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
 0R7  chir_03  C1'  O4'  C2'  N1   positiv
 0R7  chir_04  C4'  O4'  C3'  C5'  negativ
 0R7  chir_05  P1   O1   O5'  O10  both
 0R7  chir_06  P2   O8   O3   O9   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
 0R7  plan-1  C1'  0.020
 0R7  plan-1  N1   0.020
 0R7  plan-1  C6   0.020
 0R7  plan-1  C5   0.020
 0R7  plan-1  C1   0.020
 0R7  plan-1  C3   0.020
 0R7  plan-1  N2   0.020
 0R7  plan-1  C4   0.020
 0R7  plan-1  C2   0.020
 0R7  plan-1  O2   0.020
 0R7  plan-1  N3   0.020
 0R7  plan-1  H6   0.020
 0R7  plan-1  H7   0.020
 0R7  plan-1  H8   0.020
 0R7  plan-2  C1   0.020
 0R7  plan-2  C3   0.020
 0R7  plan-2  C01  0.020
 0R7  plan-2  C02  0.020
 0R7  plan-2  C03  0.020
 0R7  plan-2  C04  0.020
 0R7  plan-2  C05  0.020
 0R7  plan-2  C    0.020
 0R7  plan-2  C7   0.020
 0R7  plan-2  C8   0.020
 0R7  plan-2  H16  0.020
 0R7  plan-2  H17  0.020
 0R7  plan-2  H18  0.020
 0R7  plan-2  H19  0.020

