# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jul  4 00:30:04 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: [[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-[[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]methyl]phosphinic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](C[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@H](O)[C@@H](O)[C@H]1O
#
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
 URM  URM  '[[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-[[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]methyl]phosphinic acid'  ligand  60  36  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_URM
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
 URM  C1    C  CH1    0   0.206   4.6992   0.3679   1.4468
 URM  C2    C  CH1    0  -0.048   5.6631   1.4240   0.8737
 URM  C3    C  CH1    0  -0.032   4.8077   2.1505  -0.1818
 URM  C4    C  CH1    0   0.012   3.3837   1.8954   0.3053
 URM  C5    C  CH2    0  -0.147   2.3684   1.8783  -0.8084
 URM  O6    O  O2     0  -0.488   3.4207   0.6330   0.9496
 URM  O7    O  OH1    0  -0.663   5.0542   3.5339  -0.2175
 URM  O8    O  O2     0  -0.625   1.0771   1.8008  -0.2509
 URM  P9    P  P      0   1.335  -0.1999   1.5772  -1.2775
 URM  O10   O  OP    -1  -0.798  -0.3821   0.1114  -1.5294
 URM  O11   O  O      0  -0.807  -0.0561   2.5229  -2.4314
 URM  O12   O  O2     0  -0.748  -1.2959   2.1232  -0.2023
 URM  N13   N  NR6    0  -0.569   5.0390  -1.0250   1.1837
 URM  N15   N  NR16   0  -0.734   5.4701  -2.7991  -0.2422
 URM  C17   C  CR16   0  -0.513   5.4417  -3.1976   2.0873
 URM  C18   C  CR16   0   0.104   5.1565  -1.8942   2.2319
 URM  C19   C  CR6    0   0.747   5.1854  -1.4655  -0.1165
 URM  O19   O  O      0  -0.468   5.0794  -0.7351  -1.0777
 URM  C20   C  CR6    0   0.568   5.6247  -3.7408   0.7644
 URM  O20   O  O      0  -0.463   5.8864  -4.8979   0.4941
 URM  O21   O  OH1    0  -0.674   6.0025   2.3001   1.9169
 URM  P22   P  P      0   1.306  -2.9430   1.8375  -0.2742
 URM  O23   O  OP    -1  -0.806  -3.5332   2.8477   0.6731
 URM  O24   O  O      0  -0.791  -3.3510   1.8077  -1.7180
 URM  O36   O  O2     0  -0.496  -5.4720   0.0570   0.2175
 URM  C37   C  CH1    0   0.019  -5.5282  -0.8802  -0.8353
 URM  C38   C  CH1    0  -0.034  -5.6596  -2.3100  -0.2957
 URM  C39   C  CH1    0   0.004  -4.5166  -2.5770   0.6814
 URM  C40   C  CH1    0   0.040  -4.4901  -1.5018   1.7591
 URM  C41   C  CH1    0  -0.012  -4.3916  -0.1120   1.1144
 URM  O42   O  OH1    0  -0.673  -6.8784  -2.5234   0.3807
 URM  O43   O  OH1    0  -0.675  -4.6239  -3.8253   1.3243
 URM  O44   O  OH1    0  -0.678  -3.4062  -1.6665   2.6414
 URM  C45   C  CH2    0  -0.781  -3.0303   0.1764   0.4899
 URM  H1    H  HCH1   0   0.261   4.7173   0.4547   2.5373
 URM  H2    H  HCH1   0   0.250   6.5607   0.9696   0.4407
 URM  H3    H  HCH1   0   0.259   4.9668   1.6981  -1.1618
 URM  H4    H  HCH1   0   0.233   3.1154   2.6779   1.0302
 URM  H5    H  HCH2   0   0.213   2.4917   2.7940  -1.3979
 URM  H5A   H  HCH2   0   0.206   2.5822   1.0307  -1.4725
 URM  HO7   H  HOH1   0   0.470   5.7323   3.7132  -0.8764
 URM  H17   H  HCR6   0   0.294   5.5287  -3.8409   2.9488
 URM  H18   H  HCR6   0   0.329   5.0054  -1.4603   3.2102
 URM  HO21  H  HOH1   0   0.448   6.0030   3.1923   1.5426
 URM  H38   H  HCH1   0   0.230  -5.5619  -2.9998  -1.1469
 URM  H39   H  HCH1   0   0.219  -3.5793  -2.5220   0.1093
 URM  H40   H  HCH1   0   0.218  -5.4402  -1.5400   2.3134
 URM  H41   H  HCH1   0   0.241  -4.5570   0.6356   1.8946
 URM  HO42  H  HOH1   0   0.455  -7.5620  -2.7181  -0.2658
 URM  HO43  H  HOH1   0   0.454  -4.4022  -4.5173   0.6938
 URM  HO44  H  HOH1   0   0.448  -3.4470  -2.5622   2.9925
 URM  H45   H  HCH2   0   0.247  -2.7357  -0.5666  -0.2530
 URM  H45A  H  HCH2   0   0.257  -2.2829   0.1241   1.2834
 URM  HO47  H  HOH1   0   0.450  -7.2464   0.8865  -2.9089
 URM  HN15  H  HNR6   0   0.427   5.5857  -3.1251  -1.1942
 URM  C46   C  CH2    0  -0.175  -6.7048  -0.5310  -1.7228
 URM  O47   O  OH1    0  -0.657  -6.4685   0.6890  -2.3798
 URM  H46   H  HCH2   0   0.197  -6.8362  -1.3539  -2.4402
 URM  H46A  H  HCH2   0   0.193  -7.6172  -0.4867  -1.1141
 URM  H37   H  HCH1   0   0.217  -4.6147  -0.8325  -1.4457

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
 URM  N13  C1    single  1.458  0.020  1.458
 URM  C1   O6    single  1.397  0.020  1.397
 URM  C1   C2    single  1.540  0.020  1.540
 URM  C1   H1    single  0.970  0.020  1.090
 URM  O21  C2    single  1.404  0.020  1.404
 URM  C2   C3    single  1.541  0.020  1.541
 URM  C2   H2    single  0.970  0.020  1.090
 URM  C4   C3    single  1.526  0.020  1.526
 URM  C3   O7    single  1.406  0.020  1.406
 URM  C3   H3    single  0.970  0.020  1.090
 URM  O6   C4    single  1.418  0.020  1.418
 URM  C4   C5    single  1.507  0.020  1.507
 URM  C4   H4    single  0.970  0.020  1.090
 URM  O8   C5    single  1.409  0.020  1.409
 URM  C5   H5    single  0.970  0.020  1.090
 URM  C5   H5A   single  0.970  0.020  1.090
 URM  O7   HO7   single  0.850  0.020  0.980
 URM  O8   P9    single  1.654  0.020  1.654
 URM  O11  P9    deloc   1.499  0.020  1.499
 URM  O12  P9    single  1.629  0.020  1.629
 URM  P9   O10   deloc   1.498  0.020  1.498
 URM  O12  P22   single  1.673  0.020  1.673
 URM  C19  N13   single  1.381  0.020  1.381
 URM  N13  C18   single  1.367  0.020  1.367
 URM  N15  C19   single  1.369  0.020  1.369
 URM  N15  C20   single  1.387  0.020  1.387
 URM  C20  C17   single  1.442  0.020  1.442
 URM  C17  C18   double  1.342  0.020  1.342
 URM  C17  H17   single  0.930  0.020  1.080
 URM  C18  H18   single  0.930  0.020  1.080
 URM  O19  C19   double  1.212  0.020  1.212
 URM  O20  C20   double  1.217  0.020  1.217
 URM  O21  HO21  single  0.850  0.020  0.980
 URM  O24  P22   deloc   1.501  0.020  1.501
 URM  P22  O23   deloc   1.505  0.020  1.505
 URM  P22  C45   single  1.830  0.020  1.830
 URM  O36  C41   single  1.414  0.020  1.414
 URM  O36  C37   single  1.411  0.020  1.411
 URM  C46  C37   single  1.515  0.020  1.515
 URM  C37  C38   single  1.534  0.020  1.534
 URM  C37  H37   single  0.970  0.020  1.090
 URM  C38  O42   single  1.410  0.020  1.410
 URM  C38  C39   single  1.527  0.020  1.527
 URM  C38  H38   single  0.970  0.020  1.090
 URM  C40  C39   single  1.523  0.020  1.523
 URM  C39  O43   single  1.408  0.020  1.408
 URM  C39  H39   single  0.970  0.020  1.090
 URM  C41  C40   single  1.535  0.020  1.535
 URM  C40  O44   single  1.407  0.020  1.407
 URM  C40  H40   single  0.970  0.020  1.090
 URM  C45  C41   single  1.525  0.020  1.525
 URM  C41  H41   single  0.970  0.020  1.090
 URM  O42  HO42  single  0.850  0.020  0.980
 URM  O43  HO43  single  0.850  0.020  0.980
 URM  O44  HO44  single  0.850  0.020  0.980
 URM  C45  H45   single  0.970  0.020  1.090
 URM  C45  H45A  single  0.970  0.020  1.090
 URM  C46  O47   single  1.406  0.020  1.406
 URM  C46  H46   single  0.970  0.020  1.090
 URM  C46  H46A  single  0.970  0.020  1.090
 URM  O47  HO47  single  0.850  0.020  0.980
 URM  N15  HN15  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
 URM  H1    C1   N13  104.59  3.000
 URM  H1    C1   O6   110.78  3.000
 URM  N13   C1   O6   109.29  3.000
 URM  H1    C1   C2   107.82  3.000
 URM  O6    C1   C2   108.07  3.000
 URM  N13   C1   C2   116.24  3.000
 URM  H2    C2   O21  110.76  3.000
 URM  H2    C2   C3   112.32  3.000
 URM  O21   C2   C3   110.43  3.000
 URM  H2    C2   C1   112.05  3.000
 URM  C3    C2   C1   103.34  3.000
 URM  O21   C2   C1   107.62  3.000
 URM  H3    C3   O7   111.09  3.000
 URM  H3    C3   C4   110.69  3.000
 URM  O7    C3   C4   109.64  3.000
 URM  H3    C3   C2   109.81  3.000
 URM  O7    C3   C2   112.59  3.000
 URM  C4    C3   C2   102.74  3.000
 URM  H4    C4   O6   109.89  3.000
 URM  H4    C4   C5   109.32  3.000
 URM  O6    C4   C5   110.07  3.000
 URM  H4    C4   C3   108.60  3.000
 URM  C5    C4   C3   113.24  3.000
 URM  O6    C4   C3   105.63  3.000
 URM  H5A   C5   H5   107.32  3.000
 URM  H5A   C5   O8   112.05  3.000
 URM  H5    C5   O8   111.22  3.000
 URM  H5A   C5   C4   108.94  3.000
 URM  H5    C5   C4   108.19  3.000
 URM  O8    C5   C4   109.01  3.000
 URM  C4    O6   C1   110.76  3.000
 URM  HO7   O7   C3   108.92  3.000
 URM  P9    O8   C5   118.02  3.000
 URM  O12   P9   O11  111.17  3.000
 URM  O12   P9   O10  110.91  3.000
 URM  O11   P9   O10  119.96  3.000
 URM  O10   P9   O8   109.30  3.000
 URM  O12   P9   O8    93.70  3.000
 URM  O11   P9   O8   108.57  3.000
 URM  P22   O12  P9   125.21  3.000
 URM  C19   N13  C18  120.68  3.000
 URM  C18   N13  C1   119.29  3.000
 URM  C19   N13  C1   119.97  3.000
 URM  HN15  N15  C20  116.80  3.000
 URM  HN15  N15  C19  115.05  3.000
 URM  C20   N15  C19  128.15  3.000
 URM  H17   C17  C20  119.86  3.000
 URM  H17   C17  C18  120.68  3.000
 URM  C20   C17  C18  119.46  3.000
 URM  H18   C18  C17  121.14  3.000
 URM  H18   C18  N13  115.27  3.000
 URM  C17   C18  N13  123.59  3.000
 URM  O19   C19  N15  122.17  3.000
 URM  O19   C19  N13  123.05  3.000
 URM  N15   C19  N13  114.78  3.000
 URM  O20   C20  C17  126.12  3.000
 URM  O20   C20  N15  120.56  3.000
 URM  C17   C20  N15  113.33  3.000
 URM  HO21  O21  C2   106.75  3.000
 URM  C45   P22  O24  111.75  3.000
 URM  C45   P22  O23  109.12  3.000
 URM  O24   P22  O23  120.81  3.000
 URM  C45   P22  O12  100.60  3.000
 URM  O23   P22  O12  104.14  3.000
 URM  O24   P22  O12  108.20  3.000
 URM  C41   O36  C37  115.11  3.000
 URM  H37   C37  C46  108.06  3.000
 URM  H37   C37  C38  107.88  3.000
 URM  C46   C37  C38  110.76  3.000
 URM  H37   C37  O36  110.63  3.000
 URM  C38   C37  O36  111.11  3.000
 URM  C46   C37  O36  108.36  3.000
 URM  H38   C38  O42  110.68  3.000
 URM  H38   C38  C39  108.60  3.000
 URM  O42   C38  C39  108.27  3.000
 URM  H38   C38  C37  107.74  3.000
 URM  C39   C38  C37  108.90  3.000
 URM  O42   C38  C37  112.57  3.000
 URM  H39   C39  O43  110.29  3.000
 URM  H39   C39  C40  108.55  3.000
 URM  O43   C39  C40  107.71  3.000
 URM  H39   C39  C38  107.24  3.000
 URM  O43   C39  C38  112.96  3.000
 URM  C40   C39  C38  110.02  3.000
 URM  H40   C40  O44  110.18  3.000
 URM  H40   C40  C41  107.36  3.000
 URM  O44   C40  C41  108.65  3.000
 URM  H40   C40  C39  108.47  3.000
 URM  O44   C40  C39  111.99  3.000
 URM  C41   C40  C39  110.07  3.000
 URM  H41   C41  C45  107.34  3.000
 URM  H41   C41  C40  108.04  3.000
 URM  C45   C41  C40  113.60  3.000
 URM  H41   C41  O36  104.79  3.000
 URM  C45   C41  O36  113.55  3.000
 URM  C40   C41  O36  109.00  3.000
 URM  HO42  O42  C38  108.84  3.000
 URM  HO43  O43  C39  108.71  3.000
 URM  HO44  O44  C40  107.75  3.000
 URM  H45A  C45  H45  106.11  3.000
 URM  H45A  C45  C41  107.72  3.000
 URM  H45   C45  C41  113.01  3.000
 URM  H45A  C45  P22  108.32  3.000
 URM  H45   C45  P22  108.72  3.000
 URM  C41   C45  P22  112.65  3.000
 URM  H46A  C46  H46  107.02  3.000
 URM  H46A  C46  O47  111.34  3.000
 URM  H46   C46  O47  111.38  3.000
 URM  H46A  C46  C37  109.28  3.000
 URM  H46   C46  C37  107.61  3.000
 URM  O47   C46  C37  110.08  3.000
 URM  HO47  O47  C46  107.43  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
 URM  CONST_01  N15   C19  N13  C1   180.00   0.0  0
 URM  CONST_02  C20   N15  C19  N13    0.00   0.0  0
 URM  CONST_03  C18   N13  C19  N15    0.00   0.0  0
 URM  CONST_04  C19   N15  C20  C17    0.00   0.0  0
 URM  CONST_05  O19   C19  N13  C1     0.00   0.0  0
 URM  CONST_06  O19   C19  N13  C18  180.00   0.0  0
 URM  CONST_07  O20   C20  N15  C19  180.00   0.0  0
 URM  CONST_08  C20   N15  C19  O19  180.00   0.0  0
 URM  CONST_09  HN15  N15  C19  N13  180.00   0.0  0
 URM  Var_01    C41   C45  P22  O12  155.04  30.0  3
 URM  Var_02    O11   P9   O8   C5   -46.41  30.0  3
 URM  Var_03    O24   P22  O12  P9   -34.63  30.0  3
 URM  Var_04    H5    C5   O8   P9    68.31  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
 URM  chir_01  C1   N13  O6   C2   positiv
 URM  chir_02  C2   O21  C1   C3   negativ
 URM  chir_03  C3   O7   C4   C2   positiv
 URM  chir_04  C4   O6   C3   C5   negativ
 URM  chir_07  C37  O36  C46  C38  positiv
 URM  chir_08  C38  O42  C37  C39  negativ
 URM  chir_09  C39  O43  C38  C40  negativ
 URM  chir_10  C40  O44  C41  C39  negativ
 URM  chir_11  C41  O36  C45  C40  positiv

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
 URM  plan-1  C1    0.020
 URM  plan-1  N13   0.020
 URM  plan-1  N15   0.020
 URM  plan-1  C17   0.020
 URM  plan-1  C18   0.020
 URM  plan-1  C19   0.020
 URM  plan-1  O19   0.020
 URM  plan-1  C20   0.020
 URM  plan-1  O20   0.020
 URM  plan-1  H17   0.020
 URM  plan-1  H18   0.020
 URM  plan-1  HN15  0.020

