# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:45:24 2022
#   Inital geometry file: a 147 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-[[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)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
 660  660  '[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-[[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]methyl]phosphinic acid'  ligand  60  36  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_660
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
 660  C1   C  CH1    0   0.212  -3.9292   0.6928  -1.0963
 660  C2   C  CH1    0  -0.044  -4.7230   0.7596   0.2067
 660  C3   C  CH1    0  -0.035  -4.8888   2.2757   0.3643
 660  C4   C  CH1    0  -0.037  -3.5292   2.7645  -0.1154
 660  C5   C  CH2    0  -0.155  -2.5357   2.8629   1.0300
 660  O6   O  O2     0  -0.488  -3.0934   1.8104  -1.0900
 660  O7   O  OH1    0  -0.668  -5.8843   2.7630  -0.4975
 660  O8   O  O2     0  -0.620  -1.2475   3.0499   0.5027
 660  P9   P  P      0   1.354   0.0389   2.4738   1.3678
 660  O10  O  OP    -1  -0.791  -0.2085   1.0305   1.7086
 660  O11  O  O      0  -0.795   0.3569   3.4462   2.4610
 660  O12  O  O2     0  -0.747   1.0814   2.6203   0.1272
 660  N13  N  NR6    0  -0.569  -3.1170  -0.5096  -1.2453
 660  N15  N  NR16   0  -0.732  -2.6816  -2.5550  -2.2384
 660  C17  C  CR16   0  -0.510  -1.1573  -1.7219  -0.6410
 660  C18  C  CR16   0   0.079  -1.9626  -0.6544  -0.5260
 660  C19  C  CR6    0   0.734  -3.5241  -1.4779  -2.1413
 660  O19  O  O      0  -0.478  -4.5409  -1.3982  -2.7986
 660  C20  C  CR6    0   0.578  -1.4926  -2.7748  -1.5627
 660  O20  O  O      0  -0.473  -0.8394  -3.7826  -1.7775
 660  O21  O  OH1    0  -0.653  -5.9160   0.0463   0.0768
 660  P22  P  P      0   1.307   2.5995   1.9122   0.0557
 660  O23  O  OP    -1  -0.803   3.2716   2.5938  -1.1044
 660  O24  O  O      0  -0.790   3.1922   1.9608   1.4337
 660  O36  O  O2     0  -0.496   4.5241  -0.4901  -0.4241
 660  C37  C  CH1    0   0.002   4.5567  -1.1406   0.8276
 660  C38  C  CH1    0   0.005   4.2119  -2.6298   0.6688
 660  C39  C  CH1    0  -0.031   2.9077  -2.8016  -0.0952
 660  C40  C  CH1    0   0.056   2.9651  -2.0185  -1.3984
 660  C41  C  CH1    0  -0.013   3.2888  -0.5468  -1.1095
 660  O42  O  OH1    0  -0.674   4.0549  -3.2674   1.9194
 660  O43  O  OH1    0  -0.673   2.6623  -4.1513  -0.4216
 660  O44  O  OH1    0  -0.678   1.7680  -2.0979  -2.1265
 660  C45  C  CH2    0  -0.783   2.1557   0.1990  -0.4118
 660  H1   H  HCH1   0   0.269  -4.6120   0.7102  -1.9485
 660  H2   H  HCH1   0   0.249  -4.1151   0.3751   1.0362
 660  H3   H  HCH1   0   0.252  -5.0793   2.5619   1.4074
 660  H4   H  HCH1   0   0.261  -3.6116   3.7367  -0.6107
 660  H5   H  HCH2   0   0.229  -2.8344   3.7055   1.6655
 660  H6   H  HCH2   0   0.203  -2.5882   1.9633   1.6544
 660  H7   H  HOH1   0   0.449  -6.6609   2.1989  -0.4018
 660  H9   H  HNR6   0   0.425  -2.9722  -3.2689  -2.8952
 660  H10  H  HCR6   0   0.283  -0.2501  -1.7773  -0.0625
 660  H11  H  HCR6   0   0.344  -1.6900   0.1483   0.1462
 660  H12  H  HOH1   0   0.469  -6.2708  -0.1275   0.9546
 660  H15  H  HCH1   0   0.213   5.0095  -3.1107   0.0826
 660  H16  H  HCH1   0   0.216   2.0886  -2.4078   0.5250
 660  H17  H  HCH1   0   0.209   3.8009  -2.4256  -1.9919
 660  H18  H  HCH1   0   0.242   3.4787  -0.0448  -2.0621
 660  H19  H  HOH1   0   0.458   4.9097  -3.5850   2.2221
 660  H20  H  HOH1   0   0.454   2.4172  -4.6172   0.3833
 660  H21  H  HOH1   0   0.449   1.3785  -2.9708  -1.9969
 660  H22  H  HCH2   0   0.245   1.7956  -0.3122   0.4815
 660  H23  H  HCH2   0   0.263   1.3070   0.2285  -1.0961
 660  H26  H  HOH1   0   0.451   7.1341   0.4026   1.9973
 660  C46  C  CH2    0  -0.160   5.9589  -0.9923   1.3820
 660  O47  O  OH1    0  -0.658   6.2498   0.3604   1.6228
 660  H24  H  HCH2   0   0.189   6.0242  -1.5843   2.3038
 660  H25  H  HCH2   0   0.190   6.6648  -1.4407   0.6674
 660  H14  H  HCH1   0   0.220   3.8456  -0.6770   1.5247

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
 660  O24  P22  deloc   1.501  0.020  1.501
 660  O36  C41  single  1.414  0.020  1.414
 660  O36  C37  single  1.411  0.020  1.411
 660  C41  C40  single  1.534  0.020  1.534
 660  C41  C45  single  1.525  0.020  1.525
 660  C40  O44  single  1.403  0.020  1.403
 660  C40  C39  single  1.521  0.020  1.521
 660  P22  O23  deloc   1.504  0.020  1.504
 660  P22  C45  single  1.830  0.020  1.830
 660  P22  O12  single  1.677  0.020  1.677
 660  O47  C46  single  1.404  0.020  1.404
 660  C46  C37  single  1.515  0.020  1.515
 660  C37  C38  single  1.537  0.020  1.537
 660  O12  P9   single  1.627  0.020  1.627
 660  C38  C39  single  1.521  0.020  1.521
 660  C38  O42  single  1.412  0.020  1.412
 660  C39  O43  single  1.410  0.020  1.410
 660  P9   O11  deloc   1.497  0.020  1.497
 660  P9   O10  deloc   1.504  0.020  1.504
 660  P9   O8   single  1.654  0.020  1.654
 660  O8   C5   single  1.404  0.020  1.404
 660  C5   C4   single  1.519  0.020  1.519
 660  C4   C3   single  1.522  0.020  1.522
 660  C4   O6   single  1.432  0.020  1.432
 660  C3   O7   single  1.404  0.020  1.404
 660  C3   C2   single  1.533  0.020  1.533
 660  O6   C1   single  1.396  0.020  1.396
 660  C2   C1   single  1.527  0.020  1.527
 660  C2   O21  single  1.396  0.020  1.396
 660  C18  C17  double  1.342  0.020  1.342
 660  C18  N13  single  1.368  0.020  1.368
 660  C1   N13  single  1.459  0.020  1.459
 660  C17  C20  single  1.439  0.020  1.439
 660  N13  C19  single  1.381  0.020  1.381
 660  C20  O20  double  1.220  0.020  1.220
 660  C20  N15  single  1.385  0.020  1.385
 660  C19  N15  single  1.371  0.020  1.371
 660  C19  O19  double  1.213  0.020  1.213
 660  C1   H1   single  0.970  0.020  1.090
 660  C2   H2   single  0.970  0.020  1.090
 660  C3   H3   single  0.970  0.020  1.090
 660  C4   H4   single  0.970  0.020  1.090
 660  C5   H5   single  0.970  0.020  1.090
 660  C5   H6   single  0.970  0.020  1.090
 660  O7   H7   single  0.850  0.020  0.980
 660  N15  H9   single  0.860  0.020  1.020
 660  C17  H10  single  0.930  0.020  1.080
 660  C18  H11  single  0.930  0.020  1.080
 660  O21  H12  single  0.850  0.020  0.980
 660  C37  H14  single  0.970  0.020  1.090
 660  C38  H15  single  0.970  0.020  1.090
 660  C39  H16  single  0.970  0.020  1.090
 660  C40  H17  single  0.970  0.020  1.090
 660  C41  H18  single  0.970  0.020  1.090
 660  O42  H19  single  0.850  0.020  0.980
 660  O43  H20  single  0.850  0.020  0.980
 660  O44  H21  single  0.850  0.020  0.980
 660  C45  H22  single  0.970  0.020  1.090
 660  C45  H23  single  0.970  0.020  1.090
 660  C46  H24  single  0.970  0.020  1.090
 660  C46  H25  single  0.970  0.020  1.090
 660  O47  H26  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
 660  H1   C1   N13  106.36  3.000
 660  H1   C1   O6   111.42  3.000
 660  N13  C1   O6   109.09  3.000
 660  H1   C1   C2   109.89  3.000
 660  N13  C1   C2   114.37  3.000
 660  O6   C1   C2   105.81  3.000
 660  H2   C2   O21  111.38  3.000
 660  H2   C2   C3   109.18  3.000
 660  O21  C2   C3   114.98  3.000
 660  H2   C2   C1   109.97  3.000
 660  O21  C2   C1   110.02  3.000
 660  C3   C2   C1   100.79  3.000
 660  H3   C3   O7   111.69  3.000
 660  H3   C3   C4   111.75  3.000
 660  O7   C3   C4   109.17  3.000
 660  H3   C3   C2   111.97  3.000
 660  O7   C3   C2   110.91  3.000
 660  C4   C3   C2   100.86  3.000
 660  H4   C4   O6   107.88  3.000
 660  H4   C4   C5   109.44  3.000
 660  O6   C4   C5   110.93  3.000
 660  H4   C4   C3   111.14  3.000
 660  O6   C4   C3   105.81  3.000
 660  C5   C4   C3   111.54  3.000
 660  H6   C5   H5   106.70  3.000
 660  H6   C5   O8   111.53  3.000
 660  H5   C5   O8   111.41  3.000
 660  H6   C5   C4   110.18  3.000
 660  H5   C5   C4   107.97  3.000
 660  O8   C5   C4   108.99  3.000
 660  C4   O6   C1   110.76  3.000
 660  H7   O7   C3   107.88  3.000
 660  P9   O8   C5   118.08  3.000
 660  O12  P9   O11  111.23  3.000
 660  O11  P9   O10  119.54  3.000
 660  O12  P9   O10  111.39  3.000
 660  O10  P9   O8   108.96  3.000
 660  O11  P9   O8   108.72  3.000
 660  O12  P9   O8    93.91  3.000
 660  P22  O12  P9   125.07  3.000
 660  C19  N13  C18  121.05  3.000
 660  C19  N13  C1   118.70  3.000
 660  C18  N13  C1   120.23  3.000
 660  H9   N15  C20  116.80  3.000
 660  H9   N15  C19  115.05  3.000
 660  C20  N15  C19  128.14  3.000
 660  H10  C17  C20  120.17  3.000
 660  H10  C17  C18  120.01  3.000
 660  C20  C17  C18  119.80  3.000
 660  H11  C18  C17  119.48  3.000
 660  H11  C18  N13  117.44  3.000
 660  C17  C18  N13  123.06  3.000
 660  O19  C19  N15  121.88  3.000
 660  O19  C19  N13  123.54  3.000
 660  N15  C19  N13  114.57  3.000
 660  O20  C20  C17  126.33  3.000
 660  O20  C20  N15  120.32  3.000
 660  C17  C20  N15  113.35  3.000
 660  H12  O21  C2   108.81  3.000
 660  C45  P22  O24  111.13  3.000
 660  C45  P22  O23  109.60  3.000
 660  O24  P22  O23  121.14  3.000
 660  C45  P22  O12  100.76  3.000
 660  O23  P22  O12  104.25  3.000
 660  O24  P22  O12  107.74  3.000
 660  C41  O36  C37  115.58  3.000
 660  H14  C37  C46  109.00  3.000
 660  H14  C37  C38  109.23  3.000
 660  C46  C37  C38  109.89  3.000
 660  H14  C37  O36  110.70  3.000
 660  C38  C37  O36  110.48  3.000
 660  C46  C37  O36  107.51  3.000
 660  H15  C38  O42  110.79  3.000
 660  H15  C38  C39  107.73  3.000
 660  O42  C38  C39  107.36  3.000
 660  H15  C38  C37  108.41  3.000
 660  O42  C38  C37  111.77  3.000
 660  C39  C38  C37  110.71  3.000
 660  H16  C39  O43  110.09  3.000
 660  H16  C39  C40  109.06  3.000
 660  O43  C39  C40  107.51  3.000
 660  H16  C39  C38  108.35  3.000
 660  O43  C39  C38  111.94  3.000
 660  C40  C39  C38  109.86  3.000
 660  H17  C40  O44  110.27  3.000
 660  H17  C40  C41  107.18  3.000
 660  O44  C40  C41  109.38  3.000
 660  H17  C40  C39  107.43  3.000
 660  O44  C40  C39  112.53  3.000
 660  C41  C40  C39  109.90  3.000
 660  H18  C41  C45  107.64  3.000
 660  H18  C41  C40  108.24  3.000
 660  C45  C41  C40  113.47  3.000
 660  H18  C41  O36  104.61  3.000
 660  C45  C41  O36  114.06  3.000
 660  C40  C41  O36  108.30  3.000
 660  H19  O42  C38  109.22  3.000
 660  H20  O43  C39  108.31  3.000
 660  H21  O44  C40  109.01  3.000
 660  H23  C45  H22  105.65  3.000
 660  H23  C45  C41  107.72  3.000
 660  H22  C45  C41  113.01  3.000
 660  H23  C45  P22  108.88  3.000
 660  H22  C45  P22  108.04  3.000
 660  C41  C45  P22  113.22  3.000
 660  H25  C46  H24  106.72  3.000
 660  H25  C46  O47  111.78  3.000
 660  H24  C46  O47  111.30  3.000
 660  H25  C46  C37  108.44  3.000
 660  H24  C46  C37  108.04  3.000
 660  O47  C46  C37  110.41  3.000
 660  H26  O47  C46  107.44  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
 660  CONST_01  N15  C19  N13  C1   180.00   0.0  0
 660  CONST_02  C20  N15  C19  N13    0.00   0.0  0
 660  CONST_03  C18  N13  C19  N15    0.00   0.0  0
 660  CONST_04  C19  N15  C20  C17    0.00   0.0  0
 660  CONST_05  O19  C19  N13  C1     0.00   0.0  0
 660  CONST_06  O19  C19  N13  C18  180.00   0.0  0
 660  CONST_07  O20  C20  N15  C19  180.00   0.0  0
 660  CONST_08  C20  N15  C19  O19  180.00   0.0  0
 660  CONST_09  H9   N15  C19  N13  180.00   0.0  0
 660  Var_01    C41  C45  P22  O12  156.03  30.0  3
 660  Var_02    O12  P9   O8   C5   165.93  30.0  1
 660  Var_03    O24  P22  O12  P9   -37.40  30.0  2
 660  Var_04    H5   C5   O8   P9    90.32  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
 660  chir_01  C1   O6   C2   N13  positiv
 660  chir_02  C2   O21  C1   C3   negativ
 660  chir_03  C3   O7   C4   C2   positiv
 660  chir_04  C4   O6   C3   C5   negativ
 660  chir_07  C37  O36  C46  C38  positiv
 660  chir_08  C38  O42  C37  C39  positiv
 660  chir_09  C39  O43  C38  C40  negativ
 660  chir_10  C40  O44  C41  C39  negativ
 660  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
 660  plan-1  C1   0.020
 660  plan-1  N13  0.020
 660  plan-1  N15  0.020
 660  plan-1  C17  0.020
 660  plan-1  C18  0.020
 660  plan-1  C19  0.020
 660  plan-1  O19  0.020
 660  plan-1  C20  0.020
 660  plan-1  O20  0.020
 660  plan-1  H9   0.020
 660  plan-1  H10  0.020
 660  plan-1  H11  0.020

