# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 12:18:33 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-(2-hydroxyethyl)phosphinic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)CCO)[C@@H](O)[C@H]2O
#
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
 7XL  7XL  '[[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-(2-hydroxyethyl)phosphinic acid'  ligand  46  27  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_7XL
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
 7XL  O1   O  O     0  -0.509  -3.4534  -0.0047  -1.5530
 7XL  C1   C  CR6   0   0.605  -3.8899   0.8745  -0.8232
 7XL  N1   N  N     0  -0.540  -4.4298   2.0127  -1.3006
 7XL  C2   C  CR6   0   0.516  -4.9060   2.9356  -0.4875
 7XL  N2   N  NH2   0  -0.807  -5.4298   4.0374  -1.0199
 7XL  C3   C  CR16  0  -0.476  -4.8718   2.7866   0.9335
 7XL  C4   C  CR16  0   0.102  -4.3183   1.6520   1.4007
 7XL  N3   N  NR6   0  -0.557  -3.8355   0.6955   0.5688
 7XL  C5   C  CR15  0   0.205  -3.2182  -0.4875   1.1412
 7XL  O2   O  O     0  -0.489  -1.8499  -0.4995   0.8315
 7XL  C6   C  CR15  0  -0.046  -3.8088  -1.8449   0.7197
 7XL  O3   O  OH1   0  -0.675  -4.0424  -2.5844   1.8911
 7XL  C7   C  CR15  0  -0.035  -2.6817  -2.4921  -0.1053
 7XL  O4   O  OH1   0  -0.663  -2.5740  -3.8765   0.1078
 7XL  C8   C  CR15  0   0.025  -1.4345  -1.7885   0.4327
 7XL  C9   C  CH2   0  -0.195  -0.3597  -1.6833  -0.6157
 7XL  O5   O  O2    0  -0.578   0.7855  -1.0200  -0.0535
 7XL  P1   P  P     0   1.469   2.2437  -1.4251  -0.5354
 7XL  O6   O  O     0  -0.690   2.4647  -1.5897  -1.9795
 7XL  O7   O  OH1   0  -0.723   2.6609  -2.7373   0.2573
 7XL  O8   O  O2    0  -0.691   3.0498  -0.2218   0.1752
 7XL  P2   P  P     0   1.382   4.3720   0.5634  -0.3923
 7XL  O9   O  O     0  -0.680   4.1400   1.3224  -1.6355
 7XL  O10  O  OH1   0  -0.741   5.4617  -0.5842  -0.6246
 7XL  C10  C  CH2   0  -0.768   4.8344   1.5111   1.0604
 7XL  C11  C  CH2   0  -0.141   6.1038   2.3205   0.8310
 7XL  O11  O  OH1   0  -0.666   6.3492   3.0548   2.0061
 7XL  H1   H  HNH2  0   0.404  -5.4505   4.1580  -2.0182
 7XL  H2   H  HNH2  0   0.415  -5.8068   4.7715  -0.4470
 7XL  H3   H  HCR6  0   0.290  -5.2571   3.5401   1.6034
 7XL  H4   H  HCR6  0   0.321  -4.2386   1.4526   2.4604
 7XL  H5   H  HCR5  0   0.256  -3.3581  -0.3869   2.2218
 7XL  H6   H  HCR5  0   0.249  -4.7304  -1.7295   0.1393
 7XL  H7   H  HOH1  0   0.448  -3.8053  -3.5014   1.6961
 7XL  H8   H  HCR5  0   0.266  -2.8254  -2.2633  -1.1613
 7XL  H9   H  HOH1  0   0.471  -3.0704  -4.3367  -0.5762
 7XL  H10  H  HCR5  0   0.244  -1.0567  -2.3522   1.2966
 7XL  H11  H  HCH2  0   0.253  -0.1120  -2.6922  -0.9564
 7XL  H12  H  HCH2  0   0.259  -0.7115  -1.1050  -1.4717
 7XL  H13  H  HOH1  0   0.503   2.5221  -2.7273   1.2147
 7XL  H14  H  HOH1  0   0.499   5.7404  -1.0837   0.1551
 7XL  H15  H  HCH2  0   0.303   3.9987   2.1777   1.2888
 7XL  H16  H  HCH2  0   0.299   4.9572   0.8340   1.9090
 7XL  H17  H  HCH2  0   0.211   6.9360   1.6457   0.5981
 7XL  H18  H  HCH2  0   0.214   5.9679   2.9776  -0.0357
 7XL  H19  H  HOH1  0   0.459   7.1643   3.5502   1.8831

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
 7XL  C11  C10  single  1.523  0.020  1.523
 7XL  C11  O11  single  1.407  0.020  1.407
 7XL  C10  P2   single  1.795  0.020  1.795
 7XL  O9   P2   double  1.475  0.020  1.475
 7XL  P2   O8   single  1.639  0.020  1.639
 7XL  P2   O10  single  1.599  0.020  1.599
 7XL  O8   P1   single  1.613  0.020  1.613
 7XL  O6   P1   double  1.470  0.020  1.470
 7XL  P1   O7   single  1.589  0.020  1.589
 7XL  P1   O5   single  1.588  0.020  1.588
 7XL  C9   O5   single  1.438  0.020  1.438
 7XL  C9   C8   single  1.505  0.020  1.505
 7XL  C8   C7   single  1.530  0.020  1.530
 7XL  C8   O2   single  1.412  0.020  1.412
 7XL  C7   O4   single  1.405  0.020  1.405
 7XL  C7   C6   single  1.539  0.020  1.539
 7XL  O2   C5   single  1.403  0.020  1.403
 7XL  C6   O3   single  1.405  0.020  1.405
 7XL  C6   C5   single  1.539  0.020  1.539
 7XL  C5   N3   single  1.452  0.020  1.452
 7XL  C4   N3   single  1.357  0.020  1.357
 7XL  C4   C3   double  1.346  0.020  1.346
 7XL  N3   C1   single  1.405  0.020  1.405
 7XL  C3   C2   single  1.429  0.020  1.429
 7XL  C1   O1   double  1.223  0.020  1.223
 7XL  C1   N1   single  1.347  0.020  1.347
 7XL  C2   N1   double  1.319  0.020  1.319
 7XL  C2   N2   single  1.331  0.020  1.331
 7XL  N2   H1   single  0.860  0.020  1.020
 7XL  N2   H2   single  0.860  0.020  1.020
 7XL  C3   H3   single  0.930  0.020  1.080
 7XL  C4   H4   single  0.930  0.020  1.080
 7XL  C5   H5   single  0.970  0.020  1.090
 7XL  C6   H6   single  0.970  0.020  1.090
 7XL  O3   H7   single  0.850  0.020  0.980
 7XL  C7   H8   single  0.970  0.020  1.090
 7XL  O4   H9   single  0.850  0.020  0.980
 7XL  C8   H10  single  0.970  0.020  1.090
 7XL  C9   H11  single  0.970  0.020  1.090
 7XL  C9   H12  single  0.970  0.020  1.090
 7XL  O7   H13  single  0.850  0.020  0.980
 7XL  O10  H14  single  0.850  0.020  0.980
 7XL  C10  H15  single  0.970  0.020  1.090
 7XL  C10  H16  single  0.970  0.020  1.090
 7XL  C11  H17  single  0.970  0.020  1.090
 7XL  C11  H18  single  0.970  0.020  1.090
 7XL  O11  H19  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
 7XL  N3   C1   N1   118.32  3.000
 7XL  N1   C1   O1   122.61  3.000
 7XL  N3   C1   O1   119.07  3.000
 7XL  C2   N1   C1   121.16  3.000
 7XL  C3   C2   N2   119.56  3.000
 7XL  N2   C2   N1   118.34  3.000
 7XL  C3   C2   N1   122.10  3.000
 7XL  H2   N2   H1   118.08  3.000
 7XL  H2   N2   C2   121.63  3.000
 7XL  H1   N2   C2   120.28  3.000
 7XL  H3   C3   C4   121.31  3.000
 7XL  H3   C3   C2   122.40  3.000
 7XL  C4   C3   C2   116.28  3.000
 7XL  H4   C4   N3   116.41  3.000
 7XL  H4   C4   C3   121.73  3.000
 7XL  N3   C4   C3   121.86  3.000
 7XL  C5   N3   C4   118.95  3.000
 7XL  C4   N3   C1   120.27  3.000
 7XL  C5   N3   C1   120.73  3.000
 7XL  H5   C5   C6   107.61  3.000
 7XL  H5   C5   O2   110.08  3.000
 7XL  C6   C5   O2   107.83  3.000
 7XL  H5   C5   N3   105.07  3.000
 7XL  C6   C5   N3   116.58  3.000
 7XL  O2   C5   N3   109.55  3.000
 7XL  C8   O2   C5   110.93  3.000
 7XL  H6   C6   C7   112.12  3.000
 7XL  H6   C6   O3   110.94  3.000
 7XL  C7   C6   O3   110.32  3.000
 7XL  H6   C6   C5   112.03  3.000
 7XL  O3   C6   C5   107.44  3.000
 7XL  C7   C6   C5   103.69  3.000
 7XL  H7   O3   C6   106.87  3.000
 7XL  H8   C7   C8   110.59  3.000
 7XL  H8   C7   O4   111.34  3.000
 7XL  C8   C7   O4   109.72  3.000
 7XL  H8   C7   C6   109.54  3.000
 7XL  O4   C7   C6   112.90  3.000
 7XL  C8   C7   C6   102.42  3.000
 7XL  H9   O4   C7   108.90  3.000
 7XL  H10  C8   C9   109.76  3.000
 7XL  H10  C8   C7   108.72  3.000
 7XL  C9   C8   C7   111.68  3.000
 7XL  H10  C8   O2   110.34  3.000
 7XL  C7   C8   O2   106.22  3.000
 7XL  C9   C8   O2   110.07  3.000
 7XL  H12  C9   H11  108.52  3.000
 7XL  H12  C9   O5   108.60  3.000
 7XL  H11  C9   O5   111.53  3.000
 7XL  H12  C9   C8   110.68  3.000
 7XL  H11  C9   C8   108.32  3.000
 7XL  O5   C9   C8   109.18  3.000
 7XL  P1   O5   C9   119.66  3.000
 7XL  O8   P1   O7   105.37  3.000
 7XL  O7   P1   O6   110.98  3.000
 7XL  O8   P1   O6   116.17  3.000
 7XL  O7   P1   O5   107.48  3.000
 7XL  O6   P1   O5   117.68  3.000
 7XL  O8   P1   O5    97.75  3.000
 7XL  H13  O7   P1   116.59  3.000
 7XL  P2   O8   P1   127.44  3.000
 7XL  C10  P2   O10  108.71  3.000
 7XL  O10  P2   O9   110.73  3.000
 7XL  C10  P2   O9   116.80  3.000
 7XL  O10  P2   O8   104.84  3.000
 7XL  O9   P2   O8   114.30  3.000
 7XL  C10  P2   O8   100.40  3.000
 7XL  H14  O10  P2   116.74  3.000
 7XL  H16  C10  H15  107.55  3.000
 7XL  H16  C10  C11  110.65  3.000
 7XL  H15  C10  C11  110.16  3.000
 7XL  H16  C10  P2   109.29  3.000
 7XL  H15  C10  P2   107.11  3.000
 7XL  C11  C10  P2   111.93  3.000
 7XL  H18  C11  H17  107.16  3.000
 7XL  H18  C11  O11  111.66  3.000
 7XL  H17  C11  O11  111.48  3.000
 7XL  H18  C11  C10  109.54  3.000
 7XL  H17  C11  C10  109.73  3.000
 7XL  O11  C11  C10  107.27  3.000
 7XL  H19  O11  C11  108.04  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
 7XL  CONST_01  C3   C2   N1   C1     0.00   0.0  0
 7XL  CONST_02  C5   N3   C1   N1   180.00   0.0  0
 7XL  CONST_03  C4   N3   C1   N1     0.00   0.0  0
 7XL  CONST_04  N3   C1   N1   C2     0.00   0.0  0
 7XL  CONST_05  C5   N3   C1   O1     0.00   0.0  0
 7XL  CONST_06  C4   N3   C1   O1   180.00   0.0  0
 7XL  CONST_07  C2   N1   C1   O1   180.00   0.0  0
 7XL  CONST_08  N2   C2   N1   C1   180.00   0.0  0
 7XL  CONST_09  H1   N2   C2   N1     0.00   0.0  0
 7XL  CONST_10  H2   N2   C2   N1   180.00   0.0  0
 7XL  Var_01    O8   P1   O5   C9   169.84  30.0  1
 7XL  Var_02    C10  P2   O8   P1  -170.03  30.0  1
 7XL  Var_03    C11  C10  P2   O8   177.77  30.0  1
 7XL  Var_04    O11  C11  C10  P2   178.05  30.0  1
 7XL  Var_05    H11  C9   O5   P1    27.09  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
 7XL  chir_01  C5  O2  C6   N3   positiv
 7XL  chir_02  C6  O3  C5   C7   negativ
 7XL  chir_03  C7  O4  C8   C6   positiv
 7XL  chir_04  C8  O2  C7   C9   negativ
 7XL  chir_05  P1  O6  O7   O5   both
 7XL  chir_06  P2  O8  O10  C10  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
 7XL  plan-1  O1  0.020
 7XL  plan-1  C1  0.020
 7XL  plan-1  N1  0.020
 7XL  plan-1  C2  0.020
 7XL  plan-1  N2  0.020
 7XL  plan-1  C3  0.020
 7XL  plan-1  C4  0.020
 7XL  plan-1  N3  0.020
 7XL  plan-1  C5  0.020
 7XL  plan-1  H1  0.020
 7XL  plan-1  H2  0.020
 7XL  plan-1  H3  0.020
 7XL  plan-1  H4  0.020

