# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 09:23:29 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  44  27  .  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_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  -0.508  -3.4903  -0.1293  -1.5336
 7XL  C1   C  CR6    0   0.603  -3.9233   0.8011  -0.8686
 7XL  N1   N  N      0  -0.541  -4.4358   1.9154  -1.4270
 7XL  C2   C  CR6    0   0.515  -4.9055   2.8975  -0.6827
 7XL  N2   N  NH2    0  -0.808  -5.3991   3.9725  -1.2942
 7XL  C3   C  CR16   0  -0.477  -4.8958   2.8400   0.7449
 7XL  C4   C  CR16   0   0.102  -4.3711   1.7276   1.2928
 7XL  N3   N  NR6    0  -0.556  -3.8952   0.7106   0.5329
 7XL  C5   C  CH1    0   0.207  -3.2951  -0.4383   1.1910
 7XL  O2   O  O2     0  -0.491  -1.9213  -0.4635   0.9231
 7XL  C6   C  CH1    0  -0.045  -3.8752  -1.8177   0.8315
 7XL  O3   O  OH1    0  -0.678  -4.1682  -2.4835   2.0344
 7XL  C7   C  CH1    0  -0.034  -2.7159  -2.5173   0.0990
 7XL  O4   O  OH1    0  -0.665  -2.6194  -3.8840   0.4176
 7XL  C8   C  CH1    0   0.018  -1.4849  -1.7758   0.6176
 7XL  C9   C  CH2    0  -0.158  -0.3739  -1.7275  -0.4017
 7XL  O5   O  O2     0  -0.624   0.7495  -1.0732   0.1457
 7XL  P1   P  P      0   1.337   2.1960  -1.3318  -0.6106
 7XL  O6   O  O      0  -0.805   2.0659  -0.9715  -2.0580
 7XL  O7   O  OP    -1  -0.797   2.7106  -2.6817  -0.2145
 7XL  O8   O  O2     0  -0.750   2.9817  -0.1709   0.2286
 7XL  P2   P  P      0   1.275   4.2152   0.7596  -0.3924
 7XL  O9   O  O      0  -0.805   3.6217   1.9660  -1.0664
 7XL  O10  O  OP    -1  -0.811   5.1704  -0.1277  -1.1430
 7XL  C10  C  CH2    0  -0.738   4.9594   1.2673   1.2013
 7XL  C11  C  CH2    0  -0.147   6.1416   2.1910   0.9787
 7XL  O11  O  OH1    0  -0.677   6.6842   2.5580   2.2324
 7XL  H1   H  HNH2   0   0.403  -5.4035   4.0267  -2.2984
 7XL  H2   H  HNH2   0   0.414  -5.7727   4.7482  -0.7767
 7XL  H3   H  HCR6   0   0.289  -5.2766   3.6424   1.3582
 7XL  H4   H  HCR6   0   0.320  -4.3095   1.5966   2.3644
 7XL  H5   H  HCH1   0   0.251  -3.4719  -0.2760   2.2591
 7XL  H6   H  HCH1   0   0.245  -4.7700  -1.7366   0.2053
 7XL  H7   H  HOH1   0   0.447  -3.8971  -3.4043   1.9155
 7XL  H8   H  HCH1   0   0.259  -2.8222  -2.3700  -0.9763
 7XL  H9   H  HOH1   0   0.469  -3.1030  -4.3917  -0.2414
 7XL  H10  H  HCH1   0   0.229  -1.1248  -2.2747   1.5295
 7XL  H11  H  HCH2   0   0.209  -0.1453  -2.7630  -0.6844
 7XL  H12  H  HCH2   0   0.213  -0.7303  -1.2105  -1.2999
 7XL  H15  H  HCH2   0   0.239   4.2049   1.7746   1.8089
 7XL  H16  H  HCH2   0   0.238   5.2827   0.3803   1.7537
 7XL  H17  H  HCH2   0   0.191   6.8891   1.6805   0.3592
 7XL  H18  H  HCH2   0   0.191   5.8114   3.0734   0.4167
 7XL  H19  H  HOH1   0   0.449   7.4420   3.1277   2.0718

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  1.517  0.020  1.517
 7XL  C11  O11  single  1.415  0.020  1.415
 7XL  C10  P2   single  1.831  0.020  1.831
 7XL  O9   P2   deloc   1.504  0.020  1.504
 7XL  P2   O8   single  1.665  0.020  1.665
 7XL  P2   O10  deloc   1.504  0.020  1.504
 7XL  O8   P1   single  1.634  0.020  1.634
 7XL  O6   P1   deloc   1.497  0.020  1.497
 7XL  P1   O7   deloc   1.498  0.020  1.498
 7XL  P1   O5   single  1.653  0.020  1.653
 7XL  C9   O5   single  1.411  0.020  1.411
 7XL  C9   C8   single  1.508  0.020  1.508
 7XL  C8   C7   single  1.528  0.020  1.528
 7XL  C8   O2   single  1.416  0.020  1.416
 7XL  C7   O4   single  1.407  0.020  1.407
 7XL  C7   C6   single  1.539  0.020  1.539
 7XL  O2   C5   single  1.400  0.020  1.400
 7XL  C6   O3   single  1.406  0.020  1.406
 7XL  C6   C5   single  1.539  0.020  1.539
 7XL  C5   N3   single  1.454  0.020  1.454
 7XL  C4   N3   single  1.356  0.020  1.356
 7XL  C4   C3   double  1.347  0.020  1.347
 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  1.348  0.020  1.348
 7XL  C2   N1   double  1.319  0.020  1.319
 7XL  C2   N2   single  1.332  0.020  1.332
 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  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   118.31  3.000
 7XL  N1   C1   O1   122.57  3.000
 7XL  N3   C1   O1   119.11  3.000
 7XL  C2   N1   C1   121.16  3.000
 7XL  C3   C2   N2   119.59  3.000
 7XL  N2   C2   N1   118.30  3.000
 7XL  C3   C2   N1   122.11  3.000
 7XL  H2   N2   H1   118.11  3.000
 7XL  H2   N2   C2   121.65  3.000
 7XL  H1   N2   C2   120.24  3.000
 7XL  H3   C3   C4   121.36  3.000
 7XL  H3   C3   C2   122.38  3.000
 7XL  C4   C3   C2   116.26  3.000
 7XL  H4   C4   N3   116.40  3.000
 7XL  H4   C4   C3   121.70  3.000
 7XL  N3   C4   C3   121.90  3.000
 7XL  C5   N3   C4   118.95  3.000
 7XL  C4   N3   C1   120.26  3.000
 7XL  C5   N3   C1   120.72  3.000
 7XL  H5   C5   C6   107.45  3.000
 7XL  H5   C5   O2   110.36  3.000
 7XL  C6   C5   O2   108.01  3.000
 7XL  H5   C5   N3   104.94  3.000
 7XL  C6   C5   N3   116.55  3.000
 7XL  O2   C5   N3   109.44  3.000
 7XL  C8   O2   C5   111.12  3.000
 7XL  H6   C6   C7   112.14  3.000
 7XL  H6   C6   O3   110.73  3.000
 7XL  C7   C6   O3   110.42  3.000
 7XL  H6   C6   C5   112.04  3.000
 7XL  O3   C6   C5   107.65  3.000
 7XL  C7   C6   C5   103.57  3.000
 7XL  H7   O3   C6   106.70  3.000
 7XL  H8   C7   C8   110.35  3.000
 7XL  H8   C7   O4   111.18  3.000
 7XL  C8   C7   O4   109.84  3.000
 7XL  H8   C7   C6   109.53  3.000
 7XL  O4   C7   C6   112.67  3.000
 7XL  C8   C7   C6   102.98  3.000
 7XL  H9   O4   C7   108.84  3.000
 7XL  H10  C8   C9   109.48  3.000
 7XL  H10  C8   C7   108.97  3.000
 7XL  C9   C8   C7   112.31  3.000
 7XL  H10  C8   O2   110.01  3.000
 7XL  C7   C8   O2   105.94  3.000
 7XL  C9   C8   O2   110.06  3.000
 7XL  H12  C9   H11  107.56  3.000
 7XL  H12  C9   O5   110.99  3.000
 7XL  H11  C9   O5   111.82  3.000
 7XL  H12  C9   C8   109.23  3.000
 7XL  H11  C9   C8   107.29  3.000
 7XL  O5   C9   C8   109.83  3.000
 7XL  P1   O5   C9   116.54  3.000
 7XL  O8   P1   O7   109.83  3.000
 7XL  O7   P1   O6   120.15  3.000
 7XL  O8   P1   O6   111.55  3.000
 7XL  O7   P1   O5   108.71  3.000
 7XL  O6   P1   O5   109.19  3.000
 7XL  O8   P1   O5    94.28  3.000
 7XL  P2   O8   P1   124.18  3.000
 7XL  C10  P2   O10  109.86  3.000
 7XL  O10  P2   O9   120.01  3.000
 7XL  C10  P2   O9   109.16  3.000
 7XL  O10  P2   O8   109.07  3.000
 7XL  O9   P2   O8   108.85  3.000
 7XL  C10  P2   O8    97.55  3.000
 7XL  H16  C10  H15  107.43  3.000
 7XL  H16  C10  C11  109.73  3.000
 7XL  H15  C10  C11  109.68  3.000
 7XL  H16  C10  P2   109.57  3.000
 7XL  H15  C10  P2   109.38  3.000
 7XL  C11  C10  P2   110.97  3.000
 7XL  H18  C11  H17  106.87  3.000
 7XL  H18  C11  O11  111.15  3.000
 7XL  H17  C11  O11  111.09  3.000
 7XL  H18  C11  C10  109.30  3.000
 7XL  H17  C11  C10  109.31  3.000
 7XL  O11  C11  C10  109.08  3.000
 7XL  H19  O11  C11  107.94  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   170.00  30.0  1
 7XL  Var_02    C10  P2   O8   P1  -159.04  30.0  1
 7XL  Var_03    C11  C10  P2   O8  -178.64  30.0  2
 7XL  Var_04    O11  C11  C10  P2   179.97  30.0  2
 7XL  Var_05    H11  C9   O5   P1    42.33  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

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

