# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 05:37:40 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: (2~{S},3~{S},4~{S},5~{R},6~{R})-6-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4,5-tris(oxidanyl)oxane-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@@H]2O[C@@H]([C@@H](O)[C@H](O)[C@H]2O)C(O)=O
#
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
 7QO  7QO  "(2~{S},3~{S},4~{S},5~{R},6~{R})-6-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4,5-tris(oxidanyl)oxane-2-carboxylic acid"  ligand  32  20  .  2022-09-16  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7QO
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
 7QO  C01  C  CH1    0  -0.160  -0.3813  20.1985  -64.8794
 7QO  C02  C  CH1    0   0.038   0.2326  21.2959  -65.7696
 7QO  C03  C  CH1    0   0.021   1.6843  21.5053  -65.3710
 7QO  C04  C  CH1    0  -0.027   2.4236  20.1729  -65.4254
 7QO  C05  C  CH1    0   0.170   1.6840  19.1595  -64.5457
 7QO  C11  C  CR6    0   0.589   2.8557  17.2878  -63.4164
 7QO  C13  C  CR6    0   0.514   3.4340  15.4037  -64.6510
 7QO  C14  C  CR16   0  -0.472   2.8728  15.9409  -65.8511
 7QO  C15  C  CR16   0   0.099   2.3210  17.1648  -65.7561
 7QO  C18  C  C      0   0.441  -1.8566  19.9232  -65.2432
 7QO  N10  N  NR6    0  -0.566   2.3084  17.8524  -64.5865
 7QO  N12  N  N      0  -0.539   3.4118  16.0618  -63.5096
 7QO  N16  N  NH2    0  -0.807   3.9988  14.1973  -64.6733
 7QO  O06  O  O2     0  -0.482   0.3607  19.0013  -64.9703
 7QO  O07  O  OH1    0  -0.698  -0.4707  22.4963  -65.6318
 7QO  O08  O  OH1    0  -0.663   3.7336  20.3797  -64.9587
 7QO  O09  O  OH1    0  -0.664   2.2622  22.4512  -66.2327
 7QO  O17  O  O      0  -0.505   2.8120  17.9127  -62.3670
 7QO  O19  O  O      0  -0.610  -2.5375  20.9625  -65.4554
 7QO  O20  O  OC    -1  -0.550  -2.2520  18.7581  -65.2779
 7QO  H1   H  HCH1   0   0.226  -0.3612  20.5682  -63.8388
 7QO  H2   H  HCH1   0   0.189   0.2141  20.9321  -66.8129
 7QO  H3   H  HCH1   0   0.201   1.7000  21.8608  -64.3262
 7QO  H4   H  HCH1   0   0.232   2.4211  19.8261  -66.4691
 7QO  H5   H  HCH1   0   0.262   1.7298  19.4988  -63.5055
 7QO  H6   H  HCR6   0   0.286   2.8824  15.3993  -66.7851
 7QO  H7   H  HCR6   0   0.319   1.8649  17.6428  -66.6119
 7QO  H8   H  HNH2   0   0.402   4.3960  13.8099  -63.8341
 7QO  H9   H  HNH2   0   0.414   4.0404  13.6490  -65.5147
 7QO  H10  H  HOH1   0   0.437  -1.4107  22.1945  -65.5875
 7QO  H11  H  HOH1   0   0.461   4.3127  19.7086  -65.3320
 7QO  H12  H  HOH1   0   0.446   3.1836  22.5617  -65.9754

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
 7QO  O09  C03  single  1.404  0.020  1.404
 7QO  O19  C18  deloc   1.260  0.020  1.260
 7QO  C02  O07  single  1.398  0.020  1.398
 7QO  C02  C03  single  1.520  0.020  1.520
 7QO  C02  C01  single  1.541  0.020  1.541
 7QO  C14  C15  double  1.346  0.020  1.346
 7QO  C14  C13  single  1.430  0.020  1.430
 7QO  O20  C18  deloc   1.231  0.020  1.231
 7QO  C15  N10  single  1.357  0.020  1.357
 7QO  C18  C01  single  1.544  0.020  1.544
 7QO  C03  C04  single  1.525  0.020  1.525
 7QO  C04  O08  single  1.406  0.020  1.406
 7QO  C04  C05  single  1.532  0.020  1.532
 7QO  C01  O06  single  1.411  0.020  1.411
 7QO  O06  C05  single  1.399  0.020  1.399
 7QO  N16  C13  single  1.332  0.020  1.332
 7QO  C13  N12  double  1.318  0.020  1.318
 7QO  N10  C05  single  1.449  0.020  1.449
 7QO  N10  C11  single  1.410  0.020  1.410
 7QO  N12  C11  single  1.349  0.020  1.349
 7QO  C11  O17  double  1.222  0.020  1.222
 7QO  C01  H1   single  0.970  0.020  1.090
 7QO  C02  H2   single  0.970  0.020  1.090
 7QO  C03  H3   single  0.970  0.020  1.090
 7QO  C04  H4   single  0.970  0.020  1.090
 7QO  C05  H5   single  0.970  0.020  1.090
 7QO  C14  H6   single  0.930  0.020  1.080
 7QO  C15  H7   single  0.930  0.020  1.080
 7QO  N16  H8   single  0.860  0.020  1.020
 7QO  N16  H9   single  0.860  0.020  1.020
 7QO  O07  H10  single  0.850  0.020  0.980
 7QO  O08  H11  single  0.850  0.020  0.980
 7QO  O09  H12  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
 7QO  H1   C01  O06  109.57  3.000
 7QO  H1   C01  C18  107.39  3.000
 7QO  O06  C01  C18  109.62  3.000
 7QO  H1   C01  C02  107.38  3.000
 7QO  O06  C01  C02  110.95  3.000
 7QO  C18  C01  C02  111.81  3.000
 7QO  H2   C02  O07  111.55  3.000
 7QO  H2   C02  C03  107.99  3.000
 7QO  O07  C02  C03  109.65  3.000
 7QO  H2   C02  C01  107.72  3.000
 7QO  C03  C02  C01  109.09  3.000
 7QO  O07  C02  C01  110.75  3.000
 7QO  H3   C03  O09  110.98  3.000
 7QO  H3   C03  C04  107.96  3.000
 7QO  O09  C03  C04  111.55  3.000
 7QO  H3   C03  C02  107.83  3.000
 7QO  C04  C03  C02  109.47  3.000
 7QO  O09  C03  C02  108.97  3.000
 7QO  H4   C04  O08  111.31  3.000
 7QO  H4   C04  C05  109.58  3.000
 7QO  O08  C04  C05  110.88  3.000
 7QO  H4   C04  C03  107.96  3.000
 7QO  C05  C04  C03  108.87  3.000
 7QO  O08  C04  C03  108.14  3.000
 7QO  H5   C05  O06  111.28  3.000
 7QO  H5   C05  N10  106.75  3.000
 7QO  O06  C05  N10  107.28  3.000
 7QO  H5   C05  C04  108.68  3.000
 7QO  N10  C05  C04  111.87  3.000
 7QO  O06  C05  C04  110.93  3.000
 7QO  O17  C11  N12  122.59  3.000
 7QO  O17  C11  N10  119.61  3.000
 7QO  N12  C11  N10  117.81  3.000
 7QO  N16  C13  N12  118.29  3.000
 7QO  N12  C13  C14  122.20  3.000
 7QO  N16  C13  C14  119.51  3.000
 7QO  H6   C14  C15  121.39  3.000
 7QO  H6   C14  C13  122.29  3.000
 7QO  C15  C14  C13  116.32  3.000
 7QO  H7   C15  N10  117.02  3.000
 7QO  H7   C15  C14  121.27  3.000
 7QO  N10  C15  C14  121.71  3.000
 7QO  O20  C18  O19  127.03  3.000
 7QO  O20  C18  C01  118.83  3.000
 7QO  O19  C18  C01  114.13  3.000
 7QO  C15  N10  C11  120.59  3.000
 7QO  C11  N10  C05  120.34  3.000
 7QO  C15  N10  C05  119.04  3.000
 7QO  C13  N12  C11  121.37  3.000
 7QO  H9   N16  H8   118.15  3.000
 7QO  H9   N16  C13  121.71  3.000
 7QO  H8   N16  C13  120.14  3.000
 7QO  C05  O06  C01  112.45  3.000
 7QO  H10  O07  C02  102.75  3.000
 7QO  H11  O08  C04  109.25  3.000
 7QO  H12  O09  C03  107.89  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
 7QO  CONST_01  N12  C11  N10  C05   180.00   0.0  0
 7QO  CONST_02  C14  C13  N12  C11     0.00   0.0  0
 7QO  CONST_03  N10  C11  N12  C13     0.00   0.0  0
 7QO  CONST_04  N12  C11  N10  C15     0.00   0.0  0
 7QO  CONST_05  O17  C11  N10  C05     0.00   0.0  0
 7QO  CONST_06  N16  C13  N12  C11   180.00   0.0  0
 7QO  CONST_07  O17  C11  N12  C13   180.00   0.0  0
 7QO  CONST_08  O17  C11  N10  C15   180.00   0.0  0
 7QO  CONST_09  H8   N16  C13  C14   180.00   0.0  0
 7QO  CONST_10  H9   N16  C13  C14     0.00   0.0  0
 7QO  CONST_11  H8   N16  C13  N12     0.00   0.0  0
 7QO  CONST_12  H9   N16  C13  N12   180.00   0.0  0
 7QO  Var_01    H7   C15  N10  C05     0.61  30.0  1
 7QO  Var_02    H7   C15  N10  C11   178.59  30.0  1
 7QO  Var_03    H7   C15  C14  C13  -179.39  30.0  1
 7QO  Var_04    H6   C14  C15  N10  -179.83  30.0  1
 7QO  Var_05    H6   C14  C13  N12  -179.45  30.0  1
 7QO  Var_06    H6   C14  C13  N16     0.42  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
 7QO  chir_01  C01  C02  C18  O06  negativ
 7QO  chir_02  C02  O07  C01  C03  positiv
 7QO  chir_03  C03  O09  C02  C04  negativ
 7QO  chir_04  C04  O08  C03  C05  positiv
 7QO  chir_05  C05  O06  N10  C04  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
 7QO  plan-1  C05  0.020
 7QO  plan-1  C11  0.020
 7QO  plan-1  C13  0.020
 7QO  plan-1  C14  0.020
 7QO  plan-1  C15  0.020
 7QO  plan-1  N10  0.020
 7QO  plan-1  N12  0.020
 7QO  plan-1  N16  0.020
 7QO  plan-1  O17  0.020
 7QO  plan-1  H8   0.020
 7QO  plan-1  H9   0.020
 7QO  plan-2  C01  0.020
 7QO  plan-2  C18  0.020
 7QO  plan-2  O19  0.020
 7QO  plan-2  O20  0.020

