# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 06:33:24 2021
#   Inital geometry file: a 75 line input string
#   Ligand name: 5-[(2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1~{H}-pyrimidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)C2=CNC(=O)NC2=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
 FJF  FJF  5-[(2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1~{H}-pyrimidine-2,4-dione  ligand  29  17  .  2022-03-18  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FJF
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
 FJF  O01  O  O     0  -0.332  10.6863   -6.9542  46.5067
 FJF  C02  C  CR6   0   0.694   9.8694   -7.8460  46.4041
 FJF  N03  N  NR16  0  -0.690   8.8781   -7.8539  45.4605
 FJF  C04  C  CR16  0   0.014   7.9670   -8.8561  45.3405
 FJF  C05  C  CR6   0  -0.233   7.9497   -9.9244  46.1601
 FJF  C06  C  CR6   0   0.548   8.9653  -10.0141  47.1901
 FJF  O07  O  O     0  -0.551   9.0879  -10.9324  47.9796
 FJF  N08  N  NR16  0  -0.665   9.8509   -8.9463  47.2216
 FJF  C09  C  CH1   0  -0.005   6.9234  -11.0130  46.0358
 FJF  O10  O  O2    0  -0.471   6.4338  -11.0597  44.7109
 FJF  C11  C  CH1   0  -0.079   5.0109  -11.0487  44.6802
 FJF  C12  C  CH2   0  -0.141   4.4746   -9.6847  44.2796
 FJF  O13  O  OH1   0  -0.640   5.0834   -9.3008  43.0713
 FJF  C14  C  CH1   0   0.036   4.5732  -11.4397  46.0802
 FJF  O15  O  OH1   0  -0.667   4.5954  -12.8389  46.1968
 FJF  C16  C  CH1   0   0.053   5.6854  -10.8047  46.9251
 FJF  O17  O  OH1   0  -0.624   5.8641  -11.4116  48.1732
 FJF  H1   H  HCR6  0   0.314   7.2640   -8.7355  44.5277
 FJF  H3   H  HNR6  0   0.436  10.5755   -8.9817  47.9282
 FJF  H4   H  HCH1  0   0.206   7.3841  -11.9740  46.2973
 FJF  H5   H  HCH1  0   0.220   4.6840  -11.7875  43.9408
 FJF  H6   H  HCH2  0   0.196   4.6603   -8.9490  45.0746
 FJF  H7   H  HCH2  0   0.213   3.3845   -9.7697  44.1793
 FJF  H8   H  HOH1  0   0.452   4.7568   -8.4276  42.8367
 FJF  H9   H  HCH1  0   0.143   3.5860  -11.0290  46.3335
 FJF  H10  H  HOH1  0   0.444   4.7480  -13.0492  47.1262
 FJF  H11  H  HCH1  0   0.237   5.4869   -9.7320  47.0347
 FJF  H12  H  HOH1  0   0.448   5.2223  -11.0412  48.7877
 FJF  H13  H  HNR6  0   0.444   8.8276   -7.0679  44.8280

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
 FJF  O13  C12  single  1.406  0.020  1.406
 FJF  C12  C11  single  1.519  0.020  1.519
 FJF  O10  C11  single  1.423  0.020  1.423
 FJF  O10  C09  single  1.413  0.020  1.413
 FJF  C11  C14  single  1.518  0.020  1.518
 FJF  C09  C05  single  1.501  0.020  1.501
 FJF  C09  C16  single  1.538  0.020  1.538
 FJF  C14  O15  single  1.404  0.020  1.404
 FJF  C14  C16  single  1.534  0.020  1.534
 FJF  C05  C04  double  1.347  0.020  1.347
 FJF  C05  C06  single  1.449  0.020  1.449
 FJF  O07  C06  double  1.217  0.020  1.217
 FJF  C04  N03  single  1.360  0.020  1.360
 FJF  C06  N08  single  1.388  0.020  1.388
 FJF  N03  C02  single  1.369  0.020  1.369
 FJF  N08  C02  single  1.371  0.020  1.371
 FJF  C02  O01  double  1.214  0.020  1.214
 FJF  C16  O17  single  1.399  0.020  1.399
 FJF  C04  H1   single  0.930  0.020  1.080
 FJF  N08  H3   single  0.860  0.020  1.020
 FJF  C09  H4   single  0.970  0.020  1.090
 FJF  C11  H5   single  0.970  0.020  1.090
 FJF  C12  H6   single  0.970  0.020  1.090
 FJF  C12  H7   single  0.970  0.020  1.090
 FJF  O13  H8   single  0.850  0.020  0.980
 FJF  C14  H9   single  0.970  0.020  1.090
 FJF  O15  H10  single  0.850  0.020  0.980
 FJF  C16  H11  single  0.970  0.020  1.090
 FJF  O17  H12  single  0.850  0.020  0.980
 FJF  N03  H13  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
 FJF  N08  C02  N03  113.37  3.000
 FJF  N08  C02  O01  123.25  3.000
 FJF  N03  C02  O01  123.37  3.000
 FJF  H13  N03  C04  119.00  3.000
 FJF  H13  N03  C02  117.60  3.000
 FJF  C04  N03  C02  123.40  3.000
 FJF  H1   C04  C05  122.52  3.000
 FJF  H1   C04  N03  114.81  3.000
 FJF  C05  C04  N03  122.66  3.000
 FJF  C09  C05  C06  119.54  3.000
 FJF  C06  C05  C04  118.21  3.000
 FJF  C09  C05  C04  122.25  3.000
 FJF  N08  C06  O07  120.10  3.000
 FJF  N08  C06  C05  114.57  3.000
 FJF  O07  C06  C05  125.33  3.000
 FJF  H3   N08  C06  116.46  3.000
 FJF  H3   N08  C02  115.76  3.000
 FJF  C06  N08  C02  127.78  3.000
 FJF  H4   C09  C16  108.58  3.000
 FJF  H4   C09  O10  109.87  3.000
 FJF  C16  C09  O10  105.52  3.000
 FJF  H4   C09  C05  109.17  3.000
 FJF  C16  C09  C05  113.83  3.000
 FJF  O10  C09  C05  109.78  3.000
 FJF  C11  O10  C09  111.49  3.000
 FJF  H5   C11  C14  111.27  3.000
 FJF  H5   C11  C12  108.80  3.000
 FJF  C14  C11  C12  111.88  3.000
 FJF  H5   C11  O10  107.92  3.000
 FJF  C14  C11  O10  105.45  3.000
 FJF  C12  C11  O10  111.44  3.000
 FJF  H7   C12  H6   106.60  3.000
 FJF  H7   C12  O13  111.86  3.000
 FJF  H6   C12  O13  111.44  3.000
 FJF  H7   C12  C11  107.76  3.000
 FJF  H6   C12  C11  110.52  3.000
 FJF  O13  C12  C11  108.59  3.000
 FJF  H8   O13  C12  108.09  3.000
 FJF  H9   C14  C16  111.69  3.000
 FJF  H9   C14  O15  111.56  3.000
 FJF  C16  C14  O15  110.80  3.000
 FJF  H9   C14  C11  112.05  3.000
 FJF  C16  C14  C11  101.08  3.000
 FJF  O15  C14  C11  109.19  3.000
 FJF  H10  O15  C14  107.44  3.000
 FJF  H11  C16  O17  111.00  3.000
 FJF  H11  C16  C14  109.19  3.000
 FJF  O17  C16  C14  113.84  3.000
 FJF  H11  C16  C09  109.63  3.000
 FJF  O17  C16  C09  110.74  3.000
 FJF  C14  C16  C09  102.06  3.000
 FJF  H12  O17  C16  108.50  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
 FJF  CONST_01  C05  C06  N08  C02    0.00  0.0  0
 FJF  CONST_02  C06  N08  C02  N03    0.00  0.0  0
 FJF  CONST_03  N08  C02  N03  C04    0.00  0.0  0
 FJF  CONST_04  C04  N03  C02  O01  180.00  0.0  0
 FJF  CONST_05  C06  N08  C02  O01  180.00  0.0  0
 FJF  CONST_06  O07  C06  N08  C02  180.00  0.0  0
 FJF  CONST_07  H3   N08  C02  N03  180.00  0.0  0
 FJF  CONST_08  H13  N03  C02  N08  180.00  0.0  0

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
 FJF  chir_01  C09  O10  C05  C16  negativ
 FJF  chir_02  C11  O10  C12  C14  positiv
 FJF  chir_03  C14  O15  C11  C16  positiv
 FJF  chir_04  C16  O17  C14  C09  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
 FJF  plan-1  O01  0.020
 FJF  plan-1  C02  0.020
 FJF  plan-1  N03  0.020
 FJF  plan-1  C04  0.020
 FJF  plan-1  C05  0.020
 FJF  plan-1  C06  0.020
 FJF  plan-1  O07  0.020
 FJF  plan-1  N08  0.020
 FJF  plan-1  C09  0.020
 FJF  plan-1  H1   0.020
 FJF  plan-1  H3   0.020
 FJF  plan-1  H13  0.020

