# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 13:34:54 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 1-deoxy-1-{[2,6-dioxo-5-(5-phosphonopentyl)-1,2,3,6-tetrahydropyrimidin-4-yl]amino}-D-ribitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H](O)[C@@H](O)CNC1=C(CCCCC[P](O)(O)=O)C(=O)NC(=O)N1
#
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
 5YL  5YL  1-deoxy-1-{[2,6-dioxo-5-(5-phosphonopentyl)-1,2,3,6-tetrahydropyrimidin-4-yl]amino}-D-ribitol  ligand  53  27  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5YL
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
 5YL  O3P   O  OH1   0  -0.747   3.0216   0.3826  -6.4795
 5YL  P     P  P     0   1.372   2.1459  -0.5731  -5.5257
 5YL  O1P   O  O     0  -0.722   1.3588  -1.6252  -6.2146
 5YL  O2P   O  OH1   0  -0.753   3.1770  -1.2799  -4.5079
 5YL  C17   C  CH2   0  -0.758   1.2065   0.6296  -4.5730
 5YL  C16   C  CH2   0  -0.433   0.3024  -0.0350  -3.5357
 5YL  C15   C  CH2   0  -0.411  -0.4922   0.9882  -2.7338
 5YL  C14   C  CH2   0  -0.413  -1.3997   0.3391  -1.6983
 5YL  C13   C  CH2   0  -0.533  -2.1789   1.3622  -0.8663
 5YL  C5    C  CR6   0  -0.238  -3.0348   0.7397   0.1971
 5YL  C4    C  CR6   0   0.530  -4.4209   0.5242  -0.0493
 5YL  O4    O  OC    0  -0.496  -5.0274   0.8278  -1.0713
 5YL  N3    N  NR16  0  -0.722  -5.1334  -0.0909   0.9841
 5YL  C2    C  CR6   0   0.663  -4.6337  -0.5296   2.1691
 5YL  O2    O  OC    0  -0.487  -5.3015  -1.0749   3.0265
 5YL  N1    N  NR16  0  -0.752  -3.2894  -0.3077   2.3234
 5YL  C6    C  CR6   0   0.688  -2.4963   0.3067   1.3911
 5YL  N7    N  NH1   0  -0.689  -1.2028   0.4723   1.7096
 5YL  C8    C  CH2   0  -0.293  -0.5104  -0.1652   2.8107
 5YL  C9    C  CH1   0  -0.008   0.8918   0.4252   2.9091
 5YL  O9    O  OH1   0  -0.683   1.4457   0.3661   1.6158
 5YL  C10   C  CH1   0  -0.018   1.7407  -0.3479   3.9344
 5YL  O10   O  OH1   0  -0.658   1.0294  -0.5540   5.1334
 5YL  C11   C  CH1   0  -0.027   3.0854   0.3480   4.2177
 5YL  O11   O  OH1   0  -0.666   3.7767   0.6655   3.0214
 5YL  C12   C  CH2   0  -0.168   3.9499  -0.4810   5.1520
 5YL  O12   O  OH1   0  -0.668   5.1184   0.2453   5.4482
 5YL  HOP3  H  HOH1  0   0.492   3.5202  -0.0918  -7.1592
 5YL  HOP2  H  HOH1  0   0.488   3.7564  -0.6784  -4.0221
 5YL  H171  H  HCH2  0   0.284   0.6086   1.2163  -5.2755
 5YL  H172  H  HCH2  0   0.281   1.8995   1.3250  -4.0908
 5YL  H161  H  HCH2  0   0.232   0.9015  -0.6404  -2.8504
 5YL  H162  H  HCH2  0   0.235  -0.3870  -0.7200  -4.0357
 5YL  H151  H  HCH2  0   0.221  -1.0909   1.6012  -3.4154
 5YL  H152  H  HCH2  0   0.218   0.2015   1.6735  -2.2346
 5YL  H141  H  HCH2  0   0.212  -0.7989  -0.2964  -1.0386
 5YL  H142  H  HCH2  0   0.228  -2.1096  -0.3285  -2.1955
 5YL  H131  H  HCH2  0   0.256  -2.8120   1.9510  -1.5314
 5YL  H132  H  HCH2  0   0.231  -1.4811   2.0835  -0.4255
 5YL  HN3   H  HNR6  0   0.418  -6.1202  -0.2475   0.8273
 5YL  HN1   H  HNR6  0   0.441  -2.8945  -0.6383   3.1918
 5YL  HN7   H  HNH1  0   0.413  -0.6032   0.8024   0.9690
 5YL  H81   H  HCH2  0   0.252  -0.4524  -1.2512   2.6658
 5YL  H82   H  HCH2  0   0.258  -1.0336   0.0242   3.7478
 5YL  H91   H  HCH1  0   0.220   0.7950   1.4711   3.2441
 5YL  HO9   H  HOH1  0   0.456   2.3407   0.7272   1.6763
 5YL  H101  H  HCH1  0   0.241   1.9309  -1.3471   3.5229
 5YL  H10O  H  HOH1  0   0.451   0.8706   0.2976   5.5570
 5YL  H111  H  HCH1  0   0.238   2.8708   1.3130   4.6940
 5YL  H11O  H  HOH1  0   0.457   4.2060  -0.1315   2.6879
 5YL  H121  H  HCH2  0   0.197   4.1796  -1.4397   4.6613
 5YL  H122  H  HCH2  0   0.215   3.3783  -0.7178   6.0546
 5YL  H12O  H  HOH1  0   0.457   5.6460  -0.2767   6.0590

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
 5YL  O3P  P     single    1.609  0.020  1.609
 5YL  O3P  HOP3  single    0.850  0.020  0.980
 5YL  P    O1P   double    1.484  0.020  1.484
 5YL  P    O2P   single    1.612  0.020  1.612
 5YL  P    C17   single    1.799  0.020  1.799
 5YL  O2P  HOP2  single    0.850  0.020  0.980
 5YL  C17  C16   single    1.528  0.020  1.528
 5YL  C17  H171  single    0.970  0.020  1.090
 5YL  C17  H172  single    0.970  0.020  1.090
 5YL  C16  C15   single    1.524  0.020  1.524
 5YL  C16  H161  single    0.970  0.020  1.090
 5YL  C16  H162  single    0.970  0.020  1.090
 5YL  C15  C14   single    1.522  0.020  1.522
 5YL  C15  H151  single    0.970  0.020  1.090
 5YL  C15  H152  single    0.970  0.020  1.090
 5YL  C14  C13   single    1.532  0.020  1.532
 5YL  C14  H141  single    0.970  0.020  1.090
 5YL  C14  H142  single    0.970  0.020  1.090
 5YL  C13  C5    single    1.500  0.020  1.500
 5YL  C13  H131  single    0.970  0.020  1.090
 5YL  C13  H132  single    0.970  0.020  1.090
 5YL  C5   C4    aromatic  1.424  0.020  1.424
 5YL  C5   C6    aromatic  1.380  0.020  1.380
 5YL  C4   O4    double    1.227  0.020  1.227
 5YL  C4   N3    aromatic  1.398  0.020  1.398
 5YL  N3   C2    aromatic  1.359  0.020  1.359
 5YL  N3   HN3   single    0.860  0.020  1.020
 5YL  C2   O2    double    1.216  0.020  1.216
 5YL  C2   N1    aromatic  1.371  0.020  1.371
 5YL  N1   C6    aromatic  1.370  0.020  1.370
 5YL  N1   HN1   single    0.860  0.020  1.020
 5YL  C6   N7    single    1.342  0.020  1.342
 5YL  N7   C8    single    1.449  0.020  1.449
 5YL  N7   HN7   single    0.890  0.020  1.040
 5YL  C8   C9    single    1.525  0.020  1.525
 5YL  C8   H81   single    0.970  0.020  1.090
 5YL  C8   H82   single    0.970  0.020  1.090
 5YL  C9   O9    single    1.408  0.020  1.408
 5YL  C9   C10   single    1.539  0.020  1.539
 5YL  C9   H91   single    0.970  0.020  1.090
 5YL  O9   HO9   single    0.850  0.020  0.980
 5YL  C10  O10   single    1.409  0.020  1.409
 5YL  C10  C11   single    1.540  0.020  1.540
 5YL  C10  H101  single    0.970  0.020  1.090
 5YL  O10  H10O  single    0.850  0.020  0.980
 5YL  C11  O11   single    1.418  0.020  1.418
 5YL  C11  C12   single    1.519  0.020  1.519
 5YL  C11  H111  single    0.970  0.020  1.090
 5YL  O11  H11O  single    0.850  0.020  0.980
 5YL  C12  O12   single    1.407  0.020  1.407
 5YL  C12  H121  single    0.970  0.020  1.090
 5YL  C12  H122  single    0.970  0.020  1.090
 5YL  O12  H12O  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
 5YL  HOP3  O3P  P     113.93  3.000
 5YL  C17   P    O2P   107.02  3.000
 5YL  C17   P    O1P   116.29  3.000
 5YL  O2P   P    O1P   108.75  3.000
 5YL  C17   P    O3P   101.60  3.000
 5YL  O2P   P    O3P   106.65  3.000
 5YL  O1P   P    O3P   115.76  3.000
 5YL  HOP2  O2P  P     115.34  3.000
 5YL  H172  C17  H171  106.78  3.000
 5YL  H172  C17  C16   110.62  3.000
 5YL  H171  C17  C16   110.25  3.000
 5YL  H172  C17  P     109.12  3.000
 5YL  H171  C17  P     107.70  3.000
 5YL  C16   C17  P     112.19  3.000
 5YL  H162  C16  H161  106.58  3.000
 5YL  H162  C16  C15   109.44  3.000
 5YL  H161  C16  C15   109.14  3.000
 5YL  H162  C16  C17   109.59  3.000
 5YL  H161  C16  C17   110.01  3.000
 5YL  C15   C16  C17   111.95  3.000
 5YL  H152  C15  H151  106.25  3.000
 5YL  H152  C15  C14   109.53  3.000
 5YL  H151  C15  C14   109.64  3.000
 5YL  H152  C15  C16   109.25  3.000
 5YL  H151  C15  C16   109.48  3.000
 5YL  C14   C15  C16   112.49  3.000
 5YL  H142  C14  H141  106.00  3.000
 5YL  H142  C14  C13   108.93  3.000
 5YL  H141  C14  C13   109.84  3.000
 5YL  H142  C14  C15   109.75  3.000
 5YL  H141  C14  C15   109.28  3.000
 5YL  C13   C14  C15   112.83  3.000
 5YL  H132  C13  H131  105.04  3.000
 5YL  H132  C13  C5    110.56  3.000
 5YL  H131  C13  C5    108.97  3.000
 5YL  H132  C13  C14   109.52  3.000
 5YL  H131  C13  C14   108.94  3.000
 5YL  C5    C13  C14   113.46  3.000
 5YL  C6    C5   C4    118.83  3.000
 5YL  C6    C5   C13   121.40  3.000
 5YL  C4    C5   C13   119.69  3.000
 5YL  N3    C4   O4    118.22  3.000
 5YL  N3    C4   C5    115.77  3.000
 5YL  O4    C4   C5    126.01  3.000
 5YL  HN3   N3   C2    116.36  3.000
 5YL  HN3   N3   C4    116.80  3.000
 5YL  C2    N3   C4    126.82  3.000
 5YL  N1    C2   O2    122.12  3.000
 5YL  N1    C2   N3    113.98  3.000
 5YL  O2    C2   N3    123.90  3.000
 5YL  HN1   N1   C6    120.39  3.000
 5YL  HN1   N1   C2    115.29  3.000
 5YL  C6    N1   C2    124.32  3.000
 5YL  N7    C6   N1    116.86  3.000
 5YL  N7    C6   C5    122.88  3.000
 5YL  N1    C6   C5    120.26  3.000
 5YL  HN7   N7   C8    114.71  3.000
 5YL  HN7   N7   C6    116.04  3.000
 5YL  C8    N7   C6    125.93  3.000
 5YL  H82   C8   H81   108.12  3.000
 5YL  H82   C8   C9    108.58  3.000
 5YL  H81   C8   C9    110.08  3.000
 5YL  H82   C8   N7    110.34  3.000
 5YL  H81   C8   N7    111.13  3.000
 5YL  C9    C8   N7    108.56  3.000
 5YL  H91   C9   C10   108.82  3.000
 5YL  H91   C9   O9    110.70  3.000
 5YL  C10   C9   O9    111.95  3.000
 5YL  H91   C9   C8    107.83  3.000
 5YL  C10   C9   C8    110.83  3.000
 5YL  O9    C9   C8    106.63  3.000
 5YL  HO9   O9   C9    106.91  3.000
 5YL  H101  C10  C11   109.21  3.000
 5YL  H101  C10  O10   105.87  3.000
 5YL  C11   C10  O10   110.50  3.000
 5YL  H101  C10  C9    107.65  3.000
 5YL  C11   C10  C9    112.15  3.000
 5YL  O10   C10  C9    111.21  3.000
 5YL  H10O  O10  C10   109.13  3.000
 5YL  H111  C11  C12   108.92  3.000
 5YL  H111  C11  O11   105.35  3.000
 5YL  C12   C11  O11   111.33  3.000
 5YL  H111  C11  C10   107.84  3.000
 5YL  C12   C11  C10   111.30  3.000
 5YL  O11   C11  C10   111.82  3.000
 5YL  H11O  O11  C11   108.89  3.000
 5YL  H122  C12  H121  106.75  3.000
 5YL  H122  C12  O12   111.83  3.000
 5YL  H121  C12  O12   111.71  3.000
 5YL  H122  C12  C11   109.16  3.000
 5YL  H121  C12  C11   108.65  3.000
 5YL  O12   C12  C11   108.68  3.000
 5YL  H12O  O12  C12   108.00  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
 5YL  CONST_01  C2   N3   C4   C5      0.00   0.0  0
 5YL  CONST_02  C2   N1   C6   C5      0.00   0.0  0
 5YL  CONST_03  N1   C6   C5   C4      0.00   0.0  0
 5YL  CONST_04  N1   C2   N3   C4      0.00   0.0  0
 5YL  CONST_05  C6   C5   C4   N3      0.00   0.0  0
 5YL  CONST_06  C6   N1   C2   N3      0.00   0.0  0
 5YL  CONST_07  N3   C4   C5   C13   180.00   0.0  0
 5YL  CONST_08  N1   C6   C5   C13   180.00   0.0  0
 5YL  CONST_09  N7   C6   C5   C4    180.00   0.0  0
 5YL  CONST_10  O2   C2   N3   C4    180.00   0.0  0
 5YL  CONST_11  C6   C5   C4   O4    180.00   0.0  0
 5YL  CONST_12  C2   N3   C4   O4    180.00   0.0  0
 5YL  CONST_13  N7   C6   N1   C2    180.00   0.0  0
 5YL  CONST_14  C6   N1   C2   O2    180.00   0.0  0
 5YL  CONST_15  HN3  N3   C4   C5    180.00   0.0  0
 5YL  CONST_16  HN1  N1   C6   C5    180.00   0.0  0
 5YL  CONST_17  C8   N7   C6   C5    180.00   0.0  0
 5YL  CONST_18  C8   N7   C6   N1      0.00   0.0  0
 5YL  CONST_19  HN7  N7   C6   C5      0.00   0.0  0
 5YL  Var_01    C4   C5   C13  C14   -97.42  30.0  2
 5YL  Var_02    C5   C13  C14  C15  -177.60  30.0  3
 5YL  Var_03    C9   C8   N7   C6   -173.37  30.0  3
 5YL  Var_04    C16  C17  P    O3P  -178.25  30.0  3
 5YL  Var_05    C15  C16  C17  P    -179.91  30.0  3
 5YL  Var_06    C14  C15  C16  C17   179.88  30.0  3
 5YL  Var_07    C13  C14  C15  C16   178.72  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
 5YL  chir_01  C9   C8   O9   C10  positiv
 5YL  chir_02  C10  O10  C9   C11  negativ
 5YL  chir_03  C11  O11  C10  C12  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
 5YL  plan-1  C13  0.020
 5YL  plan-1  C5   0.020
 5YL  plan-1  C4   0.020
 5YL  plan-1  O4   0.020
 5YL  plan-1  N3   0.020
 5YL  plan-1  C2   0.020
 5YL  plan-1  O2   0.020
 5YL  plan-1  N1   0.020
 5YL  plan-1  C6   0.020
 5YL  plan-1  N7   0.020
 5YL  plan-1  HN3  0.020
 5YL  plan-1  HN1  0.020
 5YL  plan-2  C6   0.020
 5YL  plan-2  N7   0.020
 5YL  plan-2  C8   0.020
 5YL  plan-2  HN7  0.020

