# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 02:53:06 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 1-deoxy-1-(2,4,6,7-tetraoxo-1,3,4,5,6,7-hexahydropteridin-8(2H)-yl)-D-ribitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H](O)[C@@H](O)CN1C(=O)C(=O)NC2=C1NC(=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
 RDL  RDL  1-deoxy-1-(2,4,6,7-tetraoxo-1,3,4,5,6,7-hexahydropteridin-8(2H)-yl)-D-ribitol  ligand  37  23  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RDL
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
 RDL  O15   O  OH1   0  -0.667   1.1507  -0.9238   6.0592
 RDL  C15   C  CH2   0  -0.161   0.9222   0.1154   5.1400
 RDL  C14   C  CH1   0  -0.041   0.2835  -0.4745   3.8919
 RDL  O14   O  OH1   0  -0.662  -0.9405  -1.1156   4.1929
 RDL  C13   C  CH1   0  -0.037   0.1302   0.5918   2.7913
 RDL  O13   O  OH1   0  -0.661   1.4020   1.0992   2.4285
 RDL  C12   C  CH1   0   0.044  -0.5657   0.0659   1.5194
 RDL  O12   O  OH1   0  -0.673  -1.8448  -0.4642   1.7260
 RDL  C11   C  CH2   0  -0.404  -0.7198   1.2167   0.5230
 RDL  N9    N  NR6   0  -0.575  -0.8866   0.7367  -0.8490
 RDL  C8    C  CR6   0   0.457  -2.1559   0.6984  -1.3917
 RDL  O8    O  OC    0  -0.408  -3.1281   1.1017  -0.8060
 RDL  C7    C  CR6   0   0.443  -2.3220   0.1234  -2.7923
 RDL  O7    O  OC    0  -0.443  -3.4290   0.0648  -3.2850
 RDL  C10   C  CR66  0   0.713   0.2019   0.3035  -1.5652
 RDL  C5    C  CR66  0   0.085   0.0587  -0.2045  -2.8118
 RDL  N6    N  NR16  0  -0.709  -1.1951  -0.2931  -3.3874
 RDL  C4    C  CR6   0   0.554   1.2008  -0.6514  -3.5630
 RDL  O4    O  OC    0  -0.453   1.1366  -1.1140  -4.6868
 RDL  N3    N  NR16  0  -0.723   2.4017  -0.5159  -2.8969
 RDL  C2    C  CR6   0   0.682   2.5966  -0.0092  -1.6400
 RDL  N1    N  NR16  0  -0.766   1.4465   0.3956  -1.0081
 RDL  O2    O  OC    0  -0.461   3.6850   0.0803  -1.1174
 RDL  H15O  H  HOH1  0   0.459   1.5967  -0.5507   6.8247
 RDL  H151  H  HCH2  0   0.201   0.2493   0.8846   5.5496
 RDL  H152  H  HCH2  0   0.214   1.8514   0.6243   4.8639
 RDL  H141  H  HCH1  0   0.245   0.9348  -1.2681   3.5015
 RDL  H14O  H  HOH1  0   0.461  -1.4792  -0.5333   4.7426
 RDL  H131  H  HCH1  0   0.250  -0.4446   1.4393   3.1852
 RDL  H13O  H  HOH1  0   0.458   2.0421   0.3783   2.4290
 RDL  H121  H  HCH1  0   0.211   0.1067  -0.6988   1.0928
 RDL  H12O  H  HOH1  0   0.454  -1.8005  -1.0341   2.5078
 RDL  H111  H  HCH2  0   0.313  -1.6004   1.7992   0.7807
 RDL  H112  H  HCH2  0   0.303   0.1175   1.9110   0.5541
 RDL  HN6   H  HNR6  0   0.428  -1.2584  -0.6898  -4.3177
 RDL  HN3   H  HNR6  0   0.439   3.2346  -0.8159  -3.3893
 RDL  HN1   H  HNR6  0   0.431   1.5785   0.7867  -0.0850

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
 RDL  O15  C15   single    1.406  0.020  1.406
 RDL  O15  H15O  single    0.850  0.020  0.980
 RDL  C15  C14   single    1.521  0.020  1.521
 RDL  C15  H151  single    0.970  0.020  1.090
 RDL  C15  H152  single    0.970  0.020  1.090
 RDL  C14  O14   single    1.414  0.020  1.414
 RDL  C14  C13   single    1.540  0.020  1.540
 RDL  C14  H141  single    0.970  0.020  1.090
 RDL  O14  H14O  single    0.850  0.020  0.980
 RDL  C13  O13   single    1.417  0.020  1.417
 RDL  C13  C12   single    1.542  0.020  1.542
 RDL  C13  H131  single    0.970  0.020  1.090
 RDL  O13  H13O  single    0.850  0.020  0.980
 RDL  C12  O12   single    1.400  0.020  1.400
 RDL  C12  C11   single    1.530  0.020  1.530
 RDL  C12  H121  single    0.970  0.020  1.090
 RDL  O12  H12O  single    0.850  0.020  0.980
 RDL  C11  N9    single    1.463  0.020  1.463
 RDL  C11  H111  single    0.970  0.020  1.090
 RDL  C11  H112  single    0.970  0.020  1.090
 RDL  N9   C8    aromatic  1.381  0.020  1.381
 RDL  N9   C10   aromatic  1.373  0.020  1.373
 RDL  C8   O8    double    1.204  0.020  1.204
 RDL  C8   C7    aromatic  1.523  0.020  1.523
 RDL  C7   O7    double    1.213  0.020  1.213
 RDL  C7   N6    aromatic  1.341  0.020  1.341
 RDL  C10  C5    aromatic  1.354  0.020  1.354
 RDL  C10  N1    aromatic  1.367  0.020  1.367
 RDL  C5   N6    aromatic  1.382  0.020  1.382
 RDL  C5   C4    aromatic  1.438  0.020  1.438
 RDL  N6   HN6   single    0.860  0.020  1.020
 RDL  C4   O4    double    1.217  0.020  1.217
 RDL  C4   N3    aromatic  1.380  0.020  1.380
 RDL  N3   C2    aromatic  1.369  0.020  1.369
 RDL  N3   HN3   single    0.860  0.020  1.020
 RDL  C2   N1    aromatic  1.373  0.020  1.373
 RDL  C2   O2    double    1.211  0.020  1.211
 RDL  N1   HN1   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
 RDL  H15O  O15  C15   108.01  3.000
 RDL  H152  C15  H151  106.73  3.000
 RDL  H152  C15  C14   109.25  3.000
 RDL  H151  C15  C14   108.64  3.000
 RDL  H152  C15  O15   111.74  3.000
 RDL  H151  C15  O15   111.86  3.000
 RDL  C14   C15  O15   108.54  3.000
 RDL  H141  C14  C13   107.77  3.000
 RDL  H141  C14  O14   105.15  3.000
 RDL  C13   C14  O14   112.32  3.000
 RDL  H141  C14  C15   108.84  3.000
 RDL  C13   C14  C15   111.08  3.000
 RDL  O14   C14  C15   111.39  3.000
 RDL  H14O  O14  C14   109.32  3.000
 RDL  H131  C13  C12   108.85  3.000
 RDL  H131  C13  O13   106.60  3.000
 RDL  C12   C13  O13   108.42  3.000
 RDL  H131  C13  C14   109.29  3.000
 RDL  C12   C13  C14   113.46  3.000
 RDL  O13   C13  C14   109.98  3.000
 RDL  H13O  O13  C13   109.16  3.000
 RDL  H121  C12  C11   109.31  3.000
 RDL  H121  C12  O12   110.56  3.000
 RDL  C11   C12  O12   106.79  3.000
 RDL  H121  C12  C13   106.26  3.000
 RDL  C11   C12  C13   109.03  3.000
 RDL  O12   C12  C13   114.82  3.000
 RDL  H12O  O12  C12   107.47  3.000
 RDL  H112  C11  H111  105.94  3.000
 RDL  H112  C11  N9    108.90  3.000
 RDL  H111  C11  N9    107.80  3.000
 RDL  H112  C11  C12   112.57  3.000
 RDL  H111  C11  C12   109.29  3.000
 RDL  N9    C11  C12   112.05  3.000
 RDL  C10   N9   C8    120.99  3.000
 RDL  C10   N9   C11   120.15  3.000
 RDL  C8    N9   C11   118.85  3.000
 RDL  C7    C8   O8    119.05  3.000
 RDL  C7    C8   N9    118.17  3.000
 RDL  O8    C8   N9    122.78  3.000
 RDL  N6    C7   O7    124.87  3.000
 RDL  N6    C7   C8    115.71  3.000
 RDL  O7    C7   C8    119.42  3.000
 RDL  N1    C10  C5    119.80  3.000
 RDL  N1    C10  N9    119.21  3.000
 RDL  C5    C10  N9    120.99  3.000
 RDL  C4    C5   N6    118.87  3.000
 RDL  C4    C5   C10   120.90  3.000
 RDL  N6    C5   C10   120.23  3.000
 RDL  HN6   N6   C5    117.65  3.000
 RDL  HN6   N6   C7    118.46  3.000
 RDL  C5    N6   C7    123.89  3.000
 RDL  N3    C4   O4    121.93  3.000
 RDL  N3    C4   C5    114.11  3.000
 RDL  O4    C4   C5    123.95  3.000
 RDL  HN3   N3   C2    116.02  3.000
 RDL  HN3   N3   C4    116.87  3.000
 RDL  C2    N3   C4    127.11  3.000
 RDL  O2    C2   N1    122.17  3.000
 RDL  O2    C2   N3    123.48  3.000
 RDL  N1    C2   N3    114.35  3.000
 RDL  HN1   N1   C2    115.13  3.000
 RDL  HN1   N1   C10   121.14  3.000
 RDL  C2    N1   C10   123.73  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
 RDL  CONST_01  N6   C7   C8   N9     0.00   0.0  0
 RDL  CONST_02  N6   C5   C10  N9     0.00   0.0  0
 RDL  CONST_03  C4   C5   C10  N9   180.00   0.0  0
 RDL  CONST_04  C2   N1   C10  N9   180.00   0.0  0
 RDL  CONST_05  C5   C10  N9   C8     0.00   0.0  0
 RDL  CONST_06  N1   C10  N9   C8   180.00   0.0  0
 RDL  CONST_07  C5   N6   C7   C8     0.00   0.0  0
 RDL  CONST_08  C10  N9   C8   C7     0.00   0.0  0
 RDL  CONST_09  C10  C5   N6   C7     0.00   0.0  0
 RDL  CONST_10  C4   C5   N6   C7   180.00   0.0  0
 RDL  CONST_11  N3   C4   C5   C10    0.00   0.0  0
 RDL  CONST_12  N3   C2   N1   C10    0.00   0.0  0
 RDL  CONST_13  C2   N1   C10  C5     0.00   0.0  0
 RDL  CONST_14  C2   N3   C4   C5     0.00   0.0  0
 RDL  CONST_15  N1   C10  C5   N6   180.00   0.0  0
 RDL  CONST_16  N3   C4   C5   N6   180.00   0.0  0
 RDL  CONST_17  N1   C10  C5   C4     0.00   0.0  0
 RDL  CONST_18  N1   C2   N3   C4     0.00   0.0  0
 RDL  CONST_19  C7   C8   N9   C11  180.00   0.0  0
 RDL  CONST_20  C5   C10  N9   C11  180.00   0.0  0
 RDL  CONST_21  N1   C10  N9   C11    0.00   0.0  0
 RDL  CONST_22  O7   C7   C8   N9   180.00   0.0  0
 RDL  CONST_23  C10  N9   C8   O8   180.00   0.0  0
 RDL  CONST_24  N6   C7   C8   O8   180.00   0.0  0
 RDL  CONST_25  C5   N6   C7   O7   180.00   0.0  0
 RDL  CONST_26  O4   C4   C5   C10  180.00   0.0  0
 RDL  CONST_27  O2   C2   N1   C10  180.00   0.0  0
 RDL  CONST_28  O4   C4   C5   N6     0.00   0.0  0
 RDL  CONST_29  O2   C2   N3   C4   180.00   0.0  0
 RDL  CONST_30  C2   N3   C4   O4   180.00   0.0  0
 RDL  CONST_31  HN1  N1   C10  N9     0.00   0.0  0
 RDL  CONST_32  HN6  N6   C7   C8   180.00   0.0  0
 RDL  CONST_33  HN3  N3   C4   C5   180.00   0.0  0
 RDL  CONST_34  O8   C8   N9   C11    0.00   0.0  0
 RDL  Var_01    C8   N9   C11  C12  100.40  30.0  2

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
 RDL  chir_01  C14  C15  O14  C13  negativ
 RDL  chir_02  C13  O13  C14  C12  positiv
 RDL  chir_03  C12  O12  C13  C11  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
 RDL  plan-1  C11  0.020
 RDL  plan-1  N9   0.020
 RDL  plan-1  C8   0.020
 RDL  plan-1  O8   0.020
 RDL  plan-1  C7   0.020
 RDL  plan-1  O7   0.020
 RDL  plan-1  C10  0.020
 RDL  plan-1  C5   0.020
 RDL  plan-1  N6   0.020
 RDL  plan-1  C4   0.020
 RDL  plan-1  O4   0.020
 RDL  plan-1  N3   0.020
 RDL  plan-1  C2   0.020
 RDL  plan-1  N1   0.020
 RDL  plan-1  O2   0.020
 RDL  plan-1  HN6  0.020
 RDL  plan-1  HN3  0.020
 RDL  plan-1  HN1  0.020

