# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:35:30 2022
#   Inital geometry file: a 107 line input string
#   Ligand name: 1-deoxy-1-(8-iodo-7-methyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-D-ribitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO)c2cc1I
#
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
 IRF  IRF  1-deoxy-1-(8-iodo-7-methyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-D-ribitol  ligand  44  27  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IRF
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
 IRF  N1    N  N     0  -0.539  -6.1068  -5.4527  -3.2498
 IRF  C2    C  CR6   0   0.579  -7.0572  -5.8200  -4.1486
 IRF  O2    O  OC    0  -0.462  -7.9407  -6.6079  -3.8777
 IRF  N3    N  NR16  0  -0.717  -7.0147  -5.2759  -5.4348
 IRF  C4    C  CR6   0   0.556  -6.1243  -4.3571  -5.8964
 IRF  O4    O  OC    0  -0.419  -6.1450  -3.9120  -7.0213
 IRF  C4A   C  CR66  0  -0.033  -5.1209  -3.9517  -4.8802
 IRF  N5    N  N     0  -0.346  -4.2505  -3.0663  -5.2079
 IRF  C5A   C  CR66  0   0.201  -3.3298  -2.6936  -4.2854
 IRF  C6    C  CR16  0  -0.359  -2.3933  -1.7118  -4.6331
 IRF  C7    C  CR6   0   0.151  -1.4212  -1.2793  -3.7593
 IRF  C7M   C  CH3   0  -0.733  -0.4394  -0.2292  -4.1734
 IRF  C8    C  CR6   0  -0.280  -1.4155  -1.8810  -2.4848
 IRF  C9    C  CR16  0  -0.273  -2.3191  -2.8504  -2.1014
 IRF  C9A   C  CR66  0   0.428  -3.3008  -3.2738  -3.0035
 IRF  N10   N  NR6   0  -0.573  -4.2397  -4.2291  -2.6867
 IRF  C10   C  CR66  0   0.592  -5.1936  -4.5917  -3.5834
 IRF  C1'   C  CH2   0  -0.371  -4.1891  -4.8964  -1.3881
 IRF  C2'   C  CH1   0   0.000  -3.1090  -5.9771  -1.3694
 IRF  O2'   O  OH1   0  -0.655  -3.4451  -6.9337  -2.3413
 IRF  C3'   C  CH1   0   0.004  -3.0318  -6.5885   0.0319
 IRF  O3'   O  OH1   0  -0.671  -2.6232  -5.5528   0.8948
 IRF  C4'   C  CH1   0  -0.014  -2.0932  -7.7935   0.1198
 IRF  O4'   O  OH1   0  -0.679  -2.1616  -8.2355   1.4599
 IRF  C5'   C  CH2   0  -0.193  -0.6521  -7.4744  -0.2662
 IRF  I8    I  I     0   0.114   0.0237  -1.3086  -1.0658
 IRF  O5'   O  OH1   0  -0.666   0.2026  -8.5639   0.0145
 IRF  H3    H  HNR6  0   0.425  -7.7281  -5.5924  -6.0804
 IRF  H6    H  HCR6  0   0.287  -2.4548  -1.2937  -5.6298
 IRF  H7M1  H  HCH3  0   0.266  -0.6362   0.0967  -5.1928
 IRF  H7M2  H  HCH3  0   0.261  -0.4931   0.6469  -3.5256
 IRF  H7M3  H  HCH3  0   0.262   0.5849  -0.6023  -4.1327
 IRF  H9    H  HCR6  0   0.296  -2.2583  -3.2685  -1.1082
 IRF  H1'1  H  HCH2  0   0.312  -5.1644  -5.3410  -1.2090
 IRF  H1'2  H  HCH2  0   0.306  -4.0268  -4.1488  -0.6153
 IRF  H2'   H  HCH1  0   0.243  -2.1383  -5.5177  -1.5974
 IRF  HA    H  HOH1  0   0.462  -2.6446  -7.2468  -2.7707
 IRF  H3'   H  HCH1  0   0.228  -4.0380  -6.9483   0.3013
 IRF  HB    H  HOH1  0   0.456  -2.5534  -5.9149   1.7850
 IRF  H4'   H  HCH1  0   0.212  -2.4712  -8.5738  -0.5570
 IRF  HC    H  HOH1  0   0.449  -1.4225  -8.8362   1.6092
 IRF  H5'1  H  HCH2  0   0.210  -0.5949  -7.1884  -1.3232
 IRF  H5'2  H  HCH2  0   0.229  -0.2844  -6.6306   0.3200
 IRF  H5'   H  HOH1  0   0.454   0.0069  -9.2729  -0.6070

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
 IRF  N1   C2    aromatic  1.359  0.020  1.359
 IRF  N1   C10   aromatic  1.299  0.020  1.299
 IRF  C2   O2    double    1.214  0.020  1.214
 IRF  C2   N3    aromatic  1.397  0.020  1.397
 IRF  N3   C4    aromatic  1.360  0.020  1.360
 IRF  N3   H3    single    0.860  0.020  1.020
 IRF  C4   O4    double    1.210  0.020  1.210
 IRF  C4   C4A   aromatic  1.485  0.020  1.485
 IRF  C4A  N5    aromatic  1.284  0.020  1.284
 IRF  C4A  C10   aromatic  1.448  0.020  1.448
 IRF  N5   C5A   aromatic  1.356  0.020  1.356
 IRF  C5A  C6    aromatic  1.401  0.020  1.401
 IRF  C5A  C9A   aromatic  1.407  0.020  1.407
 IRF  C6   C7    aromatic  1.377  0.020  1.377
 IRF  C6   H6    single    0.930  0.020  1.080
 IRF  C7   C7M   single    1.496  0.020  1.496
 IRF  C7   C8    aromatic  1.409  0.020  1.409
 IRF  C7M  H7M1  single    0.970  0.020  1.090
 IRF  C7M  H7M2  single    0.970  0.020  1.090
 IRF  C7M  H7M3  single    0.970  0.020  1.090
 IRF  C8   C9    aromatic  1.380  0.020  1.380
 IRF  C8   I8    single    2.101  0.020  2.101
 IRF  C9   C9A   aromatic  1.399  0.020  1.399
 IRF  C9   H9    single    0.930  0.020  1.080
 IRF  C9A  N10   aromatic  1.376  0.020  1.376
 IRF  N10  C10   aromatic  1.358  0.020  1.358
 IRF  N10  C1'   single    1.461  0.020  1.461
 IRF  C1'  C2'   single    1.528  0.020  1.528
 IRF  C1'  H1'1  single    0.970  0.020  1.090
 IRF  C1'  H1'2  single    0.970  0.020  1.090
 IRF  C2'  O2'   single    1.404  0.020  1.404
 IRF  C2'  C3'   single    1.531  0.020  1.531
 IRF  C2'  H2'   single    0.970  0.020  1.090
 IRF  O2'  HA    single    0.850  0.020  0.980
 IRF  C3'  O3'   single    1.409  0.020  1.409
 IRF  C3'  C4'   single    1.530  0.020  1.530
 IRF  C3'  H3'   single    0.970  0.020  1.090
 IRF  O3'  HB    single    0.850  0.020  0.980
 IRF  C4'  O4'   single    1.413  0.020  1.413
 IRF  C4'  C5'   single    1.526  0.020  1.526
 IRF  C4'  H4'   single    0.970  0.020  1.090
 IRF  O4'  HC    single    0.850  0.020  0.980
 IRF  C5'  O5'   single    1.413  0.020  1.413
 IRF  C5'  H5'1  single    0.970  0.020  1.090
 IRF  C5'  H5'2  single    0.970  0.020  1.090
 IRF  O5'  H5'   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
 IRF  C10   N1   C2    120.08  3.000
 IRF  N3    C2   O2    118.70  3.000
 IRF  N3    C2   N1    118.84  3.000
 IRF  O2    C2   N1    122.46  3.000
 IRF  H3    N3   C4    117.12  3.000
 IRF  H3    N3   C2    116.34  3.000
 IRF  C4    N3   C2    126.54  3.000
 IRF  C4A   C4   O4    123.19  3.000
 IRF  C4A   C4   N3    113.24  3.000
 IRF  O4    C4   N3    123.56  3.000
 IRF  C10   C4A  N5    124.56  3.000
 IRF  C10   C4A  C4    117.28  3.000
 IRF  N5    C4A  C4    118.15  3.000
 IRF  C5A   N5   C4A   118.44  3.000
 IRF  C9A   C5A  C6    120.09  3.000
 IRF  C9A   C5A  N5    121.37  3.000
 IRF  C6    C5A  N5    118.54  3.000
 IRF  H6    C6   C7    120.21  3.000
 IRF  H6    C6   C5A   117.47  3.000
 IRF  C7    C6   C5A   122.32  3.000
 IRF  C8    C7   C7M   123.18  3.000
 IRF  C8    C7   C6    116.27  3.000
 IRF  C7M   C7   C6    120.54  3.000
 IRF  H7M3  C7M  H7M2  107.38  3.000
 IRF  H7M3  C7M  H7M1  107.89  3.000
 IRF  H7M2  C7M  H7M1  107.87  3.000
 IRF  H7M3  C7M  C7    111.46  3.000
 IRF  H7M2  C7M  C7    111.53  3.000
 IRF  H7M1  C7M  C7    110.54  3.000
 IRF  I8    C8   C9    116.91  3.000
 IRF  I8    C8   C7    119.82  3.000
 IRF  C9    C8   C7    123.27  3.000
 IRF  H9    C9   C9A   121.04  3.000
 IRF  H9    C9   C8    119.41  3.000
 IRF  C9A   C9   C8    119.55  3.000
 IRF  N10   C9A  C9    122.71  3.000
 IRF  N10   C9A  C5A   118.79  3.000
 IRF  C9    C9A  C5A   118.49  3.000
 IRF  C1'   N10  C10   119.29  3.000
 IRF  C1'   N10  C9A   119.87  3.000
 IRF  C10   N10  C9A   120.82  3.000
 IRF  N10   C10  C4A   115.98  3.000
 IRF  N10   C10  N1    120.08  3.000
 IRF  C4A   C10  N1    123.94  3.000
 IRF  H1'2  C1'  H1'1  107.35  3.000
 IRF  H1'2  C1'  C2'   111.84  3.000
 IRF  H1'1  C1'  C2'   110.06  3.000
 IRF  H1'2  C1'  N10   108.83  3.000
 IRF  H1'1  C1'  N10   107.60  3.000
 IRF  C2'   C1'  N10   111.00  3.000
 IRF  H2'   C2'  C3'   108.21  3.000
 IRF  H2'   C2'  O2'   110.67  3.000
 IRF  C3'   C2'  O2'   111.93  3.000
 IRF  H2'   C2'  C1'   109.06  3.000
 IRF  C3'   C2'  C1'   109.22  3.000
 IRF  O2'   C2'  C1'   107.71  3.000
 IRF  HA    O2'  C2'   109.38  3.000
 IRF  H3'   C3'  C4'   106.79  3.000
 IRF  H3'   C3'  O3'   110.81  3.000
 IRF  C4'   C3'  O3'   111.47  3.000
 IRF  H3'   C3'  C2'   107.94  3.000
 IRF  C4'   C3'  C2'   113.46  3.000
 IRF  O3'   C3'  C2'   106.36  3.000
 IRF  HB    O3'  C3'   108.09  3.000
 IRF  H4'   C4'  C5'   108.50  3.000
 IRF  H4'   C4'  O4'   110.19  3.000
 IRF  C5'   C4'  O4'   110.56  3.000
 IRF  H4'   C4'  C3'   108.21  3.000
 IRF  C5'   C4'  C3'   113.59  3.000
 IRF  O4'   C4'  C3'   105.73  3.000
 IRF  HC    O4'  C4'   107.74  3.000
 IRF  H5'2  C5'  H5'1  107.37  3.000
 IRF  H5'2  C5'  O5'   106.60  3.000
 IRF  H5'1  C5'  O5'   111.16  3.000
 IRF  H5'2  C5'  C4'   110.13  3.000
 IRF  H5'1  C5'  C4'   110.35  3.000
 IRF  O5'   C5'  C4'   111.09  3.000
 IRF  H5'   O5'  C5'   108.46  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
 IRF  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 IRF  CONST_02  C4    C4A  C10  N1     0.00   0.0  0
 IRF  CONST_03  N5    C4A  C10  N1   180.00   0.0  0
 IRF  CONST_04  C9A   N10  C10  N1   180.00   0.0  0
 IRF  CONST_05  C4A   C10  N1   C2     0.00   0.0  0
 IRF  CONST_06  N10   C10  N1   C2   180.00   0.0  0
 IRF  CONST_07  C4A   C4   N3   C2     0.00   0.0  0
 IRF  CONST_08  C10   N1   C2   N3     0.00   0.0  0
 IRF  CONST_09  N5    C4A  C4   N3   180.00   0.0  0
 IRF  CONST_10  C10   C4A  C4   N3     0.00   0.0  0
 IRF  CONST_11  C5A   N5   C4A  C4   180.00   0.0  0
 IRF  CONST_12  N10   C10  C4A  C4   180.00   0.0  0
 IRF  CONST_13  C6    C5A  N5   C4A  180.00   0.0  0
 IRF  CONST_14  C9A   C5A  N5   C4A    0.00   0.0  0
 IRF  CONST_15  C9A   N10  C10  C4A    0.00   0.0  0
 IRF  CONST_16  N10   C10  C4A  N5     0.00   0.0  0
 IRF  CONST_17  C7    C6   C5A  N5   180.00   0.0  0
 IRF  CONST_18  C9    C9A  C5A  N5   180.00   0.0  0
 IRF  CONST_19  N10   C9A  C5A  N5     0.00   0.0  0
 IRF  CONST_20  C10   C4A  N5   C5A    0.00   0.0  0
 IRF  CONST_21  C8    C7   C6   C5A    0.00   0.0  0
 IRF  CONST_22  C8    C9   C9A  C5A    0.00   0.0  0
 IRF  CONST_23  C10   N10  C9A  C5A    0.00   0.0  0
 IRF  CONST_24  C9    C9A  C5A  C6     0.00   0.0  0
 IRF  CONST_25  N10   C9A  C5A  C6   180.00   0.0  0
 IRF  CONST_26  C9    C8   C7   C6     0.00   0.0  0
 IRF  CONST_27  C9A   C5A  C6   C7     0.00   0.0  0
 IRF  CONST_28  C9A   C9   C8   C7     0.00   0.0  0
 IRF  CONST_29  N10   C9A  C9   C8   180.00   0.0  0
 IRF  CONST_30  C10   N10  C9A  C9   180.00   0.0  0
 IRF  CONST_31  C1'   N10  C10  N1     0.00   0.0  0
 IRF  CONST_32  O4    C4   N3   C2   180.00   0.0  0
 IRF  CONST_33  C10   N1   C2   O2   180.00   0.0  0
 IRF  CONST_34  C4    N3   C2   O2   180.00   0.0  0
 IRF  CONST_35  N5    C4A  C4   O4     0.00   0.0  0
 IRF  CONST_36  C10   C4A  C4   O4   180.00   0.0  0
 IRF  CONST_37  C1'   N10  C10  C4A  180.00   0.0  0
 IRF  CONST_38  C7M   C7   C6   C5A  180.00   0.0  0
 IRF  CONST_39  C1'   N10  C9A  C5A  180.00   0.0  0
 IRF  CONST_40  I8    C8   C7   C6   180.00   0.0  0
 IRF  CONST_41  C9    C8   C7   C7M  180.00   0.0  0
 IRF  CONST_42  C1'   N10  C9A  C9     0.00   0.0  0
 IRF  CONST_43  I8    C8   C9   C9A  180.00   0.0  0
 IRF  CONST_44  H3    N3   C2   N1   180.00   0.0  0
 IRF  CONST_45  H6    C6   C5A  N5     0.00   0.0  0
 IRF  CONST_46  H9    C9   C9A  C5A  180.00   0.0  0
 IRF  Var_01    C2'   C1'  N10  C9A  -78.09  30.0  2
 IRF  Var_02    H7M1  C7M  C7   C6     0.60  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
 IRF  chir_01  C2'  C1'  O2'  C3'  positiv
 IRF  chir_02  C3'  O3'  C2'  C4'  negativ
 IRF  chir_03  C4'  O4'  C3'  C5'  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
 IRF  plan-1  N1   0.020
 IRF  plan-1  C2   0.020
 IRF  plan-1  O2   0.020
 IRF  plan-1  N3   0.020
 IRF  plan-1  C4   0.020
 IRF  plan-1  O4   0.020
 IRF  plan-1  C4A  0.020
 IRF  plan-1  N5   0.020
 IRF  plan-1  C5A  0.020
 IRF  plan-1  C6   0.020
 IRF  plan-1  C7   0.020
 IRF  plan-1  C7M  0.020
 IRF  plan-1  C8   0.020
 IRF  plan-1  C9   0.020
 IRF  plan-1  C9A  0.020
 IRF  plan-1  N10  0.020
 IRF  plan-1  C10  0.020
 IRF  plan-1  C1'  0.020
 IRF  plan-1  I8   0.020
 IRF  plan-1  H3   0.020
 IRF  plan-1  H6   0.020
 IRF  plan-1  H9   0.020

