# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 22:11:59 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 1-deoxy-1-(7,8-dimethyl-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)c2cc1C
#
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
 RBF  RBF  1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-D-ribitol  ligand  47  27  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_RBF
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
 RBF  N1    N  N     0  -0.548   0.4880  -2.3123   0.3384
 RBF  C2    C  CR6   0   0.573   1.0723  -3.4927   0.0104
 RBF  O2    O  O     0  -0.468   0.5096  -4.5617   0.1454
 RBF  N3    N  NR16  0  -0.717   2.3714  -3.4797  -0.5039
 RBF  C4    C  CR6   0   0.552   3.1488  -2.3830  -0.7212
 RBF  O4    O  O     0  -0.425   4.2710  -2.4410  -1.1727
 RBF  C4A   C  CR66  0  -0.033   2.4841  -1.1138  -0.3473
 RBF  N5    N  N     0  -0.348   3.1284  -0.0106  -0.5124
 RBF  C5A   C  CR66  0   0.181   2.5245   1.1465  -0.1674
 RBF  C6    C  CR16  0  -0.360   3.2334   2.3481  -0.3421
 RBF  C7    C  CR6   0   0.074   2.6925   3.5604  -0.0036
 RBF  C7M   C  CH3   0  -0.736   3.4666   4.8296  -0.1860
 RBF  C8    C  CR6   0   0.093   1.3786   3.5829   0.5327
 RBF  C8M   C  CH3   0  -0.735   0.7575   4.8870   0.9226
 RBF  C9    C  CR16  0  -0.395   0.6676   2.4122   0.7049
 RBF  C9A   C  CR66  0   0.467   1.2166   1.1711   0.3629
 RBF  N10   N  NR6   0  -0.564   0.5602  -0.0260   0.5345
 RBF  C10   C  CR66  0   0.566   1.1469  -1.1984   0.1808
 RBF  C1'   C  CH2   0  -0.368  -0.7970  -0.0845   1.0787
 RBF  C2'   C  CH1   0   0.000  -1.8376  -0.1402  -0.0489
 RBF  O2'   O  OH1   0  -0.649  -1.5984   0.8501  -1.0179
 RBF  C3'   C  CH1   0  -0.040  -3.2619  -0.0436   0.5352
 RBF  O3'   O  OH1   0  -0.653  -3.3601  -0.6387   1.8087
 RBF  C4'   C  CH1   0  -0.016  -4.3364  -0.6308  -0.4021
 RBF  O4'   O  OH1   0  -0.652  -4.1124  -0.3606  -1.7620
 RBF  C5'   C  CH2   0  -0.160  -5.7189  -0.1818   0.0460
 RBF  O5'   O  OH1   0  -0.671  -6.6894  -0.8883  -0.6886
 RBF  HN3   H  HNR6  0   0.422   2.7717  -4.3815  -0.7321
 RBF  HC6   H  HCR6  0   0.274   4.2330   2.2803  -0.7533
 RBF  HC71  H  HCH3  0   0.252   2.9608   5.5139  -0.8698
 RBF  HC72  H  HCH3  0   0.251   3.5918   5.3598   0.7598
 RBF  HC73  H  HCH3  0   0.260   4.4575   4.6286  -0.5892
 RBF  HC81  H  HCH3  0   0.257   0.7507   5.5882   0.0864
 RBF  HC82  H  HCH3  0   0.262  -0.2676   4.7592   1.2643
 RBF  HC83  H  HCH3  0   0.260   1.3243   5.3612   1.7264
 RBF  HC9   H  HCR6  0   0.278  -0.3231   2.4867   1.1267
 RBF  HC11  H  HCH2  0   0.301  -0.8569  -0.9750   1.6967
 RBF  HC12  H  HCH2  0   0.293  -0.9461   0.7676   1.7378
 RBF  HC2'  H  HCH1  0   0.261  -1.7178  -1.0963  -0.5670
 RBF  HO2'  H  HOH1  0   0.446  -1.8581   1.7110  -0.6725
 RBF  HC3'  H  HCH1  0   0.237  -3.4717   1.0223   0.7042
 RBF  HO3'  H  HOH1  0   0.452  -3.3153  -1.5969   1.7128
 RBF  HC4'  H  HCH1  0   0.232  -4.2758  -1.7236  -0.3145
 RBF  HO4'  H  HOH1  0   0.441  -4.0896   0.5928  -1.8954
 RBF  HC51  H  HCH2  0   0.205  -5.8199  -0.3546   1.1234
 RBF  HC52  H  HCH2  0   0.194  -5.8002   0.9047  -0.1111
 RBF  HO5'  H  HOH1  0   0.455  -7.5564  -0.6183  -0.3737

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
 RBF  N1   C2    single    1.357  0.020  1.357
 RBF  N1   C10   double    1.304  0.020  1.304
 RBF  C2   O2    double    1.216  0.020  1.216
 RBF  C2   N3    single    1.397  0.020  1.397
 RBF  N3   C4    single    1.362  0.020  1.362
 RBF  N3   HN3   single    0.860  0.020  1.020
 RBF  C4   O4    double    1.211  0.020  1.211
 RBF  C4   C4A   single    1.481  0.020  1.481
 RBF  C4A  N5    double    1.288  0.020  1.288
 RBF  C4A  C10   single    1.440  0.020  1.440
 RBF  N5   C5A   single    1.350  0.020  1.350
 RBF  C5A  C6    aromatic  1.406  0.020  1.406
 RBF  C5A  C9A   aromatic  1.412  0.020  1.412
 RBF  C6   C7    aromatic  1.370  0.020  1.370
 RBF  C6   HC6   single    0.930  0.020  1.080
 RBF  C7   C7M   single    1.498  0.020  1.498
 RBF  C7   C8    aromatic  1.419  0.020  1.419
 RBF  C7M  HC71  single    0.970  0.020  1.090
 RBF  C7M  HC72  single    0.970  0.020  1.090
 RBF  C7M  HC73  single    0.970  0.020  1.090
 RBF  C8   C8M   single    1.496  0.020  1.496
 RBF  C8   C9    aromatic  1.380  0.020  1.380
 RBF  C8M  HC81  single    0.970  0.020  1.090
 RBF  C8M  HC82  single    0.970  0.020  1.090
 RBF  C8M  HC83  single    0.970  0.020  1.090
 RBF  C9   C9A   aromatic  1.400  0.020  1.400
 RBF  C9   HC9   single    0.930  0.020  1.080
 RBF  C9A  N10   single    1.376  0.020  1.376
 RBF  N10  C10   single    1.358  0.020  1.358
 RBF  N10  C1'   single    1.463  0.020  1.463
 RBF  C1'  C2'   single    1.535  0.020  1.535
 RBF  C1'  HC11  single    0.970  0.020  1.090
 RBF  C1'  HC12  single    0.970  0.020  1.090
 RBF  C2'  O2'   single    1.406  0.020  1.406
 RBF  C2'  C3'   single    1.542  0.020  1.542
 RBF  C2'  HC2'  single    0.970  0.020  1.090
 RBF  O2'  HO2'  single    0.850  0.020  0.980
 RBF  C3'  O3'   single    1.409  0.020  1.409
 RBF  C3'  C4'   single    1.542  0.020  1.542
 RBF  C3'  HC3'  single    0.970  0.020  1.090
 RBF  O3'  HO3'  single    0.850  0.020  0.980
 RBF  C4'  O4'   single    1.404  0.020  1.404
 RBF  C4'  C5'   single    1.521  0.020  1.521
 RBF  C4'  HC4'  single    0.970  0.020  1.090
 RBF  O4'  HO4'  single    0.850  0.020  0.980
 RBF  C5'  O5'   single    1.407  0.020  1.407
 RBF  C5'  HC51  single    0.970  0.020  1.090
 RBF  C5'  HC52  single    0.970  0.020  1.090
 RBF  O5'  HO5'  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
 RBF  C10   N1   C2    119.75  3.000
 RBF  N3    C2   O2    118.65  3.000
 RBF  N3    C2   N1    118.76  3.000
 RBF  O2    C2   N1    122.59  3.000
 RBF  HN3   N3   C4    117.10  3.000
 RBF  HN3   N3   C2    116.24  3.000
 RBF  C4    N3   C2    126.66  3.000
 RBF  C4A   C4   O4    123.45  3.000
 RBF  C4A   C4   N3    113.19  3.000
 RBF  O4    C4   N3    123.36  3.000
 RBF  C10   C4A  N5    124.17  3.000
 RBF  C10   C4A  C4    117.33  3.000
 RBF  N5    C4A  C4    118.50  3.000
 RBF  C5A   N5   C4A   118.53  3.000
 RBF  C9A   C5A  C6    119.93  3.000
 RBF  C9A   C5A  N5    121.69  3.000
 RBF  C6    C5A  N5    118.37  3.000
 RBF  HC6   C6   C7    120.90  3.000
 RBF  HC6   C6   C5A   117.33  3.000
 RBF  C7    C6   C5A   121.77  3.000
 RBF  C8    C7   C7M   120.74  3.000
 RBF  C8    C7   C6    118.22  3.000
 RBF  C7M   C7   C6    121.04  3.000
 RBF  HC73  C7M  HC72  107.83  3.000
 RBF  HC73  C7M  HC71  107.79  3.000
 RBF  HC72  C7M  HC71  106.94  3.000
 RBF  HC73  C7M  C7    111.05  3.000
 RBF  HC72  C7M  C7    111.43  3.000
 RBF  HC71  C7M  C7    111.60  3.000
 RBF  C9    C8   C8M   119.53  3.000
 RBF  C9    C8   C7    120.70  3.000
 RBF  C8M   C8   C7    119.77  3.000
 RBF  HC83  C8M  HC82  107.99  3.000
 RBF  HC83  C8M  HC81  106.76  3.000
 RBF  HC82  C8M  HC81  108.07  3.000
 RBF  HC83  C8M  C8    110.78  3.000
 RBF  HC82  C8M  C8    111.75  3.000
 RBF  HC81  C8M  C8    111.28  3.000
 RBF  HC9   C9   C9A   121.11  3.000
 RBF  HC9   C9   C8    117.58  3.000
 RBF  C9A   C9   C8    121.30  3.000
 RBF  N10   C9A  C9    123.64  3.000
 RBF  N10   C9A  C5A   118.28  3.000
 RBF  C9    C9A  C5A   118.08  3.000
 RBF  C1'   N10  C10   117.59  3.000
 RBF  C1'   N10  C9A   121.57  3.000
 RBF  C10   N10  C9A   120.83  3.000
 RBF  N10   C10  C4A   116.49  3.000
 RBF  N10   C10  N1    119.20  3.000
 RBF  C4A   C10  N1    124.31  3.000
 RBF  HC12  C1'  HC11  106.87  3.000
 RBF  HC12  C1'  C2'   112.37  3.000
 RBF  HC11  C1'  C2'   110.55  3.000
 RBF  HC12  C1'  N10   108.73  3.000
 RBF  HC11  C1'  N10   107.19  3.000
 RBF  C2'   C1'  N10   110.91  3.000
 RBF  HC2'  C2'  C3'   109.59  3.000
 RBF  HC2'  C2'  O2'   105.70  3.000
 RBF  C3'   C2'  O2'   111.96  3.000
 RBF  HC2'  C2'  C1'   107.77  3.000
 RBF  C3'   C2'  C1'   110.21  3.000
 RBF  O2'   C2'  C1'   111.43  3.000
 RBF  HO2'  O2'  C2'   109.66  3.000
 RBF  HC3'  C3'  C4'   109.25  3.000
 RBF  HC3'  C3'  O3'   104.90  3.000
 RBF  C4'   C3'  O3'   109.87  3.000
 RBF  HC3'  C3'  C2'   107.17  3.000
 RBF  C4'   C3'  C2'   112.92  3.000
 RBF  O3'   C3'  C2'   112.35  3.000
 RBF  HO3'  O3'  C3'   109.07  3.000
 RBF  HC4'  C4'  C5'   108.69  3.000
 RBF  HC4'  C4'  O4'   105.07  3.000
 RBF  C5'   C4'  O4'   111.92  3.000
 RBF  HC4'  C4'  C3'   106.98  3.000
 RBF  C5'   C4'  C3'   109.99  3.000
 RBF  O4'   C4'  C3'   113.84  3.000
 RBF  HO4'  O4'  C4'   109.17  3.000
 RBF  HC52  C5'  HC51  106.81  3.000
 RBF  HC52  C5'  O5'   111.72  3.000
 RBF  HC51  C5'  O5'   111.75  3.000
 RBF  HC52  C5'  C4'   108.45  3.000
 RBF  HC51  C5'  C4'   109.07  3.000
 RBF  O5'   C5'  C4'   108.95  3.000
 RBF  HO5'  O5'  C5'   108.06  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
 RBF  CONST_01  C8    C7   C6   C5A    0.00   0.0  0
 RBF  CONST_02  C8    C9   C9A  C5A    0.00   0.0  0
 RBF  CONST_03  C9    C9A  C5A  C6     0.00   0.0  0
 RBF  CONST_04  C9    C8   C7   C6     0.00   0.0  0
 RBF  CONST_05  C9A   C5A  C6   C7     0.00   0.0  0
 RBF  CONST_06  C9A   C9   C8   C7     0.00   0.0  0
 RBF  CONST_07  C4    N3   C2   N1     0.00   0.0  0
 RBF  CONST_08  C9A   N10  C10  N1   180.00   0.0  0
 RBF  CONST_09  C4A   C10  N1   C2     0.00   0.0  0
 RBF  CONST_10  N10   C10  N1   C2   180.00   0.0  0
 RBF  CONST_11  C10   N1   C2   N3     0.00   0.0  0
 RBF  CONST_12  C9A   N10  C10  C4A    0.00   0.0  0
 RBF  CONST_13  C7M   C7   C6   C5A  180.00   0.0  0
 RBF  CONST_14  C8M   C8   C7   C6   180.00   0.0  0
 RBF  CONST_15  C9    C8   C7   C7M  180.00   0.0  0
 RBF  CONST_16  C9A   C9   C8   C8M  180.00   0.0  0
 RBF  CONST_17  C1'   N10  C10  N1     0.00   0.0  0
 RBF  CONST_18  C10   N1   C2   O2   180.00   0.0  0
 RBF  CONST_19  C4    N3   C2   O2   180.00   0.0  0
 RBF  CONST_20  C1'   N10  C10  C4A  180.00   0.0  0
 RBF  CONST_21  HC6   C6   C5A  N5     0.00   0.0  0
 RBF  CONST_22  HC9   C9   C9A  C5A  180.00   0.0  0
 RBF  CONST_23  HN3   N3   C2   N1   180.00   0.0  0
 RBF  Var_01    C2'   C1'  N10  C9A   95.51  30.0  3
 RBF  Var_02    HC71  C7M  C7   C6   119.57  30.0  2
 RBF  Var_03    HC81  C8M  C8   C7    55.87  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
 RBF  chir_01  C2'  C1'  O2'  C3'  positiv
 RBF  chir_02  C3'  O3'  C2'  C4'  negativ
 RBF  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
 RBF  plan-1  N1   0.020
 RBF  plan-1  C2   0.020
 RBF  plan-1  O2   0.020
 RBF  plan-1  N3   0.020
 RBF  plan-1  C4   0.020
 RBF  plan-1  O4   0.020
 RBF  plan-1  C4A  0.020
 RBF  plan-1  N5   0.020
 RBF  plan-1  C5A  0.020
 RBF  plan-1  C6   0.020
 RBF  plan-1  C7   0.020
 RBF  plan-1  C7M  0.020
 RBF  plan-1  C8   0.020
 RBF  plan-1  C8M  0.020
 RBF  plan-1  C9   0.020
 RBF  plan-1  C9A  0.020
 RBF  plan-1  N10  0.020
 RBF  plan-1  C10  0.020
 RBF  plan-1  C1'  0.020
 RBF  plan-1  HN3  0.020
 RBF  plan-1  HC6  0.020
 RBF  plan-1  HC9  0.020

