# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug 17 11:36:38 2020
#
#   Final geometry file: /net/cci/nigel/work/qm/PBEh-3c.None.CPCM/y/YYG.cif
#   Ligand name: 7-{(3S)-4-methoxy-3-[(methoxycarbonyl)amino]-4-oxobutyl}-4,6-dimethyl-3-(5-O-phosphono-beta-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)N[C@@H](CCc1n2C(=O)c3ncn([C@@H]4O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]4O)c3N(C)c2nc1C)C(=O)OC
#
# Restraints Editor Exclusively Ligands (REEL)
#   - a module of PHENIX
#   - file written: Mon Aug 17 11:38:26 2020
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
YYG YYG '7-{(3S)-4-methoxy-3-[(methoxycarbonyl)amino]-4-oxobutyl}-4,6-dimethyl-3-(5-O-phosphono-beta-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one' RNA 67 40 . 
2020-08-17 2020-08-17
;
CIF prepared directly in eLBOW
;
#
data_comp_YYG
#
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
YYG         P      P   P      0   1.230    2.5831    1.1400   -6.2415
YYG         OP1    O   O      0  -0.864    2.6855    1.0339   -4.7173
YYG         OP2    O   OP    -1  -0.889    3.4478    0.1533   -7.0101
YYG         OP3    O   OP    -1  -0.896    2.6012    2.5738   -6.7568
YYG        O5'     O   O2     0  -0.655    1.0246    0.5582   -6.6163
YYG        C5'     C   CH2    0  -0.119   -0.0608    1.2836   -6.1360
YYG        C4'     C   CR15   0  -0.044   -1.1821    0.3329   -5.7580
YYG        O4'     O   O      0  -0.490   -0.7423   -0.5976   -4.7522
YYG        C3'     C   CR15   0  -0.037   -2.3804    1.0525   -5.1567
YYG        O3'     O   OH1    0  -0.670   -3.5421    0.2985   -5.3964
YYG        C2'     C   CR15   0  -0.037   -2.0139    1.0312   -3.6732
YYG        O2'     O   OH1    0  -0.654   -3.0870    1.1730   -2.7915
YYG        C1'     C   CR15   0   0.213   -1.4053   -0.3661   -3.5522
YYG         N9     N   NR5    0  -0.554   -0.4529   -0.4735   -2.4558
YYG         C8     C   CR15   0   0.028    0.8394    0.0189   -2.5244
YYG         N7     N   N      0  -0.445    1.4398   -0.0186   -1.3790
YYG         C5     C   CR56   0  -0.102    0.5276   -0.5405   -0.5017
YYG         C6     C   CR6    0   0.520    0.7161   -0.7592    0.8947
YYG         O6     O   O      0  -0.452    1.7237   -0.5447    1.5394
YYG         N1     N   N      0  -0.654   -0.4529   -1.2699    1.4854
YYG         C2     C   CR56   0   0.751   -1.6054   -1.5908    0.8068
YYG         N2     N   N      0  -0.511   -2.5141   -2.0946    1.5815
YYG         N3     N   NR6    0  -0.604   -1.7313   -1.3863   -0.5436
YYG         C3     C   CH3    0  -0.590   -2.9455   -1.8435   -1.2031
YYG         C4     C   CR56   0   0.656   -0.6547   -0.8338   -1.1587
YYG         C11    C   CR5    0   0.086   -1.9552   -2.1118    2.8384
YYG         C12    C   CR5    0   0.290   -0.6877   -1.6151    2.8235
YYG         C13    C   CH2    0  -0.511    0.2401   -1.3727    3.9622
YYG         C14    C   CH2    0  -0.474    0.2686    0.0936    4.4023
YYG         C15    C   CH1    0  -0.172    1.1320    0.3077    5.6478
YYG         C16    C   C      0   0.585    1.3352    1.8008    5.8652
YYG         O17    O   O      0  -0.450    2.1712    2.4371    5.2741
YYG         O18    O   O2     0  -0.443    0.4727    2.3170    6.7191
YYG         C19    C   CH3    0  -0.424    0.5551    3.7211    6.9709
YYG         N20    N   NH1    0  -0.668    0.5421   -0.3594    6.7770
YYG         C21    C   C      0   0.762    1.1852   -0.3855    7.9629
YYG         O22    O   O      0  -0.515    2.3170    0.0188    8.1316
YYG         O23    O   O2     0  -0.476    0.4253   -0.9235    8.9147
YYG         C24    C   CH3    0  -0.418    0.9918   -1.0147   10.2186
YYG        H5'     H   HCH2   0   0.190   -0.4608    1.9723   -6.8951
YYG        H5''    H   HCH2   0   0.177    0.1992    1.9024   -5.2658
YYG        H4'     H   HCR5   0   0.250   -1.4788   -0.2444   -6.6395
YYG        H3'     H   HCR5   0   0.249   -2.4767    2.0769   -5.5399
YYG        HO3'    H   HOH1   0   0.449   -4.2199    0.5916   -4.7762
YYG        H2'     H   HCR5   0   0.256   -1.2325    1.7790   -3.4867
YYG        HO2'    H   HOH1   0   0.472   -3.2193    2.1072   -2.6032
YYG        H1'     H   HCR5   0   0.266   -2.1868   -1.1101   -3.3926
YYG         H8     H   HCR5   0   0.357    1.2950    0.3672   -3.4533
YYG         H31    H   HCH3   0   0.299   -3.5668   -2.3307   -0.4606
YYG         H32    H   HCH3   0   0.271   -3.4978   -1.0064   -1.6222
YYG         H33    H   HCH3   0   0.270   -2.7114   -2.5681   -1.9806
YYG        H101    H   HCH3   0   0.248   -3.1414   -3.6072    3.7951
YYG        H102    H   HCH3   0   0.240   -2.1330   -2.6785    4.9004
YYG        H103    H   HCH3   0   0.248   -3.5858   -1.9602    4.2151
YYG        H131    H   HCH2   0   0.264    1.2530   -1.7056    3.7374
YYG        H132    H   HCH2   0   0.254   -0.1042   -1.9969    4.7893
YYG        H141    H   HCH2   0   0.254   -0.7489    0.4470    4.5946
YYG        H142    H   HCH2   0   0.272    0.6693    0.7058    3.5949
YYG         H15    H   HCH1   0   0.289    2.1241   -0.1084    5.4518
YYG        H191    H   HCH3   0   0.253   -0.2202    3.9398    7.6988
YYG        H192    H   HCH3   0   0.242    1.5262    3.9924    7.3840
YYG        H193    H   HCH3   0   0.242    0.3745    4.2971    6.0638
YYG        HN20    H   HNH1   0   0.402   -0.4467   -0.5575    6.7588
YYG        H241    H   HCH3   0   0.250    0.2227   -1.4570   10.8452
YYG        H242    H   HCH3   0   0.237    1.8742   -1.6543   10.2299
YYG        H243    H   HCH3   0   0.236    1.2539   -0.0335   10.6140
YYG         C10    C   CH3    0  -0.744   -2.7390   -2.6140    3.9984
#
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
YYG   P       OP1   deloc         1.531 0.020     1.531
YYG   P       OP2   deloc         1.521 0.020     1.521
YYG   P       OP3   deloc         1.524 0.020     1.524
YYG   P      O5'    single        1.705 0.020     1.705
YYG  O5'     C5'    single        1.391 0.020     1.391
YYG  C5'     C4'    single        1.518 0.020     1.518
YYG  C5'     H5'    single        0.970 0.020     1.090
YYG  C5'     H5''   single        0.970 0.020     1.090
YYG  C4'     O4'    single        1.439 0.020     1.439
YYG  C4'     C3'    single        1.522 0.020     1.522
YYG  C4'     H4'    single        0.970 0.020     1.090
YYG  O4'     C1'    single        1.390 0.020     1.390
YYG  C3'     O3'    single        1.406 0.020     1.406
YYG  C3'     C2'    single        1.528 0.020     1.528
YYG  C3'     H3'    single        0.970 0.020     1.090
YYG  O3'     HO3'   single        0.850 0.020     0.980
YYG  C2'     O2'    single        1.396 0.020     1.396
YYG  C2'     C1'    single        1.529 0.020     1.529
YYG  C2'     H2'    single        0.970 0.020     1.090
YYG  O2'     HO2'   single        0.850 0.020     0.980
YYG  C1'      N9    single        1.456 0.020     1.456
YYG  C1'     H1'    single        0.970 0.020     1.090
YYG   N9      C8    aromatic      1.385 0.020     1.385
YYG   N9      C4    aromatic      1.361 0.020     1.361
YYG   C8      N7    aromatic      1.294 0.020     1.294
YYG   C8      H8    single        0.930 0.020     1.080
YYG   N7      C5    aromatic      1.369 0.020     1.369
YYG   C5      C6    single        1.426 0.020     1.426
YYG   C5      C4    aromatic      1.384 0.020     1.384
YYG   C6      O6    double        1.215 0.020     1.215
YYG   C6      N1    single        1.406 0.020     1.406
YYG   N1      C2    aromatic      1.375 0.020     1.375
YYG   N1      C12   aromatic      1.402 0.020     1.402
YYG   C2      N2    aromatic      1.296 0.020     1.296
YYG   C2      N3    single        1.372 0.020     1.372
YYG   N2      C11   aromatic      1.376 0.020     1.376
YYG   N3      C3    single        1.455 0.020     1.455
YYG   N3      C4    single        1.357 0.020     1.357
YYG   C3      H31   single        0.970 0.020     1.090
YYG   C3      H32   single        0.970 0.020     1.090
YYG   C3      H33   single        0.970 0.020     1.090
YYG   C10     C11   single        1.487 0.020     1.487
YYG   C10    H101   single        0.970 0.020     1.090
YYG   C10    H102   single        0.970 0.020     1.090
YYG   C10    H103   single        0.970 0.020     1.090
YYG   C11     C12   aromatic      1.361 0.020     1.361
YYG   C12     C13   single        1.489 0.020     1.489
YYG   C13     C14   single        1.531 0.020     1.531
YYG   C13    H131   single        0.970 0.020     1.090
YYG   C13    H132   single        0.970 0.020     1.090
YYG   C14     C15   single        1.531 0.020     1.531
YYG   C14    H141   single        0.970 0.020     1.090
YYG   C14    H142   single        0.970 0.020     1.090
YYG   C15     C16   single        1.522 0.020     1.522
YYG   C15     N20   single        1.438 0.020     1.438
YYG   C15     H15   single        0.970 0.020     1.090
YYG   C16     O17   double        1.205 0.020     1.205
YYG   C16     O18   single        1.319 0.020     1.319
YYG   O18     C19   single        1.429 0.020     1.429
YYG   C19    H191   single        0.970 0.020     1.090
YYG   C19    H192   single        0.970 0.020     1.090
YYG   C19    H193   single        0.970 0.020     1.090
YYG   N20     C21   single        1.349 0.020     1.349
YYG   N20    HN20   single        0.860 0.020     1.020
YYG   C21     O22   double        1.214 0.020     1.214
YYG   C21     O23   single        1.331 0.020     1.331
YYG   O23     C24   single        1.425 0.020     1.425
YYG   C24    H241   single        0.970 0.020     1.090
YYG   C24    H242   single        0.970 0.020     1.090
YYG   C24    H243   single        0.970 0.020     1.090
#
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
YYG  O5'      P       OP3         104.93 3.000
YYG  O5'      P       OP2         100.80 3.000
YYG   OP3     P       OP2         115.65 3.000
YYG  O5'      P       OP1         104.84 3.000
YYG   OP3     P       OP1         113.64 3.000
YYG   OP2     P       OP1         114.85 3.000
YYG  C5'     O5'      P           117.34 3.000
YYG  H5''    C5'     H5'          106.26 3.000
YYG  H5''    C5'     C4'          109.29 3.000
YYG  H5'     C5'     C4'          107.17 3.000
YYG  H5''    C5'     O5'          112.49 3.000
YYG  H5'     C5'     O5'          111.83 3.000
YYG  C4'     C5'     O5'          109.62 3.000
YYG  H4'     C4'     C3'          110.74 3.000
YYG  H4'     C4'     O4'          107.74 3.000
YYG  C3'     C4'     O4'          105.68 3.000
YYG  H4'     C4'     C5'          109.27 3.000
YYG  C3'     C4'     C5'          112.58 3.000
YYG  O4'     C4'     C5'          110.69 3.000
YYG  C1'     O4'     C4'          110.48 3.000
YYG  H3'     C3'     C2'          111.89 3.000
YYG  H3'     C3'     O3'          111.63 3.000
YYG  C2'     C3'     O3'          110.88 3.000
YYG  H3'     C3'     C4'          111.86 3.000
YYG  C2'     C3'     C4'          100.84 3.000
YYG  O3'     C3'     C4'          109.26 3.000
YYG  HO3'    O3'     C3'          107.95 3.000
YYG  H2'     C2'     C1'          109.02 3.000
YYG  H2'     C2'     O2'          111.76 3.000
YYG  C1'     C2'     O2'          110.42 3.000
YYG  H2'     C2'     C3'          109.04 3.000
YYG  C1'     C2'     C3'          100.66 3.000
YYG  O2'     C2'     C3'          115.29 3.000
YYG  HO2'    O2'     C2'          109.14 3.000
YYG  H1'     C1'      N9          107.95 3.000
YYG  H1'     C1'     C2'          110.47 3.000
YYG   N9     C1'     C2'          112.78 3.000
YYG  H1'     C1'     O4'          110.75 3.000
YYG   N9     C1'     O4'          109.01 3.000
YYG  C2'     C1'     O4'          105.88 3.000
YYG   C4      N9      C8          106.24 3.000
YYG   C4      N9     C1'          129.79 3.000
YYG   C8      N9     C1'          123.15 3.000
YYG   H8      C8      N7          124.68 3.000
YYG   H8      C8      N9          123.03 3.000
YYG   N7      C8      N9          112.26 3.000
YYG   C5      N7      C8          105.62 3.000
YYG   C4      C5      C6          123.04 3.000
YYG   C4      C5      N7          110.23 3.000
YYG   C6      C5      N7          126.73 3.000
YYG   N1      C6      O6          122.05 3.000
YYG   N1      C6      C5          110.93 3.000
YYG   O6      C6      C5          127.01 3.000
YYG   C12     N1      C2          105.85 3.000
YYG   C12     N1      C6          129.04 3.000
YYG   C2      N1      C6          125.05 3.000
YYG   N3      C2      N2          125.60 3.000
YYG   N3      C2      N1          121.87 3.000
YYG   N2      C2      N1          112.54 3.000
YYG   C11     N2      C2          105.44 3.000
YYG   C4      N3      C3          125.75 3.000
YYG   C4      N3      C2          115.72 3.000
YYG   C3      N3      C2          118.42 3.000
YYG   H33     C3      H32         110.28 3.000
YYG   H33     C3      H31         108.27 3.000
YYG   H32     C3      H31         108.61 3.000
YYG   H33     C3      N3          110.70 3.000
YYG   H32     C3      N3          110.89 3.000
YYG   H31     C3      N3          108.00 3.000
YYG   N3      C4      C5          123.28 3.000
YYG   N3      C4      N9          131.08 3.000
YYG   C5      C4      N9          105.64 3.000
YYG   C12     C11     C10         128.48 3.000
YYG   C12     C11     N2          111.33 3.000
YYG   C10     C11     N2          120.18 3.000
YYG   C13     C12     C11         129.15 3.000
YYG   C13     C12     N1          125.85 3.000
YYG   C11     C12     N1          104.85 3.000
YYG  H132     C13    H131         105.94 3.000
YYG  H132     C13     C14         109.61 3.000
YYG  H131     C13     C14         109.55 3.000
YYG  H132     C13     C12         106.84 3.000
YYG  H131     C13     C12         111.83 3.000
YYG   C14     C13     C12         112.79 3.000
YYG  H142     C14    H141         106.90 3.000
YYG  H142     C14     C15         108.48 3.000
YYG  H141     C14     C15         109.66 3.000
YYG  H142     C14     C13         109.38 3.000
YYG  H141     C14     C13         110.03 3.000
YYG   C15     C14     C13         112.23 3.000
YYG   H15     C15     N20         109.66 3.000
YYG   H15     C15     C16         106.12 3.000
YYG   N20     C15     C16         113.43 3.000
YYG   H15     C15     C14         108.22 3.000
YYG   N20     C15     C14         110.04 3.000
YYG   C16     C15     C14         109.19 3.000
YYG   O18     C16     O17         124.36 3.000
YYG   O18     C16     C15         112.89 3.000
YYG   O17     C16     C15         122.70 3.000
YYG   C19     O18     C16         117.45 3.000
YYG  H193     C19    H192         109.37 3.000
YYG  H193     C19    H191         109.47 3.000
YYG  H192     C19    H191         109.40 3.000
YYG  H193     C19     O18         111.29 3.000
YYG  H192     C19     O18         111.28 3.000
YYG  H191     C19     O18         105.95 3.000
YYG  HN20     N20     C21         118.64 3.000
YYG  HN20     N20     C15         118.63 3.000
YYG   C21     N20     C15         120.23 3.000
YYG   O23     C21     O22         124.58 3.000
YYG   O23     C21     N20         111.35 3.000
YYG   O22     C21     N20         124.07 3.000
YYG   C24     O23     C21         116.95 3.000
YYG  H243     C24    H242         109.26 3.000
YYG  H243     C24    H241         109.13 3.000
YYG  H242     C24    H241         109.17 3.000
YYG  H243     C24     O23         111.72 3.000
YYG  H242     C24     O23         111.65 3.000
YYG  H241     C24     O23         105.81 3.000
YYG  H103     C10    H102         107.63 3.000
YYG  H103     C10    H101         107.23 3.000
YYG  H102     C10    H101         107.81 3.000
YYG  H103     C10     C11         111.19 3.000
YYG  H102     C10     C11         111.89 3.000
YYG  H101     C10     C11         110.88 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
YYG CONST_01   C5      N7      C8      N9            0.00   0.0 0
YYG CONST_02   N7      C5      C4      N9            0.00   0.0 0
YYG CONST_03   C5      C4      N9      C8            0.00   0.0 0
YYG CONST_04   C4      C5      N7      C8            0.00   0.0 0
YYG CONST_05   C4      N9      C8      N7            0.00   0.0 0
YYG CONST_06   C11     N2      C2      N1            0.00   0.0 0
YYG CONST_07   N2      C11     C12     N1            0.00   0.0 0
YYG CONST_08   C11     C12     N1      C2            0.00   0.0 0
YYG CONST_09   C12     C11     N2      C2            0.00   0.0 0
YYG CONST_10   C12     N1      C2      N2            0.00   0.0 0
YYG CONST_11   N7      C8      N9      C1'         180.00   0.0 0
YYG CONST_12   C5      C4      N9      C1'         180.00   0.0 0
YYG CONST_13   N3      C4      N9      C1'           0.00   0.0 0
YYG CONST_14   C13     C12     N1      C6            0.00   0.0 0
YYG CONST_15   C10     C11     C12     N1          180.00   0.0 0
YYG CONST_16   C13     C12     N1      C2          180.00   0.0 0
YYG CONST_17   C10     C11     N2      C2          180.00   0.0 0
YYG CONST_18   C13     C12     C11     N2          180.00   0.0 0
YYG CONST_19   H8      C8      N9      C1'           0.00   0.0 0
YYG   Var_01   C14     C13     C12     N1           75.15  30.0 2
YYG   Var_02   H31     C3      N3      C2           -2.02  30.0 3
YYG   Var_03  H101     C10     C11     N2           52.83  30.0 2
YYG   Var_04   C4'     C5'     O5'     P          -144.35  30.0 3
YYG   Var_05   C15     C14     C13     C12         175.07  30.0 3
YYG   Var_06   O22     C21     N20     C15          -7.18  30.0 2
YYG   Var_07  H191     C19     O18     C16        -179.32  30.0 3
YYG   Var_08  H241     C24     O23     C21         179.01  30.0 3
#
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
YYG plan-1    C1' 0.020
YYG plan-1    N9  0.020
YYG plan-1    C8  0.020
YYG plan-1    N7  0.020
YYG plan-1    C5  0.020
YYG plan-1    C6  0.020
YYG plan-1    O6  0.020
YYG plan-1    N1  0.020
YYG plan-1    C2  0.020
YYG plan-1    N2  0.020
YYG plan-1    N3  0.020
YYG plan-1    C3  0.020
YYG plan-1    C4  0.020
YYG plan-1    C11 0.020
YYG plan-1    C12 0.020
YYG plan-1    C13 0.020
YYG plan-1    H8  0.020
YYG plan-1    C10 0.020
YYG plan-2    C15 0.020
YYG plan-2    C16 0.020
YYG plan-2    O17 0.020
YYG plan-2    O18 0.020
YYG plan-3    N20 0.020
YYG plan-3    C21 0.020
YYG plan-3    O22 0.020
YYG plan-3    O23 0.020
#
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
YYG chir_01   C4'     C5'     O4'     C3'   negativ
YYG chir_02   C3'     O3'     C4'     C2'   positiv
YYG chir_03   C2'     O2'     C3'     C1'   positiv
YYG chir_04   C1'     O4'     N9      C2'   negativ
YYG chir_05   C15     C14     C16     N20   negativ
#
