# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug 17 11:41:20 2020
#
#   Final geometry file: /net/cci/nigel/work/qm/PBEh-3c.None.CPCM/5/5MC.cif
#   Ligand name: 5-methylcytidine 5'-(dihydrogen phosphate)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C(=O)N=C1N
#
# Restraints Editor Exclusively Ligands (REEL)
#   - a module of PHENIX
#   - file written: Mon Aug 17 11:41:54 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
5MC 5MC '5-methylcytidine 5'-(dihydrogen phosphate)' RNA 36 22 . 
2020-08-17 2020-08-17
;
CIF prepared directly in eLBOW
;
#
data_comp_5MC
#
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
5MC         P      P   P      0   1.220    1.2044   -0.3552   -4.1551
5MC         OP1    O   O      0  -0.905    1.9664    0.9427   -3.9087
5MC         OP2    O   OP    -1  -0.897    2.0719   -1.5938   -4.3333
5MC         OP3    O   OP    -1  -0.905    0.0556   -0.2237   -5.1498
5MC        O5'     O   O2     0  -0.660    0.4481   -0.7108   -2.6642
5MC        C5'     C   CH2    0  -0.133   -0.3412    0.2899   -2.1017
5MC        C4'     C   CH1    0   0.015   -1.2830   -0.2960   -1.0758
5MC        O4'     O   O2     0  -0.493   -0.5449   -0.8262    0.0145
5MC        C3'     C   CH1    0  -0.031   -2.2281    0.7372   -0.4671
5MC        O3'     O   OH1    0  -0.668   -3.4055    0.8257   -1.2348
5MC        C2'     C   CH1    0  -0.046   -2.4852    0.1823    0.9458
5MC        O2'     O   OH1    0  -0.679   -3.6174   -0.6528    0.9433
5MC        C1'     C   CH1    0   0.209   -1.2553   -0.7024    1.2131
5MC         N1     N   NT     0  -0.557   -0.3532   -0.2607    2.2655
5MC         C2     C   C      0   0.599    0.2246    1.0133    2.2245
5MC         O2     O   O      0  -0.512   -0.0876    1.7886    1.3303
5MC         N3     N   N      0  -0.539    1.1071    1.3392    3.1892
5MC         C4     C   C      0   0.483    1.4266    0.4879    4.1429
5MC         N4     N   NH2    0  -0.811    2.3075    0.8836    5.0617
5MC         C5     C   C      0  -0.114    0.8667   -0.8325    4.2256
5MC         C6     C   C1     0   0.057   -0.0108   -1.1356    3.2474
5MC         CM5    C   CH3    0  -0.745    1.2400   -1.7945    5.3081
5MC        H5'     H   HCH2   0   0.175   -0.9615    0.7996   -2.8538
5MC        H5''    H   HCH2   0   0.176    0.2630    1.0670   -1.6118
5MC        H4'     H   HCH1   0   0.214   -1.8823   -1.0925   -1.5427
5MC        H3'     H   HCH1   0   0.254   -1.7318    1.7055   -0.3957
5MC        HO3'    H   HOH1   0   0.467   -3.7648    1.7136   -1.1457
5MC        H2'     H   HCH1   0   0.241   -2.5907    0.9751    1.6938
5MC        HO2'    H   HOH1   0   0.446   -4.1898   -0.3339    0.2318
5MC        H1'     H   HCH1   0   0.246   -1.6198   -1.6804    1.5446
5MC        HN41    H   HNH2   0   0.404    2.7141    1.8018    5.0032
5MC        HN42    H   HNH2   0   0.421    2.6143    0.2832    5.8064
5MC         H6     H   H      0   0.309   -0.4890   -2.1055    3.2071
5MC        HM51    H   HCH3   0   0.250    2.3093   -2.0171    5.3007
5MC        HM52    H   HCH3   0   0.250    0.9934   -1.4069    6.2990
5MC        HM53    H   HCH3   0   0.262    0.7102   -2.7379    5.1856
#
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
5MC   P       OP1   deloc         1.525 0.020     1.525
5MC   P       OP2   deloc         1.523 0.020     1.523
5MC   P       OP3   deloc         1.525 0.020     1.525
5MC   P      O5'    single        1.709 0.020     1.709
5MC  O5'     C5'    single        1.393 0.020     1.393
5MC  C5'     C4'    single        1.511 0.020     1.511
5MC  C5'     H5'    single        0.970 0.020     1.090
5MC  C5'     H5''   single        0.970 0.020     1.090
5MC  C4'     O4'    single        1.419 0.020     1.419
5MC  C4'     C3'    single        1.527 0.020     1.527
5MC  C4'     H4'    single        0.970 0.020     1.090
5MC  O4'     C1'    single        1.399 0.020     1.399
5MC  C3'     O3'    single        1.408 0.020     1.408
5MC  C3'     C2'    single        1.540 0.020     1.540
5MC  C3'     H3'    single        0.970 0.020     1.090
5MC  O3'     HO3'   single        0.850 0.020     0.980
5MC  C2'     O2'    single        1.407 0.020     1.407
5MC  C2'     C1'    single        1.539 0.020     1.539
5MC  C2'     H2'    single        0.970 0.020     1.090
5MC  O2'     HO2'   single        0.850 0.020     0.980
5MC  C1'      N1    single        1.455 0.020     1.455
5MC  C1'     H1'    single        0.970 0.020     1.090
5MC   N1      C2    single        1.399 0.020     1.399
5MC   N1      C6    single        1.359 0.020     1.359
5MC   C2      O2    double        1.224 0.020     1.224
5MC   C2      N3    single        1.347 0.020     1.347
5MC   N3      C4    double        1.318 0.020     1.318
5MC   C4      N4    single        1.333 0.020     1.333
5MC   C4      C5    single        1.437 0.020     1.437
5MC   N4     HN41   single        0.860 0.020     1.020
5MC   N4     HN42   single        0.860 0.020     1.020
5MC   C5      C6    double        1.349 0.020     1.349
5MC   C5      CM5   single        1.495 0.020     1.495
5MC   C6      H6    single        0.930 0.020     1.080
5MC   CM5    HM51   single        0.970 0.020     1.090
5MC   CM5    HM52   single        0.970 0.020     1.090
5MC   CM5    HM53   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
5MC  O5'      P       OP3         104.69 3.000
5MC  O5'      P       OP2         100.65 3.000
5MC   OP3     P       OP2         115.02 3.000
5MC  O5'      P       OP1         104.90 3.000
5MC   OP3     P       OP1         114.10 3.000
5MC   OP2     P       OP1         115.25 3.000
5MC  C5'     O5'      P           116.96 3.000
5MC  H5''    C5'     H5'          106.68 3.000
5MC  H5''    C5'     C4'          108.31 3.000
5MC  H5'     C5'     C4'          107.01 3.000
5MC  H5''    C5'     O5'          112.09 3.000
5MC  H5'     C5'     O5'          112.10 3.000
5MC  C4'     C5'     O5'          110.41 3.000
5MC  H4'     C4'     C3'          108.77 3.000
5MC  H4'     C4'     O4'          109.80 3.000
5MC  C3'     C4'     O4'          105.57 3.000
5MC  H4'     C4'     C5'          109.39 3.000
5MC  C3'     C4'     C5'          113.21 3.000
5MC  O4'     C4'     C5'          110.02 3.000
5MC  C1'     O4'     C4'          111.16 3.000
5MC  H3'     C3'     C2'          109.63 3.000
5MC  H3'     C3'     O3'          111.13 3.000
5MC  C2'     C3'     O3'          112.54 3.000
5MC  H3'     C3'     C4'          110.20 3.000
5MC  C2'     C3'     C4'          103.02 3.000
5MC  O3'     C3'     C4'          110.04 3.000
5MC  HO3'    O3'     C3'          108.65 3.000
5MC  H2'     C2'     C1'          112.00 3.000
5MC  H2'     C2'     O2'          110.70 3.000
5MC  C1'     C2'     O2'          107.59 3.000
5MC  H2'     C2'     C3'          112.46 3.000
5MC  C1'     C2'     C3'          103.49 3.000
5MC  O2'     C2'     C3'          110.29 3.000
5MC  HO2'    O2'     C2'          106.37 3.000
5MC  H1'     C1'      N1          104.99 3.000
5MC  H1'     C1'     C2'          107.46 3.000
5MC   N1     C1'     C2'          116.54 3.000
5MC  H1'     C1'     O4'          110.45 3.000
5MC   N1     C1'     O4'          109.37 3.000
5MC  C2'     C1'     O4'          107.94 3.000
5MC   C6      N1      C2          120.21 3.000
5MC   C6      N1     C1'          118.91 3.000
5MC   C2      N1     C1'          120.75 3.000
5MC   N3      C2      O2          122.47 3.000
5MC   N3      C2      N1          118.01 3.000
5MC   O2      C2      N1          119.52 3.000
5MC   C4      N3      C2          121.38 3.000
5MC   C5      C4      N4          119.39 3.000
5MC   C5      C4      N3          122.75 3.000
5MC   N4      C4      N3          117.86 3.000
5MC  HN42     N4     HN41         117.72 3.000
5MC  HN42     N4      C4          122.37 3.000
5MC  HN41     N4      C4          119.87 3.000
5MC   CM5     C5      C6          122.88 3.000
5MC   CM5     C5      C4          122.39 3.000
5MC   C6      C5      C4          114.73 3.000
5MC   H6      C6      C5          121.06 3.000
5MC   H6      C6      N1          116.02 3.000
5MC   C5      C6      N1          122.91 3.000
5MC  HM53     CM5    HM52         107.44 3.000
5MC  HM53     CM5    HM51         107.40 3.000
5MC  HM52     CM5    HM51         107.43 3.000
5MC  HM53     CM5     C5          110.76 3.000
5MC  HM52     CM5     C5          111.84 3.000
5MC  HM51     CM5     C5          111.75 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
5MC CONST_01   N3      C2      N1      C1'         180.00   0.0 0
5MC CONST_02   C4      N3      C2      N1            0.00   0.0 0
5MC CONST_03   C5      C4      N3      C2            0.00   0.0 0
5MC CONST_04   C6      N1      C2      N3            0.00   0.0 0
5MC CONST_05   O2      C2      N1      C1'           0.00   0.0 0
5MC CONST_06   N4      C4      N3      C2          180.00   0.0 0
5MC CONST_07   C6      N1      C2      O2          180.00   0.0 0
5MC CONST_08   C4      N3      C2      O2          180.00   0.0 0
5MC CONST_09  HN41     N4      C4      N3            0.00   0.0 0
5MC CONST_10  HN42     N4      C4      N3          180.00   0.0 0
5MC   Var_01  HM51     CM5     C5      C4          -59.92  30.0 3
5MC   Var_02   C4'     C5'     O5'     P           161.18  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
5MC plan-1    C1' 0.020
5MC plan-1    N1  0.020
5MC plan-1    C2  0.020
5MC plan-1    O2  0.020
5MC plan-1    N3  0.020
5MC plan-1    C4  0.020
5MC plan-1    N4  0.020
5MC plan-1    C5  0.020
5MC plan-1    C6  0.020
5MC plan-1    CM5 0.020
5MC plan-1   HN41 0.020
5MC plan-1   HN42 0.020
5MC plan-1    H6  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
5MC chir_01   C4'     C5'     O4'     C3'   negativ
5MC chir_02   C3'     O3'     C4'     C2'   positiv
5MC chir_03   C2'     O2'     C3'     C1'   positiv
5MC chir_04   C1'     O4'     N1      C2'   negativ
#
