# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug 17 11:24:31 2020
#
#   Final geometry file: /net/cci/nigel/work/qm/PBEh-3c.None.CPCM/o/OMC.cif
#   Ligand name: 2'-O-methylcytidine 5'-(dihydrogen phosphate)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=NC2=O)N
#
# Restraints Editor Exclusively Ligands (REEL)
#   - a module of PHENIX
#   - file written: Mon Aug 17 11:25:13 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
OMC OMC '2'-O-methylcytidine 5'-(dihydrogen phosphate)' RNA 36 22 . 
2020-08-17 2020-08-17
;
CIF prepared directly in eLBOW
;
#
data_comp_OMC
#
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
OMC         N1     N   NR6    0  -0.566   -0.2044   -0.5295   -2.2423
OMC         C2     C   CR6    0   0.601   -1.1554    0.4892   -2.0297
OMC         N3     N   N      0  -0.542   -2.1491    0.6288   -2.9330
OMC         C4     C   CR6    0   0.514   -2.2316   -0.1505   -3.9919
OMC         C5     C   CR16   0  -0.477   -1.2823   -1.1876   -4.2444
OMC         C6     C   CR16   0   0.096   -0.3026   -1.3312   -3.3328
OMC         O2     O   O      0  -0.500   -1.0585    1.2136   -1.0517
OMC         N4     N   NH2    0  -0.809   -3.2357    0.0433   -4.8457
OMC        C1'     C   CH1    0   0.242    0.8783   -0.7782   -1.3049
OMC        C2'     C   CH1    0  -0.017    1.8339    0.3854   -1.0471
OMC        O2'     O   O2     0  -0.484    2.7338    0.4728   -2.1070
OMC         CM2    C   CH3    0  -0.409    3.5891    1.5882   -2.0241
OMC        C3'     C   CH1    0  -0.051    2.4232   -0.0217    0.3064
OMC        C4'     C   CH1    0  -0.028    1.2120   -0.6672    0.9895
OMC        O4'     O   O2     0  -0.494    0.3806   -1.1691   -0.0637
OMC        O3'     O   OH1    0  -0.673    3.4620   -0.9376    0.0599
OMC        C5'     C   CH2    0  -0.116    0.4535    0.2891    1.8880
OMC        O5'     O   O2     0  -0.661   -0.6543   -0.3568    2.4343
OMC         P      P   P      0   1.218   -1.2283    0.2391    3.9275
OMC         OP1    O   O      0  -0.905   -1.4339    1.7339    3.7021
OMC         OP2    O   OP    -1  -0.899   -2.5045   -0.5762    4.0888
OMC         OP3    O   OP    -1  -0.905   -0.1257   -0.0890    4.9297
OMC         H5     H   HCR6   0   0.288   -1.3437   -1.8332   -5.1069
OMC         H6     H   HCR6   0   0.319    0.4522   -2.0988   -3.4319
OMC        HN41    H   HNH2   0   0.402   -3.9256    0.7523   -4.6642
OMC        HN42    H   HNH2   0   0.413   -3.3539   -0.5355   -5.6584
OMC        H1'     H   HCH1   0   0.237    1.4608   -1.5886   -1.7613
OMC        H2'     H   HCH1   0   0.258    1.2852    1.3246   -0.9198
OMC        HM21    H   HCH3   0   0.237    4.1918    1.6099   -2.9308
OMC        HM22    H   HCH3   0   0.209    3.0280    2.5272   -1.9581
OMC        HM23    H   HCH3   0   0.215    4.2627    1.5323   -1.1639
OMC        H3'     H   HCH1   0   0.245    2.7820    0.8426    0.8798
OMC        H4'     H   HCH1   0   0.230    1.5396   -1.5212    1.5947
OMC        HO3'    H   HOH1   0   0.454    3.8088   -1.2334    0.9073
OMC        H5'     H   HCH2   0   0.169    1.1622    0.6142    2.6636
OMC        H5''    H   HCH2   0   0.188    0.1651    1.1849    1.3253
#
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
OMC   N1      C2    single        1.410 0.020     1.410
OMC   N1      C6    single        1.357 0.020     1.357
OMC   N1     C1'    single        1.454 0.020     1.454
OMC   C2      N3    single        1.350 0.020     1.350
OMC   C2      O2    double        1.221 0.020     1.221
OMC   N3      C4    double        1.317 0.020     1.317
OMC   C4      C5    single        1.428 0.020     1.428
OMC   C4      N4    single        1.332 0.020     1.332
OMC   C5      C6    double        1.346 0.020     1.346
OMC   C5      H5    single        0.930 0.020     1.080
OMC   C6      H6    single        0.930 0.020     1.080
OMC   N4     HN41   single        0.860 0.020     1.020
OMC   N4     HN42   single        0.860 0.020     1.020
OMC  C1'     C2'    single        1.528 0.020     1.528
OMC  C1'     O4'    single        1.393 0.020     1.393
OMC  C1'     H1'    single        0.970 0.020     1.090
OMC  C2'     O2'    single        1.393 0.020     1.393
OMC  C2'     C3'    single        1.531 0.020     1.531
OMC  C2'     H2'    single        0.970 0.020     1.090
OMC  O2'      CM2   single        1.408 0.020     1.408
OMC   CM2    HM21   single        0.970 0.020     1.090
OMC   CM2    HM22   single        0.970 0.020     1.090
OMC   CM2    HM23   single        0.970 0.020     1.090
OMC  C3'     C4'    single        1.533 0.020     1.533
OMC  C3'     O3'    single        1.407 0.020     1.407
OMC  C3'     H3'    single        0.970 0.020     1.090
OMC  C4'     O4'    single        1.433 0.020     1.433
OMC  C4'     C5'    single        1.516 0.020     1.516
OMC  C4'     H4'    single        0.970 0.020     1.090
OMC  O3'     HO3'   single        0.850 0.020     0.980
OMC  C5'     O5'    single        1.394 0.020     1.394
OMC  C5'     H5'    single        0.970 0.020     1.090
OMC  C5'     H5''   single        0.970 0.020     1.090
OMC  O5'      P     single        1.707 0.020     1.707
OMC   P       OP1   deloc         1.526 0.020     1.526
OMC   P       OP2   deloc         1.523 0.020     1.523
OMC   P       OP3   deloc         1.526 0.020     1.526
#
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
OMC  C1'      N1      C6          118.11 3.000
OMC  C1'      N1      C2          121.93 3.000
OMC   C6      N1      C2          119.95 3.000
OMC   O2      C2      N3          122.21 3.000
OMC   O2      C2      N1          119.74 3.000
OMC   N3      C2      N1          118.06 3.000
OMC   C4      N3      C2          121.51 3.000
OMC   N4      C4      C5          119.55 3.000
OMC   N4      C4      N3          118.44 3.000
OMC   C5      C4      N3          122.00 3.000
OMC   H5      C5      C6          121.27 3.000
OMC   H5      C5      C4          122.53 3.000
OMC   C6      C5      C4          116.20 3.000
OMC   H6      C6      C5          121.46 3.000
OMC   H6      C6      N1          116.27 3.000
OMC   C5      C6      N1          122.27 3.000
OMC  HN42     N4     HN41         118.12 3.000
OMC  HN42     N4      C4          121.55 3.000
OMC  HN41     N4      C4          120.26 3.000
OMC  H1'     C1'     O4'          110.66 3.000
OMC  H1'     C1'     C2'          107.50 3.000
OMC  O4'     C1'     C2'          106.67 3.000
OMC  H1'     C1'      N1          104.68 3.000
OMC  O4'     C1'      N1          110.88 3.000
OMC  C2'     C1'      N1          116.39 3.000
OMC  H2'     C2'     C3'          108.55 3.000
OMC  H2'     C2'     O2'          111.00 3.000
OMC  C3'     C2'     O2'          116.14 3.000
OMC  H2'     C2'     C1'          111.06 3.000
OMC  C3'     C2'     C1'          100.80 3.000
OMC  O2'     C2'     C1'          108.87 3.000
OMC   CM2    O2'     C2'          113.41 3.000
OMC  HM23     CM2    HM22         108.16 3.000
OMC  HM23     CM2    HM21         108.35 3.000
OMC  HM22     CM2    HM21         108.45 3.000
OMC  HM23     CM2    O2'          112.33 3.000
OMC  HM22     CM2    O2'          111.79 3.000
OMC  HM21     CM2    O2'          107.64 3.000
OMC  H3'     C3'     O3'          111.28 3.000
OMC  H3'     C3'     C4'          110.92 3.000
OMC  O3'     C3'     C4'          112.79 3.000
OMC  H3'     C3'     C2'          112.23 3.000
OMC  O3'     C3'     C2'          107.60 3.000
OMC  C4'     C3'     C2'          101.64 3.000
OMC  H4'     C4'     C5'          108.28 3.000
OMC  H4'     C4'     O4'          107.83 3.000
OMC  C5'     C4'     O4'          111.50 3.000
OMC  H4'     C4'     C3'          109.74 3.000
OMC  C5'     C4'     C3'          113.20 3.000
OMC  O4'     C4'     C3'          106.17 3.000
OMC  C4'     O4'     C1'          110.44 3.000
OMC  HO3'    O3'     C3'          108.18 3.000
OMC  H5''    C5'     H5'          106.86 3.000
OMC  H5''    C5'     O5'          111.76 3.000
OMC  H5'     C5'     O5'          111.88 3.000
OMC  H5''    C5'     C4'          110.05 3.000
OMC  H5'     C5'     C4'          106.39 3.000
OMC  O5'     C5'     C4'          109.74 3.000
OMC   P      O5'     C5'          116.63 3.000
OMC   OP3     P       OP2         114.89 3.000
OMC   OP3     P       OP1         113.90 3.000
OMC   OP2     P       OP1         115.29 3.000
OMC   OP3     P      O5'          104.86 3.000
OMC   OP2     P      O5'          100.81 3.000
OMC   OP1     P      O5'          104.96 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
OMC CONST_01   C4      N3      C2      N1            0.00   0.0 0
OMC CONST_02   C5      C4      N3      C2            0.00   0.0 0
OMC CONST_03   C6      N1      C2      N3            0.00   0.0 0
OMC CONST_04   C1'     N1      C2      N3          180.00   0.0 0
OMC CONST_05   N4      C4      N3      C2          180.00   0.0 0
OMC CONST_06   O2      C2      N3      C4          180.00   0.0 0
OMC CONST_07   O2      C2      N1      C6          180.00   0.0 0
OMC CONST_08   C1'     N1      C2      O2            0.00   0.0 0
OMC CONST_09  HN41     N4      C4      N3            0.00   0.0 0
OMC CONST_10  HN42     N4      C4      N3          180.00   0.0 0
OMC   Var_01  HM21     CM2     O2'     C2'        -175.50  30.0 3
OMC   Var_02   OP1     P       O5'     C5'          52.93  30.0 3
OMC   Var_03   H5'     C5'     O5'     P            36.07  30.0 2
#
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
OMC plan-1    N1  0.020
OMC plan-1    C2  0.020
OMC plan-1    N3  0.020
OMC plan-1    C4  0.020
OMC plan-1    C5  0.020
OMC plan-1    C6  0.020
OMC plan-1    O2  0.020
OMC plan-1    N4  0.020
OMC plan-1    C1' 0.020
OMC plan-1    H5  0.020
OMC plan-1    H6  0.020
OMC plan-1   HN41 0.020
OMC plan-1   HN42 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
OMC chir_01   C1'     N1      C2'     O4'   negativ
OMC chir_02   C2'     O2'     C3'     C1'   positiv
OMC chir_03   C3'     O3'     C2'     C4'   negativ
OMC chir_04   C4'     O4'     C3'     C5'   negativ
#
