# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug 17 10:59:28 2020
#
#   Final geometry file: /net/cci/nigel/work/qm/PBEh-3c.None.CPCM/2/2MG.pdb
#   Ligand name: N-methylguanosine 5'-(dihydrogen phosphate)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
#
# Restraints Editor Exclusively Ligands (REEL)
#   - a module of PHENIX
#   - file written: Mon Aug 17 11:07:43 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
2MG 2MG 'N-methylguanosine 5'-(dihydrogen phosphate)' RNA 39 25 . 
#
data_comp_2MG
#
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
2MG         P      P   P     0     1.224     -0.7339    0.3548   -5.2066
2MG         OP1    O   O     0     -0.905    -2.0659   -0.2944   -4.8482
2MG         OP2    O   OP    -1    -0.896    -0.8210    1.7914   -5.7017
2MG         OP3    O   OP    -1    -0.904     0.2045   -0.5470   -6.0015
2MG         O5'    O   O2    0     -0.655     0.0541    0.5895   -3.7058
2MG         C5'    C   CH2   0     -0.125     0.2811   -0.5414   -2.9289
2MG         C4'    C   CH1   0     0.003      1.2567   -0.2199   -1.8214
2MG         O4'    O   O2    0     -0.496     0.7001    0.7396   -0.9191
2MG         C3'    C   CH1   0     -0.044     1.6158   -1.4138   -0.9437
2MG         O3'    O   OH1   0     -0.658     2.6625   -2.1446   -1.5221
2MG         C2'    C   CH1   0     -0.036     2.0016   -0.7342    0.3750
2MG         O2'    O   OH1   0     -0.666     3.3002   -0.2119    0.3073
2MG         C1'    C   CH1   0     0.171      1.0240    0.4407    0.4037
2MG         N9     N   NR5   0     -0.531    -0.1944    0.1152    1.1323
2MG         C8     C   CR15  0     0.084     -1.3810   -0.3746    0.6471
2MG         N7     N   N     0     -0.445    -2.2577   -0.5868    1.5815
2MG         C5     C   CR56  0     -0.093    -1.6251   -0.2242    2.7418
2MG         C6     C   CR6   0     0.497     -2.0776   -0.2343    4.0935
2MG         O6     O   O     0     -0.476    -3.1598   -0.5855    4.5345
2MG         N1     N   NR16  0     -0.744    -1.0776    0.2364    4.9514
2MG         C2     C   CR6   0     0.746      0.1736    0.6557    4.5837
2MG         N2     N   NH1   0     -0.666     0.9837    1.0800    5.5570
2MG         CM2    C   CH3   0     -0.508     2.3281    1.5340    5.2944
2MG         N3     N   N     0     -0.516     0.5872    0.6551    3.3396
2MG         C4     C   CR56  0     0.504     -0.3411    0.2155    2.4793
2MG         H5'    H   HCH2  0     0.184      0.7214   -1.3624   -3.5135
2MG        H5''    H   HCH2  0     0.174     -0.6495   -0.9370   -2.4918
2MG         H4'    H   HCH1  0     0.23       2.1739    0.1927   -2.2621
2MG         H3'    H   HCH1  0     0.24       0.7320   -2.0463   -0.7848
2MG        HO3'    H   HOH1  0     0.468      2.6703   -3.0291   -1.1424
2MG         H2'    H   HCH1  0     0.253      1.8734   -1.3917    1.2436
2MG        HO2'    H   HOH1  0     0.45       3.8393   -0.8359   -0.1949
2MG         H1'    H   HCH1  0     0.275      1.4664    1.3058    0.9062
2MG         H8     H   HCR5  0     0.29      -1.5453   -0.5386   -0.4061
2MG         HN1    H   HNR6  0     0.422     -1.3217    0.2572    5.9331
2MG         HN2    H   HNH1  0     0.414      0.6656    1.0526    6.5107
2MG        HM21    H   HCH3  0     0.256      2.7708    1.8360    6.2388
2MG        HM22    H   HCH3  0     0.241      2.9431    0.7464    4.8583
2MG        HM23    H   HCH3  0     0.241      2.3382    2.3886    4.6180
#
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
2MG   P       OP1   deloc         1.525 0.02   1.525
2MG   P       OP2   deloc         1.522 0.02   1.522
2MG   P       OP3   deloc         1.525 0.02   1.525
2MG   P       O5'   single        1.711 0.02   1.711
2MG   O5'     C5'   single        1.391 0.02   1.391
2MG   C5'     C4'   single        1.511 0.02   1.511
2MG   C5'     H5'   single        0.970 0.02   1.09
2MG   C5'    H5''   single        0.970 0.02   1.09
2MG   C4'     O4'   single        1.430 0.02   1.43
2MG   C4'     C3'   single        1.525 0.02   1.525
2MG   C4'     H4'   single        0.970 0.02   1.09
2MG   O4'     C1'   single        1.394 0.02   1.394
2MG   C3'     O3'   single        1.401 0.02   1.401
2MG   C3'     C2'   single        1.533 0.02   1.533
2MG   C3'     H3'   single        0.970 0.02   1.09
2MG   O3'    HO3'   single        0.850 0.02   0.98
2MG   C2'     O2'   single        1.401 0.02   1.401
2MG   C2'     C1'   single        1.529 0.02   1.529
2MG   C2'     H2'   single        0.970 0.02   1.09
2MG   O2'    HO2'   single        0.850 0.02   0.98
2MG   C1'     N9    single        1.456 0.02   1.456
2MG   C1'     H1'   single        0.970 0.02   1.09
2MG   N9      C8    aromatic      1.372 0.02   1.372
2MG   N9      C4    aromatic      1.359 0.02   1.359
2MG   C8      N7    aromatic      1.299 0.02   1.299
2MG   C8      H8    single        0.930 0.02   1.08
2MG   N7      C5    aromatic      1.370 0.02   1.37
2MG   C5      C6    single        1.425 0.02   1.425
2MG   C5      C4    aromatic      1.382 0.02   1.382
2MG   C6      O6    double        1.220 0.02   1.22
2MG   C6      N1    single        1.399 0.02   1.399
2MG   N1      C2    single        1.370 0.02   1.37
2MG   N1      HN1   single        0.860 0.02   1.02
2MG   C2      N2    single        1.336 0.02   1.336
2MG   C2      N3    double        1.311 0.02   1.311
2MG   N2      CM2   single        1.443 0.02   1.443
2MG   N2      HN2   single        0.860 0.02   1.02
2MG   CM2    HM21   single        0.970 0.02   1.09
2MG   CM2    HM22   single        0.970 0.02   1.09
2MG   CM2    HM23   single        0.970 0.02   1.09
2MG   N3      C4    single        1.340 0.02   1.34
#
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
2MG   O5'     P       OP3         104.76 3.0
2MG   O5'     P       OP2         100.50 3.0
2MG   OP3     P       OP2         115.08 3.0
2MG   O5'     P       OP1         104.75 3.0
2MG   OP3     P       OP1         114.10 3.0
2MG   OP2     P       OP1         115.37 3.0
2MG   C5'     O5'     P           116.97 3.0
2MG  H5''     C5'     H5'         106.33 3.0
2MG  H5''     C5'     C4'         109.33 3.0
2MG   H5'     C5'     C4'         106.86 3.0
2MG  H5''     C5'     O5'         112.07 3.0
2MG   H5'     C5'     O5'         112.05 3.0
2MG   C4'     C5'     O5'         109.99 3.0
2MG   H4'     C4'     C3'         109.18 3.0
2MG   H4'     C4'     O4'         109.04 3.0
2MG   C3'     C4'     O4'         104.70 3.0
2MG   H4'     C4'     C5'         108.98 3.0
2MG   C3'     C4'     C5'         114.05 3.0
2MG   O4'     C4'     C5'         110.74 3.0
2MG   C1'     O4'     C4'         111.37 3.0
2MG   H3'     C3'     C2'         109.48 3.0
2MG   H3'     C3'     O3'         111.12 3.0
2MG   C2'     C3'     O3'         113.47 3.0
2MG   H3'     C3'     C4'         110.16 3.0
2MG   C2'     C3'     C4'         101.97 3.0
2MG   O3'     C3'     C4'         110.28 3.0
2MG  HO3'     O3'     C3'         108.81 3.0
2MG   H2'     C2'     C1'         111.78 3.0
2MG   H2'     C2'     O2'         111.72 3.0
2MG   C1'     C2'     O2'         107.88 3.0
2MG   H2'     C2'     C3'         112.71 3.0
2MG   C1'     C2'     C3'         101.30 3.0
2MG   O2'     C2'     C3'         110.91 3.0
2MG  HO2'     O2'     C2'         107.56 3.0
2MG   H1'     C1'     N9          106.57 3.0
2MG   H1'     C1'     C2'         110.97 3.0
2MG   N9      C1'     C2'         111.87 3.0
2MG   H1'     C1'     O4'         111.11 3.0
2MG   N9      C1'     O4'         109.16 3.0
2MG   C2'     C1'     O4'         107.19 3.0
2MG   C4      N9      C8          106.47 3.0
2MG   C4      N9      C1'         124.73 3.0
2MG   C8      N9      C1'         128.77 3.0
2MG   H8      C8      N7          125.10 3.0
2MG   H8      C8      N9          122.09 3.0
2MG   N7      C8      N9          112.80 3.0
2MG   C5      N7      C8          104.74 3.0
2MG   C4      C5      C6          118.50 3.0
2MG   C4      C5      N7          110.62 3.0
2MG   C6      C5      N7          130.88 3.0
2MG   N1      C6      O6          120.60 3.0
2MG   N1      C6      C5          110.62 3.0
2MG   O6      C6      C5          128.78 3.0
2MG   HN1     N1      C2          118.33 3.0
2MG   HN1     N1      C6          115.43 3.0
2MG   C2      N1      C6          126.24 3.0
2MG   N3      C2      N2          120.02 3.0
2MG   N3      C2      N1          122.87 3.0
2MG   N2      C2      N1          117.11 3.0
2MG   HN2     N2      CM2         118.41 3.0
2MG   HN2     N2      C2          119.38 3.0
2MG   CM2     N2      C2          122.17 3.0
2MG  HM23     CM2    HM22         108.23 3.0
2MG  HM23     CM2    HM21         108.54 3.0
2MG  HM22     CM2    HM21         108.59 3.0
2MG  HM23     CM2     N2          111.60 3.0
2MG  HM22     CM2     N2          111.77 3.0
2MG  HM21     CM2     N2          108.00 3.0
2MG   C4      N3      C2          113.01 3.0
2MG   N3      C4      C5          128.75 3.0
2MG   N3      C4      N9          125.87 3.0
2MG   C5      C4      N9          105.37 3.0
#
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
2MG CONST_01   C5      N7      C8      N9            0.00   0.0 0
2MG CONST_02   N7      C5      C4      N9            0.00   0.0 0
2MG CONST_03   C5      C4      N9      C8            0.00   0.0 0
2MG CONST_04   C4      C5      N7      C8            0.00   0.0 0
2MG CONST_05   C4      N9      C8      N7            0.00   0.0 0
2MG CONST_06   N7      C8      N9      C1'         180.00   0.0 0
2MG CONST_07   C5      C4      N9      C1'         180.00   0.0 0
2MG CONST_08   N3      C4      N9      C1'           0.00   0.0 0
2MG CONST_09   C2      N1      C6      C5            0.00   0.0 0
2MG CONST_10   N3      C2      N1      C6            0.00   0.0 0
2MG CONST_11   C4      N3      C2      N1            0.00   0.0 0
2MG CONST_12   N2      C2      N1      C6          180.00   0.0 0
2MG CONST_13   C2      N1      C6      O6          180.00   0.0 0
2MG CONST_14   C4      N3      C2      N2          180.00   0.0 0
2MG CONST_15   H8      C8      N9      C1'           0.00   0.0 0
2MG CONST_16   HN1     N1      C6      C5          180.00   0.0 0
2MG CONST_17   CM2     N2      C2      N1          180.00   0.0 0
2MG CONST_18   N3      C2      N2      CM2           0.00   0.0 0
2MG CONST_19   HN2     N2      C2      N1            0.00   0.0 0
2MG   Var_01   C4'     C5'     O5'     P           166.55  30.0 3
2MG   Var_02  HM21     CM2     N2      C2          179.22  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
2MG plan-1    C1' 0.020
2MG plan-1    N9  0.020
2MG plan-1    C8  0.020
2MG plan-1    N7  0.020
2MG plan-1    C5  0.020
2MG plan-1    C6  0.020
2MG plan-1    O6  0.020
2MG plan-1    N1  0.020
2MG plan-1    C2  0.020
2MG plan-1    N2  0.020
2MG plan-1    CM2 0.020
2MG plan-1    N3  0.020
2MG plan-1    C4  0.020
2MG plan-1    H8  0.020
2MG plan-1    HN1 0.020
2MG plan-1    HN2 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
2MG chir_01   C4'     C5'     O4'     C3'   negativ
2MG chir_02   C3'     O3'     C4'     C2'   positiv
2MG chir_03   C2'     O2'     C3'     C1'   positiv
2MG chir_04   C1'     O4'     N9      C2'   negativ
#
