# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug 17 11:52:37 2020
#
#   Final geometry file: /net/cci/nigel/work/qm/PBEh-3c.None.CPCM/1/1MA.cif
#   Ligand name: 1-methyladenosine 5'-(dihydrogen phosphate)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C=Nc2n(cnc2C1=N)[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 11:53:12 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
1MA 1MA '1-methyladenosine 5'-(dihydrogen phosphate)' RNA 38 24 . 
2020-08-17 2020-08-17
;
CIF prepared directly in eLBOW
;
#
data_comp_1MA
#
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
1MA         P      P   P      0   1.233   -3.4291   -1.8088   -0.0003
1MA         OP1    O   O      0  -0.897   -4.5520   -1.6471   -1.0171
1MA         OP2    O   OP    -1  -0.890   -3.7940   -2.5630    1.2686
1MA         OP3    O   OP    -1  -0.867   -2.0900   -2.2098   -0.6258
1MA        O5'     O   O2     0  -0.655   -3.1671   -0.2431    0.6224
1MA        C5'     C   CH2    0  -0.120   -2.7816    0.7482   -0.2736
1MA        C4'     C   CH1    0  -0.049   -1.9094    1.7649    0.4444
1MA        O4'     O   O2     0  -0.493   -0.7758    1.1334    1.0561
1MA        C3'     C   CH1    0  -0.026   -1.3304    2.8095   -0.4963
1MA        O3'     O   OH1    0  -0.672   -1.0627    3.9846    0.2266
1MA        C2'     C   CH1    0  -0.054   -0.0298    2.1274   -0.9281
1MA        O2'     O   OH1    0  -0.655    0.9749    2.9961   -1.3638
1MA        C1'     C   CH1    0   0.228    0.3980    1.4433    0.3729
1MA         N9     N   NR5    0  -0.529    1.1663    0.2353    0.1626
1MA         C8     C   CR15   0   0.022    0.6985   -1.0012   -0.1898
1MA         N7     N   N      0  -0.460    1.6669   -1.8650   -0.3530
1MA         C5     C   CR5    0   0.016    2.8135   -1.1693   -0.1026
1MA         C6     C   C      0   0.401    4.1804   -1.6103   -0.1334
1MA         N6     N   N      0  -0.674    4.5402   -2.7974   -0.4319
1MA         N1     N   NT     0  -0.514    5.0532   -0.5530    0.2092
1MA         CM1    C   CH3    0  -0.559    6.4785   -0.8344    0.2336
1MA         C2     C   C1     0   0.153    4.6270    0.6996    0.5204
1MA         N3     N   N      0  -0.457    3.4037    1.1080    0.5435
1MA         C4     C   CR5    0   0.459    2.5233    0.1330    0.2210
1MA        H5'     H   HCH2   0   0.175   -2.2381    0.3392   -1.1367
1MA        H5''    H   HCH2   0   0.189   -3.6458    1.2923   -0.6845
1MA        H4'     H   HCH1   0   0.247   -2.4924    2.2381    1.2410
1MA        H3'     H   HCH1   0   0.244   -1.9952    3.0016   -1.3493
1MA        HO3'    H   HOH1   0   0.447   -0.3907    4.4818   -0.2544
1MA        H2'     H   HCH1   0   0.249   -0.2525    1.3638   -1.6833
1MA        HO2'    H   HOH1   0   0.468    0.8292    3.1941   -2.2943
1MA        H1'     H   HCH1   0   0.253    1.0384    2.1157    0.9549
1MA         H8     H   HCR5   0   0.350   -0.3614   -1.2367   -0.2961
1MA        HN61    H   H      0   0.344    5.5437   -2.9303   -0.4078
1MA        HM11    H   HCH3   0   0.266    6.8283   -1.1476   -0.7496
1MA        HM12    H   HCH3   0   0.275    7.0195    0.0626    0.5184
1MA        HM13    H   HCH3   0   0.266    6.7041   -1.6165    0.9578
1MA         H2     H   H      0   0.287    5.4139    1.4005    0.7689
#
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
1MA   P       OP1   deloc         1.523 0.020     1.523
1MA   P       OP2   deloc         1.521 0.020     1.521
1MA   P       OP3   deloc         1.531 0.020     1.531
1MA   P      O5'    single        1.705 0.020     1.705
1MA  O5'     C5'    single        1.391 0.020     1.391
1MA  C5'     C4'    single        1.520 0.020     1.520
1MA  C5'     H5'    single        0.970 0.020     1.090
1MA  C5'     H5''   single        0.970 0.020     1.090
1MA  C4'     O4'    single        1.435 0.020     1.435
1MA  C4'     C3'    single        1.520 0.020     1.520
1MA  C4'     H4'    single        0.970 0.020     1.090
1MA  O4'     C1'    single        1.393 0.020     1.393
1MA  C3'     O3'    single        1.405 0.020     1.405
1MA  C3'     C2'    single        1.531 0.020     1.531
1MA  C3'     H3'    single        0.970 0.020     1.090
1MA  O3'     HO3'   single        0.850 0.020     0.980
1MA  C2'     O2'    single        1.398 0.020     1.398
1MA  C2'     C1'    single        1.531 0.020     1.531
1MA  C2'     H2'    single        0.970 0.020     1.090
1MA  O2'     HO2'   single        0.850 0.020     0.980
1MA  C1'      N9    single        1.447 0.020     1.447
1MA  C1'     H1'    single        0.970 0.020     1.090
1MA   N9      C8    aromatic      1.368 0.020     1.368
1MA   N9      C4    aromatic      1.362 0.020     1.362
1MA   C8      N7    aromatic      1.308 0.020     1.308
1MA   C8      H8    single        0.930 0.020     1.080
1MA   N7      C5    aromatic      1.364 0.020     1.364
1MA   C5      C6    single        1.437 0.020     1.437
1MA   C5      C4    aromatic      1.373 0.020     1.373
1MA   C6      N6    double        1.276 0.020     1.276
1MA   C6      N1    single        1.413 0.020     1.413
1MA   N6     HN61   single        0.890 0.020     1.040
1MA   N1      CM1   single        1.453 0.020     1.453
1MA   N1      C2    single        1.359 0.020     1.359
1MA   CM1    HM11   single        0.970 0.020     1.090
1MA   CM1    HM12   single        0.970 0.020     1.090
1MA   CM1    HM13   single        0.970 0.020     1.090
1MA   C2      N3    double        1.290 0.020     1.290
1MA   C2      H2    single        0.930 0.020     1.080
1MA   N3      C4    single        1.353 0.020     1.353
#
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
1MA  O5'      P       OP3         104.78 3.000
1MA  O5'      P       OP2         100.81 3.000
1MA   OP3     P       OP2         114.89 3.000
1MA  O5'      P       OP1         105.04 3.000
1MA   OP3     P       OP1         113.56 3.000
1MA   OP2     P       OP1         115.65 3.000
1MA  C5'     O5'      P           117.50 3.000
1MA  H5''    C5'     H5'          106.21 3.000
1MA  H5''    C5'     C4'          107.23 3.000
1MA  H5'     C5'     C4'          109.65 3.000
1MA  H5''    C5'     O5'          112.04 3.000
1MA  H5'     C5'     O5'          112.20 3.000
1MA  C4'     C5'     O5'          109.36 3.000
1MA  H4'     C4'     C3'          110.86 3.000
1MA  H4'     C4'     O4'          107.50 3.000
1MA  C3'     C4'     O4'          105.39 3.000
1MA  H4'     C4'     C5'          109.11 3.000
1MA  C3'     C4'     C5'          112.70 3.000
1MA  O4'     C4'     C5'          111.13 3.000
1MA  C1'     O4'     C4'          111.02 3.000
1MA  H3'     C3'     C2'          111.91 3.000
1MA  H3'     C3'     O3'          111.63 3.000
1MA  C2'     C3'     O3'          110.84 3.000
1MA  H3'     C3'     C4'          111.72 3.000
1MA  C2'     C3'     C4'          101.07 3.000
1MA  O3'     C3'     C4'          109.19 3.000
1MA  HO3'    O3'     C3'          107.89 3.000
1MA  H2'     C2'     C1'          109.32 3.000
1MA  H2'     C2'     O2'          111.35 3.000
1MA  C1'     C2'     O2'          109.98 3.000
1MA  H2'     C2'     C3'          109.39 3.000
1MA  C1'     C2'     C3'          101.35 3.000
1MA  O2'     C2'     C3'          114.94 3.000
1MA  HO2'    O2'     C2'          108.69 3.000
1MA  H1'     C1'      N9          106.21 3.000
1MA  H1'     C1'     C2'          109.90 3.000
1MA   N9     C1'     C2'          113.45 3.000
1MA  H1'     C1'     O4'          111.62 3.000
1MA   N9     C1'     O4'          109.45 3.000
1MA  C2'     C1'     O4'          106.31 3.000
1MA   C4      N9      C8          106.49 3.000
1MA   C4      N9     C1'          125.83 3.000
1MA   C8      N9     C1'          127.61 3.000
1MA   H8      C8      N7          124.37 3.000
1MA   H8      C8      N9          123.53 3.000
1MA   N7      C8      N9          112.08 3.000
1MA   C5      N7      C8          105.22 3.000
1MA   C4      C5      C6          119.83 3.000
1MA   C4      C5      N7          110.45 3.000
1MA   C6      C5      N7          129.73 3.000
1MA   N1      C6      N6          125.36 3.000
1MA   N1      C6      C5          110.65 3.000
1MA   N6      C6      C5          123.99 3.000
1MA  HN61     N6      C6          113.33 3.000
1MA   C2      N1      CM1         118.83 3.000
1MA   C2      N1      C6          123.46 3.000
1MA   CM1     N1      C6          117.71 3.000
1MA  HM13     CM1    HM12         108.40 3.000
1MA  HM13     CM1    HM11         109.08 3.000
1MA  HM12     CM1    HM11         108.32 3.000
1MA  HM13     CM1     N1          110.69 3.000
1MA  HM12     CM1     N1          109.47 3.000
1MA  HM11     CM1     N1          110.82 3.000
1MA   H2      C2      N3          118.70 3.000
1MA   H2      C2      N1          114.91 3.000
1MA   N3      C2      N1          126.39 3.000
1MA   C4      N3      C2          112.63 3.000
1MA   N3      C4      C5          127.04 3.000
1MA   N3      C4      N9          127.19 3.000
1MA   C5      C4      N9          105.77 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
1MA CONST_01   C5      N7      C8      N9            0.00   0.0 0
1MA CONST_02   N7      C5      C4      N9            0.00   0.0 0
1MA CONST_03   C5      C4      N9      C8            0.00   0.0 0
1MA CONST_04   C4      C5      N7      C8            0.00   0.0 0
1MA CONST_05   C4      N9      C8      N7            0.00   0.0 0
1MA CONST_06   N7      C8      N9      C1'         180.00   0.0 0
1MA CONST_07   C5      C4      N9      C1'         180.00   0.0 0
1MA CONST_08   N3      C4      N9      C1'           0.00   0.0 0
1MA CONST_09   C2      N1      C6      C5            0.00   0.0 0
1MA CONST_10   N3      C2      N1      C6            0.00   0.0 0
1MA CONST_11   C4      N3      C2      N1            0.00   0.0 0
1MA CONST_12   CM1     N1      C6      C5          180.00   0.0 0
1MA CONST_13   C2      N1      C6      N6          180.00   0.0 0
1MA CONST_14   N3      C2      N1      CM1         180.00   0.0 0
1MA CONST_15   H8      C8      N9      C1'           0.00   0.0 0
1MA CONST_16   H2      C2      N1      C6          180.00   0.0 0
1MA CONST_17   CM1     N1      C6      N6            0.00   0.0 0
1MA CONST_18  HN61     N6      C6      C5          180.00   0.0 0
1MA   Var_01  HM11     CM1     N1      C6           61.03  30.0 3
1MA   Var_02   C4'     C5'     O5'     P          -149.60  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
1MA plan-1    C1' 0.020
1MA plan-1    N9  0.020
1MA plan-1    C8  0.020
1MA plan-1    N7  0.020
1MA plan-1    C5  0.020
1MA plan-1    C6  0.020
1MA plan-1    N6  0.020
1MA plan-1    N1  0.020
1MA plan-1    CM1 0.020
1MA plan-1    C2  0.020
1MA plan-1    N3  0.020
1MA plan-1    C4  0.020
1MA plan-1    H8  0.020
1MA plan-1   HN61 0.020
1MA plan-1    H2  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
1MA chir_01   C4'     C5'     O4'     C3'   negativ
1MA chir_02   C3'     O3'     C4'     C2'   positiv
1MA chir_03   C2'     O2'     C3'     C1'   positiv
1MA chir_04   C1'     O4'     N9      C2'   negativ
#
