# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Oct 21 17:35:05 2020
#
#   Inital geometry file: a 109 line input string
#   Ligand name: [2-[3-[(4-amino-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-3-ium-5-yl]ethoxy-hydroxy-phosphoryl] hydrogen phosphate
#   CSD Mogul values: True
#   Random seed: 3628800
#   SMILES string: Cc1ncc(C[n+]2csc(CCO[P@](O)(=O)O[P](O)([O-])=O)c2C)c(N)n1
#
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
TDP        TDP '[2-[3-[(4-amino-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-3-ium-5-yl]ethoxy-hydroxy-phosphoryl] hydrogen phosphate' ligand 42 26 .
2020-10-21 2020-10-21
;
CIF prepared directly in eLBOW
;
#
data_comp_TDP
#
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
TDP        N1'     N   N      0    .      -6.5270   -9.5340  108.8420
TDP        C2'     C   CR6    0    .      -5.1860   -9.8350  109.0420
TDP         C2A    C   CH3    0    .      -4.1430   -8.7560  109.0940
TDP        N3'     N   N      0    .      -4.7780  -11.0890  109.1960
TDP        C4'     C   CR6    0    .      -5.6960  -12.1350  109.1610
TDP        N4'     N   NH2    0    .      -5.1880  -13.3540  109.3240
TDP        C5'     C   CR6    0    .      -7.1000  -11.8740  108.9590
TDP        C6'     C   CR16   0    .      -7.4370  -10.5640  108.8080
TDP         C35    C   CH2    0    .      -8.1400  -12.9880  108.9090
TDP         N3     N   NR5    1    .      -7.9780  -13.7930  107.6090
TDP         C2     C   CR15   0    .      -7.2960  -14.9300  107.6450
TDP         S1     S   S2     0    .      -7.1510  -15.7280  106.1910
TDP         C5     C   CR5    0    .      -8.0580  -14.4980  105.4120
TDP         C4     C   CR5    0    .      -8.4380  -13.5160  106.3190
TDP         C4A    C   CH3    0    .      -9.2300  -12.3130  105.9590
TDP         C5A    C   CH2    0    .      -8.3050  -14.6150  103.9530
TDP         C5B    C   CH2    0    .      -7.1840  -14.0870  103.0870
TDP         O5G    O   O2     0    .      -7.2870  -14.5610  101.7840
TDP         P1     P   P      0    .      -6.2950  -14.6650  100.5520
TDP         O11    O   O2     0    .      -5.6780  -16.0660  100.8100
TDP         O12    O   O      0    .      -7.0190  -14.6260   99.2930
TDP         O13    O   OP    -1    .      -5.2170  -13.6750  100.7960
TDP         P2     P   P      0    .      -6.2660  -17.5600  100.7830
TDP         O21    O   O      0    .      -5.0830  -18.4600  100.4010
TDP         O22    O   OP    -1    .      -7.0330  -17.7290  102.0100
TDP         O23    O   OP    -1    .      -7.2020  -17.5030   99.5940
TDP        H2A1    H   HCH3   0    .      -3.0660   -8.9970  109.2540
TDP        H2A2    H   HCH3   0    .      -4.2240   -8.1530  108.1590
TDP        H2A3    H   HCH3   0    .      -4.4490   -8.0180  109.8710
TDP        H4'1    H   HNH2   0    .      -5.8600  -14.1200  109.2980
TDP        H4'2    H   HNH2   0    .      -4.6480  -13.3930  110.1880
TDP        H6'     H   HCR6   0    .      -8.5020  -10.3240  108.6500
TDP        H351    H   HCH2   0    .      -8.1000  -13.6390  109.8130
TDP        H352    H   HCH2   0    .      -9.1770  -12.5990  109.0350
TDP         H2     H   HCR5   0    .      -6.9300  -15.1600  108.6590
TDP        H4A1    H   HCH3   0    .      -9.5970  -12.0920  104.9290
TDP        H4A2    H   HCH3   0    .     -10.1170  -12.2910  106.6330
TDP        H4A3    H   HCH3   0    .      -8.6460  -11.4240  106.2950
TDP        H5A1    H   HCH2   0    .      -8.5420  -15.6700  103.6810
TDP        H5A2    H   HCH2   0    .      -9.2690  -14.1260  103.6810
TDP        H5B1    H   HCH2   0    .      -7.1340  -12.9730  103.1140
TDP        H5B2    H   HCH2   0    .      -6.1850  -14.3130  103.5270
#
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
TDP  N1'     C2'    aromatic      1.338 0.020     1.338
TDP  N1'     C6'    aromatic      1.337 0.010     1.337
TDP  C2'      C2A   single        1.495 0.012     1.495
TDP  C2'     N3'    aromatic      1.337 0.011     1.337
TDP   C2A    H2A1   single        0.970 0.011     1.090
TDP   C2A    H2A2   single        0.970 0.011     1.090
TDP   C2A    H2A3   single        0.970 0.011     1.090
TDP  N3'     C4'    aromatic      1.345 0.011     1.345
TDP  C4'     N4'    single        1.337 0.011     1.337
TDP  C4'     C5'    aromatic      1.428 0.014     1.428
TDP  N4'     H4'1   single        0.890 0.010     1.040
TDP  N4'     H4'2   single        0.890 0.010     1.040
TDP  C5'     C6'    aromatic      1.378 0.010     1.378
TDP  C5'      C35   single        1.506 0.013     1.506
TDP  C6'     H6'    single        0.930 0.010     1.080
TDP   C35     N3    single        1.481 0.010     1.481
TDP   C35    H351   single        0.970 0.012     1.090
TDP   C35    H352   single        0.970 0.012     1.090
TDP   N3      C2    aromatic      1.318 0.012     1.318
TDP   N3      C4    aromatic      1.394 0.010     1.394
TDP   C2      S1    aromatic      1.675 0.010     1.675
TDP   C2      H2    single        0.930 0.010     1.080
TDP   S1      C5    aromatic      1.726 0.010     1.726
TDP   C5      C4    aromatic      1.353 0.029     1.353
TDP   C5      C5A   single        1.503 0.010     1.503
TDP   C4      C4A   single        1.490 0.012     1.490
TDP   C4A    H4A1   single        0.970 0.010     1.090
TDP   C4A    H4A2   single        0.970 0.010     1.090
TDP   C4A    H4A3   single        0.970 0.010     1.090
TDP   C5A     C5B   single        1.511 0.010     1.511
TDP   C5A    H5A1   single        0.970 0.011     1.090
TDP   C5A    H5A2   single        0.970 0.011     1.090
TDP   C5B     O5G   single        1.449 0.011     1.449
TDP   C5B    H5B1   single        0.970 0.016     1.090
TDP   C5B    H5B2   single        0.970 0.016     1.090
TDP   O5G     P1    single        1.579 0.016     1.579
TDP   P1      O11   single        1.592 0.010     1.592
TDP   P1      O12   deloc         1.477 0.011     1.477
TDP   P1      O13   deloc         1.529 0.022     1.529
TDP   O11     P2    single        1.600 0.030     1.600
TDP   P2      O21   deloc         1.533 0.022     1.533
TDP   P2      O22   deloc         1.491 0.028     1.491
TDP   P2      O23   deloc         1.533 0.032     1.533
#
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
TDP  C6'     N1'     C2'          116.11 1.279
TDP  N3'     C2'      C2A         117.10 1.068
TDP  N3'     C2'     N1'          125.71 1.011
TDP   C2A    C2'     N1'          117.40 1.000
TDP  H2A3     C2A    H2A2         101.92 3.000
TDP  H2A3     C2A    H2A1         107.95 3.000
TDP  H2A2     C2A    H2A1         107.89 3.000
TDP  H2A3     C2A    C2'          108.02 3.000
TDP  H2A2     C2A    C2'          108.00 3.000
TDP  H2A1     C2A    C2'          121.37 3.000
TDP  C4'     N3'     C2'          118.08 1.000
TDP  C5'     C4'     N4'          121.96 1.066
TDP  C5'     C4'     N3'          121.43 1.000
TDP  N4'     C4'     N3'          117.09 1.242
TDP  H4'2    N4'     H4'1         110.00 3.000
TDP  H4'2    N4'     C4'          109.94 3.000
TDP  H4'1    N4'     C4'          115.70 3.000
TDP   C35    C5'     C6'          120.87 1.274
TDP   C35    C5'     C4'          123.03 1.000
TDP  C6'     C5'     C4'          115.50 1.000
TDP  H6'     C6'     C5'          117.78 3.000
TDP  H6'     C6'     N1'          117.78 3.000
TDP  C5'     C6'     N1'          124.43 1.055
TDP  H352     C35    H351          98.37 3.000
TDP  H352     C35     N3          112.10 3.000
TDP  H351     C35     N3          112.09 3.000
TDP  H352     C35    C5'          112.08 3.000
TDP  H351     C35    C5'          112.06 3.000
TDP   N3      C35    C5'          113.03 1.000
TDP   C4      N3      C2          114.14 1.000
TDP   C4      N3      C35         122.12 1.103
TDP   C2      N3      C35         123.84 1.000
TDP   H2      C2      S1          123.83 3.000
TDP   H2      C2      N3          123.83 3.000
TDP   S1      C2      N3          112.34 1.000
TDP   C5      S1      C2           91.33 1.000
TDP   C5A     C5      C4          128.26 1.000
TDP   C5A     C5      S1          120.84 2.360
TDP   C4      C5      S1          110.16 2.167
TDP   C4A     C4      C5          127.63 1.696
TDP   C4A     C4      N3          120.70 1.000
TDP   C5      C4      N3          111.86 1.344
TDP  H4A3     C4A    H4A2         102.64 3.000
TDP  H4A3     C4A    H4A1         107.01 3.000
TDP  H4A2     C4A    H4A1         107.02 3.000
TDP  H4A3     C4A     C4          107.07 3.000
TDP  H4A2     C4A     C4          107.10 3.000
TDP  H4A1     C4A     C4          124.05 3.000
TDP  H5A2     C5A    H5A1          99.89 3.000
TDP  H5A2     C5A     C5B         110.38 3.000
TDP  H5A1     C5A     C5B         110.39 3.000
TDP  H5A2     C5A     C5          110.44 3.000
TDP  H5A1     C5A     C5          110.47 3.000
TDP   C5B     C5A     C5          113.13 1.004
TDP  H5B2     C5B    H5B1          98.79 3.000
TDP  H5B2     C5B     O5G         111.54 3.000
TDP  H5B1     C5B     O5G         111.50 3.000
TDP  H5B2     C5B     C5A         111.57 3.000
TDP  H5B1     C5B     C5A         111.60 3.000
TDP   O5G     C5B     C5A         108.47 1.091
TDP   P1      O5G     C5B         124.29 1.000
TDP   O13     P1      O12         114.42 3.527
TDP   O13     P1      O11         106.94 1.880
TDP   O12     P1      O11         111.24 2.719
TDP   O13     P1      O5G         108.07 2.651
TDP   O12     P1      O5G         110.65 3.490
TDP   O11     P1      O5G         102.67 2.380
TDP   P2      O11     P1          139.87 1.000
TDP   O23     P2      O22         113.32 2.534
TDP   O23     P2      O21         108.70 2.785
TDP   O22     P2      O21         113.32 2.534
TDP   O23     P2      O11         104.48 1.135
TDP   O22     P2      O11         110.47 1.644
TDP   O21     P2      O11         104.48 1.135
#
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
TDP CONST_01      C4'     N3'     C2'     N1'           -0.07   0.0 0
TDP CONST_02      C4'     C5'     C6'     N1'           -0.08   0.0 0
TDP CONST_03      C5'     C6'     N1'     C2'           -0.05   0.0 0
TDP CONST_04      C5'     C4'     N3'     C2'           -0.06   0.0 0
TDP CONST_05      C6'     N1'     C2'     N3'            0.13   0.0 0
TDP CONST_06      C6'     C5'     C4'     N3'            0.14   0.0 0
TDP CONST_07       C5      S1      C2      N3           -0.06   0.0 0
TDP CONST_08       S1      C5      C4      N3            0.18   0.0 0
TDP CONST_09       C5      C4      N3      C2           -0.23   0.0 0
TDP CONST_10       C4      C5      S1      C2           -0.07   0.0 0
TDP CONST_11       C4      N3      C2      S1            0.18   0.0 0
TDP CONST_12       C35    C5'     C6'     N1'         -179.74   0.0 0
TDP CONST_13      N4'     C4'     N3'     C2'          179.94   0.0 0
TDP CONST_14      C6'     N1'     C2'      C2A        -179.79   0.0 0
TDP CONST_15      C4'     N3'     C2'      C2A         179.85   0.0 0
TDP CONST_16       C35    C5'     C4'     N3'          179.79   0.0 0
TDP CONST_17      C6'     C5'     C4'     N4'         -179.87   0.0 0
TDP CONST_18       S1      C2      N3      C35        -179.21   0.0 0
TDP CONST_19       C5      C4      N3      C35         179.08   0.0 0
TDP CONST_20       C5A     C5      C4      N3         -179.31   0.0 0
TDP CONST_21       C4A     C4      N3      C2         -179.87   0.0 0
TDP CONST_22       C5A     C5      S1      C2          179.49   0.0 0
TDP CONST_23       C4A     C4      C5      S1          179.82   0.0 0
TDP CONST_24      H6'     C6'     N1'     C2'          179.95   0.0 0
TDP CONST_25       H2      C2      S1      C5          179.99   0.0 0
TDP CONST_26      H4'1    N4'     C4'     N3'         -179.98   0.0 0
TDP CONST_27      H4'2    N4'     C4'     N3'           54.69   0.0 0
TDP Var_01         N3      C35    C5'     C4'          -70.86  30.0 2
TDP Var_02         C2      N3      C35    C5'           97.82  30.0 2
TDP Var_03         C5B     C5A     C5      S1          -84.38  30.0 2
TDP Var_04        H2A1     C2A    C2'     N1'         -179.97  30.0 2
TDP Var_05        H4A1     C4A     C4      N3          179.99  30.0 2
TDP Var_06         O5G     C5B     C5A     C5          162.74  30.0 3
TDP Var_07         O11     P1      O5G     C5B          89.72  30.0 3
TDP Var_08         O21     P2      O11     P1          151.06  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
TDP plan-1    C35 0.020
TDP plan-1     N3 0.020
TDP plan-1     C2 0.020
TDP plan-1     S1 0.020
TDP plan-1     C5 0.020
TDP plan-1     C4 0.020
TDP plan-1    C4A 0.020
TDP plan-1    C5A 0.020
TDP plan-1     H2 0.020
TDP plan-2    N1' 0.020
TDP plan-2    C2' 0.020
TDP plan-2    C2A 0.020
TDP plan-2    N3' 0.020
TDP plan-2    C4' 0.020
TDP plan-2    N4' 0.020
TDP plan-2    C5' 0.020
TDP plan-2    C6' 0.020
TDP plan-2    C35 0.020
TDP plan-2    H6' 0.020
TDP plan-3    C4' 0.020
TDP plan-3    N4' 0.020
TDP plan-3   H4'1 0.020
TDP plan-3   H4'2 0.020
