# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Oct  8 13:37:56 2018
#
#   Inital geometry file: a 111 line input string
#   Ligand name: 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium
#   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
#
# Restraints Editor Exclusively Ligands (REEL)
#   - a module of PHENIX
#   - file written: Mon Oct  8 13:39:48 2018
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
TPP TPP '3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium' ligand 42 26 . 
2018-10-08 2018-10-08
;
CIF prepared directly in eLBOW
;
#
data_comp_TPP
#
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
TPP         N1'    N   N     0     .         -6.0960   -2.2730   -0.0220
TPP         C2'    C   CR6   0     .         -7.0120   -1.6120    0.6560
TPP         CM2    C   CH3   0     .         -8.0350   -2.3820    1.4510
TPP         N3'    N   N     0     .         -7.0580   -0.2950    0.6600
TPP         C4'    C   CR6   0     .         -6.1720    0.4170   -0.0300
TPP         N4'    N   NH2   0     .         -6.2230    1.8010   -0.0240
TPP         C5'    C   CR6   0     .         -5.1880   -0.2540   -0.7600
TPP         C6'    C   CR16  0     .         -5.1780   -1.6340   -0.7330
TPP         C7'    C   CH2   0     .         -4.1620    0.5110   -1.5570
TPP         N3     N   NR5   1     .         -3.0860    0.9560   -0.6680
TPP         C2     C   CR15  0     .         -3.1220    2.1120   -0.0950
TPP         S1     S   S2    0     .         -1.7300    2.3340    0.8730
TPP         C5     C   CR5   0     .         -1.1430    0.7380    0.4100
TPP         C4     C   CR5   0     .         -2.0430    0.1920   -0.4140
TPP         CM4    C   CH3   0     .         -1.8750   -1.1820   -1.0090
TPP         C6     C   CH2   0     .          0.1420    0.0990    0.8690
TPP         C7     C   CH2   0     .          1.2670    0.4630   -0.1020
TPP         O7     O   O2    0     .          2.4860   -0.1440    0.3320
TPP         PA     P   P     0     .          3.8800    0.0270   -0.4550
TPP         O1A    O   O     0     .          4.1810    1.4670   -0.6170
TPP         O2A    O   OP    -1    .          3.7650   -0.6630   -1.9050
TPP         O3A    O   O2    0     .          5.0600   -0.6770    0.3830
TPP         PB     P   P     0     .          6.6640   -0.5360    0.3920
TPP         O1B    O   O     0     .          7.1540   -0.3930   -0.9970
TPP         O2B    O   OP    -1    .          7.0830    0.7630    1.2460
TPP         O3B    O   OP    -1    .          7.3140   -1.8490    1.0590
TPP        HM21    H   HCH3  0     .         -7.6600   -2.5480    2.4610
TPP        HM22    H   HCH3  0     .         -8.9640   -1.8140    1.4960
TPP        HM23    H   HCH3  0     .         -8.2200   -3.3430    0.9700
TPP        HN41    H   HNH2  0     .         -6.9090    2.2590    0.4860
TPP        HN42    H   HNH2  0     .         -5.5720    2.3130   -0.5300
TPP         H6'    H   HCR6  0     .         -4.4320   -2.1860   -1.2850
TPP        H7'1    H   HCH2  0     .         -3.7480   -0.1360   -2.3310
TPP        H7'2    H   HCH2  0     .         -4.6330    1.3770   -2.0200
TPP         H2     H   HCR5  0     .         -3.9160    2.8350   -0.2100
TPP        HM41    H   HCH3  0     .         -1.2560   -1.1170   -1.9040
TPP        HM42    H   HCH3  0     .         -1.3940   -1.8360   -0.2820
TPP        HM43    H   HCH3  0     .         -2.8520   -1.5860   -1.2720
TPP         H61    H   HCH2  0     .          0.3920    0.4600    1.8660
TPP         H62    H   HCH2  0     .          0.0200   -0.9840    0.8950
TPP         H71    H   HCH2  0     .          1.0170    0.1010   -1.1000
TPP         H72    H   HCH2  0     .          1.3890    1.5450   -0.1280
#
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
TPP   N1'     C2'   aromatic      1.339 0.02   1.339
TPP   N1'     C6'   aromatic      1.337 0.01   1.337
TPP   C2'     CM2   single        1.494 0.011   1.494
TPP   C2'     N3'   aromatic      1.336 0.012   1.336
TPP   CM2    HM21   single        0.970 0.01   1.09
TPP   CM2    HM22   single        0.970 0.01   1.09
TPP   CM2    HM23   single        0.970 0.01   1.09
TPP   N3'     C4'   aromatic      1.345 0.01   1.345
TPP   C4'     N4'   single        1.337 0.011   1.337
TPP   C4'     C5'   aromatic      1.427 0.014   1.427
TPP   N4'    HN41   single        0.860 0.01   1.02
TPP   N4'    HN42   single        0.860 0.01   1.02
TPP   C5'     C6'   aromatic      1.377 0.01   1.377
TPP   C5'     C7'   single        1.504 0.013   1.504
TPP   C6'     H6'   single        0.930 0.01   1.08
TPP   C7'     N3    single        1.482 0.01   1.482
TPP   C7'    H7'1   single        0.970 0.013   1.09
TPP   C7'    H7'2   single        0.970 0.013   1.09
TPP   N3      C2    aromatic      1.318 0.013   1.318
TPP   N3      C4    aromatic      1.394 0.01   1.394
TPP   C2      S1    aromatic      1.675 0.01   1.675
TPP   C2      H2    single        0.930 0.01   1.08
TPP   S1      C5    aromatic      1.727 0.01   1.727
TPP   C5      C4    aromatic      1.353 0.029   1.353
TPP   C5      C6    single        1.503 0.01   1.503
TPP   C4      CM4   single        1.490 0.012   1.49
TPP   CM4    HM41   single        0.970 0.01   1.09
TPP   CM4    HM42   single        0.970 0.01   1.09
TPP   CM4    HM43   single        0.970 0.01   1.09
TPP   C6      C7    single        1.511 0.01   1.511
TPP   C6      H61   single        0.970 0.011   1.09
TPP   C6      H62   single        0.970 0.011   1.09
TPP   C7      O7    single        1.449 0.011   1.449
TPP   C7      H71   single        0.970 0.016   1.09
TPP   C7      H72   single        0.970 0.016   1.09
TPP   O7      PA    single        1.575 0.016   1.575
TPP   PA      O1A   deloc         1.479 0.01   1.479
TPP   PA      O2A   deloc         1.527 0.023   1.527
TPP   PA      O3A   single        1.592 0.032   1.592
TPP   O3A     PB    single        1.587 0.011   1.587
TPP   PB      O1B   deloc         1.492 0.016   1.492
TPP   PB      O2B   deloc         1.532 0.036   1.532
TPP   PB      O3B   deloc         1.532 0.03   1.532
#
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
TPP   C6'     N1'     C2'         115.93 1.255
TPP   N3'     C2'     CM2         117.21 1.174
TPP   N3'     C2'     N1'         125.71 1.066
TPP   CM2     C2'     N1'         117.31 1.0
TPP  HM23     CM2    HM22         109.45 3.0
TPP  HM23     CM2    HM21         109.44 3.0
TPP  HM22     CM2    HM21         109.53 3.0
TPP  HM23     CM2     C2'         109.43 3.0
TPP  HM22     CM2     C2'         109.52 3.0
TPP  HM21     CM2     C2'         109.45 3.0
TPP   C4'     N3'     C2'         118.07 1.0
TPP   C5'     C4'     N4'         122.04 1.022
TPP   C5'     C4'     N3'         121.39 1.0
TPP   N4'     C4'     N3'         117.10 1.261
TPP  HN42     N4'    HN41         119.97 3.0
TPP  HN42     N4'     C4'         120.01 3.0
TPP  HN41     N4'     C4'         120.02 3.0
TPP   C7'     C5'     C6'         120.87 1.274
TPP   C7'     C5'     C4'         123.03 1.0
TPP   C6'     C5'     C4'         115.50 1.0
TPP   H6'     C6'     C5'         117.73 3.0
TPP   H6'     C6'     N1'         117.73 3.0
TPP   C5'     C6'     N1'         124.54 1.01
TPP  H7'2     C7'    H7'1         109.53 3.0
TPP  H7'2     C7'     N3          109.52 3.0
TPP  H7'1     C7'     N3          109.40 3.0
TPP  H7'2     C7'     C5'         109.50 3.0
TPP  H7'1     C7'     C5'         109.42 3.0
TPP   N3      C7'     C5'         113.16 1.0
TPP   C4      N3      C2          114.14 1.0
TPP   C4      N3      C7'         122.01 1.0
TPP   C2      N3      C7'         123.84 1.0
TPP   H2      C2      S1          123.83 3.0
TPP   H2      C2      N3          123.83 3.0
TPP   S1      C2      N3          112.34 1.0
TPP   C5      S1      C2           91.33 1.0
TPP   C6      C5      C4          128.26 1.0
TPP   C6      C5      S1          120.84 2.36
TPP   C4      C5      S1          110.16 2.167
TPP   CM4     C4      C5          127.63 1.696
TPP   CM4     C4      N3          120.67 1.0
TPP   C5      C4      N3          111.86 1.344
TPP  HM43     CM4    HM42         109.53 3.0
TPP  HM43     CM4    HM41         109.46 3.0
TPP  HM42     CM4    HM41         109.44 3.0
TPP  HM43     CM4     C4          109.48 3.0
TPP  HM42     CM4     C4          109.45 3.0
TPP  HM41     CM4     C4          109.46 3.0
TPP   H62     C6      H61         109.45 3.0
TPP   H62     C6      C7          109.50 3.0
TPP   H61     C6      C7          109.46 3.0
TPP   H62     C6      C5          109.46 3.0
TPP   H61     C6      C5          109.51 3.0
TPP   C7      C6      C5          113.13 1.004
TPP   H72     C7      H71         109.48 3.0
TPP   H72     C7      O7          109.49 3.0
TPP   H71     C7      O7          109.41 3.0
TPP   H72     C7      C6          109.50 3.0
TPP   H71     C7      C6          109.46 3.0
TPP   O7      C7      C6          108.47 1.091
TPP   PA      O7      C7          124.29 1.0
TPP   O3A     PA      O2A         106.94 1.88
TPP   O3A     PA      O1A         111.24 2.719
TPP   O2A     PA      O1A         114.39 3.995
TPP   O3A     PA      O7          102.67 2.38
TPP   O2A     PA      O7          108.19 3.739
TPP   O1A     PA      O7          109.31 3.698
TPP   PB      O3A     PA          139.87 1.0
TPP   O3B     PB      O2B         108.49 3.002
TPP   O3B     PB      O1B         113.35 2.517
TPP   O2B     PB      O1B         113.35 2.517
TPP   O3B     PB      O3A         104.26 1.332
TPP   O2B     PB      O3A         104.26 1.332
TPP   O1B     PB      O3A         111.16 1.818
#
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
TPP CONST_01   C4'     N3'     C2'     N1'           0.00   0.0 0
TPP CONST_02   C4'     C5'     C6'     N1'           0.00   0.0 0
TPP CONST_03   C5'     C6'     N1'     C2'           0.00   0.0 0
TPP CONST_04   C5'     C4'     N3'     C2'           0.00   0.0 0
TPP CONST_05   C6'     N1'     C2'     N3'           0.00   0.0 0
TPP CONST_06   C6'     C5'     C4'     N3'           0.00   0.0 0
TPP CONST_07   C5      S1      C2      N3            0.00   0.0 0
TPP CONST_08   S1      C5      C4      N3            0.00   0.0 0
TPP CONST_09   C5      C4      N3      C2            0.00   0.0 0
TPP CONST_10   C4      C5      S1      C2            0.00   0.0 0
TPP CONST_11   C4      N3      C2      S1            0.00   0.0 0
TPP CONST_12   C7'     C5'     C6'     N1'         180.00   0.0 0
TPP CONST_13   N4'     C4'     N3'     C2'         180.00   0.0 0
TPP CONST_14   C6'     N1'     C2'     CM2         180.00   0.0 0
TPP CONST_15   C4'     N3'     C2'     CM2         180.00   0.0 0
TPP CONST_16   C7'     C5'     C4'     N3'         180.00   0.0 0
TPP CONST_17   C6'     C5'     C4'     N4'         180.00   0.0 0
TPP CONST_18   S1      C2      N3      C7'         180.00   0.0 0
TPP CONST_19   C5      C4      N3      C7'         180.00   0.0 0
TPP CONST_20   C6      C5      C4      N3          180.00   0.0 0
TPP CONST_21   CM4     C4      N3      C2          180.00   0.0 0
TPP CONST_22   C6      C5      S1      C2          180.00   0.0 0
TPP CONST_23   CM4     C4      C5      S1          180.00   0.0 0
TPP CONST_24   H6'     C6'     N1'     C2'         180.00   0.0 0
TPP CONST_25   H2      C2      S1      C5          180.00   0.0 0
TPP CONST_26  HN41     N4'     C4'     N3'           0.00   0.0 0
TPP CONST_27  HN42     N4'     C4'     N3'         180.00   0.0 0
TPP   Var_01   N3      C7'     C5'     C4'          81.75  30.0 2
TPP   Var_02   C2      N3      C7'     C5'         -91.94  30.0 2
TPP   Var_03   C7      C6      C5      S1          -90.03  30.0 2
TPP   Var_04  HM21     CM2     C2'     N1'          89.93  30.0 2
TPP   Var_05  HM41     CM4     C4      N3           95.53  30.0 2
TPP   Var_06   O7      C7      C6      C5         -179.94  30.0 3
TPP   Var_07   O1A     PA      O7      C7           54.92  30.0 3
TPP   Var_08   O1B     PB      O3A     PA          -39.96  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
TPP plan-1    C7' 0.020
TPP plan-1    N3  0.020
TPP plan-1    C2  0.020
TPP plan-1    S1  0.020
TPP plan-1    C5  0.020
TPP plan-1    C4  0.020
TPP plan-1    CM4 0.020
TPP plan-1    C6  0.020
TPP plan-1    H2  0.020
TPP plan-2    N1' 0.020
TPP plan-2    C2' 0.020
TPP plan-2    CM2 0.020
TPP plan-2    N3' 0.020
TPP plan-2    C4' 0.020
TPP plan-2    N4' 0.020
TPP plan-2    C5' 0.020
TPP plan-2    C6' 0.020
TPP plan-2    C7' 0.020
TPP plan-2    H6' 0.020
TPP plan-3    C4' 0.020
TPP plan-3    N4' 0.020
TPP plan-3   HN41 0.020
TPP plan-3   HN42 0.020
#
