# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Oct 21 13:27:56 2020
#
#   Inital geometry file: a 92 line input string
#   Ligand name: 5'-thymidylic acid
#   CSD Mogul values: True
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O
#
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
TMP        TMP '5'-thymidylic acid       ' ligand 34 21 .
2020-10-21 2020-10-21
;
CIF prepared directly in eLBOW
;
#
data_comp_TMP
#
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
TMP         P      P   P      0    .      -4.1710    1.0040   -0.0950
TMP         O1P    O   O      0    .      -3.6670    1.7600    1.0730
TMP         O2P    O   OP    -1    .      -4.8720    2.0180   -1.1300
TMP         O3P    O   OP    -1    .      -5.2450   -0.0900    0.3970
TMP        O5'     O   O2     0    .      -2.9430    0.2590   -0.8230
TMP        C5'     C   CH2    0    .      -2.2910   -0.5330    0.1720
TMP        C4'     C   CR15   0    .      -1.1080   -1.2710   -0.4570
TMP        O4'     O   O      0    .      -0.0420   -0.3490   -0.7800
TMP        C3'     C   CR15   0    .      -0.4580   -2.2350    0.5680
TMP        O3'     O   OH1    0    .      -1.1230   -3.5000    0.5710
TMP        C2'     C   CH2    0    .       0.9830   -2.3690    0.0180
TMP        C1'     C   CR15   0    .       1.1660   -1.1240   -0.8700
TMP         N1     N   NR6    0    .       2.3020   -0.3320   -0.3920
TMP         C2     C   CR6    0    .       2.2490    0.2420    0.8240
TMP         O2     O   O      0    .       1.2570    0.0970    1.5130
TMP         N3     N   NR16   0    .       3.2790    0.9730    1.2890
TMP         C4     C   CR6    0    .       4.3870    1.1390    0.5400
TMP         O4     O   O      0    .       5.3190    1.8010    0.9600
TMP         C5     C   CR6    0    .       4.4540    0.5450   -0.7430
TMP         C5M    C   CH3    0    .       5.6800    0.7190   -1.6020
TMP         C6     C   CR16   0    .       3.4070   -0.1840   -1.1850
TMP        H5'1    H   HCH2   0    .      -2.9970   -1.2580    0.5780
TMP        H5'2    H   HCH2   0    .      -1.9320    0.1130    0.9730
TMP        H4'     H   HCR5   0    .      -1.4260   -1.8140   -1.3470
TMP        H3'     H   HCR5   0    .      -0.4550   -1.7970    1.5660
TMP        HO3'    H   HOH1   0    .      -0.6170   -4.0800    1.1570
TMP        H2'1    H   HCH2   0    .       1.0820   -3.2790   -0.5740
TMP        H2'2    H   HCH2   0    .       1.7040   -2.3640    0.8350
TMP        H1'     H   HCR5   0    .       1.3350   -1.4270   -1.9040
TMP         HN3    H   HNR6   0    .       3.2240    1.3800    2.1680
TMP         H51    H   HCH3   0    .       5.5640    1.6050   -2.2270
TMP         H52    H   HCH3   0    .       6.5570    0.8360   -0.9650
TMP         H53    H   HCH3   0    .       5.8060   -0.1590   -2.2370
TMP         H6     H   HCR6   0    .       3.4410   -0.6480   -2.1590
#
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
TMP   P       O1P   deloc         1.491 0.020     1.491
TMP   P       O2P   deloc         1.533 0.032     1.533
TMP   P       O3P   deloc         1.533 0.028     1.533
TMP   P      O5'    single        1.601 0.028     1.601
TMP  O5'     C5'    single        1.443 0.032     1.443
TMP  C5'     C4'    single        1.508 0.015     1.508
TMP  C5'     H5'1   single        0.970 0.011     1.090
TMP  C5'     H5'2   single        0.970 0.011     1.090
TMP  C4'     O4'    single        1.444 0.011     1.444
TMP  C4'     C3'    single        1.527 0.011     1.527
TMP  C4'     H4'    single        0.970 0.012     1.090
TMP  O4'     C1'    single        1.418 0.012     1.418
TMP  C3'     O3'    single        1.428 0.013     1.428
TMP  C3'     C2'    single        1.523 0.010     1.523
TMP  C3'     H3'    single        0.970 0.011     1.090
TMP  O3'     HO3'   single        0.850 0.011     0.980
TMP  C2'     C1'    single        1.521 0.011     1.521
TMP  C2'     H2'1   single        0.970 0.012     1.090
TMP  C2'     H2'2   single        0.970 0.012     1.090
TMP  C1'      N1    single        1.475 0.012     1.475
TMP  C1'     H1'    single        0.970 0.017     1.090
TMP   N1      C2    single        1.379 0.017     1.379
TMP   N1      C6    single        1.377 0.010     1.377
TMP   C2      O2    double        1.223 0.013     1.223
TMP   C2      N3    single        1.374 0.012     1.374
TMP   N3      C4    single        1.382 0.010     1.382
TMP   N3      HN3   single        0.860 0.012     1.020
TMP   C4      O4    double        1.230 0.012     1.230
TMP   C4      C5    single        1.446 0.014     1.446
TMP   C5      C5M   single        1.502 0.010     1.502
TMP   C5      C6    double        1.342 0.018     1.342
TMP   C5M     H51   single        0.970 0.010     1.090
TMP   C5M     H52   single        0.970 0.010     1.090
TMP   C5M     H53   single        0.970 0.010     1.090
TMP   C6      H6    single        0.930 0.010     1.080
#
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
TMP  O5'      P       O3P         106.53 2.580
TMP  O5'      P       O2P         106.53 2.580
TMP   O3P     P       O2P         108.70 2.785
TMP  O5'      P       O1P         106.57 2.496
TMP   O3P     P       O1P         113.32 2.534
TMP   O2P     P       O1P         113.32 2.534
TMP  C5'     O5'      P           117.05 1.000
TMP  H5'2    C5'     H5'1         109.50 3.000
TMP  H5'2    C5'     C4'          109.48 3.000
TMP  H5'1    C5'     C4'          109.46 3.000
TMP  H5'2    C5'     O5'          109.48 3.000
TMP  H5'1    C5'     O5'          109.41 3.000
TMP  C4'     C5'     O5'          108.83 2.328
TMP  H4'     C4'     C3'          127.18 3.000
TMP  H4'     C4'     O4'          127.18 3.000
TMP  C3'     C4'     O4'          105.64 1.084
TMP  H4'     C4'     C5'          127.18 3.000
TMP  C3'     C4'     C5'          114.72 1.915
TMP  O4'     C4'     C5'          109.53 1.437
TMP  C1'     O4'     C4'          109.55 1.311
TMP  H3'     C3'     C2'          124.52 3.000
TMP  H3'     C3'     O3'          124.52 3.000
TMP  C2'     C3'     O3'          110.97 2.419
TMP  H3'     C3'     C4'          124.52 3.000
TMP  C2'     C3'     C4'          102.59 1.017
TMP  O3'     C3'     C4'          110.26 2.320
TMP  HO3'    O3'     C3'          106.77 3.000
TMP  H2'2    C2'     H2'1         110.54 3.000
TMP  H2'2    C2'     C1'          110.49 3.000
TMP  H2'1    C2'     C1'          110.54 3.000
TMP  H2'2    C2'     C3'          110.43 3.000
TMP  H2'1    C2'     C3'          110.47 3.000
TMP  C1'     C2'     C3'          102.57 1.360
TMP  H1'     C1'      N1          123.04 3.000
TMP  H1'     C1'     C2'          123.04 3.000
TMP   N1     C1'     C2'          113.92 1.278
TMP  H1'     C1'     O4'          123.04 3.000
TMP   N1     C1'     O4'          108.01 1.000
TMP  C2'     C1'     O4'          106.23 1.052
TMP   C6      N1      C2          121.30 1.000
TMP   C6      N1     C1'          120.69 1.410
TMP   C2      N1     C1'          117.69 1.459
TMP   N3      C2      O2          121.99 1.083
TMP   N3      C2      N1          114.83 1.000
TMP   O2      C2      N1          122.84 1.000
TMP   HN3     N3      C4          116.34 3.000
TMP   HN3     N3      C2          116.34 3.000
TMP   C4      N3      C2          127.33 1.000
TMP   C5      C4      O4          124.92 1.000
TMP   C5      C4      N3          115.32 1.000
TMP   O4      C4      N3          120.30 1.378
TMP   C6      C5      C5M         122.99 1.000
TMP   C6      C5      C4          118.02 1.000
TMP   C5M     C5      C4          118.77 1.000
TMP   H53     C5M     H52         109.49 3.000
TMP   H53     C5M     H51         109.43 3.000
TMP   H52     C5M     H51         109.47 3.000
TMP   H53     C5M     C5          109.44 3.000
TMP   H52     C5M     C5          109.50 3.000
TMP   H51     C5M     C5          109.51 3.000
TMP   H6      C6      C5          118.33 3.000
TMP   H6      C6      N1          118.33 3.000
TMP   C5      C6      N1          123.34 1.000
#
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
TMP CONST_01       N3      C2      N1      C1'         179.89   0.0 0
TMP CONST_02       C4      N3      C2      N1           -0.17   0.0 0
TMP CONST_03       C5      C4      N3      C2            0.40   0.0 0
TMP CONST_04       C6      N1      C2      N3           -0.04   0.0 0
TMP CONST_05       O2      C2      N1      C1'          -0.03   0.0 0
TMP CONST_06       O4      C4      N3      C2          179.96   0.0 0
TMP CONST_07       C6      N1      C2      O2         -179.96   0.0 0
TMP CONST_08       C4      N3      C2      O2          179.75   0.0 0
TMP CONST_09       HN3     N3      C2      N1          179.99   0.0 0
TMP Var_01         H51     C5M     C5      C4          -90.30  30.0 3
TMP Var_02        C4'     C5'     O5'      P          -179.99  30.0 3
#
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
TMP chir_01  C4'     C5'     O4'     C3'    negativ
TMP chir_02  C3'     O3'     C4'     C2'    positiv
TMP chir_03   C1'    O4'      N1     C2'    negativ
#
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
TMP plan-1    C1' 0.020
TMP plan-1     N1 0.020
TMP plan-1     C2 0.020
TMP plan-1     O2 0.020
TMP plan-1     N3 0.020
TMP plan-1     C4 0.020
TMP plan-1     O4 0.020
TMP plan-1     C5 0.020
TMP plan-1    C5M 0.020
TMP plan-1     C6 0.020
TMP plan-1    HN3 0.020
TMP plan-1     H6 0.020
