# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Oct 20 16:13:44 2020
#
#   Inital geometry file: a 79 line input string
#   Ligand name: thymidine
#   CSD Mogul values: True
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@H]2C[C@H](O)[C@@H](CO)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
THM        THM 'thymidine                ' ligand 31 17 .
2020-10-20 2020-10-20
;
CIF prepared directly in eLBOW
;
#
data_comp_THM
#
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
THM        O5'     O   OH1    0    .       2.2740   -0.7240   -3.7900
THM        C5'     C   CH2    0    .       1.2080    0.2020   -3.5740
THM        C4'     C   CH1    0    .       0.1160   -0.4630   -2.7350
THM        O4'     O   O2     0    .       0.6000   -0.7600   -1.4060
THM        C3'     C   CH1    0    .      -1.0550    0.5190   -2.4840
THM        O3'     O   OH1    0    .      -1.9930    0.4810   -3.5620
THM        C2'     C   CH2    0    .      -1.6810   -0.0460   -1.1860
THM        C1'     C   CH1    0    .      -0.5540   -0.8890   -0.5600
THM         N1     N   NR6    0    .      -0.2460   -0.3910    0.7820
THM         C2     C   CR6    0    .       0.1650    0.8790    0.9430
THM         O2     O   O      0    .       0.2780    1.6000   -0.0290
THM         N3     N   NR16   0    .       0.4540    1.3630    2.1650
THM         C4     C   CR6    0    .       0.3290    0.5780    3.2540
THM         O4     O   O      0    .       0.5900    1.0150    4.3600
THM         C5     C   CR6    0    .      -0.0980   -0.7620    3.0990
THM         C5M    C   CH3    0    .      -0.2410   -1.6620    4.2990
THM         C6     C   CR16   0    .      -0.3820   -1.2220    1.8610
THM        HO5'    H   HOH1   0    .       2.9390   -0.2660   -4.3220
THM        H5'1    H   HCH2   0    .       0.7920    0.5080   -4.5340
THM        H5'2    H   HCH2   0    .       1.5880    1.0770   -3.0470
THM        H4'     H   HCH1   0    .      -0.2410   -1.3700   -3.2220
THM        H3'     H   HCH1   0    .      -0.6860    1.5320   -2.3280
THM        HO3'    H   HOH1   0    .      -2.7380    1.0400   -3.3030
THM        H2'1    H   HCH2   0    .      -2.5420   -0.6730   -1.4200
THM        H2'2    H   HCH2   0    .      -1.9690    0.7640   -0.5170
THM        H1'     H   HCH1   0    .      -0.8590   -1.9340   -0.5060
THM         HN3    H   HNR6   0    .       0.7500    2.2810    2.2630
THM        HM51    H   HCH3   0    .       0.0310   -1.1120    5.2000
THM        HM52    H   HCH3   0    .      -1.2750   -1.9990    4.3780
THM        HM53    H   HCH3   0    .       0.4140   -2.5250    4.1860
THM         H6     H   HCR6   0    .      -0.7130   -2.2400    1.7230
#
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
THM  O5'     C5'    single        1.421 0.020     1.421
THM  O5'     HO5'   single        0.850 0.018     0.980
THM  C5'     C4'    single        1.511 0.018     1.511
THM  C5'     H5'1   single        0.970 0.015     1.090
THM  C5'     H5'2   single        0.970 0.015     1.090
THM  C4'     O4'    single        1.444 0.015     1.444
THM  C4'     C3'    single        1.527 0.011     1.527
THM  C4'     H4'    single        0.970 0.012     1.090
THM  O4'     C1'    single        1.418 0.012     1.418
THM  C3'     O3'    single        1.428 0.013     1.428
THM  C3'     C2'    single        1.523 0.010     1.523
THM  C3'     H3'    single        0.970 0.011     1.090
THM  O3'     HO3'   single        0.850 0.011     0.980
THM  C2'     C1'    single        1.521 0.011     1.521
THM  C2'     H2'1   single        0.970 0.012     1.090
THM  C2'     H2'2   single        0.970 0.012     1.090
THM  C1'      N1    single        1.475 0.012     1.475
THM  C1'     H1'    single        0.970 0.017     1.090
THM   N1      C2    single        1.379 0.017     1.379
THM   N1      C6    single        1.377 0.010     1.377
THM   C2      O2    double        1.223 0.013     1.223
THM   C2      N3    single        1.374 0.012     1.374
THM   N3      C4    single        1.382 0.010     1.382
THM   N3      HN3   single        0.860 0.012     1.020
THM   C4      O4    double        1.230 0.012     1.230
THM   C4      C5    single        1.446 0.014     1.446
THM   C5      C5M   single        1.502 0.010     1.502
THM   C5      C6    double        1.342 0.018     1.342
THM   C5M    HM51   single        0.970 0.010     1.090
THM   C5M    HM52   single        0.970 0.010     1.090
THM   C5M    HM53   single        0.970 0.010     1.090
THM   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
THM  HO5'    O5'     C5'          106.82 3.000
THM  H5'2    C5'     H5'1         109.48 3.000
THM  H5'2    C5'     C4'          109.44 3.000
THM  H5'1    C5'     C4'          109.43 3.000
THM  H5'2    C5'     O5'          109.47 3.000
THM  H5'1    C5'     O5'          109.49 3.000
THM  C4'     C5'     O5'          111.43 1.958
THM  H4'     C4'     C3'          127.18 3.000
THM  H4'     C4'     O4'          127.18 3.000
THM  C3'     C4'     O4'          105.64 1.084
THM  H4'     C4'     C5'          127.18 3.000
THM  C3'     C4'     C5'          114.78 1.409
THM  O4'     C4'     C5'          109.34 1.337
THM  C1'     O4'     C4'          109.55 1.311
THM  H3'     C3'     C2'          124.52 3.000
THM  H3'     C3'     O3'          124.52 3.000
THM  C2'     C3'     O3'          110.97 2.419
THM  H3'     C3'     C4'          124.52 3.000
THM  C2'     C3'     C4'          102.59 1.017
THM  O3'     C3'     C4'          110.26 2.320
THM  HO3'    O3'     C3'          106.75 3.000
THM  H2'2    C2'     H2'1         110.52 3.000
THM  H2'2    C2'     C1'          110.54 3.000
THM  H2'1    C2'     C1'          110.50 3.000
THM  H2'2    C2'     C3'          110.52 3.000
THM  H2'1    C2'     C3'          110.44 3.000
THM  C1'     C2'     C3'          102.57 1.360
THM  H1'     C1'      N1          123.04 3.000
THM  H1'     C1'     C2'          123.04 3.000
THM   N1     C1'     C2'          113.92 1.278
THM  H1'     C1'     O4'          123.04 3.000
THM   N1     C1'     O4'          108.01 1.000
THM  C2'     C1'     O4'          106.23 1.052
THM   C6      N1      C2          121.30 1.000
THM   C6      N1     C1'          120.69 1.410
THM   C2      N1     C1'          117.69 1.459
THM   N3      C2      O2          121.99 1.083
THM   N3      C2      N1          114.83 1.000
THM   O2      C2      N1          122.84 1.000
THM   HN3     N3      C4          116.34 3.000
THM   HN3     N3      C2          116.34 3.000
THM   C4      N3      C2          127.33 1.000
THM   C5      C4      O4          124.92 1.000
THM   C5      C4      N3          115.32 1.000
THM   O4      C4      N3          120.30 1.378
THM   C6      C5      C5M         122.99 1.000
THM   C6      C5      C4          118.02 1.000
THM   C5M     C5      C4          118.77 1.000
THM  HM53     C5M    HM52         109.44 3.000
THM  HM53     C5M    HM51         109.60 3.000
THM  HM52     C5M    HM51         109.43 3.000
THM  HM53     C5M     C5          109.48 3.000
THM  HM52     C5M     C5          109.41 3.000
THM  HM51     C5M     C5          109.46 3.000
THM   H6      C6      C5          118.33 3.000
THM   H6      C6      N1          118.33 3.000
THM   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
THM CONST_01       N3      C2      N1      C1'         179.96   0.0 0
THM CONST_02       C4      N3      C2      N1           -0.30   0.0 0
THM CONST_03       C5      C4      N3      C2            0.52   0.0 0
THM CONST_04       C6      N1      C2      N3            0.10   0.0 0
THM CONST_05       O2      C2      N1      C1'          -0.09   0.0 0
THM CONST_06       O4      C4      N3      C2         -179.99   0.0 0
THM CONST_07       C6      N1      C2      O2         -179.95   0.0 0
THM CONST_08       C4      N3      C2      O2          179.74   0.0 0
THM CONST_09       HN3     N3      C2      N1          179.93   0.0 0
THM Var_01        HM51     C5M     C5      C4           -0.23  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
THM chir_01  C4'     C5'     O4'     C3'    negativ
THM chir_02  C3'     O3'     C4'     C2'    positiv
THM 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
THM plan-1    C1' 0.020
THM plan-1     N1 0.020
THM plan-1     C2 0.020
THM plan-1     O2 0.020
THM plan-1     N3 0.020
THM plan-1     C4 0.020
THM plan-1     O4 0.020
THM plan-1     C5 0.020
THM plan-1    C5M 0.020
THM plan-1     C6 0.020
THM plan-1    HN3 0.020
THM plan-1     H6 0.020
