# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 00:19:28 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 2'-deoxy-5-iodouridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](C[C@@H]1O)N2C=C(I)C(=O)NC2=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
 ID2  ID2  '2'-deoxy-5-iodouridine   '  ligand  28  17  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ID2
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
 ID2  C2    C  CR6   0   0.755   1.4026  -0.0714   1.0289
 ID2  C4    C  CR6   0   0.605   1.6547   0.3437  -1.4050
 ID2  C5    C  CR6   0  -0.485   0.2256   0.1366  -1.5139
 ID2  C6    C  CR16  0   0.130  -0.4974  -0.1498  -0.4164
 ID2  O2    O  O     0  -0.457   1.9300  -0.1500   2.1146
 ID2  O5'   O  OH1   0  -0.671  -0.8087   2.3543   5.0397
 ID2  C5'   C  CH2   0  -0.164  -0.0439   1.1738   4.9850
 ID2  C4'   C  CH1   0   0.019  -0.7781   0.1381   4.1714
 ID2  O4'   O  O2    0  -0.488  -0.8473   0.5443   2.8140
 ID2  C1'   C  CH1   0   0.220  -0.8256  -0.5632   1.9644
 ID2  N1    N  NR6   0  -0.564   0.0501  -0.2711   0.8252
 ID2  N3    N  NR16  0  -0.734   2.1143   0.2186  -0.1069
 ID2  O4    O  O     0  -0.436   2.4100   0.6033  -2.3171
 ID2  I     I  I     0   0.114  -0.6411   0.3021  -3.3954
 ID2  C2'   C  CH2   0  -0.562  -0.4455  -1.7886   2.8010
 ID2  C3'   C  CH1   0   0.025  -0.0846  -1.2241   4.1762
 ID2  O3'   O  OH1   0  -0.668  -0.5617  -1.9733   5.2646
 ID2  H6    H  HCR6  0   0.339  -1.5666  -0.3041  -0.4642
 ID2  HO5'  H  HOH1  0   0.457  -0.3385   2.9907   5.5856
 ID2  H5'1  H  HCH2  0   0.201   0.9428   1.3430   4.5342
 ID2  H5'2  H  HCH2  0   0.205   0.1240   0.7491   5.9833
 ID2  H4'   H  HCH1  0   0.229  -1.7951   0.0098   4.5709
 ID2  H1'   H  HCH1  0   0.259  -1.8085  -0.7156   1.5121
 ID2  HN3   H  HNR6  0   0.434   3.1085   0.3561   0.0334
 ID2  H2'1  H  HCH2  0   0.270  -1.3233  -2.4295   2.8956
 ID2  H2'2  H  HCH2  0   0.278   0.3468  -2.3849   2.3518
 ID2  H3'   H  HCH1  0   0.232   0.9982  -1.0856   4.2497
 ID2  HO3'  H  HOH1  0   0.458   0.0321  -2.7167   5.4021

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
 ID2  C2   O2    double  1.210  0.020  1.210
 ID2  C2   N1    single  1.382  0.020  1.382
 ID2  C2   N3    single  1.371  0.020  1.371
 ID2  C4   C5    single  1.448  0.020  1.448
 ID2  C4   N3    single  1.383  0.020  1.383
 ID2  C4   O4    double  1.212  0.020  1.212
 ID2  C5   C6    double  1.345  0.020  1.345
 ID2  C5   I     single  2.078  0.020  2.078
 ID2  C6   N1    single  1.362  0.020  1.362
 ID2  C6   H6    single  0.930  0.020  1.080
 ID2  O5'  C5'   single  1.408  0.020  1.408
 ID2  O5'  HO5'  single  0.850  0.020  0.980
 ID2  C5'  C4'   single  1.508  0.020  1.508
 ID2  C5'  H5'1  single  0.970  0.020  1.090
 ID2  C5'  H5'2  single  0.970  0.020  1.090
 ID2  C4'  O4'   single  1.419  0.020  1.419
 ID2  C4'  C3'   single  1.529  0.020  1.529
 ID2  C4'  H4'   single  0.970  0.020  1.090
 ID2  O4'  C1'   single  1.396  0.020  1.396
 ID2  C1'  N1    single  1.466  0.020  1.466
 ID2  C1'  C2'   single  1.532  0.020  1.532
 ID2  C1'  H1'   single  0.970  0.020  1.090
 ID2  N3   HN3   single  0.860  0.020  1.020
 ID2  C2'  C3'   single  1.530  0.020  1.530
 ID2  C2'  H2'1  single  0.970  0.020  1.090
 ID2  C2'  H2'2  single  0.970  0.020  1.090
 ID2  C3'  O3'   single  1.405  0.020  1.405
 ID2  C3'  H3'   single  0.970  0.020  1.090
 ID2  O3'  HO3'  single  0.850  0.020  0.980

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
 ID2  N3    C2   N1    114.60  3.000
 ID2  N3    C2   O2    122.06  3.000
 ID2  N1    C2   O2    123.34  3.000
 ID2  O4    C4   N3    121.24  3.000
 ID2  O4    C4   C5    126.07  3.000
 ID2  N3    C4   C5    112.69  3.000
 ID2  I     C5   C6    122.11  3.000
 ID2  I     C5   C4    117.92  3.000
 ID2  C6    C5   C4    119.96  3.000
 ID2  H6    C6   N1    115.15  3.000
 ID2  H6    C6   C5    121.72  3.000
 ID2  N1    C6   C5    123.13  3.000
 ID2  HO5'  O5'  C5'   108.15  3.000
 ID2  H5'2  C5'  H5'1  107.19  3.000
 ID2  H5'2  C5'  C4'   107.43  3.000
 ID2  H5'1  C5'  C4'   108.78  3.000
 ID2  H5'2  C5'  O5'   111.85  3.000
 ID2  H5'1  C5'  O5'   112.02  3.000
 ID2  C4'   C5'  O5'   109.42  3.000
 ID2  H4'   C4'  C3'   108.32  3.000
 ID2  H4'   C4'  O4'   109.62  3.000
 ID2  C3'   C4'  O4'   106.28  3.000
 ID2  H4'   C4'  C5'   109.53  3.000
 ID2  C3'   C4'  C5'   112.92  3.000
 ID2  O4'   C4'  C5'   110.08  3.000
 ID2  C1'   O4'  C4'   110.76  3.000
 ID2  H1'   C1'  C2'   109.74  3.000
 ID2  H1'   C1'  N1    104.09  3.000
 ID2  C2'   C1'  N1    115.82  3.000
 ID2  H1'   C1'  O4'   110.40  3.000
 ID2  C2'   C1'  O4'   107.83  3.000
 ID2  N1    C1'  O4'   108.91  3.000
 ID2  C1'   N1   C6    119.06  3.000
 ID2  C1'   N1   C2    119.91  3.000
 ID2  C6    N1   C2    120.98  3.000
 ID2  HN3   N3   C4    116.34  3.000
 ID2  HN3   N3   C2    115.03  3.000
 ID2  C4    N3   C2    128.62  3.000
 ID2  H2'2  C2'  H2'1  107.43  3.000
 ID2  H2'2  C2'  C3'   113.67  3.000
 ID2  H2'1  C2'  C3'   109.19  3.000
 ID2  H2'2  C2'  C1'   113.17  3.000
 ID2  H2'1  C2'  C1'   108.52  3.000
 ID2  C3'   C2'  C1'   104.73  3.000
 ID2  H3'   C3'  O3'   110.58  3.000
 ID2  H3'   C3'  C2'   109.91  3.000
 ID2  O3'   C3'  C2'   114.80  3.000
 ID2  H3'   C3'  C4'   109.66  3.000
 ID2  O3'   C3'  C4'   108.88  3.000
 ID2  C2'   C3'  C4'   102.65  3.000
 ID2  HO3'  O3'  C3'   108.27  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
 ID2  CONST_01  C5   C4  N3  C2     0.00  0.0  0
 ID2  CONST_02  N1   C2  N3  C4     0.00  0.0  0
 ID2  CONST_03  N3   C2  N1  C6     0.00  0.0  0
 ID2  CONST_04  N3   C2  N1  C1'  180.00  0.0  0
 ID2  CONST_05  O4   C4  N3  C2   180.00  0.0  0
 ID2  CONST_06  O2   C2  N3  C4   180.00  0.0  0
 ID2  CONST_07  O2   C2  N1  C6   180.00  0.0  0
 ID2  CONST_08  C1'  N1  C2  O2     0.00  0.0  0
 ID2  CONST_09  HN3  N3  C4  C5   180.00  0.0  0

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
 ID2  chir_01  C4'  C5'  O4'  C3'  negativ
 ID2  chir_02  C1'  O4'  N1   C2'  negativ
 ID2  chir_03  C3'  O3'  C4'  C2'  positiv

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
 ID2  plan-1  C2   0.020
 ID2  plan-1  C4   0.020
 ID2  plan-1  C5   0.020
 ID2  plan-1  C6   0.020
 ID2  plan-1  O2   0.020
 ID2  plan-1  C1'  0.020
 ID2  plan-1  N1   0.020
 ID2  plan-1  N3   0.020
 ID2  plan-1  O4   0.020
 ID2  plan-1  I    0.020
 ID2  plan-1  H6   0.020
 ID2  plan-1  HN3  0.020

