# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 17:37:51 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 1,5-anhydro-2,3-dideoxy-2-(5-iodo-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-D-arabino-hexitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1OC[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
 AHU  AHU  1,5-anhydro-2,3-dideoxy-2-(5-iodo-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-D-arabino-hexitol  ligand  31  18  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AHU
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
 AHU  C4'   C  CH1   0  -0.005   1.3490   0.0398   3.2571
 AHU  C7'   C  CH2   0  -0.160   2.6334  -0.7480   3.1204
 AHU  O7'   O  OH1   0  -0.668   3.7267   0.1222   3.2778
 AHU  O5'   O  O2    0  -0.487   1.3189   0.9838   2.2023
 AHU  C6'   C  CH2   0  -0.238   0.2054   1.8436   2.2389
 AHU  C1'   C  CH1   0  -0.133  -1.1225   1.1064   2.1725
 AHU  C2'   C  CH2   0  -0.474  -1.1485   0.0033   3.2272
 AHU  C3'   C  CH1   0   0.030   0.1051  -0.8597   3.1961
 AHU  O3'   O  OH1   0  -0.666   0.0405  -1.7308   4.3019
 AHU  N1    N  NR6   0  -0.541  -1.4416   0.5928   0.8239
 AHU  C6    C  CR16  0   0.120  -0.4806   0.2366  -0.0723
 AHU  C2    C  CR6   0   0.750  -2.7817   0.4635   0.5070
 AHU  O2    O  O     0  -0.471  -3.6726   0.7477   1.2781
 AHU  N3    N  NR16  0  -0.735  -3.0353  -0.0065  -0.7552
 AHU  C4    C  CR6   0   0.603  -2.1326  -0.3764  -1.7347
 AHU  O4    O  O     0  -0.440  -2.5079  -0.7767  -2.8167
 AHU  C5    C  CR6   0  -0.482  -0.7602  -0.2285  -1.3054
 AHU  I     I  I     0   0.107   0.7403  -0.7572  -2.6442
 AHU  H4'   H  HCH1  0   0.222   1.3423   0.5645   4.2272
 AHU  H7'1  H  HCH2  0   0.200   2.6416  -1.2460   2.1400
 AHU  H7'2  H  HCH2  0   0.200   2.6406  -1.5379   3.8805
 AHU  HO'7  H  HOH1  0   0.457   4.5325  -0.3972   3.2069
 AHU  H6'1  H  HCH2  0   0.259   0.1960   2.4283   3.1681
 AHU  H6'2  H  HCH2  0   0.275   0.3116   2.5490   1.4125
 AHU  H1'   H  HCH1  0   0.303  -1.8964   1.8373   2.4007
 AHU  H2'1  H  HCH2  0   0.256  -1.2120   0.4889   4.2061
 AHU  H2'2  H  HCH2  0   0.272  -2.0394  -0.6177   3.1215
 AHU  H3'   H  HCH1  0   0.218   0.1331  -1.4332   2.2573
 AHU  HO'3  H  HOH1  0   0.457   0.5837  -2.5042   4.1268
 AHU  H6    H  HCR6  0   0.339   0.5391   0.3438   0.2660
 AHU  HN3   H  HNR6  0   0.433  -4.0166  -0.0925  -0.9926

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
 AHU  C4'  C7'   single  1.513  0.020  1.513
 AHU  C4'  O5'   single  1.416  0.020  1.416
 AHU  C4'  C3'   single  1.536  0.020  1.536
 AHU  C4'  H4'   single  0.970  0.020  1.090
 AHU  C7'  O7'   single  1.406  0.020  1.406
 AHU  C7'  H7'1  single  0.970  0.020  1.090
 AHU  C7'  H7'2  single  0.970  0.020  1.090
 AHU  O7'  HO'7  single  0.850  0.020  0.980
 AHU  O5'  C6'   single  1.407  0.020  1.407
 AHU  C6'  C1'   single  1.520  0.020  1.520
 AHU  C6'  H6'1  single  0.970  0.020  1.090
 AHU  C6'  H6'2  single  0.970  0.020  1.090
 AHU  C1'  C2'   single  1.526  0.020  1.526
 AHU  C1'  N1    single  1.478  0.020  1.478
 AHU  C1'  H1'   single  0.970  0.020  1.090
 AHU  C2'  C3'   single  1.522  0.020  1.522
 AHU  C2'  H2'1  single  0.970  0.020  1.090
 AHU  C2'  H2'2  single  0.970  0.020  1.090
 AHU  C3'  O3'   single  1.409  0.020  1.409
 AHU  C3'  H3'   single  0.970  0.020  1.090
 AHU  O3'  HO'3  single  0.850  0.020  0.980
 AHU  N1   C6    single  1.361  0.020  1.361
 AHU  N1   C2    single  1.383  0.020  1.383
 AHU  C6   C5    double  1.347  0.020  1.347
 AHU  C6   H6    single  0.930  0.020  1.080
 AHU  C2   O2    double  1.212  0.020  1.212
 AHU  C2   N3    single  1.370  0.020  1.370
 AHU  N3   C4    single  1.383  0.020  1.383
 AHU  N3   HN3   single  0.860  0.020  1.020
 AHU  C4   O4    double  1.213  0.020  1.213
 AHU  C4   C5    single  1.446  0.020  1.446
 AHU  C5   I     single  2.079  0.020  2.079

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
 AHU  H4'   C4'  C3'   107.97  3.000
 AHU  H4'   C4'  O5'   109.76  3.000
 AHU  C3'   C4'  O5'   110.10  3.000
 AHU  H4'   C4'  C7'   109.41  3.000
 AHU  C3'   C4'  C7'   112.26  3.000
 AHU  O5'   C4'  C7'   107.33  3.000
 AHU  H7'2  C7'  H7'1  106.97  3.000
 AHU  H7'2  C7'  O7'   111.29  3.000
 AHU  H7'1  C7'  O7'   111.98  3.000
 AHU  H7'2  C7'  C4'   108.55  3.000
 AHU  H7'1  C7'  C4'   108.83  3.000
 AHU  O7'   C7'  C4'   109.12  3.000
 AHU  HO'7  O7'  C7'   108.00  3.000
 AHU  C6'   O5'  C4'   113.88  3.000
 AHU  H6'2  C6'  H6'1  107.30  3.000
 AHU  H6'2  C6'  C1'   111.42  3.000
 AHU  H6'1  C6'  C1'   106.72  3.000
 AHU  H6'2  C6'  O5'   107.34  3.000
 AHU  H6'1  C6'  O5'   110.75  3.000
 AHU  C1'   C6'  O5'   113.18  3.000
 AHU  H1'   C1'  N1    105.73  3.000
 AHU  H1'   C1'  C2'   109.16  3.000
 AHU  N1    C1'  C2'   112.07  3.000
 AHU  H1'   C1'  C6'   106.63  3.000
 AHU  N1    C1'  C6'   113.39  3.000
 AHU  C2'   C1'  C6'   109.58  3.000
 AHU  H2'2  C2'  H2'1  106.97  3.000
 AHU  H2'2  C2'  C3'   110.36  3.000
 AHU  H2'1  C2'  C3'   108.52  3.000
 AHU  H2'2  C2'  C1'   110.99  3.000
 AHU  H2'1  C2'  C1'   107.35  3.000
 AHU  C3'   C2'  C1'   112.42  3.000
 AHU  H3'   C3'  O3'   110.39  3.000
 AHU  H3'   C3'  C2'   109.50  3.000
 AHU  O3'   C3'  C2'   107.25  3.000
 AHU  H3'   C3'  C4'   108.57  3.000
 AHU  O3'   C3'  C4'   111.59  3.000
 AHU  C2'   C3'  C4'   109.52  3.000
 AHU  HO'3  O3'  C3'   109.18  3.000
 AHU  C2    N1   C6    120.57  3.000
 AHU  C2    N1   C1'   116.79  3.000
 AHU  C6    N1   C1'   122.63  3.000
 AHU  H6    C6   C5    121.14  3.000
 AHU  H6    C6   N1    115.74  3.000
 AHU  C5    C6   N1    123.12  3.000
 AHU  N3    C2   O2    122.03  3.000
 AHU  N3    C2   N1    114.98  3.000
 AHU  O2    C2   N1    122.99  3.000
 AHU  HN3   N3   C4    116.34  3.000
 AHU  HN3   N3   C2    115.09  3.000
 AHU  C4    N3   C2    128.57  3.000
 AHU  C5    C4   O4    126.33  3.000
 AHU  C5    C4   N3    112.46  3.000
 AHU  O4    C4   N3    121.21  3.000
 AHU  I     C5   C4    117.89  3.000
 AHU  I     C5   C6    121.83  3.000
 AHU  C4    C5   C6    120.28  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
 AHU  CONST_01  N3   C2   N1   C1'  180.00   0.0  0
 AHU  CONST_02  C4   N3   C2   N1     0.00   0.0  0
 AHU  CONST_03  N3   C2   N1   C6     0.00   0.0  0
 AHU  CONST_04  C5   C4   N3   C2     0.00   0.0  0
 AHU  CONST_05  O2   C2   N1   C1'    0.00   0.0  0
 AHU  CONST_06  O2   C2   N1   C6   180.00   0.0  0
 AHU  CONST_07  O4   C4   N3   C2   180.00   0.0  0
 AHU  CONST_08  C4   N3   C2   O2   180.00   0.0  0
 AHU  CONST_09  HN3  N3   C2   N1   180.00   0.0  0
 AHU  Var_01    C1'  C6'  O5'  C4'  -59.12  30.0  1

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
 AHU  chir_01  C4'  C7'  O5'  C3'  negativ
 AHU  chir_02  C1'  N1   C2'  C6'  negativ
 AHU  chir_03  C3'  O3'  C2'  C4'  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
 AHU  plan-1  C1'  0.020
 AHU  plan-1  N1   0.020
 AHU  plan-1  C6   0.020
 AHU  plan-1  C2   0.020
 AHU  plan-1  O2   0.020
 AHU  plan-1  N3   0.020
 AHU  plan-1  C4   0.020
 AHU  plan-1  O4   0.020
 AHU  plan-1  C5   0.020
 AHU  plan-1  I    0.020
 AHU  plan-1  H6   0.020
 AHU  plan-1  HN3  0.020

