# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 20:46:29 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: 2'-deoxy-5-ethynyluridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](C[C@@H]1O)N2C=C(C#C)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
 EDU  EDU  2'-deoxy-5-ethynyluridine  ligand  30  18  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EDU
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
 EDU  O01  O  OH1   0  -0.672  -3.7108  -1.1535   2.1284
 EDU  C03  C  CH2   0  -0.163  -3.5684  -0.9934   0.7370
 EDU  C06  C  CH1   0   0.019  -2.9095   0.3324   0.4491
 EDU  O08  O  O2    0  -0.488  -1.5810   0.3339   0.9481
 EDU  C09  C  CH1   0   0.024  -2.8096   0.6351  -1.0466
 EDU  O10  O  OH1   0  -0.668  -3.9652   1.3258  -1.4492
 EDU  C13  C  CH2   0  -0.561  -1.5162   1.4468  -1.1396
 EDU  C16  C  CH1   0   0.220  -0.7457   1.1034   0.1379
 EDU  N18  N  NR6   0  -0.565   0.5225   0.3891  -0.0520
 EDU  C19  C  CR6   0   0.754   0.5393  -0.8194  -0.7279
 EDU  O20  O  O     0  -0.453  -0.4495  -1.3210  -1.2096
 EDU  N21  N  NR16  0  -0.735   1.7744  -1.4067  -0.8178
 EDU  C23  C  CR6   0   0.552   2.9801  -0.9510  -0.3205
 EDU  O24  O  O     0  -0.431   4.0052  -1.5799  -0.4784
 EDU  C25  C  CR6   0  -0.354   2.8707   0.3154   0.3847
 EDU  C26  C  CR16  0   0.098   1.6559   0.9048   0.4840
 EDU  C28  C  CSP   0   0.319   4.0328   0.8961   0.9514
 EDU  C29  C  CSP1  0  -0.540   5.0247   1.3849   1.4264
 EDU  H1   H  HOH1  0   0.457  -4.1326  -2.0023   2.2888
 EDU  H2   H  HCH2  0   0.202  -2.9644  -1.7937   0.2906
 EDU  H3   H  HCH2  0   0.203  -4.5394  -0.9953   0.2249
 EDU  H4   H  HCH1  0   0.230  -3.4828   1.1394   0.9287
 EDU  H5   H  HCH1  0   0.233  -2.7069  -0.2985  -1.6075
 EDU  H6   H  HOH1  0   0.458  -4.0225   1.2843  -2.4081
 EDU  H7   H  HCH2  0   0.279  -0.9467   1.2607  -2.0484
 EDU  H8   H  HCH2  0   0.271  -1.7619   2.5097  -1.1187
 EDU  H9   H  HCH1  0   0.259  -0.4544   2.0224   0.6517
 EDU  H10  H  HNR6  0   0.434   1.7947  -2.2868  -1.3199
 EDU  H11  H  HCR6  0   0.337   1.5410   1.8429   1.0090
 EDU  H12  H  H     0   0.285   5.8984   1.8303   1.8442

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
 EDU  C29  C28  triple  1.203  0.020  1.203
 EDU  C28  C25  single  1.417  0.020  1.417
 EDU  O24  C23  double  1.213  0.020  1.213
 EDU  C25  C23  single  1.454  0.020  1.454
 EDU  C25  C26  double  1.354  0.020  1.354
 EDU  C23  N21  single  1.382  0.020  1.382
 EDU  C03  O01  single  1.408  0.020  1.408
 EDU  C03  C06  single  1.508  0.020  1.508
 EDU  C26  N18  single  1.356  0.020  1.356
 EDU  O08  C06  single  1.419  0.020  1.419
 EDU  O08  C16  single  1.395  0.020  1.395
 EDU  N21  C19  single  1.371  0.020  1.371
 EDU  C06  C09  single  1.529  0.020  1.529
 EDU  N18  C19  single  1.385  0.020  1.385
 EDU  N18  C16  single  1.468  0.020  1.468
 EDU  C19  O20  double  1.209  0.020  1.209
 EDU  C16  C13  single  1.531  0.020  1.531
 EDU  C09  C13  single  1.530  0.020  1.530
 EDU  C09  O10  single  1.405  0.020  1.405
 EDU  O01  H1   single  0.832  0.020  0.971
 EDU  C03  H2   single  0.939  0.020  1.096
 EDU  C03  H3   single  0.939  0.020  1.096
 EDU  C06  H4   single  0.939  0.020  1.096
 EDU  C09  H5   single  0.939  0.020  1.096
 EDU  O10  H6   single  0.832  0.020  0.971
 EDU  C13  H7   single  0.939  0.020  1.096
 EDU  C13  H8   single  0.939  0.020  1.096
 EDU  C16  H9   single  0.939  0.020  1.096
 EDU  N21  H10  single  0.868  0.020  1.013
 EDU  C26  H11  single  0.930  0.020  1.086
 EDU  C29  H12  single  0.913  0.020  1.066

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
 EDU  H1   O01  C03  108.04  3.000
 EDU  H3   C03  H2   107.20  3.000
 EDU  H3   C03  C06  107.39  3.000
 EDU  H2   C03  C06  108.84  3.000
 EDU  H3   C03  O01  111.80  3.000
 EDU  H2   C03  O01  112.01  3.000
 EDU  C06  C03  O01  109.44  3.000
 EDU  H4   C06  C09  108.38  3.000
 EDU  H4   C06  O08  109.50  3.000
 EDU  C09  C06  O08  106.41  3.000
 EDU  H4   C06  C03  109.51  3.000
 EDU  C09  C06  C03  112.91  3.000
 EDU  O08  C06  C03  110.05  3.000
 EDU  C16  O08  C06  110.91  3.000
 EDU  H5   C09  C13  110.02  3.000
 EDU  H5   C09  O10  110.47  3.000
 EDU  C13  C09  O10  114.65  3.000
 EDU  H5   C09  C06  109.79  3.000
 EDU  O10  C09  C06  108.89  3.000
 EDU  C13  C09  C06  102.69  3.000
 EDU  H6   O10  C09  108.27  3.000
 EDU  H8   C13  H7   107.48  3.000
 EDU  H8   C13  C16  108.41  3.000
 EDU  H7   C13  C16  113.26  3.000
 EDU  H8   C13  C09  108.99  3.000
 EDU  H7   C13  C09  113.73  3.000
 EDU  C16  C13  C09  104.82  3.000
 EDU  H9   C16  N18  103.88  3.000
 EDU  H9   C16  C13  109.76  3.000
 EDU  N18  C16  C13  115.85  3.000
 EDU  H9   C16  O08  110.52  3.000
 EDU  C13  C16  O08  107.88  3.000
 EDU  N18  C16  O08  108.91  3.000
 EDU  C26  N18  C19  120.99  3.000
 EDU  C19  N18  C16  119.89  3.000
 EDU  C26  N18  C16  119.08  3.000
 EDU  N21  C19  O20  122.22  3.000
 EDU  O20  C19  N18  123.14  3.000
 EDU  N21  C19  N18  114.64  3.000
 EDU  H10  N21  C23  116.58  3.000
 EDU  H10  N21  C19  115.00  3.000
 EDU  C23  N21  C19  128.42  3.000
 EDU  C25  C23  O24  125.35  3.000
 EDU  C25  C23  N21  113.35  3.000
 EDU  O24  C23  N21  121.30  3.000
 EDU  C28  C25  C26  121.87  3.000
 EDU  C26  C25  C23  118.84  3.000
 EDU  C28  C25  C23  119.29  3.000
 EDU  H11  C26  C25  120.58  3.000
 EDU  H11  C26  N18  115.67  3.000
 EDU  C25  C26  N18  123.75  3.000
 EDU  C29  C28  C25  180.00  3.000
 EDU  H12  C29  C28  180.00  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
 EDU  CONST_01  N21  C19  N18  C16  180.00  0.0  0
 EDU  CONST_02  C23  N21  C19  N18    0.00  0.0  0
 EDU  CONST_03  C25  C23  N21  C19    0.00  0.0  0
 EDU  CONST_04  C26  N18  C19  N21    0.00  0.0  0
 EDU  CONST_05  O20  C19  N18  C16    0.00  0.0  0
 EDU  CONST_06  O24  C23  N21  C19  180.00  0.0  0
 EDU  CONST_07  C23  N21  C19  O20  180.00  0.0  0
 EDU  CONST_08  C26  N18  C19  O20  180.00  0.0  0
 EDU  CONST_09  H10  N21  C19  N18  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
 EDU  chir_01  C06  C03  O08  C09  negativ
 EDU  chir_02  C09  O10  C06  C13  positiv
 EDU  chir_03  C16  O08  N18  C13  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
 EDU  plan-1  C16  0.020
 EDU  plan-1  N18  0.020
 EDU  plan-1  C19  0.020
 EDU  plan-1  O20  0.020
 EDU  plan-1  N21  0.020
 EDU  plan-1  C23  0.020
 EDU  plan-1  O24  0.020
 EDU  plan-1  C25  0.020
 EDU  plan-1  C26  0.020
 EDU  plan-1  C28  0.020
 EDU  plan-1  C29  0.020
 EDU  plan-1  H10  0.020
 EDU  plan-1  H11  0.020

