# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 03:15:55 2022
#   Inital geometry file: a 89 line input string
#   Ligand name: 1-(2-deoxy-2-methyl-beta-D-arabinofuranosyl)-5-ethynylpyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1[C@H](O)[C@@H](CO)O[C@H]1N2C=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
 EDV  EDV  1-(2-deoxy-2-methyl-beta-D-arabinofuranosyl)-5-ethynylpyrimidine-2,4(1H,3H)-dione  ligand  33  19  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EDV
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
 EDV  O01  O  OH1   0  -0.667  -3.5000  -2.3628   1.4341
 EDV  C03  C  CH2   0  -0.165  -3.4299  -1.6925   0.2010
 EDV  C06  C  CH1   0  -0.012  -2.8316  -0.3245   0.4031
 EDV  O08  O  O2    0  -0.499  -1.4793  -0.4479   0.8104
 EDV  C09  C  CH1   0   0.039  -2.7919   0.5175  -0.8816
 EDV  O11  O  OH1   0  -0.661  -3.8908   1.3790  -1.0189
 EDV  C13  C  CH1   0  -0.329  -1.4870   1.3211  -0.7628
 EDV  C15  C  CH3   0  -0.681  -0.6234   1.2160  -2.0107
 EDV  C16  C  CH1   0   0.243  -0.8499   0.7648   0.5322
 EDV  N18  N  NR6   0  -0.567   0.5879   0.5037   0.4436
 EDV  C19  C  CR6   0   0.740   1.4419   1.5482   0.7488
 EDV  O20  O  O     0  -0.463   1.0420   2.6417   1.0820
 EDV  N21  N  NR16  0  -0.734   2.7725   1.2496   0.6380
 EDV  C23  C  CR6   0   0.556   3.3495   0.0632   0.2232
 EDV  O24  O  O     0  -0.431   4.5540  -0.0586   0.1521
 EDV  C25  C  CR6   0  -0.353   2.3791  -0.9680  -0.1052
 EDV  C26  C  CR16  0   0.081   1.0582  -0.6956   0.0227
 EDV  C28  C  CSP   0   0.318   2.8396  -2.2359  -0.5409
 EDV  C29  C  CSP1  0  -0.541   3.2332  -3.3197  -0.8854
 EDV  H1   H  HOH1  0   0.459  -3.9891  -3.1799   1.3030
 EDV  H2   H  HCH2  0   0.203  -2.8214  -2.2395  -0.5331
 EDV  H3   H  HCH2  0   0.208  -4.4230  -1.5571  -0.2482
 EDV  H4   H  HCH1  0   0.236  -3.4028   0.2282   1.1632
 EDV  H5   H  HCH1  0   0.225  -2.7207  -0.1540  -1.7494
 EDV  H6   H  HOH1  0   0.455  -4.6727   0.8526  -1.2128
 EDV  H7   H  HCH1  0   0.274  -1.7373   2.3712  -0.5987
 EDV  H8   H  HCH3  0   0.259  -1.1915   1.5614  -2.8750
 EDV  H9   H  HCH3  0   0.243   0.2703   1.8381  -1.9489
 EDV  H10  H  HCH3  0   0.232  -0.3120   0.1904  -2.2184
 EDV  H11  H  HCH1  0   0.278  -0.9889   1.4730   1.3525
 EDV  H12  H  HNR6  0   0.435   3.4058   2.0073   0.8652
 EDV  H13  H  HCR6  0   0.334   0.3160  -1.4468  -0.2013
 EDV  H14  H  H     0   0.285   3.5874  -4.2744  -1.2010

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
 EDV  C29  C28  triple  1.203  0.020  1.203
 EDV  C28  C25  single  1.418  0.020  1.418
 EDV  C25  C26  double  1.355  0.020  1.355
 EDV  C25  C23  single  1.454  0.020  1.454
 EDV  O24  C23  double  1.213  0.020  1.213
 EDV  C03  O01  single  1.405  0.020  1.405
 EDV  C03  C06  single  1.507  0.020  1.507
 EDV  C26  N18  single  1.355  0.020  1.355
 EDV  C23  N21  single  1.383  0.020  1.383
 EDV  O08  C06  single  1.418  0.020  1.418
 EDV  O08  C16  single  1.394  0.020  1.394
 EDV  C06  C09  single  1.537  0.020  1.537
 EDV  N21  C19  single  1.368  0.020  1.368
 EDV  N18  C19  single  1.383  0.020  1.383
 EDV  N18  C16  single  1.464  0.020  1.464
 EDV  C19  O20  double  1.211  0.020  1.211
 EDV  C16  C13  single  1.547  0.020  1.547
 EDV  C09  O11  single  1.403  0.020  1.403
 EDV  C09  C13  single  1.537  0.020  1.537
 EDV  C13  C15  single  1.521  0.020  1.521
 EDV  O01  H1   single  0.832  0.020  0.971
 EDV  C03  H2   single  0.939  0.020  1.096
 EDV  C03  H3   single  0.939  0.020  1.096
 EDV  C06  H4   single  0.939  0.020  1.096
 EDV  C09  H5   single  0.939  0.020  1.096
 EDV  O11  H6   single  0.832  0.020  0.971
 EDV  C13  H7   single  0.939  0.020  1.096
 EDV  C15  H8   single  0.939  0.020  1.096
 EDV  C15  H9   single  0.939  0.020  1.096
 EDV  C15  H10  single  0.939  0.020  1.096
 EDV  C16  H11  single  0.939  0.020  1.096
 EDV  N21  H12  single  0.868  0.020  1.013
 EDV  C26  H13  single  0.930  0.020  1.086
 EDV  C29  H14  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
 EDV  H1   O01  C03  108.13  3.000
 EDV  H3   C03  H2   106.78  3.000
 EDV  H3   C03  C06  107.58  3.000
 EDV  H2   C03  C06  108.76  3.000
 EDV  H3   C03  O01  111.87  3.000
 EDV  H2   C03  O01  112.10  3.000
 EDV  C06  C03  O01  109.58  3.000
 EDV  H4   C06  C09  108.41  3.000
 EDV  H4   C06  O08  109.92  3.000
 EDV  C09  C06  O08  105.27  3.000
 EDV  H4   C06  C03  110.04  3.000
 EDV  C09  C06  C03  113.30  3.000
 EDV  O08  C06  C03  109.77  3.000
 EDV  C16  O08  C06  107.31  3.000
 EDV  H5   C09  C13  108.99  3.000
 EDV  H5   C09  O11  110.40  3.000
 EDV  C13  C09  O11  110.58  3.000
 EDV  H5   C09  C06  109.08  3.000
 EDV  C13  C09  C06  104.10  3.000
 EDV  O11  C09  C06  113.45  3.000
 EDV  H6   O11  C09  108.67  3.000
 EDV  H7   C13  C16  108.33  3.000
 EDV  H7   C13  C15  108.65  3.000
 EDV  C16  C13  C15  115.35  3.000
 EDV  H7   C13  C09  108.65  3.000
 EDV  C15  C13  C09  112.48  3.000
 EDV  C16  C13  C09  103.09  3.000
 EDV  H10  C15  H9   108.23  3.000
 EDV  H10  C15  H8   107.18  3.000
 EDV  H9   C15  H8   106.92  3.000
 EDV  H10  C15  C13  112.52  3.000
 EDV  H9   C15  C13  112.30  3.000
 EDV  H8   C15  C13  109.43  3.000
 EDV  H11  C16  N18  106.62  3.000
 EDV  H11  C16  C13  110.07  3.000
 EDV  N18  C16  C13  114.71  3.000
 EDV  H11  C16  O08  110.89  3.000
 EDV  C13  C16  O08  107.09  3.000
 EDV  N18  C16  O08  107.47  3.000
 EDV  C26  N18  C19  121.50  3.000
 EDV  C19  N18  C16  117.28  3.000
 EDV  C26  N18  C16  121.16  3.000
 EDV  N21  C19  O20  122.71  3.000
 EDV  O20  C19  N18  122.59  3.000
 EDV  N21  C19  N18  114.69  3.000
 EDV  H12  N21  C23  116.61  3.000
 EDV  H12  N21  C19  115.24  3.000
 EDV  C23  N21  C19  128.12  3.000
 EDV  C25  C23  O24  125.35  3.000
 EDV  O24  C23  N21  121.21  3.000
 EDV  C25  C23  N21  113.44  3.000
 EDV  C28  C25  C26  121.70  3.000
 EDV  C26  C25  C23  119.14  3.000
 EDV  C28  C25  C23  119.15  3.000
 EDV  H13  C26  C25  120.72  3.000
 EDV  H13  C26  N18  116.21  3.000
 EDV  C25  C26  N18  123.06  3.000
 EDV  C29  C28  C25  180.00  3.000
 EDV  H14  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
 EDV  CONST_01  N21  C19  N18  C16  180.00  0.0  0
 EDV  CONST_02  C23  N21  C19  N18    0.00  0.0  0
 EDV  CONST_03  C25  C23  N21  C19    0.00  0.0  0
 EDV  CONST_04  C26  N18  C19  N21    0.00  0.0  0
 EDV  CONST_05  O20  C19  N18  C16    0.00  0.0  0
 EDV  CONST_06  O24  C23  N21  C19  180.00  0.0  0
 EDV  CONST_07  C23  N21  C19  O20  180.00  0.0  0
 EDV  CONST_08  C26  N18  C19  O20  180.00  0.0  0
 EDV  CONST_09  H12  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
 EDV  chir_01  C06  C03  O08  C09  negativ
 EDV  chir_02  C09  O11  C06  C13  positiv
 EDV  chir_03  C13  C16  C09  C15  positiv
 EDV  chir_04  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
 EDV  plan-1  C16  0.020
 EDV  plan-1  N18  0.020
 EDV  plan-1  C19  0.020
 EDV  plan-1  O20  0.020
 EDV  plan-1  N21  0.020
 EDV  plan-1  C23  0.020
 EDV  plan-1  O24  0.020
 EDV  plan-1  C25  0.020
 EDV  plan-1  C26  0.020
 EDV  plan-1  C28  0.020
 EDV  plan-1  C29  0.020
 EDV  plan-1  H12  0.020
 EDV  plan-1  H13  0.020

