# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 11:26:44 2022
#   Inital geometry file: a 83 line input string
#   Ligand name: 2'-deoxy-5-ethynyl-2',2'-difluorouridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](N2C=C(C#C)C(=O)NC2=O)C(F)(F)[C@@H]1O
#
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
 F2U  F2U  2'-deoxy-5-ethynyl-2',2'-difluorouridine  ligand  30  20  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_F2U
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
 F2U  O01  O  OH1   0  -0.669  -3.6487  -2.3646   1.4254
 F2U  C03  C  CH2   0  -0.158  -3.4577  -1.5853   0.2709
 F2U  C06  C  CR15  0  -0.011  -2.7948  -0.2881   0.6599
 F2U  O08  O  O     0  -0.479  -1.4659  -0.5384   1.1147
 F2U  C09  C  CR15  0  -0.099  -2.6693   0.6893  -0.5084
 F2U  O11  O  OH1   0  -0.653  -3.8190   1.4669  -0.6025
 F2U  C13  C  CR5   0   0.714  -1.4093   1.4637  -0.1205
 F2U  F14  F  F     0  -0.322  -0.6680   1.8817  -1.1711
 F2U  F15  F  F     0  -0.331  -1.7411   2.5792   0.5760
 F2U  C16  C  CR15  0   0.095  -0.6222   0.5212   0.8190
 F2U  N18  N  NR6   0  -0.568   0.6424   0.0435   0.2859
 F2U  C19  C  CR6   0   0.763   0.6598  -0.7473  -0.8543
 F2U  O20  O  O     0  -0.453  -0.3408  -1.0459  -1.4618
 F2U  N21  N  NR16  0  -0.736   1.9052  -1.1625  -1.2386
 F2U  C23  C  CR6   0   0.558   3.1250  -0.8708  -0.6575
 F2U  O24  O  O     0  -0.424   4.1603  -1.3014  -1.1159
 F2U  C25  C  CR6   0  -0.352   3.0174  -0.0234   0.5212
 F2U  C26  C  CR16  0   0.103   1.7937   0.3787   0.9288
 F2U  C28  C  CSP   0   0.321   4.1969   0.3500   1.2131
 F2U  C29  C  CSP1  0  -0.534   5.2007   0.6624   1.7979
 F2U  H1   H  HOH1  0   0.460  -4.0723  -3.1871   1.1641
 F2U  H2   H  HCH2  0   0.209  -2.8335  -2.0944  -0.4743
 F2U  H3   H  HCH2  0   0.212  -4.4088  -1.3335  -0.2157
 F2U  H4   H  HCR5  0   0.255  -3.3717   0.1943   1.4613
 F2U  H5   H  HCR5  0   0.273  -2.4624   0.1440  -1.4338
 F2U  H6   H  HOH1  0   0.469  -3.8863   1.8254  -1.4927
 F2U  H7   H  HCR5  0   0.294  -0.3573   1.0806   1.7214
 F2U  H8   H  HNR6  0   0.437   1.9267  -1.7458  -2.0674
 F2U  H9   H  HCR6  0   0.343   1.6790   1.0017   1.8046
 F2U  H10  H  H     0   0.286   6.0862   0.9405   2.3224

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
 F2U  C29  C28  triple  1.203  0.020  1.203
 F2U  C28  C25  single  1.417  0.020  1.417
 F2U  C25  C26  double  1.351  0.020  1.351
 F2U  C25  C23  single  1.456  0.020  1.456
 F2U  O24  C23  double  1.211  0.020  1.211
 F2U  C03  O01  single  1.406  0.020  1.406
 F2U  C03  C06  single  1.508  0.020  1.508
 F2U  C26  N18  single  1.361  0.020  1.361
 F2U  C23  N21  single  1.382  0.020  1.382
 F2U  O08  C06  single  1.427  0.020  1.427
 F2U  O08  C16  single  1.386  0.020  1.386
 F2U  C06  C09  single  1.528  0.020  1.528
 F2U  N18  C16  single  1.453  0.020  1.453
 F2U  N18  C19  single  1.388  0.020  1.388
 F2U  N21  C19  single  1.368  0.020  1.368
 F2U  C16  C13  single  1.546  0.020  1.546
 F2U  C19  O20  double  1.208  0.020  1.208
 F2U  C09  C13  single  1.529  0.020  1.529
 F2U  C09  O11  single  1.391  0.020  1.391
 F2U  F14  C13  single  1.352  0.020  1.352
 F2U  C13  F15  single  1.356  0.020  1.356
 F2U  O01  H1   single  0.832  0.020  0.971
 F2U  C03  H2   single  0.939  0.020  1.096
 F2U  C03  H3   single  0.939  0.020  1.096
 F2U  C06  H4   single  0.939  0.020  1.096
 F2U  C09  H5   single  0.939  0.020  1.096
 F2U  O11  H6   single  0.832  0.020  0.971
 F2U  C16  H7   single  0.939  0.020  1.096
 F2U  N21  H8   single  0.868  0.020  1.013
 F2U  C26  H9   single  0.930  0.020  1.086
 F2U  C29  H10  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
 F2U  H1   O01  C03  108.11  3.000
 F2U  H3   C03  H2   107.36  3.000
 F2U  H3   C03  C06  107.34  3.000
 F2U  H2   C03  C06  108.92  3.000
 F2U  H3   C03  O01  111.93  3.000
 F2U  H2   C03  O01  112.20  3.000
 F2U  C06  C03  O01  108.95  3.000
 F2U  H4   C06  C09  108.65  3.000
 F2U  H4   C06  O08  109.48  3.000
 F2U  C09  C06  O08  106.22  3.000
 F2U  H4   C06  C03  109.57  3.000
 F2U  C09  C06  C03  112.90  3.000
 F2U  O08  C06  C03  109.93  3.000
 F2U  C16  O08  C06  111.39  3.000
 F2U  H5   C09  C13  108.14  3.000
 F2U  H5   C09  O11  112.19  3.000
 F2U  C13  C09  O11  114.52  3.000
 F2U  H5   C09  C06  110.09  3.000
 F2U  O11  C09  C06  109.96  3.000
 F2U  C13  C09  C06  101.40  3.000
 F2U  H6   O11  C09  109.19  3.000
 F2U  C16  C13  F15  108.29  3.000
 F2U  F15  C13  F14  106.19  3.000
 F2U  C16  C13  F14  112.43  3.000
 F2U  F15  C13  C09  110.20  3.000
 F2U  F14  C13  C09  114.28  3.000
 F2U  C16  C13  C09  105.36  3.000
 F2U  H7   C16  N18  105.07  3.000
 F2U  H7   C16  C13  108.22  3.000
 F2U  N18  C16  C13  114.86  3.000
 F2U  H7   C16  O08  111.23  3.000
 F2U  C13  C16  O08  106.60  3.000
 F2U  N18  C16  O08  110.89  3.000
 F2U  C26  N18  C19  121.20  3.000
 F2U  C19  N18  C16  119.98  3.000
 F2U  C26  N18  C16  118.82  3.000
 F2U  N21  C19  O20  122.53  3.000
 F2U  O20  C19  N18  122.93  3.000
 F2U  N21  C19  N18  114.53  3.000
 F2U  H8   N21  C23  116.52  3.000
 F2U  H8   N21  C19  115.06  3.000
 F2U  C23  N21  C19  128.41  3.000
 F2U  C25  C23  O24  125.20  3.000
 F2U  O24  C23  N21  121.34  3.000
 F2U  C25  C23  N21  113.46  3.000
 F2U  C28  C25  C26  121.87  3.000
 F2U  C26  C25  C23  118.98  3.000
 F2U  C28  C25  C23  119.15  3.000
 F2U  H9   C26  C25  120.81  3.000
 F2U  H9   C26  N18  115.79  3.000
 F2U  C25  C26  N18  123.40  3.000
 F2U  C29  C28  C25  180.00  3.000
 F2U  H10  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
 F2U  CONST_01  N21  C19  N18  C16  180.00  0.0  0
 F2U  CONST_02  C23  N21  C19  N18    0.00  0.0  0
 F2U  CONST_03  C25  C23  N21  C19    0.00  0.0  0
 F2U  CONST_04  C26  N18  C19  N21    0.00  0.0  0
 F2U  CONST_05  O20  C19  N18  C16    0.00  0.0  0
 F2U  CONST_06  O24  C23  N21  C19  180.00  0.0  0
 F2U  CONST_07  C26  N18  C19  O20  180.00  0.0  0
 F2U  CONST_08  C23  N21  C19  O20  180.00  0.0  0
 F2U  CONST_09  H8   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
 F2U  chir_01  C06  C03  O08  C09  negativ
 F2U  chir_02  C09  O11  C06  C13  positiv
 F2U  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
 F2U  plan-1  C16  0.020
 F2U  plan-1  N18  0.020
 F2U  plan-1  C19  0.020
 F2U  plan-1  O20  0.020
 F2U  plan-1  N21  0.020
 F2U  plan-1  C23  0.020
 F2U  plan-1  O24  0.020
 F2U  plan-1  C25  0.020
 F2U  plan-1  C26  0.020
 F2U  plan-1  C28  0.020
 F2U  plan-1  C29  0.020
 F2U  plan-1  H8   0.020
 F2U  plan-1  H9   0.020

