# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 09:58:05 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 2',3'-dideoxy-2'-fluoro-3'-triaza-1,2-dien-2-ium-1-yluridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](F)[C@@H]1N=[N+]=N)N2C=CC(=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
 0NP  0NP  2',3'-dideoxy-2'-fluoro-3'-triaza-1,2-dien-2-ium-1-yluridine  ligand  30  19  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0NP
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
 0NP  C2   C  CR6   0   0.765  -1.6952  -0.2414   0.8008
 0NP  O2   O  O     0  -0.472  -0.8159  -0.4261   1.6164
 0NP  C6   C  CR16  0   0.110  -2.4319   0.3228  -1.4083
 0NP  N19  N  N     0  -0.324   4.0665   2.7422   0.7789
 0NP  N18  N  N     1   0.524   3.5891   1.6879   0.6340
 0NP  C3'  C  CH1   0  -0.241   1.8514   0.1028   0.5304
 0NP  C4'  C  CH1   0   0.036   1.8198  -1.1116  -0.4071
 0NP  C5'  C  CH2   0  -0.152   2.0977  -2.4099   0.3121
 0NP  O5'  O  OH1   0  -0.663   2.1147  -3.4424  -0.6360
 0NP  O4'  O  O2    0  -0.469   0.5020  -1.1055  -0.9146
 0NP  C2'  C  CH1   0   0.135   0.8717   1.0899  -0.0955
 0NP  F2'  F  F     0  -0.360   1.5759   1.9119  -0.9621
 0NP  C1'  C  CH1   0   0.152  -0.0447   0.1813  -0.9353
 0NP  N1   N  NR6   0  -0.569  -1.4221   0.1220  -0.5035
 0NP  N3   N  NR16  0  -0.735  -3.0200  -0.3622   1.0994
 0NP  C5   C  CR16  0  -0.509  -3.7281   0.2050  -1.0907
 0NP  C4   C  CR6   0   0.574  -4.1051  -0.1646   0.2537
 0NP  O4   O  O     0  -0.451  -5.2393  -0.3059   0.6636
 0NP  H1   H  HCR6  0   0.336  -2.1151   0.5902  -2.4061
 0NP  H2   H  H     0   0.501   4.4137   3.2087  -0.0677
 0NP  H3   H  HCH1  0   0.384   1.5530  -0.1631   1.5451
 0NP  H4   H  HCH1  0   0.280   2.5460  -0.9701  -1.2177
 0NP  H5   H  HCH2  0   0.219   3.0600  -2.3096   0.8316
 0NP  H6   H  HCH2  0   0.218   1.3275  -2.5561   1.0797
 0NP  H7   H  HOH1  0   0.464   2.2358  -4.2756  -0.1717
 0NP  H8   H  HCH1  0   0.312   0.3573   1.7239   0.6238
 0NP  H9   H  HCH1  0   0.300  -0.0668   0.5870  -1.9508
 0NP  H10  H  HNR6  0   0.433  -3.2272  -0.6229   2.0566
 0NP  H11  H  HCR6  0   0.301  -4.4933   0.3770  -1.8313
 0NP  N3'  N  N     0  -0.099   3.2180   0.5953   0.6667

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
 0NP  C5'  C4'  single  1.510  0.020  1.510
 0NP  C5'  O5'  single  1.402  0.020  1.402
 0NP  C4'  O4'  single  1.412  0.020  1.412
 0NP  C4'  C3'  single  1.535  0.020  1.535
 0NP  O4'  C1'  single  1.398  0.020  1.398
 0NP  N3'  C3'  single  1.459  0.020  1.459
 0NP  N3'  N18  double  1.154  0.020  1.154
 0NP  C3'  C2'  single  1.525  0.020  1.525
 0NP  C1'  N1   single  1.445  0.020  1.445
 0NP  C1'  C2'  single  1.540  0.020  1.540
 0NP  N18  N19  double  1.166  0.020  1.166
 0NP  N1   C6   single  1.371  0.020  1.371
 0NP  N1   C2   single  1.381  0.020  1.381
 0NP  O2   C2   double  1.213  0.020  1.213
 0NP  C6   C5   double  1.340  0.020  1.340
 0NP  C2'  F2'  single  1.387  0.020  1.387
 0NP  C2   N3   single  1.363  0.020  1.363
 0NP  C5   C4   single  1.444  0.020  1.444
 0NP  N3   C4   single  1.390  0.020  1.390
 0NP  C4   O4   double  1.214  0.020  1.214
 0NP  C6   H1   single  0.930  0.020  1.080
 0NP  N19  H2   single  0.890  0.020  1.040
 0NP  C3'  H3   single  0.970  0.020  1.090
 0NP  C4'  H4   single  0.970  0.020  1.090
 0NP  C5'  H5   single  0.970  0.020  1.090
 0NP  C5'  H6   single  0.970  0.020  1.090
 0NP  O5'  H7   single  0.850  0.020  0.980
 0NP  C2'  H8   single  0.970  0.020  1.090
 0NP  C1'  H9   single  0.970  0.020  1.090
 0NP  N3   H10  single  0.860  0.020  1.020
 0NP  C5   H11  single  0.930  0.020  1.080

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
 0NP  N3   C2   N1   114.98  3.000
 0NP  N3   C2   O2   122.92  3.000
 0NP  N1   C2   O2   122.10  3.000
 0NP  H1   C6   C5   121.63  3.000
 0NP  H1   C6   N1   115.46  3.000
 0NP  C5   C6   N1   122.92  3.000
 0NP  H2   N19  N18  116.52  3.000
 0NP  N3'  N18  N19  169.61  3.000
 0NP  H3   C3'  C2'  111.34  3.000
 0NP  H3   C3'  C4'  111.71  3.000
 0NP  C2'  C3'  C4'  104.37  3.000
 0NP  H3   C3'  N3'  104.57  3.000
 0NP  C2'  C3'  N3'  114.93  3.000
 0NP  C4'  C3'  N3'  110.09  3.000
 0NP  H4   C4'  O4'  110.58  3.000
 0NP  H4   C4'  C5'  109.93  3.000
 0NP  O4'  C4'  C5'  110.28  3.000
 0NP  H4   C4'  C3'  109.61  3.000
 0NP  O4'  C4'  C3'  103.61  3.000
 0NP  C5'  C4'  C3'  112.69  3.000
 0NP  H6   C5'  H5   107.24  3.000
 0NP  H6   C5'  O5'  112.55  3.000
 0NP  H5   C5'  O5'  112.13  3.000
 0NP  H6   C5'  C4'  108.58  3.000
 0NP  H5   C5'  C4'  107.94  3.000
 0NP  O5'  C5'  C4'  108.26  3.000
 0NP  H7   O5'  C5'  108.25  3.000
 0NP  C1'  O4'  C4'  111.97  3.000
 0NP  H8   C2'  C1'  115.03  3.000
 0NP  H8   C2'  F2'  107.93  3.000
 0NP  C1'  C2'  F2'  108.13  3.000
 0NP  H8   C2'  C3'  114.17  3.000
 0NP  F2'  C2'  C3'  108.30  3.000
 0NP  C1'  C2'  C3'  102.96  3.000
 0NP  H9   C1'  N1   105.87  3.000
 0NP  H9   C1'  C2'  107.43  3.000
 0NP  N1   C1'  C2'  115.38  3.000
 0NP  H9   C1'  O4'  111.29  3.000
 0NP  C2'  C1'  O4'  107.60  3.000
 0NP  N1   C1'  O4'  109.31  3.000
 0NP  C1'  N1   C6   119.94  3.000
 0NP  C6   N1   C2   121.08  3.000
 0NP  C1'  N1   C2   118.78  3.000
 0NP  H10  N3   C4   116.85  3.000
 0NP  H10  N3   C2   115.36  3.000
 0NP  C4   N3   C2   127.79  3.000
 0NP  H11  C5   C4   119.65  3.000
 0NP  H11  C5   C6   120.63  3.000
 0NP  C4   C5   C6   119.71  3.000
 0NP  O4   C4   C5   126.00  3.000
 0NP  O4   C4   N3   120.48  3.000
 0NP  C5   C4   N3   113.52  3.000
 0NP  C3'  N3'  N18  128.17  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
 0NP  CONST_01  C5   C4  N3  C2     0.00  0.0  0
 0NP  CONST_02  N3   C2  N1  C6     0.00  0.0  0
 0NP  CONST_03  N3   C2  N1  C1'  180.00  0.0  0
 0NP  CONST_04  C4   N3  C2  N1     0.00  0.0  0
 0NP  CONST_05  O4   C4  N3  C2   180.00  0.0  0
 0NP  CONST_06  C1'  N1  C2  O2     0.00  0.0  0
 0NP  CONST_07  C6   N1  C2  O2   180.00  0.0  0
 0NP  CONST_08  C4   N3  C2  O2   180.00  0.0  0
 0NP  CONST_09  H10  N3  C2  N1   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
 0NP  chir_01  C3'  C4'  N3'  C2'  negativ
 0NP  chir_02  C4'  O4'  C3'  C5'  negativ
 0NP  chir_03  C2'  F2'  C3'  C1'  positiv
 0NP  chir_04  C1'  O4'  N1   C2'  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
 0NP  plan-1  C2   0.020
 0NP  plan-1  O2   0.020
 0NP  plan-1  C6   0.020
 0NP  plan-1  C1'  0.020
 0NP  plan-1  N1   0.020
 0NP  plan-1  N3   0.020
 0NP  plan-1  C5   0.020
 0NP  plan-1  C4   0.020
 0NP  plan-1  O4   0.020
 0NP  plan-1  H1   0.020
 0NP  plan-1  H10  0.020
 0NP  plan-1  H11  0.020
 0NP  plan-2  N19  0.020
 0NP  plan-2  N18  0.020
 0NP  plan-2  C3'  0.020
 0NP  plan-2  C4'  0.020
 0NP  plan-2  C2'  0.020
 0NP  plan-2  H2   0.020
 0NP  plan-2  H3   0.020
 0NP  plan-2  N3'  0.020

