# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 22:27:50 2021
#   Inital geometry file: a 120 line input string
#   Ligand name: 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=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
 1FZ  1FZ  5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine  ligand  47  29  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1FZ
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
 1FZ  O2   O  O     0  -0.488  28.7050  26.7280  72.5251
 1FZ  O4   O  O     0  -0.456  33.2274  26.5591  72.4429
 1FZ  C4   C  CR6   0   0.561  32.1909  26.4946  71.8068
 1FZ  C5   C  CR6   0  -0.183  32.1029  26.3012  70.3743
 1FZ  C6   C  CR16  0   0.047  30.8807  26.2426  69.8144
 1FZ  C5M  C  CH3   0  -0.706  33.3643  26.1613  69.5873
 1FZ  N3   N  NR16  0  -0.731  30.9672  26.6082  72.4426
 1FZ  C2   C  CR6   0   0.734  29.7220  26.5754  71.8761
 1FZ  N1   N  NR6   0  -0.563  29.7147  26.3610  70.5197
 1FZ  C1'  C  CH1   0   0.199  28.3901  26.3298  69.8685
 1FZ  C2'  C  CH2   0  -0.540  27.8627  27.7246  69.5367
 1FZ  C3'  C  CH1   0   0.026  28.2438  27.8783  68.0705
 1FZ  O3'  O  OH1   0  -0.685  27.5124  28.8399  67.3538
 1FZ  O4'  O  O2    0  -0.493  28.5004  25.6377  68.6566
 1FZ  C4'  C  CH1   0   0.009  28.0606  26.4422  67.5709
 1FZ  C5'  C  CH2   0  -0.242  28.7591  26.0348  66.2976
 1FZ  O5'  O  O2    0  -0.575  30.1688  26.2987  66.3670
 1FZ  PA   P  P     0   1.506  30.9169  27.2505  65.3333
 1FZ  O1A  O  O     0  -0.711  30.8353  26.7945  63.9155
 1FZ  O2A  O  OH1   0  -0.710  32.3507  27.3817  65.9887
 1FZ  N3A  N  NH1   0  -0.975  30.3278  28.8016  65.5270
 1FZ  PB   P  P     0   1.439  29.0886  29.4561  64.6023
 1FZ  O1B  O  OH1   0  -0.731  28.4646  30.5748  65.5198
 1FZ  O2B  O  O     0  -0.680  28.2334  28.4077  64.0171
 1FZ  O3B  O  O2    0  -0.683  29.8064  30.3859  63.4992
 1FZ  PG   P  P     0   1.448  30.2490  29.8803  61.9979
 1FZ  O1G  O  OH1   0  -0.772  31.2908  28.7282  62.2347
 1FZ  O3G  O  O     0  -0.688  29.0863  29.6302  61.1312
 1FZ  O2G  O  OH1   0  -0.717  31.2331  31.0493  61.5715
 1FZ  H2   H  HCH3  0   0.247  33.9447  25.2983  69.9160
 1FZ  H3   H  HCH3  0   0.239  33.1495  26.0349  68.5276
 1FZ  H4   H  HCH3  0   0.247  34.0018  27.0395  69.6953
 1FZ  H5   H  HNR6  0   0.426  30.9841  26.7530  73.4446
 1FZ  H6   H  HCH1  0   0.284  27.7262  25.7922  70.5447
 1FZ  H7   H  HCH2  0   0.291  28.2730  28.5017  70.1790
 1FZ  H8   H  HCH2  0   0.275  26.7750  27.7358  69.6448
 1FZ  H9   H  HCH1  0   0.261  29.2894  28.1828  67.9895
 1FZ  H10  H  HOH1  0   0.474  26.5665  28.6544  67.4015
 1FZ  H11  H  HCH1  0   0.261  26.9899  26.2645  67.3894
 1FZ  H12  H  HCH2  0   0.270  28.2878  26.5542  65.4630
 1FZ  H13  H  HCH2  0   0.285  28.6352  24.9644  66.1308
 1FZ  H14  H  HOH1  0   0.518  32.9897  26.7050  65.7225
 1FZ  H15  H  HNH1  0   0.453  30.8339  29.4259  66.1475
 1FZ  H16  H  HOH1  0   0.512  28.0373  30.1577  66.3064
 1FZ  H17  H  HOH1  0   0.500  31.0525  27.9281  62.7903
 1FZ  H18  H  HOH1  0   0.507  30.8168  31.7285  61.0240
 1FZ  H1   H  HCR6  0   0.311  30.7699  26.0820  68.7532

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
 1FZ  O3G  PG   double  1.472  0.020  1.472
 1FZ  O1G  PG   single  1.571  0.020  1.571
 1FZ  O2G  PG   single  1.586  0.020  1.586
 1FZ  PG   O3B  single  1.645  0.020  1.645
 1FZ  O1A  PA   double  1.492  0.020  1.492
 1FZ  O3B  PB   single  1.611  0.020  1.611
 1FZ  O2B  PB   double  1.474  0.020  1.474
 1FZ  PB   N3A  single  1.679  0.020  1.679
 1FZ  PB   O1B  single  1.576  0.020  1.576
 1FZ  PA   N3A  single  1.670  0.020  1.670
 1FZ  PA   O2A  single  1.582  0.020  1.582
 1FZ  PA   O5'  single  1.592  0.020  1.592
 1FZ  C5'  O5'  single  1.436  0.020  1.436
 1FZ  C5'  C4'  single  1.508  0.020  1.508
 1FZ  O3'  C3'  single  1.405  0.020  1.405
 1FZ  C4'  C3'  single  1.531  0.020  1.531
 1FZ  C4'  O4'  single  1.421  0.020  1.421
 1FZ  C3'  C2'  single  1.523  0.020  1.523
 1FZ  O4'  C1'  single  1.400  0.020  1.400
 1FZ  C5M  C5   single  1.493  0.020  1.493
 1FZ  C2'  C1'  single  1.528  0.020  1.528
 1FZ  C6   C5   double  1.346  0.020  1.346
 1FZ  C6   N1   single  1.368  0.020  1.368
 1FZ  C1'  N1   single  1.476  0.020  1.476
 1FZ  C5   C4   single  1.448  0.020  1.448
 1FZ  N1   C2   single  1.373  0.020  1.373
 1FZ  C4   O4   double  1.218  0.020  1.218
 1FZ  C4   N3   single  1.384  0.020  1.384
 1FZ  C2   N3   single  1.368  0.020  1.368
 1FZ  C2   O2   double  1.216  0.020  1.216
 1FZ  C6   H1   single  0.930  0.020  1.080
 1FZ  C5M  H2   single  0.970  0.020  1.090
 1FZ  C5M  H3   single  0.970  0.020  1.090
 1FZ  C5M  H4   single  0.970  0.020  1.090
 1FZ  N3   H5   single  0.860  0.020  1.020
 1FZ  C1'  H6   single  0.970  0.020  1.090
 1FZ  C2'  H7   single  0.970  0.020  1.090
 1FZ  C2'  H8   single  0.970  0.020  1.090
 1FZ  C3'  H9   single  0.970  0.020  1.090
 1FZ  O3'  H10  single  0.850  0.020  0.980
 1FZ  C4'  H11  single  0.970  0.020  1.090
 1FZ  C5'  H12  single  0.970  0.020  1.090
 1FZ  C5'  H13  single  0.970  0.020  1.090
 1FZ  O2A  H14  single  0.850  0.020  0.980
 1FZ  N3A  H15  single  0.860  0.020  1.020
 1FZ  O1B  H16  single  0.850  0.020  0.980
 1FZ  O1G  H17  single  0.850  0.020  0.980
 1FZ  O2G  H18  single  0.850  0.020  0.980

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
 1FZ  N3   C4   C5   114.31  3.000
 1FZ  N3   C4   O4   120.55  3.000
 1FZ  C5   C4   O4   125.14  3.000
 1FZ  C5M  C5   C6   122.94  3.000
 1FZ  C6   C5   C4   118.21  3.000
 1FZ  C5M  C5   C4   118.85  3.000
 1FZ  H1   C6   N1   115.63  3.000
 1FZ  H1   C6   C5   120.59  3.000
 1FZ  N1   C6   C5   123.77  3.000
 1FZ  H4   C5M  H3   107.77  3.000
 1FZ  H4   C5M  H2   107.23  3.000
 1FZ  H3   C5M  H2   107.85  3.000
 1FZ  H4   C5M  C5   111.48  3.000
 1FZ  H3   C5M  C5   110.93  3.000
 1FZ  H2   C5M  C5   111.40  3.000
 1FZ  H5   N3   C2   115.36  3.000
 1FZ  H5   N3   C4   116.85  3.000
 1FZ  C2   N3   C4   127.78  3.000
 1FZ  N1   C2   N3   114.68  3.000
 1FZ  N3   C2   O2   122.49  3.000
 1FZ  N1   C2   O2   122.83  3.000
 1FZ  C1'  N1   C2   116.35  3.000
 1FZ  C2   N1   C6   121.22  3.000
 1FZ  C1'  N1   C6   122.38  3.000
 1FZ  H6   C1'  O4'  109.95  3.000
 1FZ  H6   C1'  C2'  112.02  3.000
 1FZ  O4'  C1'  C2'  106.89  3.000
 1FZ  H6   C1'  N1   106.47  3.000
 1FZ  C2'  C1'  N1   112.73  3.000
 1FZ  O4'  C1'  N1   108.76  3.000
 1FZ  H8   C2'  H7   108.03  3.000
 1FZ  H8   C2'  C3'  110.08  3.000
 1FZ  H7   C2'  C3'  113.69  3.000
 1FZ  H8   C2'  C1'  109.36  3.000
 1FZ  H7   C2'  C1'  113.17  3.000
 1FZ  C3'  C2'  C1'  102.41  3.000
 1FZ  H9   C3'  C4'  110.60  3.000
 1FZ  H9   C3'  O3'  105.66  3.000
 1FZ  C4'  C3'  O3'  114.40  3.000
 1FZ  H9   C3'  C2'  109.83  3.000
 1FZ  C4'  C3'  C2'  100.92  3.000
 1FZ  O3'  C3'  C2'  115.47  3.000
 1FZ  H10  O3'  C3'  110.71  3.000
 1FZ  C4'  O4'  C1'  110.92  3.000
 1FZ  H11  C4'  C5'  105.53  3.000
 1FZ  H11  C4'  O4'  109.62  3.000
 1FZ  C5'  C4'  O4'  110.40  3.000
 1FZ  H11  C4'  C3'  108.77  3.000
 1FZ  O4'  C4'  C3'  104.16  3.000
 1FZ  C5'  C4'  C3'  118.25  3.000
 1FZ  H13  C5'  H12  107.55  3.000
 1FZ  H13  C5'  O5'  107.42  3.000
 1FZ  H12  C5'  O5'  111.95  3.000
 1FZ  H13  C5'  C4'  109.98  3.000
 1FZ  H12  C5'  C4'  108.50  3.000
 1FZ  O5'  C5'  C4'  111.36  3.000
 1FZ  PA   O5'  C5'  122.68  3.000
 1FZ  N3A  PA   O2A  101.22  3.000
 1FZ  O2A  PA   O1A  117.95  3.000
 1FZ  N3A  PA   O1A  112.01  3.000
 1FZ  O2A  PA   O5'  101.92  3.000
 1FZ  N3A  PA   O5'  108.31  3.000
 1FZ  O1A  PA   O5'  114.13  3.000
 1FZ  H14  O2A  PA   115.23  3.000
 1FZ  H15  N3A  PB   117.69  3.000
 1FZ  H15  N3A  PA   117.78  3.000
 1FZ  PB   N3A  PA   123.94  3.000
 1FZ  O3B  PB   O2B  113.40  3.000
 1FZ  O2B  PB   O1B  120.42  3.000
 1FZ  O3B  PB   O1B   99.52  3.000
 1FZ  O1B  PB   N3A  104.38  3.000
 1FZ  O2B  PB   N3A  111.69  3.000
 1FZ  O3B  PB   N3A  105.86  3.000
 1FZ  H16  O1B  PB   109.59  3.000
 1FZ  PG   O3B  PB   124.56  3.000
 1FZ  O2G  PG   O3G  117.20  3.000
 1FZ  O2G  PG   O1G   99.76  3.000
 1FZ  O3G  PG   O1G  119.21  3.000
 1FZ  O2G  PG   O3B  100.70  3.000
 1FZ  O1G  PG   O3B  105.44  3.000
 1FZ  O3G  PG   O3B  112.16  3.000
 1FZ  H17  O1G  PG   120.73  3.000
 1FZ  H18  O2G  PG   113.76  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
 1FZ  CONST_01  N1   C2   N3   C4      0.00   0.0  0
 1FZ  CONST_02  C2   N3   C4   C5      0.00   0.0  0
 1FZ  CONST_03  N3   C2   N1   C6      0.00   0.0  0
 1FZ  CONST_04  C1'  N1   C2   N3    180.00   0.0  0
 1FZ  CONST_05  C6   N1   C2   O2    180.00   0.0  0
 1FZ  CONST_06  C1'  N1   C2   O2      0.00   0.0  0
 1FZ  CONST_07  C4   N3   C2   O2    180.00   0.0  0
 1FZ  CONST_08  C2   N3   C4   O4    180.00   0.0  0
 1FZ  CONST_09  H5   N3   C4   C5    180.00   0.0  0
 1FZ  Var_01    H2   C5M  C5   C4     60.56  30.0  3
 1FZ  Var_02    O1A  PA   O5'  C5'   -60.65  30.0  1
 1FZ  Var_03    PB   N3A  PA   O5'   -94.99  30.0  3
 1FZ  Var_04    O3B  PB   N3A  PA   -100.59  30.0  1
 1FZ  Var_05    O3G  PG   O3B  PB     70.00  30.0  1
 1FZ  Var_06    H12  C5'  O5'  PA      0.34  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
 1FZ  chir_01  C1'  O4'  C2'  N1   positiv
 1FZ  chir_02  C3'  O3'  C4'  C2'  positiv
 1FZ  chir_03  C4'  O4'  C3'  C5'  negativ
 1FZ  chir_04  PA   N3A  O2A  O5'  both
 1FZ  chir_05  PB   O2B  O3B  N3A  both

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
 1FZ  plan-1  O2   0.020
 1FZ  plan-1  O4   0.020
 1FZ  plan-1  C4   0.020
 1FZ  plan-1  C5   0.020
 1FZ  plan-1  C6   0.020
 1FZ  plan-1  C5M  0.020
 1FZ  plan-1  N3   0.020
 1FZ  plan-1  C2   0.020
 1FZ  plan-1  N1   0.020
 1FZ  plan-1  C1'  0.020
 1FZ  plan-1  H5   0.020
 1FZ  plan-1  H1   0.020

