# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 20:35:18 2021
#   Inital geometry file: a 115 line input string
#   Ligand name: 2-[(2~{R})-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2-oxidanyl-2~{H}-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CN2[C@H](O)SC(=C2C)CCO[P](O)(=O)O[P](O)(O)=O)c(N)n1
#
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
 8FL  8FL  '2-[(2~{R})-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2-oxidanyl-2~{H}-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate'  ligand  47  27  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8FL
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
 8FL  C4'  C  CR6   0   0.384  13.1173  33.2829  -26.1062
 8FL  C5'  C  CR6   0   0.004  13.3055  33.3633  -27.5076
 8FL  C6'  C  CR16  0  -0.029  12.1956  33.0679  -28.2606
 8FL  N1'  N  N     0  -0.467  11.0069  32.7232  -27.7609
 8FL  N3'  N  N     0  -0.345  11.9292  32.9387  -25.6017
 8FL  C2'  C  CR6   0   0.294  10.9357  32.6732  -26.4379
 8FL  CM2  C  CH3   0  -0.721   9.6218  32.3033  -25.8231
 8FL  C7   C  CH2   0  -0.175  15.1882  39.3459  -27.5256
 8FL  C7'  C  CH2   0  -0.475  14.6219  33.6563  -28.1669
 8FL  C4   C  CR5   0   0.388  14.7324  36.1548  -28.3209
 8FL  C5   C  CR5   0  -0.363  15.6569  37.1108  -28.4884
 8FL  C2   C  CR15  0   0.064  16.5732  34.9789  -27.3857
 8FL  N4'  N  NH2   0  -0.817  14.1062  33.5047  -25.2286
 8FL  N3   N  NR5   0  -0.440  15.2186  34.9441  -27.8369
 8FL  O3B  O  OH1   0  -0.735  19.7659  40.3185  -25.4568
 8FL  O1A  O  O     0  -0.696  16.8710  42.8169  -27.1437
 8FL  OC2  O  OH1   0  -0.680  16.5954  35.0232  -25.9898
 8FL  O2B  O  OH1   0  -0.756  18.3754  38.3633  -25.7175
 8FL  O1B  O  O     0  -0.642  18.6847  39.8953  -27.8209
 8FL  O2A  O  OH1   0  -0.744  15.2319  41.7631  -25.3910
 8FL  O7   O  O2    0  -0.509  15.6044  40.7077  -27.7030
 8FL  O3A  O  O2    0  -0.707  17.2905  40.6208  -25.7788
 8FL  PB   P  P     0   1.453  18.5737  39.7943  -26.3555
 8FL  PA   P  P     0   1.476  16.2774  41.5976  -26.5767
 8FL  S1   S  S2    0   0.047  17.2804  36.5008  -28.1271
 8FL  H1   H  HCR6  0   0.287  12.2653  33.1085  -29.3446
 8FL  H2   H  HCH3  0   0.275  12.9348  35.6645  -29.3918
 8FL  H3   H  HCH3  0   0.247  12.6751  36.1136  -27.7108
 8FL  H4   H  HCH3  0   0.277  13.0681  37.3449  -28.9084
 8FL  H5   H  HCH3  0   0.241   8.9407  31.9012  -26.5691
 8FL  H6   H  HCH3  0   0.261   9.7578  31.5694  -25.0297
 8FL  H7   H  HCH3  0   0.225   9.1539  33.1807  -25.3725
 8FL  H8   H  HCH2  0   0.301  14.1199  39.3300  -27.3053
 8FL  H9   H  HCH2  0   0.254  15.6949  38.8876  -26.6741
 8FL  H10  H  HCH2  0   0.283  16.4214  38.9406  -29.2357
 8FL  H11  H  HCH2  0   0.234  14.7148  38.7188  -29.5429
 8FL  H12  H  HCH2  0   0.277  14.5002  33.5520  -29.2500
 8FL  H13  H  HCH2  0   0.308  15.3457  32.8914  -27.8753
 8FL  H14  H  HCR5  0   0.280  17.1443  34.1248  -27.7560
 8FL  H15  H  HNH2  0   0.384  13.8642  33.5118  -24.2517
 8FL  H16  H  HNH2  0   0.399  14.9552  33.9889  -25.4855
 8FL  H17  H  HOH1  0   0.499  20.1025  41.1919  -25.7010
 8FL  H18  H  HOH1  0   0.441  17.4454  34.6954  -25.6715
 8FL  H19  H  HOH1  0   0.481  18.0489  37.6868  -26.3520
 8FL  H20  H  HOH1  0   0.489  14.6389  42.5208  -25.4911
 8FL  CM4  C  CH3   0  -0.737  13.2778  36.3251  -28.5939
 8FL  C6   C  CH2   0  -0.517  15.4958  38.5610  -28.7976

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
 8FL  CM4  C4   single    1.490  0.020  1.490
 8FL  C4   C5   double    1.340  0.020  1.340
 8FL  C4   N3   single    1.392  0.020  1.392
 8FL  C6   C5   single    1.491  0.020  1.491
 8FL  C6   C7   single    1.526  0.020  1.526
 8FL  C7'  N3   single    1.457  0.020  1.457
 8FL  C7'  C5'  single    1.501  0.020  1.501
 8FL  C6'  N1'  aromatic  1.335  0.020  1.335
 8FL  C6'  C5'  aromatic  1.373  0.020  1.373
 8FL  C5   S1   single    1.771  0.020  1.771
 8FL  N3   C2   single    1.428  0.020  1.428
 8FL  O1B  PB   double    1.473  0.020  1.473
 8FL  O7   C7   single    1.435  0.020  1.435
 8FL  O7   PA   single    1.585  0.020  1.585
 8FL  N1'  C2'  aromatic  1.326  0.020  1.326
 8FL  C5'  C4'  aromatic  1.416  0.020  1.416
 8FL  C2   S1   single    1.835  0.020  1.835
 8FL  C2   OC2  single    1.397  0.020  1.397
 8FL  O1A  PA   double    1.470  0.020  1.470
 8FL  PA   O3A  single    1.618  0.020  1.618
 8FL  PA   O2A  single    1.589  0.020  1.589
 8FL  O3B  PB   single    1.582  0.020  1.582
 8FL  PB   O3A  single    1.632  0.020  1.632
 8FL  PB   O2B  single    1.579  0.020  1.579
 8FL  C2'  CM2  single    1.497  0.020  1.497
 8FL  C2'  N3'  aromatic  1.326  0.020  1.326
 8FL  C4'  N3'  aromatic  1.336  0.020  1.336
 8FL  C4'  N4'  single    1.341  0.020  1.341
 8FL  C6'  H1   single    0.930  0.020  1.080
 8FL  CM4  H2   single    0.970  0.020  1.090
 8FL  CM4  H3   single    0.970  0.020  1.090
 8FL  CM4  H4   single    0.970  0.020  1.090
 8FL  CM2  H5   single    0.970  0.020  1.090
 8FL  CM2  H6   single    0.970  0.020  1.090
 8FL  CM2  H7   single    0.970  0.020  1.090
 8FL  C7   H8   single    0.970  0.020  1.090
 8FL  C7   H9   single    0.970  0.020  1.090
 8FL  C6   H10  single    0.970  0.020  1.090
 8FL  C6   H11  single    0.970  0.020  1.090
 8FL  C7'  H12  single    0.970  0.020  1.090
 8FL  C7'  H13  single    0.970  0.020  1.090
 8FL  C2   H14  single    0.970  0.020  1.090
 8FL  N4'  H15  single    0.890  0.020  1.040
 8FL  N4'  H16  single    0.890  0.020  1.040
 8FL  O3B  H17  single    0.850  0.020  0.980
 8FL  OC2  H18  single    0.850  0.020  0.980
 8FL  O2B  H19  single    0.850  0.020  0.980
 8FL  O2A  H20  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
 8FL  N4'  C4'  N3'  116.84  3.000
 8FL  N4'  C4'  C5'  122.70  3.000
 8FL  N3'  C4'  C5'  120.43  3.000
 8FL  C7'  C5'  C6'  120.65  3.000
 8FL  C6'  C5'  C4'  115.02  3.000
 8FL  C7'  C5'  C4'  124.21  3.000
 8FL  H1   C6'  N1'  116.11  3.000
 8FL  H1   C6'  C5'  119.14  3.000
 8FL  N1'  C6'  C5'  124.75  3.000
 8FL  C2'  N1'  C6'  115.54  3.000
 8FL  C2'  N3'  C4'  118.68  3.000
 8FL  CM2  C2'  N3'  116.63  3.000
 8FL  N3'  C2'  N1'  125.57  3.000
 8FL  CM2  C2'  N1'  117.80  3.000
 8FL  H7   CM2  H6   107.11  3.000
 8FL  H7   CM2  H5   108.17  3.000
 8FL  H6   CM2  H5   109.20  3.000
 8FL  H7   CM2  C2'  110.32  3.000
 8FL  H6   CM2  C2'  110.86  3.000
 8FL  H5   CM2  C2'  111.07  3.000
 8FL  H9   C7   H8   106.91  3.000
 8FL  H9   C7   O7   111.11  3.000
 8FL  H8   C7   O7   108.84  3.000
 8FL  H9   C7   C6   109.92  3.000
 8FL  H8   C7   C6   110.99  3.000
 8FL  O7   C7   C6   109.06  3.000
 8FL  H13  C7'  H12  105.72  3.000
 8FL  H13  C7'  N3   106.68  3.000
 8FL  H12  C7'  N3   110.72  3.000
 8FL  H13  C7'  C5'  109.09  3.000
 8FL  H12  C7'  C5'  108.57  3.000
 8FL  N3   C7'  C5'  115.60  3.000
 8FL  N3   C4   C5   115.03  3.000
 8FL  N3   C4   CM4  120.29  3.000
 8FL  C5   C4   CM4  124.68  3.000
 8FL  S1   C5   C4   111.16  3.000
 8FL  S1   C5   C6   118.43  3.000
 8FL  C4   C5   C6   130.16  3.000
 8FL  H14  C2   S1   108.07  3.000
 8FL  H14  C2   OC2  110.81  3.000
 8FL  S1   C2   OC2  111.80  3.000
 8FL  H14  C2   N3   111.71  3.000
 8FL  OC2  C2   N3   109.36  3.000
 8FL  S1   C2   N3   104.96  3.000
 8FL  H16  N4'  H15  116.45  3.000
 8FL  H16  N4'  C4'  122.18  3.000
 8FL  H15  N4'  C4'  117.34  3.000
 8FL  C2   N3   C4   114.84  3.000
 8FL  C2   N3   C7'  118.78  3.000
 8FL  C4   N3   C7'  123.17  3.000
 8FL  H17  O3B  PB   114.70  3.000
 8FL  H18  OC2  C2   109.45  3.000
 8FL  H19  O2B  PB   113.85  3.000
 8FL  H20  O2A  PA   114.05  3.000
 8FL  PA   O7   C7   124.61  3.000
 8FL  PA   O3A  PB   128.61  3.000
 8FL  O3A  PB   O1B  112.09  3.000
 8FL  O3A  PB   O2B  102.56  3.000
 8FL  O1B  PB   O2B  118.26  3.000
 8FL  O2B  PB   O3B   99.51  3.000
 8FL  O3A  PB   O3B  102.94  3.000
 8FL  O1B  PB   O3B  119.05  3.000
 8FL  O3A  PA   O7   106.10  3.000
 8FL  O3A  PA   O2A   96.13  3.000
 8FL  O7   PA   O2A  108.01  3.000
 8FL  O2A  PA   O1A  117.84  3.000
 8FL  O3A  PA   O1A  115.99  3.000
 8FL  O7   PA   O1A  111.28  3.000
 8FL  C2   S1   C5    90.85  3.000
 8FL  H4   CM4  H3   108.04  3.000
 8FL  H4   CM4  H2   107.20  3.000
 8FL  H3   CM4  H2   107.53  3.000
 8FL  H4   CM4  C4   110.39  3.000
 8FL  H3   CM4  C4   111.67  3.000
 8FL  H2   CM4  C4   111.82  3.000
 8FL  H11  C6   H10  106.40  3.000
 8FL  H11  C6   C5   111.08  3.000
 8FL  H10  C6   C5   109.24  3.000
 8FL  H11  C6   C7   110.53  3.000
 8FL  H10  C6   C7   109.05  3.000
 8FL  C5   C6   C7   110.43  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
 8FL  CONST_01  N1'  C6'  C5'  C4'    0.00   0.0  0
 8FL  CONST_02  N1'  C2'  N3'  C4'    0.00   0.0  0
 8FL  CONST_03  C2'  N1'  C6'  C5'    0.00   0.0  0
 8FL  CONST_04  C2'  N3'  C4'  C5'    0.00   0.0  0
 8FL  CONST_05  N3'  C2'  N1'  C6'    0.00   0.0  0
 8FL  CONST_06  N3'  C4'  C5'  C6'    0.00   0.0  0
 8FL  CONST_07  CM2  C2'  N3'  C4'  180.00   0.0  0
 8FL  CONST_08  CM2  C2'  N1'  C6'  180.00   0.0  0
 8FL  CONST_09  N4'  C4'  C5'  C6'  180.00   0.0  0
 8FL  CONST_10  C7'  C5'  C6'  N1'  180.00   0.0  0
 8FL  CONST_11  C7'  C5'  C4'  N3'  180.00   0.0  0
 8FL  CONST_12  N4'  C4'  N3'  C2'  180.00   0.0  0
 8FL  CONST_13  H1   C6'  C5'  C4'  180.00   0.0  0
 8FL  CONST_14  H15  N4'  C4'  C5'  180.00   0.0  0
 8FL  Var_01    C2   N3   C4   C5    10.02  30.0  1
 8FL  Var_02    S1   C5   C4   N3     3.54  30.0  1
 8FL  Var_03    N3   C7'  C5'  C4'  -60.93  30.0  2
 8FL  Var_04    C4   N3   C7'  C5'  -73.04  30.0  3
 8FL  Var_05    C4   C5   C6   C7    81.86  30.0  3
 8FL  Var_06    H5   CM2  C2'  N1'   12.92  30.0  2
 8FL  Var_07    H2   CM4  C4   C5   116.93  30.0  3
 8FL  Var_08    O7   C7   C6   C5   155.04  30.0  3
 8FL  Var_09    O1A  PA   O7   C7   166.55  30.0  3

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
 8FL  chir_01  C2  N3   S1   OC2  negativ
 8FL  chir_02  PA  O1A  O3A  O2A  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
 8FL  plan-1  C4'  0.020
 8FL  plan-1  C5'  0.020
 8FL  plan-1  C6'  0.020
 8FL  plan-1  N1'  0.020
 8FL  plan-1  N3'  0.020
 8FL  plan-1  C2'  0.020
 8FL  plan-1  CM2  0.020
 8FL  plan-1  C7'  0.020
 8FL  plan-1  N4'  0.020
 8FL  plan-1  H1   0.020
 8FL  plan-2  C4'  0.020
 8FL  plan-2  N4'  0.020
 8FL  plan-2  H15  0.020
 8FL  plan-2  H16  0.020
 8FL  plan-3  C7'  0.020
 8FL  plan-3  C4   0.020
 8FL  plan-3  C2   0.020
 8FL  plan-3  N3   0.020

