# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jun 13 20:27:02 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: [(2~{R},4~{a}~{R},6~{R},7~{a}~{R})-6-[2,4-bis(oxidanylidene)-5-[(~{E})-3-phosphonoprop-1-enyl]pyrimidin-1-yl]-2-phenyl-4~{a},6,7,7~{a}-tetrahydro-4~{H}-furo[3,2-d][1,3]dioxin-2-yl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)C\C=C\C1=CN([C@H]2C[C@H]3O[C@](OC[C@H]3O2)(c4ccccc4)[P](O)(O)=O)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
 O84  O84  '[(2~{R},4~{a}~{R},6~{R},7~{a}~{R})-6-[2,4-bis(oxidanylidene)-5-[(~{E})-3-phosphonoprop-1-enyl]pyrimidin-1-yl]-2-phenyl-4~{a},6,7,7~{a}-tetrahydro-4~{H}-furo[3,2-d][1,3]dioxin-2-yl]phosphonic acid'  ligand  52  34  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_O84
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
 O84  OP2  O  OP    -1  -0.891  -5.6450   1.9559  -1.3765
 O84  P    P  P      0   1.173  -4.9705   1.9988  -0.0058
 O84  OP1  O  O      0  -0.882  -4.3531   3.3491   0.3508
 O84  OP3  O  OP    -1  -0.882  -5.7754   1.3462   1.1161
 O84  CAB  C  CT     0   0.170  -3.4563   0.8520  -0.1963
 O84  C2   C  CR6    0   0.031  -2.6814   0.8445   1.0983
 O84  CAA  C  CR16   0  -0.271  -1.6719   1.7754   1.3357
 O84  C9   C  CR16   0  -0.254  -1.0124   1.8208   2.5567
 O84  C10  C  CR16   0  -0.276  -1.3696   0.9523   3.5794
 O84  C11  C  CR16   0  -0.254  -2.3931   0.0382   3.3632
 O84  C12  C  CR16   0  -0.266  -3.0459  -0.0080   2.1398
 O84  O3'  O  O2     0  -0.507  -3.9710  -0.4305  -0.5102
 O84  O7   O  O2     0  -0.498  -2.6959   1.3604  -1.2624
 O84  C5'  C  CH2    0  -0.220  -1.6248   0.5367  -1.6635
 O84  C4'  C  CH1    0  -0.023  -2.2004  -0.7682  -2.1872
 O84  O4'  O  O2     0  -0.500  -1.2070  -1.7649  -2.3924
 O84  C3'  C  CH1    0  -0.000  -3.1390  -1.3649  -1.1419
 O84  C2'  C  CH2    0  -0.564  -2.1581  -2.1619  -0.2731
 O84  C1'  C  CH1    0   0.239  -1.1514  -2.6521  -1.3101
 O84  N9   N  NR6    0  -0.571   0.2346  -2.7021  -0.7917
 O84  C4   C  CR16   0   0.025   1.1954  -1.8162  -1.1764
 O84  C8   C  CR6    0   0.733   0.5149  -3.7051   0.1001
 O84  O2   O  O      0  -0.488  -0.3112  -4.5229   0.4585
 O84  N1   N  NR16   0  -0.731   1.8034  -3.7088   0.5586
 O84  C6   C  CR6    0   0.535   2.8372  -2.8427   0.2393
 O84  O6   O  O      0  -0.452   3.9264  -2.9960   0.7611
 O84  C5   C  CR6    0  -0.126   2.4745  -1.8176  -0.7249
 O84  C17  C  C1     0  -0.307   3.4028  -0.8195  -1.2456
 O84  C18  C  C1     0  -0.190   4.7110  -0.6615  -1.0065
 O84  C19  C  CH2    0  -0.773   5.5396   0.4122  -1.6005
 O84  P2   P  P      0   1.164   6.2564   1.5858  -0.3160
 O84  O11  O  O      0  -0.909   7.0772   0.6796   0.6098
 O84  O9   O  OP    -1  -0.911   7.1062   2.5585  -1.1449
 O84  O10  O  OP    -1  -0.903   5.0486   2.2393   0.3605
 O84  H3   H  HCR6   0   0.237  -1.3887   2.4702   0.5570
 O84  H4   H  HCR6   0   0.243  -0.2204   2.5436   2.7095
 O84  H5   H  HCR6   0   0.243  -0.8587   0.9885   4.5333
 O84  H6   H  HCR6   0   0.241  -2.6891  -0.6403   4.1540
 O84  H7   H  HCR6   0   0.233  -3.8389  -0.7271   1.9904
 O84  H8   H  HCH2   0   0.254  -1.0745   1.0673  -2.4431
 O84  H9   H  HCH2   0   0.204  -0.9230   0.3569  -0.8370
 O84  H10  H  HCH1   0   0.262  -2.7000  -0.5970  -3.1431
 O84  H11  H  HCH1   0   0.261  -3.8152  -2.0716  -1.6334
 O84  H12  H  HCH2   0   0.270  -1.6665  -1.5309   0.4666
 O84  H13  H  HCH2   0   0.280  -2.6354  -2.9853   0.2525
 O84  H14  H  HCH1   0   0.270  -1.3864  -3.6593  -1.6609
 O84  H15  H  HCR6   0   0.310   0.8860  -1.0846  -1.9073
 O84  H16  H  HNR6   0   0.424   2.0227  -4.4427   1.2210
 O84  H17  H  H      0   0.217   2.9356  -0.1249  -1.9408
 O84  H18  H  H      0   0.231   5.2200  -1.3267  -0.3212
 O84  H19  H  HCH2   0   0.202   6.3905  -0.0359  -2.1268
 O84  H20  H  HCH2   0   0.199   4.9652   0.9753  -2.3439

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
 O84  O11  P2   deloc     1.534  0.020  1.534
 O84  O6   C6   double    1.217  0.020  1.217
 O84  O9   P2   deloc     1.535  0.020  1.535
 O84  P2   O10  deloc     1.531  0.020  1.531
 O84  P2   C19  single    1.882  0.020  1.882
 O84  C18  C19  single    1.481  0.020  1.481
 O84  C18  C17  double    1.339  0.020  1.339
 O84  C6   N1   single    1.386  0.020  1.386
 O84  C6   C5   single    1.453  0.020  1.453
 O84  N1   C8   single    1.368  0.020  1.368
 O84  C17  C5   single    1.459  0.020  1.459
 O84  C5   C4   double    1.356  0.020  1.356
 O84  C8   O2   double    1.216  0.020  1.216
 O84  C8   N9   single    1.371  0.020  1.371
 O84  C4   N9   single    1.362  0.020  1.362
 O84  N9   C1'  single    1.481  0.020  1.481
 O84  C1'  C2'  single    1.526  0.020  1.526
 O84  C1'  O4'  single    1.401  0.020  1.401
 O84  C2'  C3'  single    1.534  0.020  1.534
 O84  C11  C12  aromatic  1.387  0.020  1.387
 O84  C11  C10  aromatic  1.389  0.020  1.389
 O84  O4'  C4'  single    1.422  0.020  1.422
 O84  C12  C2   aromatic  1.394  0.020  1.394
 O84  O3'  C3'  single    1.402  0.020  1.402
 O84  O3'  CAB  single    1.417  0.020  1.417
 O84  C3'  C4'  single    1.526  0.020  1.526
 O84  C10  C9   aromatic  1.388  0.020  1.388
 O84  C4'  C5'  single    1.519  0.020  1.519
 O84  C2   CAB  single    1.509  0.020  1.509
 O84  C2   CAA  aromatic  1.394  0.020  1.394
 O84  C9   CAA  aromatic  1.388  0.020  1.388
 O84  CAB  O7   single    1.405  0.020  1.405
 O84  CAB  P    single    1.909  0.020  1.909
 O84  O7   C5'  single    1.409  0.020  1.409
 O84  OP1  P    deloc     1.527  0.020  1.527
 O84  P    OP2  deloc     1.528  0.020  1.528
 O84  P    OP3  deloc     1.527  0.020  1.527
 O84  CAA  H3   single    0.930  0.020  1.080
 O84  C9   H4   single    0.930  0.020  1.080
 O84  C10  H5   single    0.930  0.020  1.080
 O84  C11  H6   single    0.930  0.020  1.080
 O84  C12  H7   single    0.930  0.020  1.080
 O84  C5'  H8   single    0.970  0.020  1.090
 O84  C5'  H9   single    0.970  0.020  1.090
 O84  C4'  H10  single    0.970  0.020  1.090
 O84  C3'  H11  single    0.970  0.020  1.090
 O84  C2'  H12  single    0.970  0.020  1.090
 O84  C2'  H13  single    0.970  0.020  1.090
 O84  C1'  H14  single    0.970  0.020  1.090
 O84  C4   H15  single    0.930  0.020  1.080
 O84  N1   H16  single    0.860  0.020  1.020
 O84  C17  H17  single    0.930  0.020  1.080
 O84  C18  H18  single    0.930  0.020  1.080
 O84  C19  H19  single    0.970  0.020  1.090
 O84  C19  H20  single    0.970  0.020  1.090

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
 O84  CAB  P    OP3  103.57  3.000
 O84  OP3  P    OP1  114.80  3.000
 O84  CAB  P    OP1  103.52  3.000
 O84  OP3  P    OP2  114.47  3.000
 O84  OP1  P    OP2  114.37  3.000
 O84  CAB  P    OP2  104.11  3.000
 O84  O7   CAB  O3'  110.86  3.000
 O84  O7   CAB  C2   112.02  3.000
 O84  O3'  CAB  C2   111.84  3.000
 O84  O7   CAB  P    106.72  3.000
 O84  C2   CAB  P    108.95  3.000
 O84  O3'  CAB  P    106.12  3.000
 O84  C12  C2   CAA  118.07  3.000
 O84  CAA  C2   CAB  120.99  3.000
 O84  C12  C2   CAB  120.64  3.000
 O84  H3   CAA  C9   119.20  3.000
 O84  H3   CAA  C2   119.75  3.000
 O84  C9   CAA  C2   121.05  3.000
 O84  H4   C9   C10  120.11  3.000
 O84  H4   C9   CAA  119.56  3.000
 O84  C10  C9   CAA  120.34  3.000
 O84  H5   C10  C11  120.45  3.000
 O84  H5   C10  C9   120.44  3.000
 O84  C11  C10  C9   119.11  3.000
 O84  H6   C11  C12  119.62  3.000
 O84  H6   C11  C10  119.99  3.000
 O84  C12  C11  C10  120.38  3.000
 O84  H7   C12  C11  119.29  3.000
 O84  H7   C12  C2   119.69  3.000
 O84  C11  C12  C2   121.01  3.000
 O84  C3'  O3'  CAB  119.18  3.000
 O84  C5'  O7   CAB  114.57  3.000
 O84  H9   C5'  H8   107.13  3.000
 O84  H9   C5'  C4'  111.14  3.000
 O84  H8   C5'  C4'  111.24  3.000
 O84  H9   C5'  O7   111.52  3.000
 O84  H8   C5'  O7   107.59  3.000
 O84  C4'  C5'  O7   108.19  3.000
 O84  H10  C4'  C3'  112.30  3.000
 O84  H10  C4'  O4'  107.65  3.000
 O84  C3'  C4'  O4'  104.74  3.000
 O84  H10  C4'  C5'  109.90  3.000
 O84  C3'  C4'  C5'  109.43  3.000
 O84  O4'  C4'  C5'  112.77  3.000
 O84  C1'  O4'  C4'  111.11  3.000
 O84  H11  C3'  C2'  108.30  3.000
 O84  H11  C3'  C4'  108.95  3.000
 O84  C2'  C3'  C4'  101.41  3.000
 O84  H11  C3'  O3'  105.43  3.000
 O84  C4'  C3'  O3'  114.40  3.000
 O84  C2'  C3'  O3'  118.09  3.000
 O84  H13  C2'  H12  107.97  3.000
 O84  H13  C2'  C1'  112.02  3.000
 O84  H12  C2'  C1'  110.47  3.000
 O84  H13  C2'  C3'  112.74  3.000
 O84  H12  C2'  C3'  111.85  3.000
 O84  C1'  C2'  C3'  101.76  3.000
 O84  H14  C1'  N9   106.42  3.000
 O84  H14  C1'  C2'  111.87  3.000
 O84  N9   C1'  C2'  112.98  3.000
 O84  H14  C1'  O4'  109.11  3.000
 O84  C2'  C1'  O4'  107.19  3.000
 O84  N9   C1'  O4'  109.22  3.000
 O84  C8   N9   C4   121.01  3.000
 O84  C4   N9   C1'  122.63  3.000
 O84  C8   N9   C1'  116.35  3.000
 O84  H15  C4   C5   119.76  3.000
 O84  H15  C4   N9   115.46  3.000
 O84  C5   C4   N9   124.77  3.000
 O84  N1   C8   O2   122.63  3.000
 O84  O2   C8   N9   123.00  3.000
 O84  N1   C8   N9   114.37  3.000
 O84  H16  N1   C6   116.23  3.000
 O84  H16  N1   C8   115.17  3.000
 O84  C6   N1   C8   128.60  3.000
 O84  C5   C6   O6   126.62  3.000
 O84  C5   C6   N1   114.04  3.000
 O84  O6   C6   N1   119.34  3.000
 O84  C17  C5   C6   124.09  3.000
 O84  C17  C5   C4   118.71  3.000
 O84  C6   C5   C4   117.19  3.000
 O84  H17  C17  C18  117.27  3.000
 O84  H17  C17  C5   113.05  3.000
 O84  C18  C17  C5   129.67  3.000
 O84  H18  C18  C19  115.88  3.000
 O84  H18  C18  C17  120.00  3.000
 O84  C19  C18  C17  124.09  3.000
 O84  H20  C19  H19  106.93  3.000
 O84  H20  C19  P2   110.03  3.000
 O84  H19  C19  P2   106.68  3.000
 O84  H20  C19  C18  110.58  3.000
 O84  H19  C19  C18  109.30  3.000
 O84  P2   C19  C18  113.05  3.000
 O84  O10  P2   O9   113.89  3.000
 O84  O10  P2   O11  114.06  3.000
 O84  O9   P2   O11  113.84  3.000
 O84  O10  P2   C19  105.51  3.000
 O84  O9   P2   C19  103.74  3.000
 O84  O11  P2   C19  104.32  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
 O84  CONST_01  C10  C11  C12  C2      0.00   0.0  0
 O84  CONST_02  C10  C9   CAA  C2      0.00   0.0  0
 O84  CONST_03  C11  C12  C2   CAA     0.00   0.0  0
 O84  CONST_04  C11  C10  C9   CAA     0.00   0.0  0
 O84  CONST_05  C12  C11  C10  C9      0.00   0.0  0
 O84  CONST_06  C12  C2   CAA  C9      0.00   0.0  0
 O84  CONST_07  C11  C12  C2   CAB   180.00   0.0  0
 O84  CONST_08  C9   CAA  C2   CAB   180.00   0.0  0
 O84  CONST_09  N1   C8   N9   C1'   180.00   0.0  0
 O84  CONST_10  C6   N1   C8   N9      0.00   0.0  0
 O84  CONST_11  N1   C8   N9   C4      0.00   0.0  0
 O84  CONST_12  C5   C6   N1   C8      0.00   0.0  0
 O84  CONST_13  O2   C8   N9   C1'     0.00   0.0  0
 O84  CONST_14  O2   C8   N9   C4    180.00   0.0  0
 O84  CONST_15  O6   C6   N1   C8    180.00   0.0  0
 O84  CONST_16  C6   N1   C8   O2    180.00   0.0  0
 O84  CONST_17  H7   C12  C2   CAB     0.00   0.0  0
 O84  CONST_18  H3   CAA  C2   CAB     0.00   0.0  0
 O84  CONST_19  H6   C11  C12  C2    180.00   0.0  0
 O84  CONST_20  H4   C9   CAA  C2    180.00   0.0  0
 O84  CONST_21  H5   C10  C9   CAA   180.00   0.0  0
 O84  CONST_22  H16  N1   C8   N9    180.00   0.0  0
 O84  CONST_23  C19  C18  C17  C5    180.00   0.0  0
 O84  CONST_24  H18  C18  C17  C5      0.00   0.0  0
 O84  CONST_25  H17  C17  C18  C19     0.00   0.0  0
 O84  Var_01    C4'  C5'  O7   CAB    63.60  30.0  1
 O84  Var_02    C18  C17  C5   C4   -176.43  30.0  2
 O84  Var_03    P2   C19  C18  C17   117.18  30.0  3
 O84  Var_04    O11  P2   C19  C18    58.34  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
 O84  chir_01  CAB  C2   O7   O3'  negativ
 O84  chir_02  C4'  O4'  C3'  C5'  negativ
 O84  chir_03  C3'  O3'  C2'  C4'  positiv
 O84  chir_04  C1'  O4'  N9   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
 O84  plan-1  CAB  0.020
 O84  plan-1  C2   0.020
 O84  plan-1  CAA  0.020
 O84  plan-1  C9   0.020
 O84  plan-1  C10  0.020
 O84  plan-1  C11  0.020
 O84  plan-1  C12  0.020
 O84  plan-1  H3   0.020
 O84  plan-1  H4   0.020
 O84  plan-1  H5   0.020
 O84  plan-1  H6   0.020
 O84  plan-1  H7   0.020
 O84  plan-2  C1'  0.020
 O84  plan-2  N9   0.020
 O84  plan-2  C4   0.020
 O84  plan-2  C8   0.020
 O84  plan-2  O2   0.020
 O84  plan-2  N1   0.020
 O84  plan-2  C6   0.020
 O84  plan-2  O6   0.020
 O84  plan-2  C5   0.020
 O84  plan-2  C17  0.020
 O84  plan-2  H15  0.020
 O84  plan-2  H16  0.020
 O84  plan-3  C5   0.020
 O84  plan-3  C17  0.020
 O84  plan-3  C18  0.020
 O84  plan-3  C19  0.020
 O84  plan-3  H17  0.020
 O84  plan-3  H18  0.020

