# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 04:40:46 2021
#   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  56  34  .  2021-08-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_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  OH1   0  -0.739  -4.9500  25.7972  32.8147
 O84  P    P  P     0   1.365  -5.4405  24.5497  31.9370
 O84  OP1  O  O     0  -0.689  -6.9050  24.4257  31.7586
 O84  OP3  O  OH1   0  -0.737  -4.7035  23.3569  32.7178
 O84  CAB  C  CT    0   0.274  -4.5159  24.6615  30.3053
 O84  C2   C  CR6   0  -0.076  -4.8431  23.3643  29.5897
 O84  CAA  C  CR16  0  -0.272  -3.9797  22.2743  29.6674
 O84  C9   C  CR16  0  -0.228  -4.3064  21.0791  29.0408
 O84  C10  C  CR16  0  -0.269  -5.4979  20.9591  28.3412
 O84  C11  C  CR16  0  -0.247  -6.3588  22.0458  28.2581
 O84  C12  C  CR16  0  -0.242  -6.0384  23.2415  28.8829
 O84  O3'  O  O2    0  -0.502  -5.0289  25.6987  29.5286
 O84  O7   O  O2    0  -0.487  -3.1394  24.7313  30.4470
 O84  C5'  C  CH2   0  -0.228  -2.5927  25.9694  30.8756
 O84  C4'  C  CH1   0   0.005  -3.1544  27.1360  30.0995
 O84  O4'  O  O2    0  -0.490  -2.5835  27.1812  28.7999
 O84  C3'  C  CH1   0  -0.022  -4.6544  27.0318  29.8592
 O84  C2'  C  CH2   0  -0.539  -4.8312  27.8795  28.6142
 O84  C1'  C  CH1   0   0.179  -3.4619  27.8176  27.9124
 O84  N9   N  NR6   0  -0.568  -3.4353  27.0778  26.6498
 O84  C4   C  CR16  0   0.069  -3.5667  25.7229  26.6511
 O84  C8   C  CR6   0   0.735  -3.1924  27.7646  25.4779
 O84  O2   O  O     0  -0.475  -3.0764  28.9705  25.4174
 O84  N1   N  NR16  0  -0.734  -3.0964  26.9660  24.3710
 O84  C6   C  CR6   0   0.552  -3.1940  25.5875  24.2846
 O84  O6   O  O     0  -0.444  -3.0634  25.0399  23.2070
 O84  C5   C  CR6   0  -0.144  -3.4619  24.9351  25.5559
 O84  C17  C  C1    0  -0.250  -3.6025  23.4945  25.7172
 O84  C18  C  C1    0  -0.258  -3.3969  22.5298  24.8175
 O84  C19  C  CH2   0  -0.799  -3.5511  21.0822  25.1637
 O84  P2   P  P     0   1.363  -1.9503  20.3250  25.5048
 O84  O11  O  O     0  -0.721  -0.9294  20.4017  24.4280
 O84  O9   O  OH1   0  -0.748  -2.3749  18.8260  25.9132
 O84  O10  O  OH1   0  -0.737  -1.5306  21.0533  26.8741
 O84  H1   H  HOH1  0   0.503  -5.6705  26.2584  33.2670
 O84  H2   H  HOH1  0   0.498  -4.9840  22.4693  32.4580
 O84  H3   H  HCR6  0   0.265  -3.0461  22.3449  30.2081
 O84  H4   H  HCR6  0   0.258  -3.6227  20.2428  29.0975
 O84  H5   H  HCR6  0   0.270  -5.7569  20.0236  27.8617
 O84  H6   H  HCR6  0   0.262  -7.2878  21.9617  27.7097
 O84  H7   H  HCR6  0   0.261  -6.7260  24.0723  28.8144
 O84  H8   H  HCH2  0   0.273  -1.5166  25.8922  30.7210
 O84  H9   H  HCH2  0   0.249  -2.7573  26.1364  31.9413
 O84  H10  H  HCH1  0   0.268  -2.9369  28.0619  30.6454
 O84  H11  H  HCH1  0   0.276  -5.2359  27.4038  30.7055
 O84  H12  H  HCH2  0   0.290  -5.0360  28.9091  28.9065
 O84  H13  H  HCH2  0   0.294  -5.6574  27.5482  27.9859
 O84  H14  H  HCH1  0   0.280  -3.1130  28.8216  27.6751
 O84  H15  H  HCR6  0   0.319  -3.7684  25.2762  27.6125
 O84  H16  H  HNR6  0   0.429  -2.9146  27.4562  23.5036
 O84  H17  H  H     0   0.249  -3.9026  23.1932  26.7187
 O84  H18  H  H     0   0.270  -3.0906  22.7595  23.8074
 O84  H19  H  HCH2  0   0.304  -3.9974  20.5273  24.3347
 O84  H20  H  HCH2  0   0.304  -4.1964  20.9474  26.0338
 O84  H21  H  HOH1  0   0.491  -1.6795  18.1705  25.7678
 O84  H22  H  HOH1  0   0.489  -0.5859  21.0004  27.0708

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   double    1.486  0.020  1.486
 O84  O6   C6   double    1.216  0.020  1.216
 O84  O9   P2   single    1.611  0.020  1.611
 O84  P2   O10  single    1.607  0.020  1.607
 O84  P2   C19  single    1.803  0.020  1.803
 O84  C18  C19  single    1.496  0.020  1.496
 O84  C18  C17  double    1.335  0.020  1.335
 O84  C6   N1   single    1.385  0.020  1.385
 O84  C6   C5   single    1.454  0.020  1.454
 O84  N1   C8   single    1.368  0.020  1.368
 O84  C17  C5   single    1.456  0.020  1.456
 O84  C5   C4   double    1.353  0.020  1.353
 O84  C8   O2   double    1.213  0.020  1.213
 O84  C8   N9   single    1.380  0.020  1.380
 O84  C4   N9   single    1.361  0.020  1.361
 O84  N9   C1'  single    1.464  0.020  1.464
 O84  C1'  C2'  single    1.540  0.020  1.540
 O84  C1'  O4'  single    1.402  0.020  1.402
 O84  C2'  C3'  single    1.517  0.020  1.517
 O84  C11  C12  aromatic  1.387  0.020  1.387
 O84  C11  C10  aromatic  1.389  0.020  1.389
 O84  O4'  C4'  single    1.420  0.020  1.420
 O84  C12  C2   aromatic  1.394  0.020  1.394
 O84  O3'  C3'  single    1.424  0.020  1.424
 O84  O3'  CAB  single    1.394  0.020  1.394
 O84  C3'  C4'  single    1.523  0.020  1.523
 O84  C10  C9   aromatic  1.387  0.020  1.387
 O84  C4'  C5'  single    1.510  0.020  1.510
 O84  C2   CAB  single    1.517  0.020  1.517
 O84  C2   CAA  aromatic  1.393  0.020  1.393
 O84  C9   CAA  aromatic  1.388  0.020  1.388
 O84  CAB  O7   single    1.386  0.020  1.386
 O84  CAB  P    single    1.879  0.020  1.879
 O84  O7   C5'  single    1.420  0.020  1.420
 O84  OP1  P    double    1.481  0.020  1.481
 O84  P    OP2  single    1.602  0.020  1.602
 O84  P    OP3  single    1.605  0.020  1.605
 O84  OP2  H1   single    0.850  0.020  0.980
 O84  OP3  H2   single    0.850  0.020  0.980
 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
 O84  O9   H21  single    0.850  0.020  0.980
 O84  O10  H22  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
 O84  H1   OP2  P    113.53  3.000
 O84  CAB  P    OP3  103.93  3.000
 O84  OP3  P    OP1  116.78  3.000
 O84  CAB  P    OP1  112.77  3.000
 O84  OP3  P    OP2   99.88  3.000
 O84  OP1  P    OP2  115.72  3.000
 O84  CAB  P    OP2  106.19  3.000
 O84  H2   OP3  P    114.75  3.000
 O84  O7   CAB  O3'  112.66  3.000
 O84  O7   CAB  C2   107.79  3.000
 O84  O3'  CAB  C2   107.10  3.000
 O84  O7   CAB  P    113.77  3.000
 O84  C2   CAB  P    104.64  3.000
 O84  O3'  CAB  P    110.31  3.000
 O84  C12  C2   CAA  119.40  3.000
 O84  CAA  C2   CAB  120.61  3.000
 O84  C12  C2   CAB  119.96  3.000
 O84  H3   CAA  C9   119.02  3.000
 O84  H3   CAA  C2   120.80  3.000
 O84  C9   CAA  C2   120.18  3.000
 O84  H4   C9   C10  120.17  3.000
 O84  H4   C9   CAA  119.55  3.000
 O84  C10  C9   CAA  120.28  3.000
 O84  H5   C10  C11  120.09  3.000
 O84  H5   C10  C9   120.25  3.000
 O84  C11  C10  C9   119.67  3.000
 O84  H6   C11  C12  119.59  3.000
 O84  H6   C11  C10  120.11  3.000
 O84  C12  C11  C10  120.31  3.000
 O84  H7   C12  C11  119.17  3.000
 O84  H7   C12  C2   120.66  3.000
 O84  C11  C12  C2   120.16  3.000
 O84  C3'  O3'  CAB  118.08  3.000
 O84  C5'  O7   CAB  117.22  3.000
 O84  H9   C5'  H8   107.35  3.000
 O84  H9   C5'  C4'  109.13  3.000
 O84  H8   C5'  C4'  110.44  3.000
 O84  H9   C5'  O7   111.73  3.000
 O84  H8   C5'  O7   106.00  3.000
 O84  C4'  C5'  O7   112.06  3.000
 O84  H10  C4'  C3'  109.37  3.000
 O84  H10  C4'  O4'  110.43  3.000
 O84  C3'  C4'  O4'  104.70  3.000
 O84  H10  C4'  C5'  108.83  3.000
 O84  C3'  C4'  C5'  113.25  3.000
 O84  O4'  C4'  C5'  110.21  3.000
 O84  C1'  O4'  C4'  110.00  3.000
 O84  H11  C3'  C2'  112.56  3.000
 O84  H11  C3'  C4'  112.27  3.000
 O84  C2'  C3'  C4'  101.89  3.000
 O84  H11  C3'  O3'  111.03  3.000
 O84  C4'  C3'  O3'  111.09  3.000
 O84  C2'  C3'  O3'  107.58  3.000
 O84  H13  C2'  H12  107.42  3.000
 O84  H13  C2'  C1'  113.53  3.000
 O84  H12  C2'  C1'  109.11  3.000
 O84  H13  C2'  C3'  113.07  3.000
 O84  H12  C2'  C3'  109.26  3.000
 O84  C1'  C2'  C3'  104.36  3.000
 O84  H14  C1'  N9   105.80  3.000
 O84  H14  C1'  C2'  110.31  3.000
 O84  N9   C1'  C2'  115.45  3.000
 O84  H14  C1'  O4'  110.84  3.000
 O84  C2'  C1'  O4'  106.67  3.000
 O84  N9   C1'  O4'  107.78  3.000
 O84  C8   N9   C4   120.87  3.000
 O84  C4   N9   C1'  120.04  3.000
 O84  C8   N9   C1'  118.96  3.000
 O84  H15  C4   C5   119.64  3.000
 O84  H15  C4   N9   115.53  3.000
 O84  C5   C4   N9   124.83  3.000
 O84  N1   C8   O2   122.22  3.000
 O84  O2   C8   N9   123.64  3.000
 O84  N1   C8   N9   114.14  3.000
 O84  H16  N1   C6   116.17  3.000
 O84  H16  N1   C8   115.03  3.000
 O84  C6   N1   C8   128.80  3.000
 O84  C5   C6   O6   126.35  3.000
 O84  C5   C6   N1   113.90  3.000
 O84  O6   C6   N1   119.75  3.000
 O84  C17  C5   C6   123.96  3.000
 O84  C17  C5   C4   118.60  3.000
 O84  C6   C5   C4   117.44  3.000
 O84  H17  C17  C18  117.56  3.000
 O84  H17  C17  C5   113.74  3.000
 O84  C18  C17  C5   128.70  3.000
 O84  H18  C18  C19  116.82  3.000
 O84  H18  C18  C17  121.35  3.000
 O84  C19  C18  C17  121.82  3.000
 O84  H20  C19  H19  107.49  3.000
 O84  H20  C19  P2   108.79  3.000
 O84  H19  C19  P2   107.02  3.000
 O84  H20  C19  C18  111.39  3.000
 O84  H19  C19  C18  110.96  3.000
 O84  P2   C19  C18  111.01  3.000
 O84  O10  P2   O9   105.95  3.000
 O84  O10  P2   O11  114.50  3.000
 O84  O9   P2   O11  114.39  3.000
 O84  O10  P2   C19  101.70  3.000
 O84  O9   P2   C19  101.82  3.000
 O84  O11  P2   C19  116.81  3.000
 O84  H21  O9   P2   113.79  3.000
 O84  H22  O10  P2   113.83  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   -47.66  30.0  1
 O84  Var_02    C18  C17  C5   C4   -172.12  30.0  1
 O84  Var_03    P2   C19  C18  C17   -98.96  30.0  3
 O84  Var_04    O11  P2   C19  C18   -57.30  30.0  2

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

