# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 11:26:18 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 2-[[7-[(2~{R},3~{R},4~{S},5~{R})-5-[(~{R})-(4-chlorophenyl)-oxidanyl-methyl]-3,4-bis(oxidanyl)oxolan-2-yl]pyrrolo[2,3-d]pyrimidin-4-yl]amino]ethanal
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1[C@H](O)c2ccc(Cl)cc2)n3ccc4c(NCC=O)ncnc34
#
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
 CUX  CUX  2-[[7-[(2~{R},3~{R},4~{S},5~{R})-5-[(~{R})-(4-chlorophenyl)-oxidanyl-methyl]-3,4-bis(oxidanyl)oxolan-2-yl]pyrrolo[2,3-d]pyrimidin-4-yl]amino]ethanal  ligand  48  29  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_CUX
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
 CUX  C4   C   CR56  0   0.516   2.2373  -0.6448  -0.2602
 CUX  C5   C   CR56  0  -0.066   2.8858   0.2988   0.5390
 CUX  C6   C   CR6   0   0.501   4.0990   0.7870   0.0192
 CUX  N1   N   N     0  -0.494   4.5350   0.3428  -1.1599
 CUX  N3   N   N     0  -0.462   2.6635  -1.0975  -1.4408
 CUX  CBB  C   C1    0   0.175   6.0384   2.6835  -1.2427
 CUX  CBA  C   CH2   0  -0.391   6.1369   2.0911   0.1426
 CUX  NAA  N   NH1   0  -0.670   4.8499   1.7048   0.6508
 CUX  C2   C   CR16  0   0.054   3.8037  -0.5575  -1.8159
 CUX  CAI  C   CR15  0  -0.445   2.0801   0.4985   1.7000
 CUX  CAH  C   CR15  0  -0.003   1.0021  -0.3185   1.5595
 CUX  NAG  N   NR5   0  -0.555   1.0939  -1.0232   0.3765
 CUX  CAK  C   CH1   0   0.212   0.1223  -1.9346  -0.1507
 CUX  OAL  O   O2    0  -0.489  -1.0554  -1.2369  -0.4775
 CUX  CAP  C   CH1   0  -0.057  -0.3148  -3.0293   0.8187
 CUX  OAQ  O   OH1   0  -0.654   0.6159  -4.0704   0.8125
 CUX  CAN  C   CH1   0  -0.023  -1.6882  -3.3909   0.2505
 CUX  OAO  O   OH1   0  -0.671  -1.5580  -4.1924  -0.8968
 CUX  CAM  C   CH1   0  -0.019  -2.2060  -2.0208  -0.1786
 CUX  CAR  C   CH1   0  -0.091  -3.0409  -1.3084   0.8959
 CUX  OAS  O   OH1   0  -0.648  -4.2047  -2.0416   1.1859
 CUX  CAT  C   CR6   0   0.176  -3.3301   0.1162   0.4814
 CUX  CAU  C   CR16  0  -0.311  -2.5795   1.1681   0.9915
 CUX  CAV  C   CR16  0  -0.196  -2.8160   2.4782   0.6017
 CUX  CAW  C   CR6   0  -0.056  -3.8225   2.7347  -0.3145
 CUX  CLA  CL  CL    0  -0.130  -4.1347   4.3674  -0.8065
 CUX  CAX  C   CR16  0  -0.194  -4.5882   1.7054  -0.8399
 CUX  CAY  C   CR16  0  -0.325  -4.3351   0.4028  -0.4377
 CUX  H1   H   H     0   0.197   5.0641   3.1517  -1.4717
 CUX  H4   H   HCH2  0   0.270   6.8591   1.2700   0.1398
 CUX  H5   H   HCR6  0   0.251   4.2025  -0.8805  -2.7712
 CUX  H6   H   HCR5  0   0.260   2.2642   1.1564   2.5340
 CUX  H7   H   HCR5  0   0.292   0.1646  -0.4528   2.2247
 CUX  H8   H   HCH1  0   0.257   0.5732  -2.3840  -1.0413
 CUX  H9   H   HCH1  0   0.249  -0.4451  -2.6148   1.8270
 CUX  H10  H   HOH1  0   0.470   0.5213  -4.5787   1.6242
 CUX  H11  H   HCH1  0   0.254  -2.3346  -3.8610   1.0005
 CUX  H12  H   HOH1  0   0.450  -0.9378  -4.9028  -0.6943
 CUX  H13  H   HCH1  0   0.258  -2.8168  -2.1153  -1.0861
 CUX  H14  H   HCH1  0   0.256  -2.4689  -1.2825   1.8298
 CUX  H15  H   HOH1  0   0.454  -4.6927  -2.2132   0.3733
 CUX  H16  H   HCR6  0   0.254  -1.7975   0.9762   1.7154
 CUX  H17  H   HCR6  0   0.281  -2.2231   3.2845   1.0112
 CUX  H18  H   HCR6  0   0.281  -5.3751   1.9112  -1.5526
 CUX  H19  H   HCR6  0   0.255  -4.9458  -0.3852  -0.8626
 CUX  H20  H   HCH2  0   0.299   6.5306   2.8697   0.8006
 CUX  H21  H   HNH1  0   0.412   4.5846   2.0075   1.5721
 CUX  O5   O   O     0  -0.385   6.9570   2.7163  -2.0200

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
 CUX  OAS  CAR  single    1.406  0.020  1.406
 CUX  CLA  CAW  single    1.734  0.020  1.734
 CUX  CAW  CAV  aromatic  1.385  0.020  1.385
 CUX  CAW  CAX  aromatic  1.386  0.020  1.386
 CUX  CAV  CAU  aromatic  1.387  0.020  1.387
 CUX  CAX  CAY  aromatic  1.387  0.020  1.387
 CUX  CAU  CAT  aromatic  1.389  0.020  1.389
 CUX  CAY  CAT  aromatic  1.392  0.020  1.392
 CUX  CAT  CAR  single    1.512  0.020  1.512
 CUX  CAR  CAM  single    1.536  0.020  1.536
 CUX  CBB  CBA  single    1.510  0.020  1.510
 CUX  OAL  CAM  single    1.424  0.020  1.424
 CUX  OAL  CAK  single    1.407  0.020  1.407
 CUX  CAM  CAN  single    1.526  0.020  1.526
 CUX  CBA  NAA  single    1.437  0.020  1.437
 CUX  CAH  CAI  aromatic  1.360  0.020  1.360
 CUX  CAH  NAG  aromatic  1.380  0.020  1.380
 CUX  CAI  C5   aromatic  1.427  0.020  1.427
 CUX  NAG  CAK  single    1.433  0.020  1.433
 CUX  NAG  C4   aromatic  1.362  0.020  1.362
 CUX  CAN  CAP  single    1.530  0.020  1.530
 CUX  CAN  OAO  single    1.406  0.020  1.406
 CUX  CAK  CAP  single    1.526  0.020  1.526
 CUX  C5   C4   aromatic  1.396  0.020  1.396
 CUX  C5   C6   aromatic  1.407  0.020  1.407
 CUX  NAA  C6   single    1.344  0.020  1.344
 CUX  C4   N3   aromatic  1.334  0.020  1.334
 CUX  C6   N1   aromatic  1.333  0.020  1.333
 CUX  CAP  OAQ  single    1.396  0.020  1.396
 CUX  N3   C2   aromatic  1.316  0.020  1.316
 CUX  N1   C2   aromatic  1.333  0.020  1.333
 CUX  CBB  H1   single    0.930  0.020  1.080
 CUX  CBA  H4   single    0.970  0.020  1.090
 CUX  C2   H5   single    0.930  0.020  1.080
 CUX  CAI  H6   single    0.930  0.020  1.080
 CUX  CAH  H7   single    0.930  0.020  1.080
 CUX  CAK  H8   single    0.970  0.020  1.090
 CUX  CAP  H9   single    0.970  0.020  1.090
 CUX  OAQ  H10  single    0.850  0.020  0.980
 CUX  CAN  H11  single    0.970  0.020  1.090
 CUX  OAO  H12  single    0.850  0.020  0.980
 CUX  CAM  H13  single    0.970  0.020  1.090
 CUX  CAR  H14  single    0.970  0.020  1.090
 CUX  OAS  H15  single    0.850  0.020  0.980
 CUX  CAU  H16  single    0.930  0.020  1.080
 CUX  CAV  H17  single    0.930  0.020  1.080
 CUX  CAX  H18  single    0.930  0.020  1.080
 CUX  CAY  H19  single    0.930  0.020  1.080
 CUX  CBA  H20  single    0.970  0.020  1.090
 CUX  NAA  H21  single    0.860  0.020  1.020
 CUX  CBB  O5   double    1.204  0.020  1.204

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
 CUX  NAG  C4   N3   125.97  3.000
 CUX  N3   C4   C5   125.97  3.000
 CUX  NAG  C4   C5   108.06  3.000
 CUX  CAI  C5   C6   137.61  3.000
 CUX  C6   C5   C4   115.05  3.000
 CUX  CAI  C5   C4   107.33  3.000
 CUX  NAA  C6   N1   117.42  3.000
 CUX  N1   C6   C5   119.54  3.000
 CUX  NAA  C6   C5   123.04  3.000
 CUX  C2   N1   C6   118.75  3.000
 CUX  C2   N3   C4   112.93  3.000
 CUX  O5   CBB  H1   121.84  3.000
 CUX  O5   CBB  CBA  123.59  3.000
 CUX  H1   CBB  CBA  114.46  3.000
 CUX  H20  CBA  H4   107.38  3.000
 CUX  H20  CBA  NAA  107.53  3.000
 CUX  H4   CBA  NAA  112.99  3.000
 CUX  H20  CBA  CBB  107.25  3.000
 CUX  H4   CBA  CBB  109.59  3.000
 CUX  NAA  CBA  CBB  111.81  3.000
 CUX  H21  NAA  CBA  118.66  3.000
 CUX  H21  NAA  C6   119.27  3.000
 CUX  CBA  NAA  C6   121.20  3.000
 CUX  H5   C2   N3   116.58  3.000
 CUX  H5   C2   N1   115.66  3.000
 CUX  N3   C2   N1   127.76  3.000
 CUX  H6   CAI  CAH  125.58  3.000
 CUX  H6   CAI  C5   128.19  3.000
 CUX  CAH  CAI  C5   106.22  3.000
 CUX  H7   CAH  NAG  121.14  3.000
 CUX  H7   CAH  CAI  128.83  3.000
 CUX  NAG  CAH  CAI  110.03  3.000
 CUX  CAK  NAG  CAH  126.52  3.000
 CUX  CAK  NAG  C4   125.03  3.000
 CUX  CAH  NAG  C4   108.34  3.000
 CUX  H8   CAK  CAP  109.89  3.000
 CUX  H8   CAK  OAL  111.06  3.000
 CUX  CAP  CAK  OAL  105.28  3.000
 CUX  H8   CAK  NAG  106.33  3.000
 CUX  CAP  CAK  NAG  114.64  3.000
 CUX  OAL  CAK  NAG  109.73  3.000
 CUX  CAM  OAL  CAK  110.76  3.000
 CUX  H9   CAP  CAN  108.90  3.000
 CUX  H9   CAP  OAQ  111.39  3.000
 CUX  CAN  CAP  OAQ  114.87  3.000
 CUX  H9   CAP  CAK  110.27  3.000
 CUX  OAQ  CAP  CAK  109.94  3.000
 CUX  CAN  CAP  CAK  101.00  3.000
 CUX  H10  OAQ  CAP  108.93  3.000
 CUX  H11  CAN  CAM  112.17  3.000
 CUX  H11  CAN  OAO  111.64  3.000
 CUX  CAM  CAN  OAO  108.29  3.000
 CUX  H11  CAN  CAP  112.12  3.000
 CUX  OAO  CAN  CAP  110.78  3.000
 CUX  CAM  CAN  CAP  101.35  3.000
 CUX  H12  OAO  CAN  107.95  3.000
 CUX  H13  CAM  CAR  108.41  3.000
 CUX  H13  CAM  CAN  110.11  3.000
 CUX  CAR  CAM  CAN  113.84  3.000
 CUX  H13  CAM  OAL  108.87  3.000
 CUX  CAN  CAM  OAL  106.20  3.000
 CUX  CAR  CAM  OAL  109.31  3.000
 CUX  H14  CAR  CAT  108.15  3.000
 CUX  H14  CAR  OAS  105.59  3.000
 CUX  CAT  CAR  OAS  112.94  3.000
 CUX  H14  CAR  CAM  108.87  3.000
 CUX  CAT  CAR  CAM  110.44  3.000
 CUX  OAS  CAR  CAM  110.63  3.000
 CUX  H15  OAS  CAR  109.77  3.000
 CUX  CAY  CAT  CAU  118.47  3.000
 CUX  CAY  CAT  CAR  120.89  3.000
 CUX  CAU  CAT  CAR  120.63  3.000
 CUX  H16  CAU  CAV  118.58  3.000
 CUX  H16  CAU  CAT  120.10  3.000
 CUX  CAV  CAU  CAT  121.32  3.000
 CUX  H17  CAV  CAW  120.72  3.000
 CUX  H17  CAV  CAU  120.29  3.000
 CUX  CAW  CAV  CAU  118.99  3.000
 CUX  CAX  CAW  CLA  119.49  3.000
 CUX  CAX  CAW  CAV  120.97  3.000
 CUX  CLA  CAW  CAV  119.54  3.000
 CUX  H18  CAX  CAY  120.18  3.000
 CUX  H18  CAX  CAW  120.69  3.000
 CUX  CAY  CAX  CAW  119.13  3.000
 CUX  H19  CAY  CAX  117.81  3.000
 CUX  H19  CAY  CAT  121.07  3.000
 CUX  CAX  CAY  CAT  121.12  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
 CUX  CONST_01  CAI  CAH  NAG  C4      0.00   0.0  0
 CUX  CONST_02  CAH  CAI  C5   C4      0.00   0.0  0
 CUX  CONST_03  N1   C6   C5   C4      0.00   0.0  0
 CUX  CONST_04  N1   C2   N3   C4      0.00   0.0  0
 CUX  CONST_05  NAG  CAH  CAI  C5      0.00   0.0  0
 CUX  CONST_06  CAH  NAG  C4   C5      0.00   0.0  0
 CUX  CONST_07  C2   N3   C4   C5      0.00   0.0  0
 CUX  CONST_08  C2   N1   C6   C5      0.00   0.0  0
 CUX  CONST_09  CAH  CAI  C5   C6    180.00   0.0  0
 CUX  CONST_10  NAG  C4   C5   C6    180.00   0.0  0
 CUX  CONST_11  N3   C4   C5   C6      0.00   0.0  0
 CUX  CONST_12  N3   C2   N1   C6      0.00   0.0  0
 CUX  CONST_13  CAI  C5   C6   N1    180.00   0.0  0
 CUX  CONST_14  CAH  NAG  C4   N3    180.00   0.0  0
 CUX  CONST_15  CAI  C5   C4   N3    180.00   0.0  0
 CUX  CONST_16  NAG  C4   N3   C2    180.00   0.0  0
 CUX  CONST_17  NAG  C4   C5   CAI     0.00   0.0  0
 CUX  CONST_18  CAW  CAV  CAU  CAT     0.00   0.0  0
 CUX  CONST_19  CAW  CAX  CAY  CAT     0.00   0.0  0
 CUX  CONST_20  CAX  CAW  CAV  CAU     0.00   0.0  0
 CUX  CONST_21  CAX  CAY  CAT  CAU     0.00   0.0  0
 CUX  CONST_22  CAY  CAX  CAW  CAV     0.00   0.0  0
 CUX  CONST_23  CAY  CAT  CAU  CAV     0.00   0.0  0
 CUX  CONST_24  CAK  NAG  C4   C5    180.00   0.0  0
 CUX  CONST_25  CAK  NAG  C4   N3      0.00   0.0  0
 CUX  CONST_26  CAK  NAG  CAH  CAI   180.00   0.0  0
 CUX  CONST_27  NAA  C6   C5   C4    180.00   0.0  0
 CUX  CONST_28  CAI  C5   C6   NAA     0.00   0.0  0
 CUX  CONST_29  C2   N1   C6   NAA   180.00   0.0  0
 CUX  CONST_30  CAV  CAU  CAT  CAR   180.00   0.0  0
 CUX  CONST_31  CAX  CAY  CAT  CAR   180.00   0.0  0
 CUX  CONST_32  CLA  CAW  CAV  CAU   180.00   0.0  0
 CUX  CONST_33  CAY  CAX  CAW  CLA   180.00   0.0  0
 CUX  CONST_34  H7   CAH  NAG  C4    180.00   0.0  0
 CUX  CONST_35  H6   CAI  C5   C4    180.00   0.0  0
 CUX  CONST_36  H5   C2   N3   C4    180.00   0.0  0
 CUX  CONST_37  H17  CAV  CAU  CAT   180.00   0.0  0
 CUX  CONST_38  H18  CAX  CAY  CAT   180.00   0.0  0
 CUX  CONST_39  H19  CAY  CAT  CAU   180.00   0.0  0
 CUX  CONST_40  H16  CAU  CAV  CAW   180.00   0.0  0
 CUX  CONST_41  CBA  NAA  C6   C5    180.00   0.0  0
 CUX  CONST_42  CBA  NAA  C6   N1      0.00   0.0  0
 CUX  CONST_43  H21  NAA  C6   C5      0.00   0.0  0
 CUX  Var_01    CBB  CBA  NAA  C6     60.39  30.0  1
 CUX  Var_02    O5   CBB  CBA  NAA  -157.36  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
 CUX  chir_01  CAK  OAL  NAG  CAP  negativ
 CUX  chir_02  CAP  OAQ  CAK  CAN  negativ
 CUX  chir_03  CAN  OAO  CAP  CAM  negativ
 CUX  chir_04  CAM  OAL  CAR  CAN  positiv
 CUX  chir_05  CAR  OAS  CAM  CAT  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
 CUX  plan-1  CAR  0.020
 CUX  plan-1  CAT  0.020
 CUX  plan-1  CAU  0.020
 CUX  plan-1  CAV  0.020
 CUX  plan-1  CAW  0.020
 CUX  plan-1  CLA  0.020
 CUX  plan-1  CAX  0.020
 CUX  plan-1  CAY  0.020
 CUX  plan-1  H16  0.020
 CUX  plan-1  H17  0.020
 CUX  plan-1  H18  0.020
 CUX  plan-1  H19  0.020
 CUX  plan-2  C4   0.020
 CUX  plan-2  C5   0.020
 CUX  plan-2  C6   0.020
 CUX  plan-2  N1   0.020
 CUX  plan-2  N3   0.020
 CUX  plan-2  NAA  0.020
 CUX  plan-2  C2   0.020
 CUX  plan-2  CAI  0.020
 CUX  plan-2  CAH  0.020
 CUX  plan-2  NAG  0.020
 CUX  plan-2  CAK  0.020
 CUX  plan-2  H5   0.020
 CUX  plan-2  H6   0.020
 CUX  plan-2  H7   0.020
 CUX  plan-3  C6   0.020
 CUX  plan-3  CBA  0.020
 CUX  plan-3  NAA  0.020
 CUX  plan-3  H21  0.020
 CUX  plan-4  CBB  0.020
 CUX  plan-4  CBA  0.020
 CUX  plan-4  H1   0.020
 CUX  plan-4  O5   0.020

