# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:11:39 2022
#   Inital geometry file: a 116 line input string
#   Ligand name: (1R,2S,3S,4R)-3-{[5-fluoro-2-(5-fluoro-1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-4-yl]amino}bicyclo[2.2.2]octane-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H]1C2CCC(CC2)[C@@H]1Nc3nc(ncc3F)c4c[nH]c5ncc(F)cc45
#
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
 21G  21G  '(1R,2S,3S,4R)-3-{[5-fluoro-2-(5-fluoro-1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-4-yl]amino}bicyclo[2.2.2]octane-2-carboxylic acid'  ligand  47  29  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_21G
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
 21G  C1   C  CR16   0  -0.421   4.4630  -0.6318   0.2269
 21G  C2   C  CR6    0   0.439   5.7318  -0.1051   0.3100
 21G  C3   C  CR16   0  -0.228   5.9884   1.2561   0.1515
 21G  C5   C  CR56   0   0.468   3.8068   1.6362  -0.1739
 21G  C6   C  CR56   0   0.030   3.4391   0.2785  -0.0275
 21G  C7   C  CR5    0  -0.123   2.0198   0.2189  -0.1960
 21G  N4   N  N      0  -0.409   5.0263   2.1329  -0.0910
 21G  C8   C  CR15   0  -0.013   1.6036   1.5097  -0.4319
 21G  N9   N  NR15   0  -0.666   2.6669   2.3492  -0.4187
 21G  C11  C  CR6    0   0.311   1.1481  -0.9427  -0.1261
 21G  N12  N  N      0  -0.464   1.7057  -2.1233   0.1060
 21G  C13  C  CR16   0  -0.186   0.8643  -3.1654   0.1677
 21G  C14  C  CR6    0   0.342  -0.4777  -3.0193   0.0033
 21G  C15  C  CR6    0   0.418  -1.0010  -1.7296  -0.2415
 21G  N16  N  N      0  -0.472  -0.1518  -0.7115  -0.2982
 21G  N17  N  NH1    0  -0.692  -2.3054  -1.5121  -0.4234
 21G  C18  C  CH1    0  -0.007  -2.8624  -0.1925  -0.6846
 21G  C20  C  CH1    0  -0.358  -2.8540   0.7269   0.5595
 21G  C22  C  CH1    0  -0.252  -4.3057   1.0743   0.9331
 21G  C23  C  CH2    0  -0.437  -4.9744   1.8534  -0.2015
 21G  C24  C  CH2    0  -0.425  -4.8090   1.0708  -1.5208
 21G  C25  C  CH1    0  -0.297  -4.2887  -0.3359  -1.2196
 21G  C26  C  CH2    0  -0.456  -5.2091  -0.9833  -0.1795
 21G  C27  C  CH2    0  -0.428  -5.0860  -0.2223   1.1564
 21G  C28  C  C      0   0.463  -2.0270   2.0194   0.4076
 21G  O29  O  OC    -1  -0.603  -1.7141   2.4055  -0.7382
 21G  O30  O  O      0  -0.624  -1.7657   2.6123   1.4756
 21G  F31  F  F      0  -0.308  -1.3145  -4.0709   0.0648
 21G  F32  F  F      0  -0.315   6.7745  -0.9192   0.5513
 21G  H1   H  HCR6   0   0.281   4.2734  -1.6892   0.3500
 21G  H2   H  HCR6   0   0.276   7.0040   1.6289   0.2255
 21G  H3   H  HCR5   0   0.325   0.6023   1.8726  -0.6170
 21G  H4   H  HNR5   0   0.417   2.6232   3.3458  -0.5594
 21G  H5   H  HCR6   0   0.280   1.2902  -4.1456   0.3557
 21G  H6   H  HNH1   0   0.397  -2.9326  -2.2946  -0.3410
 21G  H7   H  HCH1   0   0.250  -2.2492   0.2763  -1.4560
 21G  H8   H  HCH1   0   0.225  -2.4298   0.1690   1.4004
 21G  H9   H  HCH1   0   0.217  -4.3036   1.6679   1.8504
 21G  H10  H  HCH2   0   0.220  -6.0326   1.9920   0.0359
 21G  H11  H  HCH2   0   0.229  -4.5508   2.8548  -0.2911
 21G  H12  H  HCH2   0   0.226  -5.7591   1.0020  -2.0555
 21G  H13  H  HCH2   0   0.227  -4.1080   1.5825  -2.1833
 21G  H14  H  HCH1   0   0.230  -4.2755  -0.9330  -2.1364
 21G  H15  H  HCH2   0   0.234  -6.2348  -0.9469  -0.5545
 21G  H16  H  HCH2   0   0.231  -4.9897  -2.0461  -0.0477
 21G  H17  H  HCH2   0   0.221  -4.5753  -0.8337   1.9057
 21G  H18  H  HCH2   0   0.226  -6.0756   0.0006   1.5630

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
 21G  N9   C5   aromatic  1.367  0.020  1.367
 21G  N9   C8   aromatic  1.355  0.020  1.355
 21G  N4   C5   aromatic  1.319  0.020  1.319
 21G  N4   C3   aromatic  1.324  0.020  1.324
 21G  C5   C6   aromatic  1.414  0.020  1.414
 21G  C8   C7   aromatic  1.377  0.020  1.377
 21G  C3   C2   aromatic  1.394  0.020  1.394
 21G  C6   C7   aromatic  1.431  0.020  1.431
 21G  C6   C1   aromatic  1.393  0.020  1.393
 21G  C7   C11  single    1.454  0.020  1.454
 21G  C2   C1   aromatic  1.376  0.020  1.376
 21G  C2   F32  single    1.345  0.020  1.345
 21G  N12  C11  aromatic  1.326  0.020  1.326
 21G  N12  C13  aromatic  1.341  0.020  1.341
 21G  C11  N16  aromatic  1.331  0.020  1.331
 21G  C13  C14  aromatic  1.360  0.020  1.360
 21G  N16  C15  aromatic  1.327  0.020  1.327
 21G  C15  C14  aromatic  1.413  0.020  1.413
 21G  C15  N17  single    1.335  0.020  1.335
 21G  C14  F31  single    1.345  0.020  1.345
 21G  O30  C28  deloc     1.249  0.020  1.249
 21G  N17  C18  single    1.456  0.020  1.456
 21G  C18  C25  single    1.530  0.020  1.530
 21G  C18  C20  single    1.547  0.020  1.547
 21G  C28  O29  deloc     1.249  0.020  1.249
 21G  C28  C20  single    1.542  0.020  1.542
 21G  C24  C25  single    1.530  0.020  1.530
 21G  C24  C23  single    1.543  0.020  1.543
 21G  C25  C26  single    1.532  0.020  1.532
 21G  C20  C22  single    1.539  0.020  1.539
 21G  C23  C22  single    1.530  0.020  1.530
 21G  C26  C27  single    1.542  0.020  1.542
 21G  C22  C27  single    1.530  0.020  1.530
 21G  C1   H1   single    0.930  0.020  1.080
 21G  C3   H2   single    0.930  0.020  1.080
 21G  C8   H3   single    0.930  0.020  1.080
 21G  N9   H4   single    0.860  0.020  1.020
 21G  C13  H5   single    0.930  0.020  1.080
 21G  N17  H6   single    0.860  0.020  1.020
 21G  C18  H7   single    0.970  0.020  1.090
 21G  C20  H8   single    0.970  0.020  1.090
 21G  C22  H9   single    0.970  0.020  1.090
 21G  C23  H10  single    0.970  0.020  1.090
 21G  C23  H11  single    0.970  0.020  1.090
 21G  C24  H12  single    0.970  0.020  1.090
 21G  C24  H13  single    0.970  0.020  1.090
 21G  C25  H14  single    0.970  0.020  1.090
 21G  C26  H15  single    0.970  0.020  1.090
 21G  C26  H16  single    0.970  0.020  1.090
 21G  C27  H17  single    0.970  0.020  1.090
 21G  C27  H18  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
 21G  H1   C1   C6   122.05  3.000
 21G  H1   C1   C2   121.95  3.000
 21G  C6   C1   C2   116.00  3.000
 21G  F32  C2   C3   117.95  3.000
 21G  F32  C2   C1   119.60  3.000
 21G  C3   C2   C1   122.45  3.000
 21G  H2   C3   N4   117.74  3.000
 21G  H2   C3   C2   120.02  3.000
 21G  N4   C3   C2   122.24  3.000
 21G  N9   C5   N4   125.86  3.000
 21G  N4   C5   C6   126.52  3.000
 21G  N9   C5   C6   107.61  3.000
 21G  C7   C6   C5   106.60  3.000
 21G  C7   C6   C1   136.33  3.000
 21G  C5   C6   C1   117.07  3.000
 21G  C11  C7   C8   125.17  3.000
 21G  C11  C7   C6   128.50  3.000
 21G  C8   C7   C6   106.32  3.000
 21G  C5   N4   C3   115.72  3.000
 21G  H3   C8   N9   121.38  3.000
 21G  H3   C8   C7   128.62  3.000
 21G  N9   C8   C7   110.00  3.000
 21G  H4   N9   C8   125.28  3.000
 21G  H4   N9   C5   125.26  3.000
 21G  C8   N9   C5   109.46  3.000
 21G  N16  C11  N12  126.00  3.000
 21G  N16  C11  C7   116.13  3.000
 21G  N12  C11  C7   117.87  3.000
 21G  C13  N12  C11  115.85  3.000
 21G  H5   C13  C14  120.35  3.000
 21G  H5   C13  N12  117.63  3.000
 21G  C14  C13  N12  122.02  3.000
 21G  F31  C14  C15  119.40  3.000
 21G  F31  C14  C13  121.62  3.000
 21G  C15  C14  C13  118.98  3.000
 21G  N17  C15  N16  119.64  3.000
 21G  N17  C15  C14  122.29  3.000
 21G  N16  C15  C14  118.07  3.000
 21G  C15  N16  C11  119.08  3.000
 21G  H6   N17  C18  118.76  3.000
 21G  H6   N17  C15  118.11  3.000
 21G  C18  N17  C15  123.09  3.000
 21G  H7   C18  C25  108.48  3.000
 21G  H7   C18  C20  108.07  3.000
 21G  C25  C18  C20  109.99  3.000
 21G  H7   C18  N17  107.53  3.000
 21G  C20  C18  N17  113.10  3.000
 21G  C25  C18  N17  109.54  3.000
 21G  H8   C20  C28  107.16  3.000
 21G  H8   C20  C22  107.11  3.000
 21G  C28  C20  C22  109.92  3.000
 21G  H8   C20  C18  108.47  3.000
 21G  C22  C20  C18  108.93  3.000
 21G  C28  C20  C18  114.96  3.000
 21G  H9   C22  C27  109.81  3.000
 21G  H9   C22  C23  110.29  3.000
 21G  C27  C22  C23  108.47  3.000
 21G  H9   C22  C20  108.95  3.000
 21G  C27  C22  C20  108.99  3.000
 21G  C23  C22  C20  110.32  3.000
 21G  H11  C23  H10  106.10  3.000
 21G  H11  C23  C24  110.72  3.000
 21G  H10  C23  C24  110.72  3.000
 21G  H11  C23  C22  111.01  3.000
 21G  H10  C23  C22  109.05  3.000
 21G  C24  C23  C22  109.20  3.000
 21G  H13  C24  H12  106.92  3.000
 21G  H13  C24  C25  109.39  3.000
 21G  H12  C24  C25  109.53  3.000
 21G  H13  C24  C23  110.48  3.000
 21G  H12  C24  C23  110.93  3.000
 21G  C25  C24  C23  109.54  3.000
 21G  H14  C25  C26  110.21  3.000
 21G  H14  C25  C24  109.93  3.000
 21G  C26  C25  C24  108.53  3.000
 21G  H14  C25  C18  109.44  3.000
 21G  C26  C25  C18  111.23  3.000
 21G  C24  C25  C18  107.44  3.000
 21G  H16  C26  H15  105.19  3.000
 21G  H16  C26  C27  111.06  3.000
 21G  H15  C26  C27  110.84  3.000
 21G  H16  C26  C25  111.84  3.000
 21G  H15  C26  C25  108.47  3.000
 21G  C27  C26  C25  109.36  3.000
 21G  H18  C27  H17  106.38  3.000
 21G  H18  C27  C26  110.52  3.000
 21G  H17  C27  C26  110.79  3.000
 21G  H18  C27  C22  110.08  3.000
 21G  H17  C27  C22  109.61  3.000
 21G  C26  C27  C22  109.42  3.000
 21G  O30  C28  O29  125.82  3.000
 21G  O29  C28  C20  118.94  3.000
 21G  O30  C28  C20  115.21  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
 21G  CONST_01  N9   C5   C6   C1   180.00   0.0  0
 21G  CONST_02  N4   C5   C6   C1     0.00   0.0  0
 21G  CONST_03  C8   C7   C6   C1   180.00   0.0  0
 21G  CONST_04  C11  C7   C6   C1     0.00   0.0  0
 21G  CONST_05  N4   C3   C2   C1     0.00   0.0  0
 21G  CONST_06  C5   N4   C3   C2     0.00   0.0  0
 21G  CONST_07  C5   C6   C1   C2     0.00   0.0  0
 21G  CONST_08  C7   C6   C1   C2   180.00   0.0  0
 21G  CONST_09  N9   C5   N4   C3   180.00   0.0  0
 21G  CONST_10  C6   C5   N4   C3     0.00   0.0  0
 21G  CONST_11  C6   C1   C2   C3     0.00   0.0  0
 21G  CONST_12  C7   C8   N9   C5     0.00   0.0  0
 21G  CONST_13  C8   C7   C6   C5     0.00   0.0  0
 21G  CONST_14  C11  C7   C6   C5   180.00   0.0  0
 21G  CONST_15  C8   N9   C5   C6     0.00   0.0  0
 21G  CONST_16  N9   C8   C7   C6     0.00   0.0  0
 21G  CONST_17  N12  C11  C7   C6     0.00   0.0  0
 21G  CONST_18  N16  C11  C7   C6   180.00   0.0  0
 21G  CONST_19  N9   C5   C6   C7     0.00   0.0  0
 21G  CONST_20  N4   C5   C6   C7   180.00   0.0  0
 21G  CONST_21  C13  N12  C11  C7   180.00   0.0  0
 21G  CONST_22  C15  N16  C11  C7   180.00   0.0  0
 21G  CONST_23  C8   N9   C5   N4   180.00   0.0  0
 21G  CONST_24  N12  C11  C7   C8   180.00   0.0  0
 21G  CONST_25  N16  C11  C7   C8     0.00   0.0  0
 21G  CONST_26  C11  C7   C8   N9   180.00   0.0  0
 21G  CONST_27  C14  C13  N12  C11    0.00   0.0  0
 21G  CONST_28  C14  C15  N16  C11    0.00   0.0  0
 21G  CONST_29  C15  N16  C11  N12    0.00   0.0  0
 21G  CONST_30  C15  C14  C13  N12    0.00   0.0  0
 21G  CONST_31  N16  C11  N12  C13    0.00   0.0  0
 21G  CONST_32  N16  C15  C14  C13    0.00   0.0  0
 21G  CONST_33  F32  C2   C1   C6   180.00   0.0  0
 21G  CONST_34  F32  C2   C3   N4   180.00   0.0  0
 21G  CONST_35  N17  C15  N16  C11  180.00   0.0  0
 21G  CONST_36  F31  C14  C13  N12  180.00   0.0  0
 21G  CONST_37  N17  C15  C14  C13  180.00   0.0  0
 21G  CONST_38  F31  C14  C15  N16  180.00   0.0  0
 21G  CONST_39  C18  N17  C15  C14  180.00   0.0  0
 21G  CONST_40  C18  N17  C15  N16    0.00   0.0  0
 21G  CONST_41  H2   C3   C2   C1   180.00   0.0  0
 21G  CONST_42  H1   C1   C2   C3   180.00   0.0  0
 21G  CONST_43  H3   C8   N9   C5   180.00   0.0  0
 21G  CONST_44  H4   N9   C5   C6   180.00   0.0  0
 21G  CONST_45  H5   C13  N12  C11  180.00   0.0  0
 21G  CONST_46  H6   N17  C15  C14    0.00   0.0  0
 21G  Var_01    C25  C24  C23  C22   11.25  30.0  1
 21G  Var_02    C25  C26  C27  C22   10.86  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
 21G  chir_01  C18  N17  C25  C20  negativ
 21G  chir_02  C20  C18  C28  C22  negativ
 21G  chir_03  C22  C27  C23  C20  positiv
 21G  chir_04  C25  C18  C24  C26  positiv

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
 21G  plan-1  C7   0.020
 21G  plan-1  C11  0.020
 21G  plan-1  N12  0.020
 21G  plan-1  C13  0.020
 21G  plan-1  C14  0.020
 21G  plan-1  C15  0.020
 21G  plan-1  N16  0.020
 21G  plan-1  N17  0.020
 21G  plan-1  F31  0.020
 21G  plan-1  H5   0.020
 21G  plan-2  C1   0.020
 21G  plan-2  C2   0.020
 21G  plan-2  C3   0.020
 21G  plan-2  C5   0.020
 21G  plan-2  C6   0.020
 21G  plan-2  C7   0.020
 21G  plan-2  N4   0.020
 21G  plan-2  C8   0.020
 21G  plan-2  N9   0.020
 21G  plan-2  C11  0.020
 21G  plan-2  F32  0.020
 21G  plan-2  H1   0.020
 21G  plan-2  H2   0.020
 21G  plan-2  H3   0.020
 21G  plan-2  H4   0.020
 21G  plan-3  C15  0.020
 21G  plan-3  N17  0.020
 21G  plan-3  C18  0.020
 21G  plan-3  H6   0.020
 21G  plan-4  C20  0.020
 21G  plan-4  C28  0.020
 21G  plan-4  O29  0.020
 21G  plan-4  O30  0.020

