# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 10:33:44 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 6-{[(3R,4R)-4-(2-{[(2S)-1-(3-fluorophenyl)propan-2-yl]amino}ethoxy)pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](Cc1cccc(F)c1)NCCO[C@H]2CNC[C@H]2Cc3cc(C)cc(N)n3
#
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
 Y2F  Y2F  6-{[(3R,4R)-4-(2-{[(2S)-1-(3-fluorophenyl)propan-2-yl]amino}ethoxy)pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine  ligand  59  28  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Y2F
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
 Y2F  N01   N  N     0  -0.484  -5.3200  -0.5117  -0.7245
 Y2F  C02   C  CR6   0   0.437  -6.5019  -0.2954  -0.1588
 Y2F  N02   N  NH2   0  -0.839  -7.5188  -1.1424  -0.5006
 Y2F  C03   C  CR16  0  -0.447  -6.7091   0.7274   0.7834
 Y2F  C04   C  CR6   0   0.204  -5.6495   1.5377   1.1352
 Y2F  C05   C  CR16  0  -0.433  -4.4097   1.3006   0.5306
 Y2F  C06   C  CR6   0   0.279  -4.2923   0.2696  -0.3845
 Y2F  C07   C  CH3   0  -0.726  -5.8055   2.6301   2.1487
 Y2F  C08   C  CH2   0  -0.495  -2.9749  -0.0437  -1.0369
 Y2F  O09   O  O2    0  -0.492  -0.2693  -0.6733  -1.3531
 Y2F  N1'   N  NH1   0  -0.593  -0.7864  -2.0815   1.1640
 Y2F  C10   C  CH2   0  -0.157   0.9032  -0.8850  -2.1041
 Y2F  C11   C  CH2   0  -0.294   1.7237   0.3853  -2.0524
 Y2F  N12   N  NH1   0  -0.576   2.1398   0.6572  -0.6945
 Y2F  C13   C  CH1   0  -0.070   2.9410   1.8486  -0.5000
 Y2F  C14   C  CH3   0  -0.674   2.1875   3.1604  -0.7262
 Y2F  C15   C  CH2   0  -0.522   3.5345   1.8213   0.9161
 Y2F  C2'   C  CH2   0  -0.345  -0.5388  -2.7487  -0.1092
 Y2F  C21   C  CR6   0   0.177   4.4660   0.6668   1.1414
 Y2F  C22   C  CR16  0  -0.304   3.9976  -0.5788   1.5569
 Y2F  C23   C  CR16  0  -0.233   4.8725  -1.6403   1.7365
 Y2F  C24   C  CR16  0  -0.429   6.2334  -1.4890   1.5001
 Y2F  C25   C  CR6   0   0.536   6.6800  -0.2505   1.0855
 Y2F  F25   F  F     0  -0.321   7.9948  -0.0768   0.8553
 Y2F  C26   C  CR16  0  -0.473   5.8294   0.8229   0.9035
 Y2F  C3'   C  CH1   0   0.051  -1.0905  -1.8041  -1.1781
 Y2F  C4'   C  CH1   0  -0.300  -2.3911  -1.3538  -0.5129
 Y2F  C5'   C  CH2   0  -0.270  -2.0388  -1.3313   0.9941
 Y2F  HN02  H  HNH2  0   0.378  -7.3961  -1.6501  -1.3616
 Y2F  HN0A  H  HNH2  0   0.387  -8.4598  -0.8180  -0.3518
 Y2F  H03   H  HCR6  0   0.254  -7.6904   0.8734   1.2193
 Y2F  H05   H  HCR6  0   0.240  -3.5540   1.9200   0.7699
 Y2F  H07   H  HCH3  0   0.254  -5.3429   2.3406   3.0941
 Y2F  H07A  H  HCH3  0   0.248  -5.3142   3.5462   1.8202
 Y2F  H07B  H  HCH3  0   0.246  -6.8524   2.8543   2.3468
 Y2F  H08   H  HCH2  0   0.242  -3.1244  -0.1180  -2.1179
 Y2F  H08A  H  HCH2  0   0.243  -2.2740   0.7730  -0.8601
 Y2F  HN1'  H  HNH1  0   0.342  -0.0382  -1.4189   1.3174
 Y2F  H10   H  HCH2  0   0.198   1.4969  -1.7141  -1.6994
 Y2F  H10A  H  HCH2  0   0.206   0.6595  -1.1325  -3.1463
 Y2F  H11   H  HCH2  0   0.223   2.6123   0.2414  -2.6738
 Y2F  H11A  H  HCH2  0   0.194   1.1472   1.1982  -2.5201
 Y2F  HN12  H  HNH1  0   0.332   1.3256   0.6926  -0.0920
 Y2F  H13   H  HCH1  0   0.225   3.7721   1.8000  -1.2143
 Y2F  H14   H  HCH3  0   0.233   1.7395   3.2007  -1.7197
 Y2F  H14A  H  HCH3  0   0.216   1.3844   3.2742   0.0063
 Y2F  H14B  H  HCH3  0   0.226   2.8517   4.0210  -0.6324
 Y2F  H15   H  HCH2  0   0.246   4.0627   2.7610   1.0937
 Y2F  H15A  H  HCH2  0   0.241   2.7108   1.7861   1.6364
 Y2F  H2'   H  HCH2  0   0.243   0.5197  -2.9874  -0.2238
 Y2F  H2'A  H  HCH2  0   0.225  -1.0866  -3.6954  -0.1548
 Y2F  H22   H  HCR6  0   0.240   2.9413  -0.7191   1.7430
 Y2F  H23   H  HCR6  0   0.262   4.4951  -2.6002   2.0637
 Y2F  H24   H  HCR6  0   0.274   6.9257  -2.3089   1.6394
 Y2F  H26   H  HCR6  0   0.265   6.2267   1.7781   0.5805
 Y2F  H3'   H  HCH1  0   0.214  -1.2698  -2.3064  -2.1388
 Y2F  H4'   H  HCH1  0   0.251  -3.1263  -2.1447  -0.6924
 Y2F  H5'   H  HCH2  0   0.218  -2.8443  -1.7822   1.5791
 Y2F  H5'A  H  HCH2  0   0.226  -1.9164  -0.3102   1.3632

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
 Y2F  C02  N01   aromatic  1.328  0.020  1.328
 Y2F  C06  N01   aromatic  1.335  0.020  1.335
 Y2F  C03  C02   aromatic  1.406  0.020  1.406
 Y2F  C02  N02   single    1.367  0.020  1.367
 Y2F  N02  HN02  single    0.890  0.020  1.040
 Y2F  N02  HN0A  single    0.890  0.020  1.040
 Y2F  C04  C03   aromatic  1.380  0.020  1.380
 Y2F  C03  H03   single    0.930  0.020  1.080
 Y2F  C07  C04   single    1.498  0.020  1.498
 Y2F  C04  C05   aromatic  1.400  0.020  1.400
 Y2F  C05  C06   aromatic  1.384  0.020  1.384
 Y2F  C05  H05   single    0.930  0.020  1.080
 Y2F  C06  C08   single    1.503  0.020  1.503
 Y2F  C07  H07   single    0.970  0.020  1.090
 Y2F  C07  H07A  single    0.970  0.020  1.090
 Y2F  C07  H07B  single    0.970  0.020  1.090
 Y2F  C4'  C08   single    1.527  0.020  1.527
 Y2F  C08  H08   single    0.970  0.020  1.090
 Y2F  C08  H08A  single    0.970  0.020  1.090
 Y2F  C3'  O09   single    1.408  0.020  1.408
 Y2F  O09  C10   single    1.408  0.020  1.408
 Y2F  N1'  C5'   single    1.470  0.020  1.470
 Y2F  N1'  C2'   single    1.459  0.020  1.459
 Y2F  N1'  HN1'  single    0.890  0.020  1.040
 Y2F  C10  C11   single    1.513  0.020  1.513
 Y2F  C10  H10   single    0.970  0.020  1.090
 Y2F  C10  H10A  single    0.970  0.020  1.090
 Y2F  N12  C11   single    1.446  0.020  1.446
 Y2F  C11  H11   single    0.970  0.020  1.090
 Y2F  C11  H11A  single    0.970  0.020  1.090
 Y2F  N12  C13   single    1.449  0.020  1.449
 Y2F  N12  HN12  single    0.890  0.020  1.040
 Y2F  C13  C15   single    1.536  0.020  1.536
 Y2F  C13  C14   single    1.530  0.020  1.530
 Y2F  C13  H13   single    0.970  0.020  1.090
 Y2F  C14  H14   single    0.970  0.020  1.090
 Y2F  C14  H14A  single    0.970  0.020  1.090
 Y2F  C14  H14B  single    0.970  0.020  1.090
 Y2F  C15  C21   single    1.501  0.020  1.501
 Y2F  C15  H15   single    0.970  0.020  1.090
 Y2F  C15  H15A  single    0.970  0.020  1.090
 Y2F  C2'  C3'   single    1.529  0.020  1.529
 Y2F  C2'  H2'   single    0.970  0.020  1.090
 Y2F  C2'  H2'A  single    0.970  0.020  1.090
 Y2F  C22  C21   aromatic  1.394  0.020  1.394
 Y2F  C21  C26   aromatic  1.393  0.020  1.393
 Y2F  C22  C23   aromatic  1.387  0.020  1.387
 Y2F  C22  H22   single    0.930  0.020  1.080
 Y2F  C23  C24   aromatic  1.390  0.020  1.390
 Y2F  C23  H23   single    0.930  0.020  1.080
 Y2F  C24  C25   aromatic  1.380  0.020  1.380
 Y2F  C24  H24   single    0.930  0.020  1.080
 Y2F  C26  C25   aromatic  1.382  0.020  1.382
 Y2F  C25  F25   single    1.346  0.020  1.346
 Y2F  C26  H26   single    0.930  0.020  1.080
 Y2F  C4'  C3'   single    1.529  0.020  1.529
 Y2F  C3'  H3'   single    0.970  0.020  1.090
 Y2F  C5'  C4'   single    1.548  0.020  1.548
 Y2F  C4'  H4'   single    0.970  0.020  1.090
 Y2F  C5'  H5'   single    0.970  0.020  1.090
 Y2F  C5'  H5'A  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
 Y2F  C06   N01  C02   118.77  3.000
 Y2F  C03   C02  N02   120.58  3.000
 Y2F  N02   C02  N01   117.04  3.000
 Y2F  C03   C02  N01   122.35  3.000
 Y2F  HN0A  N02  HN02  113.76  3.000
 Y2F  HN0A  N02  C02   117.32  3.000
 Y2F  HN02  N02  C02   115.82  3.000
 Y2F  H03   C03  C04   120.92  3.000
 Y2F  H03   C03  C02   120.07  3.000
 Y2F  C04   C03  C02   119.01  3.000
 Y2F  C07   C04  C05   120.53  3.000
 Y2F  C05   C04  C03   118.08  3.000
 Y2F  C07   C04  C03   121.39  3.000
 Y2F  H05   C05  C06   120.35  3.000
 Y2F  H05   C05  C04   120.49  3.000
 Y2F  C06   C05  C04   119.15  3.000
 Y2F  C08   C06  C05   121.11  3.000
 Y2F  C08   C06  N01   116.25  3.000
 Y2F  C05   C06  N01   122.63  3.000
 Y2F  H07B  C07  H07A  108.37  3.000
 Y2F  H07B  C07  H07   107.73  3.000
 Y2F  H07A  C07  H07   107.03  3.000
 Y2F  H07B  C07  C04   111.92  3.000
 Y2F  H07A  C07  C04   111.22  3.000
 Y2F  H07   C07  C04   110.38  3.000
 Y2F  H08A  C08  H08   107.39  3.000
 Y2F  H08A  C08  C4'   109.94  3.000
 Y2F  H08   C08  C4'   109.45  3.000
 Y2F  H08A  C08  C06   109.69  3.000
 Y2F  H08   C08  C06   108.87  3.000
 Y2F  C4'   C08  C06   111.41  3.000
 Y2F  C3'   O09  C10   115.53  3.000
 Y2F  HN1'  N1'  C5'   108.28  3.000
 Y2F  HN1'  N1'  C2'   107.86  3.000
 Y2F  C5'   N1'  C2'   106.10  3.000
 Y2F  H10A  C10  H10   107.45  3.000
 Y2F  H10A  C10  C11   109.99  3.000
 Y2F  H10   C10  C11   109.17  3.000
 Y2F  H10A  C10  O09   110.80  3.000
 Y2F  H10   C10  O09   111.55  3.000
 Y2F  C11   C10  O09   107.88  3.000
 Y2F  H11A  C11  H11   106.33  3.000
 Y2F  H11A  C11  N12   114.25  3.000
 Y2F  H11   C11  N12   108.93  3.000
 Y2F  H11A  C11  C10   108.75  3.000
 Y2F  H11   C11  C10   108.10  3.000
 Y2F  N12   C11  C10   110.24  3.000
 Y2F  HN12  N12  C13   109.62  3.000
 Y2F  HN12  N12  C11   109.49  3.000
 Y2F  C13   N12  C11   116.09  3.000
 Y2F  H13   C13  C15   107.87  3.000
 Y2F  H13   C13  C14   108.35  3.000
 Y2F  C15   C13  C14   109.99  3.000
 Y2F  H13   C13  N12   107.17  3.000
 Y2F  C14   C13  N12   114.39  3.000
 Y2F  C15   C13  N12   108.84  3.000
 Y2F  H14B  C14  H14A  107.92  3.000
 Y2F  H14B  C14  H14   107.41  3.000
 Y2F  H14A  C14  H14   107.75  3.000
 Y2F  H14B  C14  C13   111.34  3.000
 Y2F  H14A  C14  C13   110.61  3.000
 Y2F  H14   C14  C13   111.64  3.000
 Y2F  H15A  C15  H15   106.53  3.000
 Y2F  H15A  C15  C21   110.09  3.000
 Y2F  H15   C15  C21   109.70  3.000
 Y2F  H15A  C15  C13   108.45  3.000
 Y2F  H15   C15  C13   108.76  3.000
 Y2F  C21   C15  C13   113.08  3.000
 Y2F  H2'A  C2'  H2'   106.98  3.000
 Y2F  H2'A  C2'  C3'   108.93  3.000
 Y2F  H2'   C2'  C3'   114.31  3.000
 Y2F  H2'A  C2'  N1'   110.30  3.000
 Y2F  H2'   C2'  N1'   110.88  3.000
 Y2F  C3'   C2'  N1'   105.44  3.000
 Y2F  C26   C21  C22   118.69  3.000
 Y2F  C26   C21  C15   119.72  3.000
 Y2F  C22   C21  C15   121.58  3.000
 Y2F  H22   C22  C23   119.62  3.000
 Y2F  H22   C22  C21   119.69  3.000
 Y2F  C23   C22  C21   120.69  3.000
 Y2F  H23   C23  C24   119.31  3.000
 Y2F  H23   C23  C22   119.87  3.000
 Y2F  C24   C23  C22   120.82  3.000
 Y2F  H24   C24  C25   120.76  3.000
 Y2F  H24   C24  C23   121.48  3.000
 Y2F  C25   C24  C23   117.76  3.000
 Y2F  C26   C25  F25   118.59  3.000
 Y2F  F25   C25  C24   118.90  3.000
 Y2F  C26   C25  C24   122.51  3.000
 Y2F  H26   C26  C25   119.89  3.000
 Y2F  H26   C26  C21   120.57  3.000
 Y2F  C25   C26  C21   119.54  3.000
 Y2F  H3'   C3'  C4'   112.10  3.000
 Y2F  H3'   C3'  C2'   112.80  3.000
 Y2F  C4'   C3'  C2'   100.65  3.000
 Y2F  H3'   C3'  O09   110.71  3.000
 Y2F  C4'   C3'  O09   108.28  3.000
 Y2F  C2'   C3'  O09   111.86  3.000
 Y2F  H4'   C4'  C5'   108.84  3.000
 Y2F  H4'   C4'  C3'   106.70  3.000
 Y2F  C5'   C4'  C3'   103.55  3.000
 Y2F  H4'   C4'  C08   107.87  3.000
 Y2F  C5'   C4'  C08   114.12  3.000
 Y2F  C3'   C4'  C08   115.38  3.000
 Y2F  H5'A  C5'  H5'   106.70  3.000
 Y2F  H5'A  C5'  C4'   111.59  3.000
 Y2F  H5'   C5'  C4'   110.33  3.000
 Y2F  H5'A  C5'  N1'   110.03  3.000
 Y2F  H5'   C5'  N1'   110.83  3.000
 Y2F  C4'   C5'  N1'   107.40  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
 Y2F  CONST_01  C04  C03  C02  N01    0.00   0.0  0
 Y2F  CONST_02  C04  C05  C06  N01    0.00   0.0  0
 Y2F  CONST_03  C05  C06  N01  C02    0.00   0.0  0
 Y2F  CONST_04  C05  C04  C03  C02    0.00   0.0  0
 Y2F  CONST_05  C06  N01  C02  C03    0.00   0.0  0
 Y2F  CONST_06  C06  C05  C04  C03    0.00   0.0  0
 Y2F  CONST_07  C24  C23  C22  C21    0.00   0.0  0
 Y2F  CONST_08  C24  C25  C26  C21    0.00   0.0  0
 Y2F  CONST_09  C25  C26  C21  C22    0.00   0.0  0
 Y2F  CONST_10  C25  C24  C23  C22    0.00   0.0  0
 Y2F  CONST_11  C26  C21  C22  C23    0.00   0.0  0
 Y2F  CONST_12  C26  C25  C24  C23    0.00   0.0  0
 Y2F  CONST_13  C08  C06  N01  C02  180.00   0.0  0
 Y2F  CONST_14  C07  C04  C03  C02  180.00   0.0  0
 Y2F  CONST_15  C06  N01  C02  N02  180.00   0.0  0
 Y2F  CONST_16  C04  C03  C02  N02  180.00   0.0  0
 Y2F  CONST_17  C08  C06  C05  C04  180.00   0.0  0
 Y2F  CONST_18  C07  C04  C05  C06  180.00   0.0  0
 Y2F  CONST_19  C23  C22  C21  C15  180.00   0.0  0
 Y2F  CONST_20  C25  C26  C21  C15  180.00   0.0  0
 Y2F  CONST_21  F25  C25  C26  C21  180.00   0.0  0
 Y2F  CONST_22  F25  C25  C24  C23  180.00   0.0  0
 Y2F  CONST_23  H03  C03  C02  N01  180.00   0.0  0
 Y2F  CONST_24  H05  C05  C06  N01  180.00   0.0  0
 Y2F  CONST_25  H23  C23  C22  C21  180.00   0.0  0
 Y2F  CONST_26  H26  C26  C21  C22  180.00   0.0  0
 Y2F  CONST_27  H24  C24  C23  C22  180.00   0.0  0
 Y2F  CONST_28  H22  C22  C23  C24  180.00   0.0  0
 Y2F  Var_01    C4'  C5'  N1'  C2'  -10.73  30.0  1
 Y2F  Var_02    C5'  N1'  C2'  C3'   32.94  30.0  1
 Y2F  Var_03    C4'  C08  C06  N01  -70.28  30.0  2
 Y2F  Var_04    C22  C21  C15  C13  -86.75  30.0  2
 Y2F  Var_05    H07  C07  C04  C03  105.15  30.0  2
 Y2F  Var_06    H10  C10  O09  C3'  -53.83  30.0  3
 Y2F  Var_07    N12  C11  C10  O09   63.70  30.0  3
 Y2F  Var_08    C13  N12  C11  C10  179.79  30.0  1

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
 Y2F  chir_01  C13  N12  C15  C14  positiv
 Y2F  chir_02  C3'  O09  C2'  C4'  negativ
 Y2F  chir_03  C4'  C08  C3'  C5'  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
 Y2F  plan-1  N01   0.020
 Y2F  plan-1  C02   0.020
 Y2F  plan-1  N02   0.020
 Y2F  plan-1  C03   0.020
 Y2F  plan-1  C04   0.020
 Y2F  plan-1  C05   0.020
 Y2F  plan-1  C06   0.020
 Y2F  plan-1  C07   0.020
 Y2F  plan-1  C08   0.020
 Y2F  plan-1  H03   0.020
 Y2F  plan-1  H05   0.020
 Y2F  plan-2  C15   0.020
 Y2F  plan-2  C21   0.020
 Y2F  plan-2  C22   0.020
 Y2F  plan-2  C23   0.020
 Y2F  plan-2  C24   0.020
 Y2F  plan-2  C25   0.020
 Y2F  plan-2  F25   0.020
 Y2F  plan-2  C26   0.020
 Y2F  plan-2  H22   0.020
 Y2F  plan-2  H23   0.020
 Y2F  plan-2  H24   0.020
 Y2F  plan-2  H26   0.020
 Y2F  plan-3  C02   0.020
 Y2F  plan-3  N02   0.020
 Y2F  plan-3  HN02  0.020
 Y2F  plan-3  HN0A  0.020

