# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 08:07:08 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: 6-{[(3R,4R)-4-{[5-(3-fluorophenyl)pentyl]oxy}pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(C[C@@H]2CNC[C@@H]2OCCCCCc3cccc(F)c3)c1
#
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
 H4W  H4W  6-{[(3R,4R)-4-{[5-(3-fluorophenyl)pentyl]oxy}pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine  ligand  57  27  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H4W
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
 H4W  F23  F  F     0  -0.319   8.6407   1.5537   1.8185
 H4W  C23  C  CR6   0   0.539   8.0278   1.2758   0.6540
 H4W  C22  C  CR16  0  -0.471   7.0694   0.2810   0.6323
 H4W  C21  C  CR6   0   0.151   6.4287  -0.0243  -0.5661
 H4W  C26  C  CR16  0  -0.322   6.7761   0.6874  -1.7134
 H4W  C25  C  CR16  0  -0.224   7.7409   1.6835  -1.6650
 H4W  C24  C  CR16  0  -0.428   8.3826   1.9915  -0.4724
 H4W  C14  C  CH2   0  -0.507   5.3434  -1.0623  -0.6040
 H4W  C13  C  CH2   0  -0.410   3.9609  -0.4440  -0.3884
 H4W  C12  C  CH2   0  -0.429   2.8407  -1.4752  -0.4268
 H4W  C11  C  CH2   0  -0.460   1.4660  -0.8468  -0.2351
 H4W  C10  C  CH2   0  -0.122   0.3535  -1.8741  -0.3074
 H4W  O09  O  O2    0  -0.492  -0.8830  -1.2287  -0.1068
 H4W  C3'  C  CH1   0   0.076  -1.9997  -2.0197  -0.4118
 H4W  C2'  C  CH2   0  -0.317  -2.2193  -3.1952   0.5513
 H4W  N1'  N  NH1   0  -0.612  -3.6586  -3.3642   0.5144
 H4W  C5'  C  CH2   0  -0.270  -4.1871  -2.0182   0.6484
 H4W  C4'  C  CH1   0  -0.299  -3.3166  -1.2026  -0.3161
 H4W  C08  C  CH2   0  -0.494  -3.1519   0.2497   0.1289
 H4W  C06  C  CR6   0   0.280  -4.4746   0.9638   0.1248
 H4W  N01  N  N     0  -0.485  -5.0127   1.1982  -1.0745
 H4W  C02  C  CR6   0   0.439  -6.1920   1.8058  -1.1379
 H4W  N02  N  NH2   0  -0.840  -6.7343   1.9818  -2.3786
 H4W  C03  C  CR16  0  -0.448  -6.8876   2.2190   0.0121
 H4W  C04  C  CR6   0   0.205  -6.3342   1.9776   1.2524
 H4W  C07  C  CH3   0  -0.727  -7.0406   2.3787   2.5112
 H4W  C05  C  CR16  0  -0.432  -5.0934   1.3319   1.3060
 H4W  H1   H  HCR6  0   0.268   6.8258  -0.2560   1.5417
 H4W  H2   H  HCR6  0   0.250   6.2877   0.4581  -2.6529
 H4W  H3   H  HCR6  0   0.265   8.0006   2.2282  -2.5635
 H4W  H4   H  HCR6  0   0.276   9.1388   2.7635  -0.4224
 H4W  H5   H  HCH2  0   0.242   5.3604  -1.5798  -1.5671
 H4W  H6   H  HCH2  0   0.241   5.5252  -1.8192   0.1634
 H4W  H7   H  HCH2  0   0.224   3.9467   0.0809   0.5721
 H4W  H8   H  HCH2  0   0.224   3.7844   0.3155  -1.1561
 H4W  H9   H  HCH2  0   0.217   2.8709  -2.0078  -1.3836
 H4W  H10  H  HCH2  0   0.218   3.0125  -2.2290   0.3485
 H4W  H11  H  HCH2  0   0.222   1.4292  -0.3352   0.7320
 H4W  H12  H  HCH2  0   0.221   1.3017  -0.0848  -1.0030
 H4W  H13  H  HCH2  0   0.192   0.3704  -2.3737  -1.2873
 H4W  H14  H  HCH2  0   0.197   0.5171  -2.6556   0.4478
 H4W  H15  H  HCH1  0   0.212  -1.8969  -2.4110  -1.4338
 H4W  H16  H  HCH2  0   0.232  -1.7038  -4.1068   0.2418
 H4W  H17  H  HCH2  0   0.198  -1.8378  -2.9138   1.5469
 H4W  H18  H  HNH1  0   0.351  -3.9851  -3.9761   1.2504
 H4W  H20  H  HCH2  0   0.230  -5.2482  -1.9774   0.3959
 H4W  H21  H  HCH2  0   0.195  -4.0787  -1.6200   1.6710
 H4W  H22  H  HCH1  0   0.251  -3.7889  -1.1951  -1.3010
 H4W  H23  H  HCH2  0   0.236  -2.7211   0.2886   1.1314
 H4W  H24  H  HCH2  0   0.247  -2.4656   0.7715  -0.5417
 H4W  H25  H  HNH2  0   0.379  -6.0978   1.9212  -3.1561
 H4W  H26  H  HNH2  0   0.387  -7.4484   2.6829  -2.4829
 H4W  H27  H  HCR6  0   0.253  -7.8427   2.7218  -0.0821
 H4W  H28  H  HCH3  0   0.253  -7.4130   1.4986   3.0387
 H4W  H29  H  HCH3  0   0.249  -6.3668   2.8980   3.1930
 H4W  H30  H  HCH3  0   0.246  -7.8899   3.0292   2.3083
 H4W  H31  H  HCR6  0   0.241  -4.6190   1.1245   2.2570

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
 H4W  C07  C04  single    1.498  0.020  1.498
 H4W  C04  C03  aromatic  1.379  0.020  1.379
 H4W  C04  C05  aromatic  1.400  0.020  1.400
 H4W  C03  C02  aromatic  1.406  0.020  1.406
 H4W  C05  C06  aromatic  1.383  0.020  1.383
 H4W  C02  N02  single    1.365  0.020  1.365
 H4W  C02  N01  aromatic  1.328  0.020  1.328
 H4W  C06  N01  aromatic  1.335  0.020  1.335
 H4W  C06  C08  single    1.503  0.020  1.503
 H4W  C5'  N1'  single    1.452  0.020  1.452
 H4W  C5'  C4'  single    1.534  0.020  1.534
 H4W  O09  C10  single    1.409  0.020  1.409
 H4W  O09  C3'  single    1.402  0.020  1.402
 H4W  C08  C4'  single    1.528  0.020  1.528
 H4W  N1'  C2'  single    1.450  0.020  1.450
 H4W  C4'  C3'  single    1.553  0.020  1.553
 H4W  C10  C11  single    1.516  0.020  1.516
 H4W  C3'  C2'  single    1.535  0.020  1.535
 H4W  C11  C12  single    1.524  0.020  1.524
 H4W  C12  C13  single    1.523  0.020  1.523
 H4W  C25  C26  aromatic  1.388  0.020  1.388
 H4W  C25  C24  aromatic  1.389  0.020  1.389
 H4W  C26  C21  aromatic  1.394  0.020  1.394
 H4W  C24  C23  aromatic  1.381  0.020  1.381
 H4W  C13  C14  single    1.530  0.020  1.530
 H4W  C21  C14  single    1.502  0.020  1.502
 H4W  C21  C22  aromatic  1.393  0.020  1.393
 H4W  C23  C22  aromatic  1.382  0.020  1.382
 H4W  C23  F23  single    1.345  0.020  1.345
 H4W  C22  H1   single    0.930  0.020  1.080
 H4W  C26  H2   single    0.930  0.020  1.080
 H4W  C25  H3   single    0.930  0.020  1.080
 H4W  C24  H4   single    0.930  0.020  1.080
 H4W  C14  H5   single    0.970  0.020  1.090
 H4W  C14  H6   single    0.970  0.020  1.090
 H4W  C13  H7   single    0.970  0.020  1.090
 H4W  C13  H8   single    0.970  0.020  1.090
 H4W  C12  H9   single    0.970  0.020  1.090
 H4W  C12  H10  single    0.970  0.020  1.090
 H4W  C11  H11  single    0.970  0.020  1.090
 H4W  C11  H12  single    0.970  0.020  1.090
 H4W  C10  H13  single    0.970  0.020  1.090
 H4W  C10  H14  single    0.970  0.020  1.090
 H4W  C3'  H15  single    0.970  0.020  1.090
 H4W  C2'  H16  single    0.970  0.020  1.090
 H4W  C2'  H17  single    0.970  0.020  1.090
 H4W  N1'  H18  single    0.890  0.020  1.040
 H4W  C5'  H20  single    0.970  0.020  1.090
 H4W  C5'  H21  single    0.970  0.020  1.090
 H4W  C4'  H22  single    0.970  0.020  1.090
 H4W  C08  H23  single    0.970  0.020  1.090
 H4W  C08  H24  single    0.970  0.020  1.090
 H4W  N02  H25  single    0.890  0.020  1.040
 H4W  N02  H26  single    0.890  0.020  1.040
 H4W  C03  H27  single    0.930  0.020  1.080
 H4W  C07  H28  single    0.970  0.020  1.090
 H4W  C07  H29  single    0.970  0.020  1.090
 H4W  C07  H30  single    0.970  0.020  1.090
 H4W  C05  H31  single    0.930  0.020  1.080

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
 H4W  C24  C23  C22  122.60  3.000
 H4W  C22  C23  F23  118.58  3.000
 H4W  C24  C23  F23  118.82  3.000
 H4W  H1   C22  C21  120.67  3.000
 H4W  H1   C22  C23  119.97  3.000
 H4W  C21  C22  C23  119.36  3.000
 H4W  C14  C21  C26  120.80  3.000
 H4W  C14  C21  C22  120.36  3.000
 H4W  C26  C21  C22  118.80  3.000
 H4W  H2   C26  C25  119.70  3.000
 H4W  H2   C26  C21  119.56  3.000
 H4W  C25  C26  C21  120.73  3.000
 H4W  H3   C25  C24  119.36  3.000
 H4W  H3   C25  C26  119.95  3.000
 H4W  C24  C25  C26  120.69  3.000
 H4W  H4   C24  C25  121.39  3.000
 H4W  H4   C24  C23  120.78  3.000
 H4W  C25  C24  C23  117.82  3.000
 H4W  H6   C14  H5   106.74  3.000
 H4W  H6   C14  C13  109.35  3.000
 H4W  H5   C14  C13  109.24  3.000
 H4W  H6   C14  C21  109.91  3.000
 H4W  H5   C14  C21  109.75  3.000
 H4W  C13  C14  C21  111.72  3.000
 H4W  H8   C13  H7   106.30  3.000
 H4W  H8   C13  C12  109.49  3.000
 H4W  H7   C13  C12  109.71  3.000
 H4W  H8   C13  C14  109.11  3.000
 H4W  H7   C13  C14  109.22  3.000
 H4W  C12  C13  C14  112.79  3.000
 H4W  H10  C12  H9   106.23  3.000
 H4W  H10  C12  C11  109.65  3.000
 H4W  H9   C12  C11  109.59  3.000
 H4W  H10  C12  C13  109.45  3.000
 H4W  H9   C12  C13  109.33  3.000
 H4W  C11  C12  C13  112.41  3.000
 H4W  H12  C11  H11  106.82  3.000
 H4W  H12  C11  C10  109.16  3.000
 H4W  H11  C11  C10  109.53  3.000
 H4W  H12  C11  C12  109.53  3.000
 H4W  H11  C11  C12  109.53  3.000
 H4W  C10  C11  C12  112.13  3.000
 H4W  H14  C10  H13  106.67  3.000
 H4W  H14  C10  O09  111.01  3.000
 H4W  H13  C10  O09  110.38  3.000
 H4W  H14  C10  C11  109.86  3.000
 H4W  H13  C10  C11  109.82  3.000
 H4W  O09  C10  C11  109.08  3.000
 H4W  C3'  O09  C10  114.18  3.000
 H4W  H15  C3'  C4'  108.90  3.000
 H4W  H15  C3'  C2'  108.90  3.000
 H4W  C4'  C3'  C2'  104.05  3.000
 H4W  H15  C3'  O09  109.19  3.000
 H4W  C2'  C3'  O09  114.17  3.000
 H4W  C4'  C3'  O09  111.42  3.000
 H4W  H17  C2'  H16  107.79  3.000
 H4W  H17  C2'  N1'  113.34  3.000
 H4W  H16  C2'  N1'  111.35  3.000
 H4W  H17  C2'  C3'  108.75  3.000
 H4W  H16  C2'  C3'  113.20  3.000
 H4W  N1'  C2'  C3'  102.43  3.000
 H4W  H18  N1'  C5'  112.10  3.000
 H4W  H18  N1'  C2'  111.88  3.000
 H4W  C5'  N1'  C2'  104.53  3.000
 H4W  H21  C5'  H20  107.25  3.000
 H4W  H21  C5'  C4'  109.59  3.000
 H4W  H20  C5'  C4'  112.73  3.000
 H4W  H21  C5'  N1'  112.61  3.000
 H4W  H20  C5'  N1'  111.53  3.000
 H4W  C4'  C5'  N1'  103.19  3.000
 H4W  H22  C4'  C08  107.61  3.000
 H4W  H22  C4'  C5'  108.98  3.000
 H4W  C08  C4'  C5'  112.54  3.000
 H4W  H22  C4'  C3'  108.35  3.000
 H4W  C08  C4'  C3'  115.26  3.000
 H4W  C5'  C4'  C3'  103.91  3.000
 H4W  H24  C08  H23  107.38  3.000
 H4W  H24  C08  C06  108.92  3.000
 H4W  H23  C08  C06  109.44  3.000
 H4W  H24  C08  C4'  110.06  3.000
 H4W  H23  C08  C4'  110.11  3.000
 H4W  C06  C08  C4'  110.85  3.000
 H4W  C05  C06  N01  122.68  3.000
 H4W  N01  C06  C08  116.13  3.000
 H4W  C05  C06  C08  121.18  3.000
 H4W  C02  N01  C06  118.75  3.000
 H4W  C03  C02  N02  120.58  3.000
 H4W  N02  C02  N01  117.07  3.000
 H4W  C03  C02  N01  122.32  3.000
 H4W  H26  N02  H25  114.24  3.000
 H4W  H26  N02  C02  117.77  3.000
 H4W  H25  N02  C02  116.29  3.000
 H4W  H27  C03  C04  120.86  3.000
 H4W  H27  C03  C02  120.09  3.000
 H4W  C04  C03  C02  119.05  3.000
 H4W  C05  C04  C07  120.62  3.000
 H4W  C05  C04  C03  118.08  3.000
 H4W  C07  C04  C03  121.30  3.000
 H4W  H30  C07  H29  108.30  3.000
 H4W  H30  C07  H28  107.79  3.000
 H4W  H29  C07  H28  107.02  3.000
 H4W  H30  C07  C04  111.79  3.000
 H4W  H29  C07  C04  111.20  3.000
 H4W  H28  C07  C04  110.55  3.000
 H4W  H31  C05  C04  120.68  3.000
 H4W  H31  C05  C06  120.20  3.000
 H4W  C04  C05  C06  119.12  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
 H4W  CONST_01  C26  C25  C24  C23     0.00   0.0  0
 H4W  CONST_02  C26  C21  C22  C23     0.00   0.0  0
 H4W  CONST_03  C25  C26  C21  C22     0.00   0.0  0
 H4W  CONST_04  C25  C24  C23  C22     0.00   0.0  0
 H4W  CONST_05  C24  C25  C26  C21     0.00   0.0  0
 H4W  CONST_06  C24  C23  C22  C21     0.00   0.0  0
 H4W  CONST_07  C03  C04  C05  C06     0.00   0.0  0
 H4W  CONST_08  C03  C02  N01  C06     0.00   0.0  0
 H4W  CONST_09  C04  C03  C02  N01     0.00   0.0  0
 H4W  CONST_10  C04  C05  C06  N01     0.00   0.0  0
 H4W  CONST_11  C05  C04  C03  C02     0.00   0.0  0
 H4W  CONST_12  C05  C06  N01  C02     0.00   0.0  0
 H4W  CONST_13  C25  C24  C23  F23   180.00   0.0  0
 H4W  CONST_14  C21  C22  C23  F23   180.00   0.0  0
 H4W  CONST_15  C14  C21  C22  C23   180.00   0.0  0
 H4W  CONST_16  C14  C21  C26  C25   180.00   0.0  0
 H4W  CONST_17  C04  C05  C06  C08   180.00   0.0  0
 H4W  CONST_18  C02  N01  C06  C08   180.00   0.0  0
 H4W  CONST_19  C07  C04  C05  C06   180.00   0.0  0
 H4W  CONST_20  N02  C02  N01  C06   180.00   0.0  0
 H4W  CONST_21  C07  C04  C03  C02   180.00   0.0  0
 H4W  CONST_22  C04  C03  C02  N02   180.00   0.0  0
 H4W  CONST_23  H3   C25  C24  C23   180.00   0.0  0
 H4W  CONST_24  H2   C26  C21  C22   180.00   0.0  0
 H4W  CONST_25  H4   C24  C23  C22   180.00   0.0  0
 H4W  CONST_26  H1   C22  C21  C26   180.00   0.0  0
 H4W  CONST_27  H27  C03  C02  N01   180.00   0.0  0
 H4W  CONST_28  H31  C05  C06  N01   180.00   0.0  0
 H4W  Var_01    C5'  N1'  C2'  C3'   -46.25  30.0  1
 H4W  Var_02    C4'  C5'  N1'  C2'    44.98  30.0  1
 H4W  Var_03    C05  C06  C08  C4'   109.67  30.0  2
 H4W  Var_04    C13  C14  C21  C22    91.34  30.0  2
 H4W  Var_05    H28  C07  C04  C03   108.68  30.0  2
 H4W  Var_06    C12  C13  C14  C21   179.81  30.0  2
 H4W  Var_07    H13  C10  O09  C3'    47.26  30.0  3
 H4W  Var_08    C11  C12  C13  C14  -179.02  30.0  1
 H4W  Var_09    C10  C11  C12  C13   178.63  30.0  2
 H4W  Var_10    O09  C10  C11  C12   179.31  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
 H4W  chir_01  C3'  O09  C4'  C2'  positiv
 H4W  chir_02  C4'  C3'  C08  C5'  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
 H4W  plan-1  F23  0.020
 H4W  plan-1  C23  0.020
 H4W  plan-1  C22  0.020
 H4W  plan-1  C21  0.020
 H4W  plan-1  C26  0.020
 H4W  plan-1  C25  0.020
 H4W  plan-1  C24  0.020
 H4W  plan-1  C14  0.020
 H4W  plan-1  H1   0.020
 H4W  plan-1  H2   0.020
 H4W  plan-1  H3   0.020
 H4W  plan-1  H4   0.020
 H4W  plan-2  C08  0.020
 H4W  plan-2  C06  0.020
 H4W  plan-2  N01  0.020
 H4W  plan-2  C02  0.020
 H4W  plan-2  N02  0.020
 H4W  plan-2  C03  0.020
 H4W  plan-2  C04  0.020
 H4W  plan-2  C07  0.020
 H4W  plan-2  C05  0.020
 H4W  plan-2  H27  0.020
 H4W  plan-2  H31  0.020
 H4W  plan-3  C02  0.020
 H4W  plan-3  N02  0.020
 H4W  plan-3  H25  0.020
 H4W  plan-3  H26  0.020

