# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 03:33:38 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: 6-{[(3S,4S)-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
 HW4  HW4  6-{[(3S,4S)-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_HW4
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
 HW4  F23  F  F     0  -0.319  -8.5950  -0.5944   2.7129
 HW4  C23  C  CR6   0   0.540  -8.0327  -0.0125   1.6385
 HW4  C24  C  CR16  0  -0.429  -8.4760   1.2359   1.2491
 HW4  C25  C  CR16  0  -0.224  -7.8855   1.8143   0.1328
 HW4  C26  C  CR16  0  -0.322  -6.8843   1.1512  -0.5623
 HW4  C22  C  CR16  0  -0.473  -7.0363  -0.6921   0.9647
 HW4  C21  C  CR6   0   0.153  -6.4486  -0.1090  -0.1551
 HW4  C14  C  CH2   0  -0.507  -5.3325  -0.8069  -0.8782
 HW4  C13  C  CH2   0  -0.411  -3.9565  -0.3727  -0.3701
 HW4  C12  C  CH2   0  -0.430  -2.8205  -1.0854  -1.0915
 HW4  C11  C  CH2   0  -0.461  -1.4464  -0.6796  -0.5738
 HW4  C10  C  CH2   0  -0.126  -0.3313  -1.3984  -1.3072
 HW4  O09  O  O2    0  -0.497   0.9029  -1.0611  -0.7206
 HW4  C3'  C  CH1   0   0.021   2.0271  -1.5994  -1.3809
 HW4  C2'  C  CH2   0  -0.308   2.2347  -3.0971  -1.0647
 HW4  N1'  N  NH1   0  -0.602   3.2771  -3.1950  -0.0329
 HW4  C5'  C  CH2   0  -0.290   3.5720  -1.8349   0.4057
 HW4  C4'  C  CH1   0  -0.279   3.2890  -0.9499  -0.8096
 HW4  C08  C  CH2   0  -0.491   3.1863   0.5501  -0.5442
 HW4  C06  C  CR6   0   0.266   4.4926   1.1111  -0.0565
 HW4  N01  N  N     0  -0.478   4.6980   1.0844   1.2614
 HW4  C02  C  CR6   0   0.442   5.8547   1.5350   1.7377
 HW4  N02  N  NH2   0  -0.840   6.0493   1.4378   3.0866
 HW4  C03  C  CR16  0  -0.447   6.8604   2.0518   0.9047
 HW4  C04  C  CR6   0   0.205   6.6497   2.0830  -0.4597
 HW4  C05  C  CR16  0  -0.427   5.4333   1.5981  -0.9490
 HW4  C07  C  CH3   0  -0.727   7.6965   2.6055  -1.3954
 HW4  H1   H  HCR6  0   0.276  -9.2589   1.7415   1.7985
 HW4  H2   H  HCR6  0   0.265  -8.2152   2.7913  -0.1953
 HW4  H3   H  HCR6  0   0.251  -6.4377   1.6157  -1.4333
 HW4  H4   H  HCR6  0   0.268  -6.7235  -1.6719   1.3061
 HW4  H5   H  HCH2  0   0.241  -5.4332  -1.8891  -0.7616
 HW4  H6   H  HCH2  0   0.243  -5.4017  -0.5994  -1.9495
 HW4  H7   H  HCH2  0   0.224  -3.8503   0.7098  -0.4930
 HW4  H8   H  HCH2  0   0.224  -3.8895  -0.5684   0.7047
 HW4  H9   H  HCH2  0   0.218  -2.9443  -2.1680  -0.9807
 HW4  H10  H  HCH2  0   0.218  -2.8883  -0.8798  -2.1651
 HW4  H11  H  HCH2  0   0.222  -1.3164   0.4020  -0.6764
 HW4  H12  H  HCH2  0   0.222  -1.3789  -0.9066   0.4947
 HW4  H13  H  HCH2  0   0.191  -0.5065  -2.4831  -1.2661
 HW4  H14  H  HCH2  0   0.194  -0.3386  -1.1228  -2.3723
 HW4  H15  H  HCH1  0   0.224   1.9356  -1.4251  -2.4617
 HW4  H16  H  HCH2  0   0.223   1.2973  -3.5431  -0.7195
 HW4  H17  H  HCH2  0   0.232   2.5320  -3.6472  -1.9590
 HW4  H18  H  HNH1  0   0.347   4.1117  -3.5782  -0.4545
 HW4  H20  H  HCH2  0   0.210   2.9216  -1.5476   1.2393
 HW4  H21  H  HCH2  0   0.236   4.5984  -1.7663   0.7650
 HW4  H22  H  HCH1  0   0.246   4.0880  -1.1205  -1.5414
 HW4  H23  H  HCH2  0   0.241   2.8886   1.0604  -1.4637
 HW4  H24  H  HCH2  0   0.240   2.4162   0.7450   0.2030
 HW4  H25  H  HNH2  0   0.378   5.2219   1.3204   3.6478
 HW4  H26  H  HNH2  0   0.387   6.7452   2.0351   3.5001
 HW4  H27  H  HCR6  0   0.254   7.7840   2.4226   1.3328
 HW4  H28  H  HCR6  0   0.240   5.2211   1.6091  -2.0113
 HW4  H29  H  HCH3  0   0.253   8.1885   1.7824  -1.9167
 HW4  H30  H  HCH3  0   0.248   7.2584   3.2498  -2.1579
 HW4  H31  H  HCH3  0   0.246   8.4649   3.1693  -0.8689

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
 HW4  C07  C04  single    1.498  0.020  1.498
 HW4  C04  C03  aromatic  1.381  0.020  1.381
 HW4  C04  C05  aromatic  1.398  0.020  1.398
 HW4  C03  C02  aromatic  1.404  0.020  1.404
 HW4  C05  C06  aromatic  1.385  0.020  1.385
 HW4  C02  N02  single    1.366  0.020  1.366
 HW4  C02  N01  aromatic  1.330  0.020  1.330
 HW4  C06  N01  aromatic  1.334  0.020  1.334
 HW4  C06  C08  single    1.503  0.020  1.503
 HW4  C4'  C5'  single    1.530  0.020  1.530
 HW4  C4'  C3'  single    1.530  0.020  1.530
 HW4  C4'  C08  single    1.527  0.020  1.527
 HW4  C5'  N1'  single    1.459  0.020  1.459
 HW4  C3'  O09  single    1.411  0.020  1.411
 HW4  C3'  C2'  single    1.545  0.020  1.545
 HW4  C10  O09  single    1.408  0.020  1.408
 HW4  C10  C11  single    1.516  0.020  1.516
 HW4  C25  C24  aromatic  1.389  0.020  1.389
 HW4  C25  C26  aromatic  1.387  0.020  1.387
 HW4  N1'  C2'  single    1.470  0.020  1.470
 HW4  C24  C23  aromatic  1.381  0.020  1.381
 HW4  C26  C21  aromatic  1.394  0.020  1.394
 HW4  C12  C11  single    1.524  0.020  1.524
 HW4  C12  C13  single    1.523  0.020  1.523
 HW4  C23  F23  single    1.345  0.020  1.345
 HW4  C23  C22  aromatic  1.382  0.020  1.382
 HW4  C21  C22  aromatic  1.393  0.020  1.393
 HW4  C21  C14  single    1.502  0.020  1.502
 HW4  C13  C14  single    1.530  0.020  1.530
 HW4  C24  H1   single    0.930  0.020  1.080
 HW4  C25  H2   single    0.930  0.020  1.080
 HW4  C26  H3   single    0.930  0.020  1.080
 HW4  C22  H4   single    0.930  0.020  1.080
 HW4  C14  H5   single    0.970  0.020  1.090
 HW4  C14  H6   single    0.970  0.020  1.090
 HW4  C13  H7   single    0.970  0.020  1.090
 HW4  C13  H8   single    0.970  0.020  1.090
 HW4  C12  H9   single    0.970  0.020  1.090
 HW4  C12  H10  single    0.970  0.020  1.090
 HW4  C11  H11  single    0.970  0.020  1.090
 HW4  C11  H12  single    0.970  0.020  1.090
 HW4  C10  H13  single    0.970  0.020  1.090
 HW4  C10  H14  single    0.970  0.020  1.090
 HW4  C3'  H15  single    0.970  0.020  1.090
 HW4  C2'  H16  single    0.970  0.020  1.090
 HW4  C2'  H17  single    0.970  0.020  1.090
 HW4  N1'  H18  single    0.890  0.020  1.040
 HW4  C5'  H20  single    0.970  0.020  1.090
 HW4  C5'  H21  single    0.970  0.020  1.090
 HW4  C4'  H22  single    0.970  0.020  1.090
 HW4  C08  H23  single    0.970  0.020  1.090
 HW4  C08  H24  single    0.970  0.020  1.090
 HW4  N02  H25  single    0.890  0.020  1.040
 HW4  N02  H26  single    0.890  0.020  1.040
 HW4  C03  H27  single    0.930  0.020  1.080
 HW4  C05  H28  single    0.930  0.020  1.080
 HW4  C07  H29  single    0.970  0.020  1.090
 HW4  C07  H30  single    0.970  0.020  1.090
 HW4  C07  H31  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
 HW4  C22  C23  C24  122.60  3.000
 HW4  C22  C23  F23  118.57  3.000
 HW4  C24  C23  F23  118.83  3.000
 HW4  H1   C24  C25  121.41  3.000
 HW4  H1   C24  C23  120.78  3.000
 HW4  C25  C24  C23  117.82  3.000
 HW4  H2   C25  C26  119.96  3.000
 HW4  H2   C25  C24  119.35  3.000
 HW4  C26  C25  C24  120.69  3.000
 HW4  H3   C26  C21  119.57  3.000
 HW4  H3   C26  C25  119.69  3.000
 HW4  C21  C26  C25  120.74  3.000
 HW4  H4   C22  C21  120.67  3.000
 HW4  H4   C22  C23  119.95  3.000
 HW4  C21  C22  C23  119.37  3.000
 HW4  C14  C21  C22  120.41  3.000
 HW4  C14  C21  C26  120.77  3.000
 HW4  C22  C21  C26  118.78  3.000
 HW4  H6   C14  H5   106.65  3.000
 HW4  H6   C14  C13  109.17  3.000
 HW4  H5   C14  C13  109.17  3.000
 HW4  H6   C14  C21  109.67  3.000
 HW4  H5   C14  C21  109.89  3.000
 HW4  C13  C14  C21  112.12  3.000
 HW4  H8   C13  H7   106.33  3.000
 HW4  H8   C13  C12  109.63  3.000
 HW4  H7   C13  C12  109.72  3.000
 HW4  H8   C13  C14  109.29  3.000
 HW4  H7   C13  C14  109.31  3.000
 HW4  C12  C13  C14  112.38  3.000
 HW4  H10  C12  H9   106.13  3.000
 HW4  H10  C12  C11  109.81  3.000
 HW4  H9   C12  C11  109.32  3.000
 HW4  H10  C12  C13  109.29  3.000
 HW4  H9   C12  C13  109.29  3.000
 HW4  C11  C12  C13  112.78  3.000
 HW4  H12  C11  H11  106.82  3.000
 HW4  H12  C11  C10  109.18  3.000
 HW4  H11  C11  C10  109.63  3.000
 HW4  H12  C11  C12  109.40  3.000
 HW4  H11  C11  C12  109.79  3.000
 HW4  C10  C11  C12  111.88  3.000
 HW4  H14  C10  H13  106.39  3.000
 HW4  H14  C10  O09  110.44  3.000
 HW4  H13  C10  O09  111.14  3.000
 HW4  H14  C10  C11  110.17  3.000
 HW4  H13  C10  C11  109.42  3.000
 HW4  O09  C10  C11  109.25  3.000
 HW4  C3'  O09  C10  114.35  3.000
 HW4  H15  C3'  C4'  111.64  3.000
 HW4  H15  C3'  C2'  111.49  3.000
 HW4  C4'  C3'  C2'  102.96  3.000
 HW4  H15  C3'  O09  109.49  3.000
 HW4  C2'  C3'  O09  112.41  3.000
 HW4  C4'  C3'  O09  108.69  3.000
 HW4  H17  C2'  H16  106.66  3.000
 HW4  H17  C2'  N1'  110.39  3.000
 HW4  H16  C2'  N1'  111.04  3.000
 HW4  H17  C2'  C3'  110.95  3.000
 HW4  H16  C2'  C3'  110.16  3.000
 HW4  N1'  C2'  C3'  107.67  3.000
 HW4  H18  N1'  C5'  108.17  3.000
 HW4  H18  N1'  C2'  108.55  3.000
 HW4  C5'  N1'  C2'  107.00  3.000
 HW4  H21  C5'  H20  106.97  3.000
 HW4  H21  C5'  C4'  113.56  3.000
 HW4  H20  C5'  C4'  110.05  3.000
 HW4  H21  C5'  N1'  110.38  3.000
 HW4  H20  C5'  N1'  110.68  3.000
 HW4  C4'  C5'  N1'  105.25  3.000
 HW4  H22  C4'  C08  108.53  3.000
 HW4  H22  C4'  C5'  107.78  3.000
 HW4  C08  C4'  C5'  116.28  3.000
 HW4  H22  C4'  C3'  106.60  3.000
 HW4  C08  C4'  C3'  115.25  3.000
 HW4  C5'  C4'  C3'  101.75  3.000
 HW4  H24  C08  H23  107.50  3.000
 HW4  H24  C08  C06  108.95  3.000
 HW4  H23  C08  C06  109.60  3.000
 HW4  H24  C08  C4'  110.01  3.000
 HW4  H23  C08  C4'  109.32  3.000
 HW4  C06  C08  C4'  111.38  3.000
 HW4  C05  C06  N01  122.62  3.000
 HW4  N01  C06  C08  116.54  3.000
 HW4  C05  C06  C08  120.83  3.000
 HW4  C02  N01  C06  118.75  3.000
 HW4  C03  C02  N02  120.65  3.000
 HW4  N02  C02  N01  116.97  3.000
 HW4  C03  C02  N01  122.36  3.000
 HW4  H26  N02  H25  114.12  3.000
 HW4  H26  N02  C02  117.52  3.000
 HW4  H25  N02  C02  116.21  3.000
 HW4  H27  C03  C04  120.85  3.000
 HW4  H27  C03  C02  120.13  3.000
 HW4  C04  C03  C02  119.02  3.000
 HW4  C07  C04  C05  120.69  3.000
 HW4  C05  C04  C03  118.09  3.000
 HW4  C07  C04  C03  121.22  3.000
 HW4  H28  C05  C04  120.67  3.000
 HW4  H28  C05  C06  120.16  3.000
 HW4  C04  C05  C06  119.17  3.000
 HW4  H31  C07  H30  108.41  3.000
 HW4  H31  C07  H29  107.66  3.000
 HW4  H30  C07  H29  107.03  3.000
 HW4  H31  C07  C04  111.82  3.000
 HW4  H30  C07  C04  111.23  3.000
 HW4  H29  C07  C04  110.50  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
 HW4  CONST_01  C26  C25  C24  C23     0.00   0.0  0
 HW4  CONST_02  C26  C21  C22  C23     0.00   0.0  0
 HW4  CONST_03  C21  C26  C25  C24     0.00   0.0  0
 HW4  CONST_04  C21  C22  C23  C24     0.00   0.0  0
 HW4  CONST_05  C22  C23  C24  C25     0.00   0.0  0
 HW4  CONST_06  C22  C21  C26  C25     0.00   0.0  0
 HW4  CONST_07  C03  C04  C05  C06     0.00   0.0  0
 HW4  CONST_08  C03  C02  N01  C06     0.00   0.0  0
 HW4  CONST_09  C04  C03  C02  N01     0.00   0.0  0
 HW4  CONST_10  C04  C05  C06  N01     0.00   0.0  0
 HW4  CONST_11  C05  C04  C03  C02     0.00   0.0  0
 HW4  CONST_12  C05  C06  N01  C02     0.00   0.0  0
 HW4  CONST_13  C25  C24  C23  F23   180.00   0.0  0
 HW4  CONST_14  C21  C22  C23  F23   180.00   0.0  0
 HW4  CONST_15  C14  C21  C22  C23   180.00   0.0  0
 HW4  CONST_16  C14  C21  C26  C25   180.00   0.0  0
 HW4  CONST_17  C04  C05  C06  C08   180.00   0.0  0
 HW4  CONST_18  C02  N01  C06  C08   180.00   0.0  0
 HW4  CONST_19  C07  C04  C05  C06   180.00   0.0  0
 HW4  CONST_20  N02  C02  N01  C06   180.00   0.0  0
 HW4  CONST_21  C07  C04  C03  C02   180.00   0.0  0
 HW4  CONST_22  C04  C03  C02  N02   180.00   0.0  0
 HW4  CONST_23  H2   C25  C24  C23   180.00   0.0  0
 HW4  CONST_24  H3   C26  C25  C24   180.00   0.0  0
 HW4  CONST_25  H4   C22  C23  C24   180.00   0.0  0
 HW4  CONST_26  H1   C24  C25  C26   180.00   0.0  0
 HW4  CONST_27  H27  C03  C02  N01   180.00   0.0  0
 HW4  CONST_28  H28  C05  C06  N01   180.00   0.0  0
 HW4  Var_01    C5'  N1'  C2'  C3'     7.35  30.0  1
 HW4  Var_02    C4'  C5'  N1'  C2'   -29.35  30.0  1
 HW4  Var_03    C05  C06  C08  C4'    90.06  30.0  2
 HW4  Var_04    C13  C14  C21  C26    84.88  30.0  2
 HW4  Var_05    H29  C07  C04  C03   104.79  30.0  2
 HW4  Var_06    C12  C13  C14  C21   179.52  30.0  1
 HW4  Var_07    H13  C10  O09  C3'    63.38  30.0  1
 HW4  Var_08    C11  C12  C13  C14  -178.89  30.0  1
 HW4  Var_09    C10  C11  C12  C13  -179.88  30.0  3
 HW4  Var_10    O09  C10  C11  C12  -175.61  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
 HW4  chir_01  C3'  C4'  O09  C2'  positiv
 HW4  chir_02  C4'  C08  C3'  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
 HW4  plan-1  F23  0.020
 HW4  plan-1  C23  0.020
 HW4  plan-1  C24  0.020
 HW4  plan-1  C25  0.020
 HW4  plan-1  C26  0.020
 HW4  plan-1  C22  0.020
 HW4  plan-1  C21  0.020
 HW4  plan-1  C14  0.020
 HW4  plan-1  H1   0.020
 HW4  plan-1  H2   0.020
 HW4  plan-1  H3   0.020
 HW4  plan-1  H4   0.020
 HW4  plan-2  C08  0.020
 HW4  plan-2  C06  0.020
 HW4  plan-2  N01  0.020
 HW4  plan-2  C02  0.020
 HW4  plan-2  N02  0.020
 HW4  plan-2  C03  0.020
 HW4  plan-2  C04  0.020
 HW4  plan-2  C05  0.020
 HW4  plan-2  C07  0.020
 HW4  plan-2  H27  0.020
 HW4  plan-2  H28  0.020
 HW4  plan-3  C02  0.020
 HW4  plan-3  N02  0.020
 HW4  plan-3  H25  0.020
 HW4  plan-3  H26  0.020

