# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 06:08:37 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: 6-{[(3S,4S)-4-{[(4E)-5-(3-fluorophenyl)pent-4-en-1-yl]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]2OCCC\C=C\c3cccc(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
 HW5  HW5  6-{[(3S,4S)-4-{[(4E)-5-(3-fluorophenyl)pent-4-en-1-yl]oxy}pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine  ligand  55  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_HW5
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
 HW5  F23  F  F     0  -0.317  -8.8533  -2.0446   0.1096
 HW5  C23  C  CR6   0   0.544  -7.9990  -1.2191  -0.5189
 HW5  C22  C  CR16  0  -0.484  -6.9241  -0.7201   0.1895
 HW5  C21  C  CR6   0   0.168  -6.0189   0.1376  -0.4390
 HW5  C26  C  CR16  0  -0.341  -6.2378   0.4676  -1.7811
 HW5  C25  C  CR16  0  -0.219  -7.3252  -0.0470  -2.4660
 HW5  C24  C  CR16  0  -0.429  -8.2267  -0.9031  -1.8426
 HW5  C14  C  C1    0  -0.299  -4.8867   0.6447   0.3424
 HW5  C13  C  C1    0  -0.201  -3.9179   1.4529  -0.0910
 HW5  C12  C  CH2   0  -0.494  -2.7780   1.9256   0.7489
 HW5  C11  C  CH2   0  -0.464  -1.4336   1.4196   0.2236
 HW5  C10  C  CH2   0  -0.128  -0.2733   2.0032   1.0059
 HW5  O09  O  O2    0  -0.496   0.9299   1.5095   0.4736
 HW5  C3'  C  CH1   0   0.016   2.0881   1.8951   1.1817
 HW5  C4'  C  CH1   0  -0.276   3.2585   1.0377   0.6977
 HW5  C5'  C  CH2   0  -0.285   3.6948   1.7984  -0.5557
 HW5  N1'  N  NH1   0  -0.605   3.5741   3.2125  -0.2109
 HW5  C2'  C  CH2   0  -0.302   2.5398   3.3250   0.8283
 HW5  C08  C  CH2   0  -0.487   2.9388  -0.4447   0.5212
 HW5  C06  C  CR6   0   0.265   4.1666  -1.2478   0.1965
 HW5  C05  C  CR16  0  -0.430   4.8615  -1.9161   1.1905
 HW5  C04  C  CR6   0   0.204   6.0215  -2.6213   0.8549
 HW5  C07  C  CH3   0  -0.726   6.8098  -3.3414   1.9062
 HW5  C03  C  CR16  0  -0.447   6.4221  -2.6220  -0.4662
 HW5  C02  C  CR6   0   0.440   5.6558  -1.9197  -1.4111
 HW5  N01  N  N     0  -0.474   4.5549  -1.2531  -1.0803
 HW5  N02  N  NH2   0  -0.839   5.9943  -1.9385  -2.7359
 HW5  H1   H  HCR6  0   0.274  -6.7868  -0.9979   1.2275
 HW5  H2   H  HCR6  0   0.256  -5.5580   1.1301  -2.3000
 HW5  H3   H  HCR6  0   0.269  -7.4794   0.2194  -3.5031
 HW5  H4   H  HCR6  0   0.279  -9.0775  -1.3103  -2.3725
 HW5  H5   H  H     0   0.244  -4.8542   0.3127   1.3769
 HW5  H7   H  H     0   0.251  -3.9155   1.7986  -1.1215
 HW5  H9   H  HCH2  0   0.239  -2.7674   3.0213   0.7493
 HW5  H10  H  HCH2  0   0.241  -2.9178   1.6108   1.7863
 HW5  H11  H  HCH2  0   0.232  -1.4058   0.3283   0.2818
 HW5  H12  H  HCH2  0   0.231  -1.3282   1.6857  -0.8322
 HW5  H13  H  HCH2  0   0.194  -0.3158   3.1009   0.9549
 HW5  H14  H  HCH2  0   0.196  -0.3614   1.7370   2.0699
 HW5  H15  H  HCH1  0   0.226   1.9172   1.7789   2.2608
 HW5  H16  H  HCH1  0   0.246   4.0529   1.1413   1.4471
 HW5  H17  H  HCH2  0   0.236   4.7119   1.5678  -0.8700
 HW5  H18  H  HCH2  0   0.207   3.0357   1.5466  -1.3940
 HW5  H19  H  HNH1  0   0.348   4.4553   3.5246   0.1718
 HW5  H21  H  HCH2  0   0.222   1.6892   3.9194   0.4801
 HW5  H22  H  HCH2  0   0.230   2.9347   3.8325   1.7106
 HW5  H23  H  HCH2  0   0.240   2.4878  -0.8268   1.4404
 HW5  H24  H  HCH2  0   0.240   2.2062  -0.5736  -0.2771
 HW5  H25  H  HCR6  0   0.240   4.5087  -1.8904   2.2142
 HW5  H26  H  HCH3  0   0.253   7.3321  -2.6306   2.5489
 HW5  H27  H  HCH3  0   0.249   6.1579  -3.9337   2.5484
 HW5  H28  H  HCH3  0   0.246   7.5550  -4.0038   1.4685
 HW5  H29  H  HCR6  0   0.254   7.3143  -3.1535  -0.7758
 HW5  H30  H  HNH2  0   0.386   6.9504  -2.1567  -2.9623
 HW5  H31  H  HNH2  0   0.378   5.6025  -1.2008  -3.2984

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
 HW5  C07  C04  single    1.498  0.020  1.498
 HW5  C04  C03  aromatic  1.380  0.020  1.380
 HW5  C04  C05  aromatic  1.398  0.020  1.398
 HW5  C03  C02  aromatic  1.405  0.020  1.405
 HW5  C05  C06  aromatic  1.385  0.020  1.385
 HW5  C02  N02  single    1.368  0.020  1.368
 HW5  C02  N01  aromatic  1.329  0.020  1.329
 HW5  C06  N01  aromatic  1.335  0.020  1.335
 HW5  C06  C08  single    1.503  0.020  1.503
 HW5  C4'  C5'  single    1.530  0.020  1.530
 HW5  C4'  C08  single    1.527  0.020  1.527
 HW5  C4'  C3'  single    1.529  0.020  1.529
 HW5  C5'  N1'  single    1.461  0.020  1.461
 HW5  C3'  O09  single    1.411  0.020  1.411
 HW5  C3'  C2'  single    1.541  0.020  1.541
 HW5  C10  O09  single    1.405  0.020  1.405
 HW5  C10  C11  single    1.516  0.020  1.516
 HW5  N1'  C2'  single    1.471  0.020  1.471
 HW5  C11  C12  single    1.530  0.020  1.530
 HW5  C12  C13  single    1.493  0.020  1.493
 HW5  C25  C24  aromatic  1.391  0.020  1.391
 HW5  C25  C26  aromatic  1.384  0.020  1.384
 HW5  C24  C23  aromatic  1.380  0.020  1.380
 HW5  C26  C21  aromatic  1.399  0.020  1.399
 HW5  C23  F23  single    1.344  0.020  1.344
 HW5  C23  C22  aromatic  1.381  0.020  1.381
 HW5  C21  C22  aromatic  1.396  0.020  1.396
 HW5  C21  C14  single    1.466  0.020  1.466
 HW5  C13  C14  double    1.334  0.020  1.334
 HW5  C22  H1   single    0.930  0.020  1.080
 HW5  C26  H2   single    0.930  0.020  1.080
 HW5  C25  H3   single    0.930  0.020  1.080
 HW5  C24  H4   single    0.930  0.020  1.080
 HW5  C14  H5   single    0.930  0.020  1.080
 HW5  C13  H7   single    0.930  0.020  1.080
 HW5  C12  H9   single    0.970  0.020  1.090
 HW5  C12  H10  single    0.970  0.020  1.090
 HW5  C11  H11  single    0.970  0.020  1.090
 HW5  C11  H12  single    0.970  0.020  1.090
 HW5  C10  H13  single    0.970  0.020  1.090
 HW5  C10  H14  single    0.970  0.020  1.090
 HW5  C3'  H15  single    0.970  0.020  1.090
 HW5  C4'  H16  single    0.970  0.020  1.090
 HW5  C5'  H17  single    0.970  0.020  1.090
 HW5  C5'  H18  single    0.970  0.020  1.090
 HW5  N1'  H19  single    0.890  0.020  1.040
 HW5  C2'  H21  single    0.970  0.020  1.090
 HW5  C2'  H22  single    0.970  0.020  1.090
 HW5  C08  H23  single    0.970  0.020  1.090
 HW5  C08  H24  single    0.970  0.020  1.090
 HW5  C05  H25  single    0.930  0.020  1.080
 HW5  C07  H26  single    0.970  0.020  1.090
 HW5  C07  H27  single    0.970  0.020  1.090
 HW5  C07  H28  single    0.970  0.020  1.090
 HW5  C03  H29  single    0.930  0.020  1.080
 HW5  N02  H30  single    0.890  0.020  1.040
 HW5  N02  H31  single    0.890  0.020  1.040

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
 HW5  C24  C23  C22  122.54  3.000
 HW5  C22  C23  F23  118.48  3.000
 HW5  C24  C23  F23  118.98  3.000
 HW5  H1   C22  C21  120.44  3.000
 HW5  H1   C22  C23  119.85  3.000
 HW5  C21  C22  C23  119.71  3.000
 HW5  C14  C21  C26  123.39  3.000
 HW5  C14  C21  C22  118.24  3.000
 HW5  C26  C21  C22  118.37  3.000
 HW5  H2   C26  C25  118.95  3.000
 HW5  H2   C26  C21  120.41  3.000
 HW5  C25  C26  C21  120.65  3.000
 HW5  H3   C25  C24  119.27  3.000
 HW5  H3   C25  C26  119.65  3.000
 HW5  C24  C25  C26  121.08  3.000
 HW5  H4   C24  C25  121.46  3.000
 HW5  H4   C24  C23  120.89  3.000
 HW5  C25  C24  C23  117.65  3.000
 HW5  H5   C14  C13  118.20  3.000
 HW5  H5   C14  C21  115.13  3.000
 HW5  C13  C14  C21  126.67  3.000
 HW5  H7   C13  C12  115.53  3.000
 HW5  H7   C13  C14  120.16  3.000
 HW5  C12  C13  C14  124.30  3.000
 HW5  H10  C12  H9   106.79  3.000
 HW5  H10  C12  C11  110.06  3.000
 HW5  H9   C12  C11  108.81  3.000
 HW5  H10  C12  C13  110.19  3.000
 HW5  H9   C12  C13  108.92  3.000
 HW5  C11  C12  C13  111.91  3.000
 HW5  H12  C11  H11  106.97  3.000
 HW5  H12  C11  C10  109.31  3.000
 HW5  H11  C11  C10  109.71  3.000
 HW5  H12  C11  C12  109.61  3.000
 HW5  H11  C11  C12  109.54  3.000
 HW5  C10  C11  C12  111.60  3.000
 HW5  H14  C10  H13  106.45  3.000
 HW5  H14  C10  O09  110.48  3.000
 HW5  H13  C10  O09  111.48  3.000
 HW5  H14  C10  C11  110.15  3.000
 HW5  H13  C10  C11  109.31  3.000
 HW5  O09  C10  C11  108.94  3.000
 HW5  C3'  O09  C10  114.62  3.000
 HW5  H15  C3'  C2'  111.66  3.000
 HW5  H15  C3'  C4'  111.75  3.000
 HW5  C2'  C3'  C4'  102.91  3.000
 HW5  H15  C3'  O09  109.65  3.000
 HW5  C2'  C3'  O09  112.28  3.000
 HW5  C4'  C3'  O09  108.42  3.000
 HW5  H16  C4'  C08  108.80  3.000
 HW5  H16  C4'  C5'  107.83  3.000
 HW5  C08  C4'  C5'  116.61  3.000
 HW5  H16  C4'  C3'  106.56  3.000
 HW5  C08  C4'  C3'  114.88  3.000
 HW5  C5'  C4'  C3'  101.47  3.000
 HW5  H18  C5'  H17  107.00  3.000
 HW5  H18  C5'  N1'  110.70  3.000
 HW5  H17  C5'  N1'  110.50  3.000
 HW5  H18  C5'  C4'  109.94  3.000
 HW5  H17  C5'  C4'  113.42  3.000
 HW5  N1'  C5'  C4'  105.34  3.000
 HW5  H19  N1'  C2'  108.80  3.000
 HW5  H19  N1'  C5'  108.45  3.000
 HW5  C2'  N1'  C5'  107.40  3.000
 HW5  H22  C2'  H21  106.60  3.000
 HW5  H22  C2'  N1'  110.62  3.000
 HW5  H21  C2'  N1'  111.31  3.000
 HW5  H22  C2'  C3'  110.61  3.000
 HW5  H21  C2'  C3'  110.44  3.000
 HW5  N1'  C2'  C3'  107.30  3.000
 HW5  H24  C08  H23  107.27  3.000
 HW5  H24  C08  C06  109.11  3.000
 HW5  H23  C08  C06  109.40  3.000
 HW5  H24  C08  C4'  109.87  3.000
 HW5  H23  C08  C4'  109.19  3.000
 HW5  C06  C08  C4'  111.89  3.000
 HW5  N01  C06  C05  122.60  3.000
 HW5  N01  C06  C08  116.53  3.000
 HW5  C05  C06  C08  120.85  3.000
 HW5  H25  C05  C04  120.60  3.000
 HW5  H25  C05  C06  120.23  3.000
 HW5  C04  C05  C06  119.17  3.000
 HW5  C03  C04  C07  121.23  3.000
 HW5  C03  C04  C05  118.08  3.000
 HW5  C07  C04  C05  120.69  3.000
 HW5  H28  C07  H27  108.39  3.000
 HW5  H28  C07  H26  107.78  3.000
 HW5  H27  C07  H26  107.04  3.000
 HW5  H28  C07  C04  111.74  3.000
 HW5  H27  C07  C04  111.09  3.000
 HW5  H26  C07  C04  110.61  3.000
 HW5  H29  C03  C02  120.14  3.000
 HW5  H29  C03  C04  120.84  3.000
 HW5  C02  C03  C04  119.02  3.000
 HW5  N02  C02  N01  116.95  3.000
 HW5  N01  C02  C03  122.36  3.000
 HW5  N02  C02  C03  120.65  3.000
 HW5  C02  N01  C06  118.76  3.000
 HW5  H31  N02  H30  113.75  3.000
 HW5  H31  N02  C02  115.76  3.000
 HW5  H30  N02  C02  117.14  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
 HW5  CONST_01  C26  C25  C24  C23     0.00   0.0  0
 HW5  CONST_02  C26  C21  C22  C23     0.00   0.0  0
 HW5  CONST_03  C25  C24  C23  C22     0.00   0.0  0
 HW5  CONST_04  C25  C26  C21  C22     0.00   0.0  0
 HW5  CONST_05  C24  C25  C26  C21     0.00   0.0  0
 HW5  CONST_06  C24  C23  C22  C21     0.00   0.0  0
 HW5  CONST_07  C03  C04  C05  C06     0.00   0.0  0
 HW5  CONST_08  C03  C02  N01  C06     0.00   0.0  0
 HW5  CONST_09  C02  C03  C04  C05     0.00   0.0  0
 HW5  CONST_10  C02  N01  C06  C05     0.00   0.0  0
 HW5  CONST_11  N01  C02  C03  C04     0.00   0.0  0
 HW5  CONST_12  N01  C06  C05  C04     0.00   0.0  0
 HW5  CONST_13  C25  C24  C23  F23   180.00   0.0  0
 HW5  CONST_14  C21  C22  C23  F23   180.00   0.0  0
 HW5  CONST_15  C14  C21  C22  C23   180.00   0.0  0
 HW5  CONST_16  C14  C21  C26  C25   180.00   0.0  0
 HW5  CONST_17  C04  C05  C06  C08   180.00   0.0  0
 HW5  CONST_18  C02  N01  C06  C08   180.00   0.0  0
 HW5  CONST_19  C07  C04  C05  C06   180.00   0.0  0
 HW5  CONST_20  N02  C02  N01  C06   180.00   0.0  0
 HW5  CONST_21  N02  C02  C03  C04   180.00   0.0  0
 HW5  CONST_22  C02  C03  C04  C07   180.00   0.0  0
 HW5  CONST_23  H3   C25  C24  C23   180.00   0.0  0
 HW5  CONST_24  H4   C24  C23  C22   180.00   0.0  0
 HW5  CONST_25  H2   C26  C21  C22   180.00   0.0  0
 HW5  CONST_26  H1   C22  C21  C26   180.00   0.0  0
 HW5  CONST_27  H29  C03  C04  C05   180.00   0.0  0
 HW5  CONST_28  H25  C05  C04  C03   180.00   0.0  0
 HW5  Var_01    C5'  N1'  C2'  C3'     3.74  30.0  1
 HW5  Var_02    C2'  N1'  C5'  C4'   -26.90  30.0  1
 HW5  Var_03    C05  C06  C08  C4'    96.45  30.0  3
 HW5  Var_04    C13  C14  C21  C22   179.01  30.0  2
 HW5  Var_05    H26  C07  C04  C05   -71.72  30.0  2
 HW5  Var_06    C12  C13  C14  C21  -179.27   0.0  2
 HW5  Var_07    H13  C10  O09  C3'    64.04  30.0  3
 HW5  Var_08    C11  C12  C13  C14   116.27  30.0  1
 HW5  Var_09    C10  C11  C12  C13   174.91  30.0  1
 HW5  Var_10    O09  C10  C11  C12  -179.65  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
 HW5  chir_01  C3'  C4'  O09  C2'  positiv
 HW5  chir_02  C4'  C3'  C08  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
 HW5  plan-1  F23  0.020
 HW5  plan-1  C23  0.020
 HW5  plan-1  C22  0.020
 HW5  plan-1  C21  0.020
 HW5  plan-1  C26  0.020
 HW5  plan-1  C25  0.020
 HW5  plan-1  C24  0.020
 HW5  plan-1  C14  0.020
 HW5  plan-1  H1   0.020
 HW5  plan-1  H2   0.020
 HW5  plan-1  H3   0.020
 HW5  plan-1  H4   0.020
 HW5  plan-2  C08  0.020
 HW5  plan-2  C06  0.020
 HW5  plan-2  C05  0.020
 HW5  plan-2  C04  0.020
 HW5  plan-2  C07  0.020
 HW5  plan-2  C03  0.020
 HW5  plan-2  C02  0.020
 HW5  plan-2  N01  0.020
 HW5  plan-2  N02  0.020
 HW5  plan-2  H25  0.020
 HW5  plan-2  H29  0.020
 HW5  plan-3  C02  0.020
 HW5  plan-3  N02  0.020
 HW5  plan-3  H30  0.020
 HW5  plan-3  H31  0.020
 HW5  plan-4  C21  0.020
 HW5  plan-4  C14  0.020
 HW5  plan-4  C13  0.020
 HW5  plan-4  C12  0.020
 HW5  plan-4  H5   0.020
 HW5  plan-4  H7   0.020

