# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 09:09:30 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 6-{[(3R,4R)-4-{[(3E)-4-(3-fluorophenyl)but-3-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]2OCC\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
 H5W  H5W  6-{[(3R,4R)-4-{[(3E)-4-(3-fluorophenyl)but-3-en-1-yl]oxy}pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine  ligand  52  26  .  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_H5W
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
 H5W  F23  F  F     0  -0.318   8.3702   1.3748  -0.9523
 H5W  C23  C  CR6   0   0.560   7.7259   0.3146  -0.4353
 H5W  C24  C  CR16  0  -0.427   8.4667  -0.6636   0.2042
 H5W  C25  C  CR16  0  -0.226   7.7837  -1.7516   0.7267
 H5W  C26  C  CR16  0  -0.331   6.4045  -1.8445   0.6074
 H5W  C22  C  CR16  0  -0.501   6.3565   0.2490  -0.5684
 H5W  C21  C  CR6   0   0.172   5.6697  -0.8479  -0.0390
 H5W  C13  C  C1    0  -0.297   4.2144  -0.9937  -0.1347
 H5W  C12  C  C1    0  -0.217   3.3597  -0.1374  -0.6961
 H5W  C11  C  CH2   0  -0.526   1.8834  -0.3520  -0.7614
 H5W  C10  C  CH2   0  -0.124   1.1308   0.7455  -0.0230
 H5W  O09  O  O2    0  -0.490  -0.2491   0.5200  -0.1737
 H5W  C3'  C  CH1   0   0.075  -1.0562   1.3910   0.5748
 H5W  C2'  C  CH2   0  -0.317  -1.0909   2.8248   0.0223
 H5W  N1'  N  NH1   0  -0.612  -2.4263   3.2682   0.3705
 H5W  C5'  C  CH2   0  -0.271  -3.2884   2.1604   0.0004
 H5W  C4'  C  CH1   0  -0.296  -2.5431   0.9415   0.5555
 H5W  C08  C  CH2   0  -0.493  -2.8268  -0.3350  -0.2337
 H5W  C06  C  CR6   0   0.280  -4.2864  -0.6893  -0.1701
 H5W  N01  N  N     0  -0.484  -4.7413  -1.0947   1.0183
 H5W  C02  C  CR6   0   0.437  -6.0297  -1.3904   1.1423
 H5W  N02  N  NH2   0  -0.839  -6.4670  -1.7556   2.3849
 H5W  C03  C  CR16  0  -0.448  -6.9297  -1.2967   0.0660
 H5W  C05  C  CR16  0  -0.430  -5.1015  -0.5736  -1.2812
 H5W  C04  C  CR6   0   0.205  -6.4612  -0.8858  -1.1644
 H5W  C07  C  CH3   0  -0.727  -7.3729  -0.7717  -2.3474
 H5W  H1   H  HCR6  0   0.280   9.5417  -0.5764   0.2892
 H5W  H2   H  HCR6  0   0.269   8.3340  -2.5348   1.2308
 H5W  H3   H  HCR6  0   0.259   5.8886  -2.7019   1.0209
 H5W  H4   H  HCR6  0   0.273   5.8356   1.0476  -1.0808
 H5W  H5   H  H     0   0.247   3.8170  -1.9051   0.3037
 H5W  H6   H  H     0   0.256   3.7228   0.7867  -1.1387
 H5W  H7   H  HCH2  0   0.247   1.5642  -0.3489  -1.8092
 H5W  H8   H  HCH2  0   0.245   1.6207  -1.3266  -0.3433
 H5W  H9   H  HCH2  0   0.203   1.4109   0.7387   1.0400
 H5W  H10  H  HCH2  0   0.204   1.4227   1.7264  -0.4229
 H5W  H11  H  HCH1  0   0.215  -0.7015   1.4098   1.6142
 H5W  H12  H  HCH2  0   0.232  -0.3312   3.4767   0.4578
 H5W  H13  H  HCH2  0   0.199  -0.9164   2.7830  -1.0656
 H5W  H14  H  HNH1  0   0.351  -2.6776   4.1219  -0.1100
 H5W  H16  H  HCH2  0   0.231  -4.2883   2.2764   0.4227
 H5W  H17  H  HCH2  0   0.195  -3.4042   2.0556  -1.0913
 H5W  H18  H  HCH1  0   0.252  -2.8613   0.7730   1.5867
 H5W  H19  H  HCH2  0   0.236  -2.5274  -0.2084  -1.2756
 H5W  H20  H  HCH2  0   0.247  -2.2426  -1.1637   0.1726
 H5W  H21  H  HNH2  0   0.378  -5.7556  -2.0708   3.0242
 H5W  H22  H  HNH2  0   0.387  -7.3232  -2.2820   2.4377
 H5W  H23  H  HCR6  0   0.254  -7.9746  -1.5450   0.2078
 H5W  H24  H  HCR6  0   0.241  -4.6912  -0.2448  -2.2280
 H5W  H25  H  HCH3  0   0.251  -7.3954   0.2527  -2.7222
 H5W  H26  H  HCH3  0   0.251  -7.0264  -1.4016  -3.1682
 H5W  H27  H  HCH3  0   0.246  -8.3927  -1.0642  -2.1023

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
 H5W  C07  C04  single    1.498  0.020  1.498
 H5W  C04  C03  aromatic  1.379  0.020  1.379
 H5W  C04  C05  aromatic  1.400  0.020  1.400
 H5W  C03  C02  aromatic  1.406  0.020  1.406
 H5W  C05  C06  aromatic  1.383  0.020  1.383
 H5W  C02  N02  single    1.367  0.020  1.367
 H5W  C02  N01  aromatic  1.328  0.020  1.328
 H5W  C5'  N1'  single    1.452  0.020  1.452
 H5W  C5'  C4'  single    1.533  0.020  1.533
 H5W  C06  N01  aromatic  1.336  0.020  1.336
 H5W  C06  C08  single    1.503  0.020  1.503
 H5W  N1'  C2'  single    1.450  0.020  1.450
 H5W  O09  C10  single    1.406  0.020  1.406
 H5W  O09  C3'  single    1.404  0.020  1.404
 H5W  C08  C4'  single    1.527  0.020  1.527
 H5W  C4'  C3'  single    1.553  0.020  1.553
 H5W  C10  C11  single    1.522  0.020  1.522
 H5W  C3'  C2'  single    1.537  0.020  1.537
 H5W  C11  C12  single    1.493  0.020  1.493
 H5W  C12  C13  double    1.334  0.020  1.334
 H5W  C13  C21  single    1.466  0.020  1.466
 H5W  C21  C26  aromatic  1.397  0.020  1.397
 H5W  C21  C22  aromatic  1.398  0.020  1.398
 H5W  C26  C25  aromatic  1.387  0.020  1.387
 H5W  C22  C23  aromatic  1.377  0.020  1.377
 H5W  C25  C24  aromatic  1.387  0.020  1.387
 H5W  C23  C24  aromatic  1.384  0.020  1.384
 H5W  C23  F23  single    1.344  0.020  1.344
 H5W  C24  H1   single    0.930  0.020  1.080
 H5W  C25  H2   single    0.930  0.020  1.080
 H5W  C26  H3   single    0.930  0.020  1.080
 H5W  C22  H4   single    0.930  0.020  1.080
 H5W  C13  H5   single    0.930  0.020  1.080
 H5W  C12  H6   single    0.930  0.020  1.080
 H5W  C11  H7   single    0.970  0.020  1.090
 H5W  C11  H8   single    0.970  0.020  1.090
 H5W  C10  H9   single    0.970  0.020  1.090
 H5W  C10  H10  single    0.970  0.020  1.090
 H5W  C3'  H11  single    0.970  0.020  1.090
 H5W  C2'  H12  single    0.970  0.020  1.090
 H5W  C2'  H13  single    0.970  0.020  1.090
 H5W  N1'  H14  single    0.890  0.020  1.040
 H5W  C5'  H16  single    0.970  0.020  1.090
 H5W  C5'  H17  single    0.970  0.020  1.090
 H5W  C4'  H18  single    0.970  0.020  1.090
 H5W  C08  H19  single    0.970  0.020  1.090
 H5W  C08  H20  single    0.970  0.020  1.090
 H5W  N02  H21  single    0.890  0.020  1.040
 H5W  N02  H22  single    0.890  0.020  1.040
 H5W  C03  H23  single    0.930  0.020  1.080
 H5W  C05  H24  single    0.930  0.020  1.080
 H5W  C07  H25  single    0.970  0.020  1.090
 H5W  C07  H26  single    0.970  0.020  1.090
 H5W  C07  H27  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
 H5W  C22  C23  C24  122.91  3.000
 H5W  C24  C23  F23  118.61  3.000
 H5W  C22  C23  F23  118.49  3.000
 H5W  H1   C24  C25  121.54  3.000
 H5W  H1   C24  C23  120.75  3.000
 H5W  C25  C24  C23  117.71  3.000
 H5W  H2   C25  C26  119.82  3.000
 H5W  H2   C25  C24  119.54  3.000
 H5W  C26  C25  C24  120.64  3.000
 H5W  H3   C26  C21  119.41  3.000
 H5W  H3   C26  C25  119.59  3.000
 H5W  C21  C26  C25  121.00  3.000
 H5W  H4   C22  C21  121.44  3.000
 H5W  H4   C22  C23  119.28  3.000
 H5W  C21  C22  C23  119.28  3.000
 H5W  C13  C21  C22  122.75  3.000
 H5W  C22  C21  C26  118.46  3.000
 H5W  C13  C21  C26  118.79  3.000
 H5W  H5   C13  C12  118.29  3.000
 H5W  H5   C13  C21  114.85  3.000
 H5W  C12  C13  C21  126.86  3.000
 H5W  H6   C12  C11  115.76  3.000
 H5W  H6   C12  C13  120.21  3.000
 H5W  C11  C12  C13  124.03  3.000
 H5W  H8   C11  H7   107.37  3.000
 H5W  H8   C11  C10  109.79  3.000
 H5W  H7   C11  C10  108.54  3.000
 H5W  H8   C11  C12  110.44  3.000
 H5W  H7   C11  C12  109.25  3.000
 H5W  C10  C11  C12  111.35  3.000
 H5W  H10  C10  H9   106.84  3.000
 H5W  H10  C10  O09  111.40  3.000
 H5W  H9   C10  O09  110.65  3.000
 H5W  H10  C10  C11  109.62  3.000
 H5W  H9   C10  C11  109.80  3.000
 H5W  O09  C10  C11  108.52  3.000
 H5W  C3'  O09  C10  114.05  3.000
 H5W  H11  C3'  C4'  109.01  3.000
 H5W  H11  C3'  C2'  109.36  3.000
 H5W  C4'  C3'  C2'  104.12  3.000
 H5W  H11  C3'  O09  109.24  3.000
 H5W  C2'  C3'  O09  113.59  3.000
 H5W  C4'  C3'  O09  111.36  3.000
 H5W  H13  C2'  H12  107.83  3.000
 H5W  H13  C2'  N1'  113.23  3.000
 H5W  H12  C2'  N1'  111.25  3.000
 H5W  H13  C2'  C3'  108.41  3.000
 H5W  H12  C2'  C3'  113.45  3.000
 H5W  N1'  C2'  C3'  102.70  3.000
 H5W  H14  N1'  C5'  112.05  3.000
 H5W  H14  N1'  C2'  111.90  3.000
 H5W  C5'  N1'  C2'  104.62  3.000
 H5W  H17  C5'  H16  107.27  3.000
 H5W  H17  C5'  C4'  109.51  3.000
 H5W  H16  C5'  C4'  112.95  3.000
 H5W  H17  C5'  N1'  112.78  3.000
 H5W  H16  C5'  N1'  111.36  3.000
 H5W  C4'  C5'  N1'  103.05  3.000
 H5W  H18  C4'  C08  107.74  3.000
 H5W  H18  C4'  C5'  108.84  3.000
 H5W  C08  C4'  C5'  112.78  3.000
 H5W  H18  C4'  C3'  108.16  3.000
 H5W  C08  C4'  C3'  115.22  3.000
 H5W  C5'  C4'  C3'  103.88  3.000
 H5W  H20  C08  H19  107.24  3.000
 H5W  H20  C08  C06  108.95  3.000
 H5W  H19  C08  C06  109.52  3.000
 H5W  H20  C08  C4'  110.03  3.000
 H5W  H19  C08  C4'  110.20  3.000
 H5W  C06  C08  C4'  110.82  3.000
 H5W  C05  C06  N01  122.66  3.000
 H5W  N01  C06  C08  116.10  3.000
 H5W  C05  C06  C08  121.23  3.000
 H5W  C02  N01  C06  118.77  3.000
 H5W  C03  C02  N02  120.59  3.000
 H5W  N02  C02  N01  117.06  3.000
 H5W  C03  C02  N01  122.33  3.000
 H5W  H22  N02  H21  113.82  3.000
 H5W  H22  N02  C02  117.36  3.000
 H5W  H21  N02  C02  115.77  3.000
 H5W  H23  C03  C04  120.84  3.000
 H5W  H23  C03  C02  120.12  3.000
 H5W  C04  C03  C02  119.03  3.000
 H5W  H24  C05  C04  120.57  3.000
 H5W  H24  C05  C06  120.30  3.000
 H5W  C04  C05  C06  119.13  3.000
 H5W  C07  C04  C05  120.55  3.000
 H5W  C05  C04  C03  118.09  3.000
 H5W  C07  C04  C03  121.37  3.000
 H5W  H27  C07  H26  108.16  3.000
 H5W  H27  C07  H25  108.08  3.000
 H5W  H26  C07  H25  106.86  3.000
 H5W  H27  C07  C04  111.83  3.000
 H5W  H26  C07  C04  110.91  3.000
 H5W  H25  C07  C04  110.82  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
 H5W  CONST_01  C26  C21  C22  C23    0.00   0.0  0
 H5W  CONST_02  C26  C25  C24  C23    0.00   0.0  0
 H5W  CONST_03  C21  C26  C25  C24    0.00   0.0  0
 H5W  CONST_04  C21  C22  C23  C24    0.00   0.0  0
 H5W  CONST_05  C22  C21  C26  C25    0.00   0.0  0
 H5W  CONST_06  C22  C23  C24  C25    0.00   0.0  0
 H5W  CONST_07  C03  C04  C05  C06    0.00   0.0  0
 H5W  CONST_08  C03  C02  N01  C06    0.00   0.0  0
 H5W  CONST_09  C04  C03  C02  N01    0.00   0.0  0
 H5W  CONST_10  C04  C05  C06  N01    0.00   0.0  0
 H5W  CONST_11  C05  C04  C03  C02    0.00   0.0  0
 H5W  CONST_12  C05  C06  N01  C02    0.00   0.0  0
 H5W  CONST_13  C21  C22  C23  F23  180.00   0.0  0
 H5W  CONST_14  C25  C24  C23  F23  180.00   0.0  0
 H5W  CONST_15  C13  C21  C22  C23  180.00   0.0  0
 H5W  CONST_16  C13  C21  C26  C25  180.00   0.0  0
 H5W  CONST_17  C04  C05  C06  C08  180.00   0.0  0
 H5W  CONST_18  C02  N01  C06  C08  180.00   0.0  0
 H5W  CONST_19  C07  C04  C05  C06  180.00   0.0  0
 H5W  CONST_20  N02  C02  N01  C06  180.00   0.0  0
 H5W  CONST_21  C07  C04  C03  C02  180.00   0.0  0
 H5W  CONST_22  C04  C03  C02  N02  180.00   0.0  0
 H5W  CONST_23  H2   C25  C24  C23  180.00   0.0  0
 H5W  CONST_24  H3   C26  C25  C24  180.00   0.0  0
 H5W  CONST_25  H4   C22  C23  C24  180.00   0.0  0
 H5W  CONST_26  H1   C24  C25  C26  180.00   0.0  0
 H5W  CONST_27  H23  C03  C02  N01  180.00   0.0  0
 H5W  CONST_28  H24  C05  C06  N01  180.00   0.0  0
 H5W  Var_01    C5'  N1'  C2'  C3'  -45.44  30.0  1
 H5W  Var_02    C4'  C5'  N1'  C2'   45.46  30.0  1
 H5W  Var_03    C05  C06  C08  C4'  109.78  30.0  2
 H5W  Var_04    C12  C13  C21  C26  179.01  30.0  3
 H5W  Var_05    H25  C07  C04  C03  119.60  30.0  2
 H5W  Var_06    C11  C12  C13  C21  179.84   0.0  2
 H5W  Var_07    H9   C10  O09  C3'   53.44  30.0  3
 H5W  Var_08    C10  C11  C12  C13  118.81  30.0  1
 H5W  Var_09    O09  C10  C11  C12  177.33  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
 H5W  chir_01  C3'  O09  C4'  C2'  positiv
 H5W  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
 H5W  plan-1  F23  0.020
 H5W  plan-1  C23  0.020
 H5W  plan-1  C24  0.020
 H5W  plan-1  C25  0.020
 H5W  plan-1  C26  0.020
 H5W  plan-1  C22  0.020
 H5W  plan-1  C21  0.020
 H5W  plan-1  C13  0.020
 H5W  plan-1  H1   0.020
 H5W  plan-1  H2   0.020
 H5W  plan-1  H3   0.020
 H5W  plan-1  H4   0.020
 H5W  plan-2  C08  0.020
 H5W  plan-2  C06  0.020
 H5W  plan-2  N01  0.020
 H5W  plan-2  C02  0.020
 H5W  plan-2  N02  0.020
 H5W  plan-2  C03  0.020
 H5W  plan-2  C05  0.020
 H5W  plan-2  C04  0.020
 H5W  plan-2  C07  0.020
 H5W  plan-2  H23  0.020
 H5W  plan-2  H24  0.020
 H5W  plan-3  C02  0.020
 H5W  plan-3  N02  0.020
 H5W  plan-3  H21  0.020
 H5W  plan-3  H22  0.020
 H5W  plan-4  C21  0.020
 H5W  plan-4  C13  0.020
 H5W  plan-4  C12  0.020
 H5W  plan-4  C11  0.020
 H5W  plan-4  H5   0.020
 H5W  plan-4  H6   0.020

