# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 09:38:47 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: 6-{[(3R,4R)-4-{[5-(3-chloro-5-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]2OCCCCCc3cc(F)cc(Cl)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
 HW6  HW6  6-{[(3R,4R)-4-{[5-(3-chloro-5-fluorophenyl)pentyl]oxy}pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine  ligand  57  28  .  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_HW6
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
 HW6  F23  F   F     0  -0.311  -7.8993  -1.1347  -2.6509
 HW6  C23  C   CR6   0   0.549  -7.3176  -0.5846  -1.5755
 HW6  C24  C   CR16  0  -0.392  -7.7970   0.6283  -1.1209
 HW6  C22  C   CR16  0  -0.467  -6.2737  -1.2535  -0.9684
 HW6  C21  C   CR6   0   0.147  -5.6711  -0.6935   0.1540
 HW6  C26  C   CR16  0  -0.284  -6.1313   0.5295   0.6369
 HW6  C25  C   CR6   0  -0.002  -7.1801   1.1685  -0.0033
 HW6  CL2  CL  CL    0  -0.120  -7.7446   2.6869   0.6080
 HW6  C14  C   CH2   0  -0.510  -4.5045  -1.3749   0.8091
 HW6  C13  C   CH2   0  -0.412  -3.1668  -0.8879   0.2492
 HW6  C12  C   CH2   0  -0.430  -1.9818  -1.5918   0.8960
 HW6  C11  C   CH2   0  -0.463  -0.6416  -1.1200   0.3466
 HW6  C10  C   CH2   0  -0.126   0.5183  -1.8416   1.0026
 HW6  O09  O   O2    0  -0.497   1.7280  -1.3858   0.4476
 HW6  C3'  C   CR15  0   0.020   2.8802  -1.9328   1.0508
 HW6  C4'  C   CR15  0  -0.278   4.1051  -1.1415   0.5923
 HW6  C5'  C   CH2   0  -0.291   4.4690  -1.8508  -0.7114
 HW6  N1'  N   NR15  0  -0.601   4.2554  -3.2702  -0.4518
 HW6  C2'  C   CH2   0  -0.308   3.1819  -3.3635   0.5479
 HW6  C08  C   CH2   0  -0.489   3.9203   0.3679   0.4871
 HW6  C06  C   CR6   0   0.283   5.2080   1.0517   0.1194
 HW6  C05  C   CR16  0  -0.438   5.3487   1.7107  -1.0895
 HW6  C04  C   CR6   0   0.204   6.5768   2.3030  -1.4039
 HW6  C07  C   CH3   0  -0.725   6.7610   3.0471  -2.6910
 HW6  C03  C   CR16  0  -0.446   7.6018   2.2005  -0.4852
 HW6  C02  C   CR6   0   0.437   7.3701   1.5178   0.7209
 HW6  N01  N   N     0  -0.485   6.1991   0.9602   1.0081
 HW6  N02  N   NH2   0  -0.839   8.3447   1.4412   1.6760
 HW6  H1   H   HCR6  0   0.298  -8.6180   1.1269  -1.6178
 HW6  H2   H   HCR6  0   0.276  -5.9370  -2.2046  -1.3621
 HW6  H3   H   HCR6  0   0.274  -5.6719   0.9763   1.5094
 HW6  H4   H   HCH2  0   0.248  -4.5308  -1.1962   1.8870
 HW6  H5   H   HCH2  0   0.247  -4.5828  -2.4556   0.6673
 HW6  H6   H   HCH2  0   0.227  -3.1456  -1.0502  -0.8330
 HW6  H7   H   HCH2  0   0.227  -3.0821   0.1928   0.4003
 HW6  H8   H   HCH2  0   0.219  -2.0134  -1.4311   1.9789
 HW6  H9   H   HCH2  0   0.219  -2.0781  -2.6725   0.7462
 HW6  H10  H   HCH2  0   0.222  -0.6090  -1.2880  -0.7344
 HW6  H11  H   HCH2  0   0.222  -0.5370  -0.0421   0.5031
 HW6  H12  H   HCH2  0   0.193   0.5056  -1.6652   2.0887
 HW6  H13  H   HCH2  0   0.192   0.3996  -2.9259   0.8632
 HW6  H14  H   HCR5  0   0.223   2.7683  -1.9049   2.1433
 HW6  H15  H   HCR5  0   0.243   4.9018  -1.3414   1.3173
 HW6  H16  H   HCH2  0   0.211   3.8177  -1.5047  -1.5229
 HW6  H17  H   HCH2  0   0.237   5.4968  -1.6713  -1.0291
 HW6  H18  H   HNR5  0   0.348   5.1030  -3.6475  -0.0508
 HW6  H20  H   HCH2  0   0.232   3.4855  -4.0147   1.3690
 HW6  H21  H   HCH2  0   0.223   2.2802  -3.8047   0.1130
 HW6  H22  H   HCH2  0   0.240   3.1573   0.6046  -0.2555
 HW6  H23  H   HCH2  0   0.244   3.5679   0.7620   1.4455
 HW6  H24  H   HCR6  0   0.242   4.5213   1.7530  -1.7868
 HW6  H25  H   HCH3  0   0.254   6.3609   4.0592  -2.6040
 HW6  H26  H   HCH3  0   0.246   7.8125   3.1316  -2.9612
 HW6  H27  H   HCH3  0   0.247   6.2319   2.5624  -3.5110
 HW6  H28  H   HCR6  0   0.253   8.5739   2.6361  -0.6850
 HW6  H29  H   HNH2  0   0.386   9.2980   1.5535   1.3742
 HW6  H30  H   HNH2  0   0.378   8.2193   0.7271   2.3746

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
 HW6  F23  C23  single    1.341  0.020  1.341
 HW6  C23  C22  aromatic  1.381  0.020  1.381
 HW6  C23  C24  aromatic  1.381  0.020  1.381
 HW6  C22  C21  aromatic  1.392  0.020  1.392
 HW6  C24  C25  aromatic  1.386  0.020  1.386
 HW6  C21  C14  single    1.501  0.020  1.501
 HW6  C21  C26  aromatic  1.393  0.020  1.393
 HW6  C11  C12  single    1.523  0.020  1.523
 HW6  C11  C10  single    1.515  0.020  1.515
 HW6  C14  C13  single    1.530  0.020  1.530
 HW6  C13  C12  single    1.523  0.020  1.523
 HW6  C25  C26  aromatic  1.385  0.020  1.385
 HW6  C25  CL2  single    1.731  0.020  1.731
 HW6  C10  O09  single    1.407  0.020  1.407
 HW6  O09  C3'  single    1.411  0.020  1.411
 HW6  C08  C06  single    1.504  0.020  1.504
 HW6  C08  C4'  single    1.524  0.020  1.524
 HW6  C3'  C4'  single    1.529  0.020  1.529
 HW6  C3'  C2'  single    1.546  0.020  1.546
 HW6  C06  N01  aromatic  1.334  0.020  1.334
 HW6  C06  C05  aromatic  1.384  0.020  1.384
 HW6  N01  C02  aromatic  1.328  0.020  1.328
 HW6  C05  C04  aromatic  1.399  0.020  1.399
 HW6  C4'  C5'  single    1.528  0.020  1.528
 HW6  C02  N02  single    1.367  0.020  1.367
 HW6  C02  C03  aromatic  1.405  0.020  1.405
 HW6  C04  C03  aromatic  1.380  0.020  1.380
 HW6  C04  C07  single    1.498  0.020  1.498
 HW6  C2'  N1'  single    1.470  0.020  1.470
 HW6  C5'  N1'  single    1.459  0.020  1.459
 HW6  C24  H1   single    0.930  0.020  1.080
 HW6  C22  H2   single    0.930  0.020  1.080
 HW6  C26  H3   single    0.930  0.020  1.080
 HW6  C14  H4   single    0.970  0.020  1.090
 HW6  C14  H5   single    0.970  0.020  1.090
 HW6  C13  H6   single    0.970  0.020  1.090
 HW6  C13  H7   single    0.970  0.020  1.090
 HW6  C12  H8   single    0.970  0.020  1.090
 HW6  C12  H9   single    0.970  0.020  1.090
 HW6  C11  H10  single    0.970  0.020  1.090
 HW6  C11  H11  single    0.970  0.020  1.090
 HW6  C10  H12  single    0.970  0.020  1.090
 HW6  C10  H13  single    0.970  0.020  1.090
 HW6  C3'  H14  single    0.970  0.020  1.090
 HW6  C4'  H15  single    0.970  0.020  1.090
 HW6  C5'  H16  single    0.970  0.020  1.090
 HW6  C5'  H17  single    0.970  0.020  1.090
 HW6  N1'  H18  single    0.890  0.020  1.040
 HW6  C2'  H20  single    0.970  0.020  1.090
 HW6  C2'  H21  single    0.970  0.020  1.090
 HW6  C08  H22  single    0.970  0.020  1.090
 HW6  C08  H23  single    0.970  0.020  1.090
 HW6  C05  H24  single    0.930  0.020  1.080
 HW6  C07  H25  single    0.970  0.020  1.090
 HW6  C07  H26  single    0.970  0.020  1.090
 HW6  C07  H27  single    0.970  0.020  1.090
 HW6  C03  H28  single    0.930  0.020  1.080
 HW6  N02  H29  single    0.890  0.020  1.040
 HW6  N02  H30  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
 HW6  C22  C23  C24  122.90  3.000
 HW6  C24  C23  F23  118.28  3.000
 HW6  C22  C23  F23  118.82  3.000
 HW6  H1   C24  C25  121.92  3.000
 HW6  H1   C24  C23  121.14  3.000
 HW6  C25  C24  C23  116.94  3.000
 HW6  H2   C22  C21  120.80  3.000
 HW6  H2   C22  C23  120.04  3.000
 HW6  C21  C22  C23  119.16  3.000
 HW6  C14  C21  C26  120.26  3.000
 HW6  C26  C21  C22  119.32  3.000
 HW6  C14  C21  C22  120.38  3.000
 HW6  H3   C26  C25  120.23  3.000
 HW6  H3   C26  C21  120.10  3.000
 HW6  C25  C26  C21  119.68  3.000
 HW6  CL2  C25  C26  119.23  3.000
 HW6  CL2  C25  C24  118.77  3.000
 HW6  C26  C25  C24  122.00  3.000
 HW6  H5   C14  H4   106.73  3.000
 HW6  H5   C14  C13  109.27  3.000
 HW6  H4   C14  C13  109.27  3.000
 HW6  H5   C14  C21  109.67  3.000
 HW6  H4   C14  C21  109.72  3.000
 HW6  C13  C14  C21  112.04  3.000
 HW6  H7   C13  H6   106.35  3.000
 HW6  H7   C13  C12  109.73  3.000
 HW6  H6   C13  C12  109.66  3.000
 HW6  H7   C13  C14  109.35  3.000
 HW6  H6   C13  C14  109.37  3.000
 HW6  C12  C13  C14  112.21  3.000
 HW6  H9   C12  H8   106.11  3.000
 HW6  H9   C12  C11  109.49  3.000
 HW6  H8   C12  C11  109.66  3.000
 HW6  H9   C12  C13  109.25  3.000
 HW6  H8   C12  C13  109.26  3.000
 HW6  C11  C12  C13  112.85  3.000
 HW6  H11  C11  H10  106.84  3.000
 HW6  H11  C11  C10  109.51  3.000
 HW6  H10  C11  C10  109.37  3.000
 HW6  H11  C11  C12  109.73  3.000
 HW6  H10  C11  C12  109.57  3.000
 HW6  C10  C11  C12  111.70  3.000
 HW6  H13  C10  H12  106.37  3.000
 HW6  H13  C10  O09  111.24  3.000
 HW6  H12  C10  O09  110.33  3.000
 HW6  H13  C10  C11  109.40  3.000
 HW6  H12  C10  C11  110.00  3.000
 HW6  O09  C10  C11  109.46  3.000
 HW6  C3'  O09  C10  114.08  3.000
 HW6  H14  C3'  C2'  111.52  3.000
 HW6  H14  C3'  C4'  111.52  3.000
 HW6  C2'  C3'  C4'  103.01  3.000
 HW6  H14  C3'  O09  109.40  3.000
 HW6  C2'  C3'  O09  112.27  3.000
 HW6  C4'  C3'  O09  109.00  3.000
 HW6  H15  C4'  C08  108.33  3.000
 HW6  H15  C4'  C5'  107.86  3.000
 HW6  C08  C4'  C5'  115.44  3.000
 HW6  H15  C4'  C3'  106.85  3.000
 HW6  C5'  C4'  C3'  101.91  3.000
 HW6  C08  C4'  C3'  115.86  3.000
 HW6  H17  C5'  H16  106.99  3.000
 HW6  H17  C5'  N1'  110.49  3.000
 HW6  H16  C5'  N1'  110.61  3.000
 HW6  H17  C5'  C4'  113.36  3.000
 HW6  H16  C5'  C4'  110.09  3.000
 HW6  N1'  C5'  C4'  105.36  3.000
 HW6  H18  N1'  C2'  108.60  3.000
 HW6  H18  N1'  C5'  108.13  3.000
 HW6  C2'  N1'  C5'  106.84  3.000
 HW6  H21  C2'  H20  106.73  3.000
 HW6  H21  C2'  N1'  110.93  3.000
 HW6  H20  C2'  N1'  110.27  3.000
 HW6  H21  C2'  C3'  109.98  3.000
 HW6  H20  C2'  C3'  111.21  3.000
 HW6  N1'  C2'  C3'  107.75  3.000
 HW6  H23  C08  H22  107.03  3.000
 HW6  H23  C08  C06  109.04  3.000
 HW6  H22  C08  C06  109.51  3.000
 HW6  H23  C08  C4'  109.58  3.000
 HW6  H22  C08  C4'  110.28  3.000
 HW6  C06  C08  C4'  111.30  3.000
 HW6  N01  C06  C05  122.61  3.000
 HW6  C05  C06  C08  121.14  3.000
 HW6  N01  C06  C08  116.23  3.000
 HW6  H24  C05  C04  120.63  3.000
 HW6  H24  C05  C06  120.22  3.000
 HW6  C04  C05  C06  119.15  3.000
 HW6  C03  C04  C07  121.16  3.000
 HW6  C07  C04  C05  120.75  3.000
 HW6  C03  C04  C05  118.09  3.000
 HW6  H27  C07  H26  108.47  3.000
 HW6  H27  C07  H25  107.12  3.000
 HW6  H26  C07  H25  107.56  3.000
 HW6  H27  C07  C04  111.46  3.000
 HW6  H26  C07  C04  111.74  3.000
 HW6  H25  C07  C04  110.30  3.000
 HW6  H28  C03  C02  120.10  3.000
 HW6  H28  C03  C04  120.90  3.000
 HW6  C02  C03  C04  119.01  3.000
 HW6  N02  C02  N01  117.00  3.000
 HW6  N02  C02  C03  120.63  3.000
 HW6  N01  C02  C03  122.33  3.000
 HW6  C02  N01  C06  118.82  3.000
 HW6  H30  N02  H29  113.91  3.000
 HW6  H30  N02  C02  115.84  3.000
 HW6  H29  N02  C02  117.37  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
 HW6  CONST_01  C26  C21  C22  C23     0.00   0.0  0
 HW6  CONST_02  C26  C25  C24  C23     0.00   0.0  0
 HW6  CONST_03  C21  C22  C23  C24     0.00   0.0  0
 HW6  CONST_04  C21  C26  C25  C24     0.00   0.0  0
 HW6  CONST_05  C25  C24  C23  C22     0.00   0.0  0
 HW6  CONST_06  C25  C26  C21  C22     0.00   0.0  0
 HW6  CONST_07  C03  C02  N01  C06     0.00   0.0  0
 HW6  CONST_08  C03  C04  C05  C06     0.00   0.0  0
 HW6  CONST_09  C02  N01  C06  C05     0.00   0.0  0
 HW6  CONST_10  C02  C03  C04  C05     0.00   0.0  0
 HW6  CONST_11  N01  C06  C05  C04     0.00   0.0  0
 HW6  CONST_12  N01  C02  C03  C04     0.00   0.0  0
 HW6  CONST_13  C21  C22  C23  F23   180.00   0.0  0
 HW6  CONST_14  C25  C24  C23  F23   180.00   0.0  0
 HW6  CONST_15  C14  C21  C22  C23   180.00   0.0  0
 HW6  CONST_16  CL2  C25  C24  C23   180.00   0.0  0
 HW6  CONST_17  CL2  C25  C26  C21   180.00   0.0  0
 HW6  CONST_18  C14  C21  C26  C25   180.00   0.0  0
 HW6  CONST_19  C02  N01  C06  C08   180.00   0.0  0
 HW6  CONST_20  C04  C05  C06  C08   180.00   0.0  0
 HW6  CONST_21  N02  C02  N01  C06   180.00   0.0  0
 HW6  CONST_22  C07  C04  C05  C06   180.00   0.0  0
 HW6  CONST_23  N02  C02  C03  C04   180.00   0.0  0
 HW6  CONST_24  C02  C03  C04  C07   180.00   0.0  0
 HW6  CONST_25  H2   C22  C23  C24   180.00   0.0  0
 HW6  CONST_26  H3   C26  C25  C24   180.00   0.0  0
 HW6  CONST_27  H1   C24  C23  C22   180.00   0.0  0
 HW6  CONST_28  H28  C03  C04  C05   180.00   0.0  0
 HW6  CONST_29  H24  C05  C04  C03   180.00   0.0  0
 HW6  Var_01    C5'  N1'  C2'  C3'    -8.16  30.0  1
 HW6  Var_02    C2'  N1'  C5'  C4'    29.73  30.0  1
 HW6  Var_03    N01  C06  C08  C4'   -64.14  30.0  2
 HW6  Var_04    C13  C14  C21  C22    91.56  30.0  2
 HW6  Var_05    H25  C07  C04  C05    81.11  30.0  2
 HW6  Var_06    C12  C13  C14  C21  -179.13  30.0  3
 HW6  Var_07    H12  C10  O09  C3'    54.91  30.0  2
 HW6  Var_08    C11  C12  C13  C14   179.87  30.0  3
 HW6  Var_09    C10  C11  C12  C13  -179.71  30.0  1
 HW6  Var_10    O09  C10  C11  C12   179.11  30.0  3

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
 HW6  chir_01  C3'  O09  C4'  C2'  positiv
 HW6  chir_02  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
 HW6  plan-1  F23  0.020
 HW6  plan-1  C23  0.020
 HW6  plan-1  C24  0.020
 HW6  plan-1  C22  0.020
 HW6  plan-1  C21  0.020
 HW6  plan-1  C26  0.020
 HW6  plan-1  C25  0.020
 HW6  plan-1  CL2  0.020
 HW6  plan-1  C14  0.020
 HW6  plan-1  H1   0.020
 HW6  plan-1  H2   0.020
 HW6  plan-1  H3   0.020
 HW6  plan-2  C08  0.020
 HW6  plan-2  C06  0.020
 HW6  plan-2  C05  0.020
 HW6  plan-2  C04  0.020
 HW6  plan-2  C07  0.020
 HW6  plan-2  C03  0.020
 HW6  plan-2  C02  0.020
 HW6  plan-2  N01  0.020
 HW6  plan-2  N02  0.020
 HW6  plan-2  H24  0.020
 HW6  plan-2  H28  0.020
 HW6  plan-3  C02  0.020
 HW6  plan-3  N02  0.020
 HW6  plan-3  H29  0.020
 HW6  plan-3  H30  0.020

