# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 16:05:04 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 6-({(3R,4R)-4-[4-(3-chloro-5-fluorophenoxy)butoxy]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]2OCCCCOc3cc(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
 HW7  HW7  6-({(3R,4R)-4-[4-(3-chloro-5-fluorophenoxy)butoxy]pyrrolidin-3-yl}methyl)-4-methylpyridin-2-amine  ligand  55  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_HW7
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
 HW7  CL2  CL  CL    0  -0.112   6.9719   2.9407   1.1148
 HW7  C25  C   CR6   0  -0.002   6.8854   1.3151   0.5278
 HW7  C24  C   CR16  0  -0.404   8.0624   0.6508   0.2360
 HW7  C23  C   CR6   0   0.544   7.9395  -0.6468  -0.2315
 HW7  F23  F   F     0  -0.309   9.0588  -1.3215  -0.5230
 HW7  C22  C   CR16  0  -0.503   6.7296  -1.2758  -0.4094
 HW7  C26  C   CR16  0  -0.353   5.6344   0.7356   0.3712
 HW7  C21  C   CR6   0   0.413   5.5611  -0.5743  -0.1011
 HW7  O14  O   O2    0  -0.469   4.4148  -1.2386  -0.2882
 HW7  C13  C   CH2   0  -0.178   3.1781  -0.5889  -0.0171
 HW7  C12  C   CH2   0  -0.465   2.0642  -1.5757  -0.2912
 HW7  C11  C   CH2   0  -0.471   0.6971  -0.9612  -0.0125
 HW7  C10  C   CH2   0  -0.124  -0.4154  -1.9593  -0.2684
 HW7  O09  O   O2    0  -0.496  -1.6504  -1.3676   0.0503
 HW7  C3'  C   CH1   0   0.028  -2.7689  -2.1656  -0.2700
 HW7  C2'  C   CH2   0  -0.319  -2.9840  -3.3143   0.7517
 HW7  C4'  C   CH1   0  -0.283  -4.0435  -1.3286  -0.1323
 HW7  C5'  C   CH2   0  -0.299  -4.4502  -1.5908   1.3188
 HW7  N1'  N   NH1   0  -0.594  -4.1814  -3.0051   1.5386
 HW7  C08  C   CH2   0  -0.489  -3.9223   0.1389  -0.5271
 HW7  C06  C   CR6   0   0.282  -5.2532   0.8343  -0.4484
 HW7  N01  N   N     0  -0.485  -6.1929   0.4073  -1.2954
 HW7  C05  C   CR16  0  -0.435  -5.4789   1.8440   0.4695
 HW7  C04  C   CR6   0   0.205  -6.7413   2.4465   0.5238
 HW7  C07  C   CH3   0  -0.726  -7.0152   3.5583   1.4898
 HW7  C03  C   CR16  0  -0.449  -7.7127   1.9964  -0.3459
 HW7  C02  C   CR6   0   0.438  -7.3961   0.9668  -1.2493
 HW7  N02  N   NH2   0  -0.839  -8.3470   0.4704  -2.0954
 HW7  H1   H   HCR6  0   0.298   9.0311   1.1122   0.3662
 HW7  H2   H   HCR6  0   0.292   6.6801  -2.2919  -0.7790
 HW7  H3   H   HCR6  0   0.304   4.7483   1.3022   0.6173
 HW7  H4   H   HCH2  0   0.229   3.1442  -0.2607   1.0277
 HW7  H5   H   HCH2  0   0.230   3.0740   0.2992  -0.6504
 HW7  H6   H   HCH2  0   0.237   2.1179  -1.9080  -1.3316
 HW7  H7   H   HCH2  0   0.236   2.2054  -2.4595   0.3373
 HW7  H8   H   HCH2  0   0.230   0.6487  -0.6231   1.0268
 HW7  H9   H   HCH2  0   0.230   0.5471  -0.0807  -0.6436
 HW7  H10  H   HCH2  0   0.196  -0.4017  -2.2730  -1.3226
 HW7  H11  H   HCH2  0   0.194  -0.2398  -2.8644   0.3306
 HW7  H12  H   HCH1  0   0.220  -2.6576  -2.5520  -1.2924
 HW7  H13  H   HCH2  0   0.236  -3.0920  -4.2840   0.2647
 HW7  H14  H   HCH2  0   0.225  -2.1090  -3.3843   1.4058
 HW7  H15  H   HCH1  0   0.244  -4.8024  -1.7923  -0.7722
 HW7  H16  H   HCH2  0   0.214  -3.8426  -0.9824   1.9990
 HW7  H17  H   HCH2  0   0.240  -5.4962  -1.3613   1.5236
 HW7  H18  H   HNH1  0   0.346  -4.9586  -3.5343   1.1654
 HW7  H20  H   HCH2  0   0.240  -3.2063   0.6482   0.1195
 HW7  H21  H   HCH2  0   0.244  -3.5423   0.2144  -1.5503
 HW7  H22  H   HCR6  0   0.241  -4.6863   2.1610   1.1353
 HW7  H23  H   HCH3  0   0.253  -6.4866   4.4648   1.1893
 HW7  H24  H   HCH3  0   0.246  -8.0767   3.7953   1.5440
 HW7  H25  H   HCH3  0   0.249  -6.6686   3.3037   2.4916
 HW7  H26  H   HCR6  0   0.254  -8.7080   2.4248  -0.3390
 HW7  H27  H   HNH2  0   0.379  -8.0083  -0.0470  -2.8903
 HW7  H28  H   HNH2  0   0.387  -9.1394   1.0572  -2.2963

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
 HW7  F23  C23  single    1.339  0.020  1.339
 HW7  C23  C22  aromatic  1.375  0.020  1.375
 HW7  C23  C24  aromatic  1.385  0.020  1.385
 HW7  C22  C21  aromatic  1.397  0.020  1.397
 HW7  C24  C25  aromatic  1.383  0.020  1.383
 HW7  C21  O14  single    1.338  0.020  1.338
 HW7  C21  C26  aromatic  1.394  0.020  1.394
 HW7  C11  C12  single    1.525  0.020  1.525
 HW7  C11  C10  single    1.516  0.020  1.516
 HW7  O14  C13  single    1.423  0.020  1.423
 HW7  C25  C26  aromatic  1.388  0.020  1.388
 HW7  C25  CL2  single    1.731  0.020  1.731
 HW7  C13  C12  single    1.513  0.020  1.513
 HW7  C10  O09  single    1.406  0.020  1.406
 HW7  O09  C3'  single    1.411  0.020  1.411
 HW7  C08  C06  single    1.504  0.020  1.504
 HW7  C08  C4'  single    1.524  0.020  1.524
 HW7  C06  N01  aromatic  1.335  0.020  1.335
 HW7  C06  C05  aromatic  1.383  0.020  1.383
 HW7  N01  C02  aromatic  1.328  0.020  1.328
 HW7  C3'  C4'  single    1.531  0.020  1.531
 HW7  C3'  C2'  single    1.552  0.020  1.552
 HW7  C4'  C5'  single    1.530  0.020  1.530
 HW7  C05  C04  aromatic  1.400  0.020  1.400
 HW7  N02  C02  single    1.366  0.020  1.366
 HW7  C02  C03  aromatic  1.406  0.020  1.406
 HW7  C04  C03  aromatic  1.379  0.020  1.379
 HW7  C04  C07  single    1.498  0.020  1.498
 HW7  C2'  N1'  single    1.466  0.020  1.466
 HW7  C5'  N1'  single    1.456  0.020  1.456
 HW7  C24  H1   single    0.930  0.020  1.080
 HW7  C22  H2   single    0.930  0.020  1.080
 HW7  C26  H3   single    0.930  0.020  1.080
 HW7  C13  H4   single    0.970  0.020  1.090
 HW7  C13  H5   single    0.970  0.020  1.090
 HW7  C12  H6   single    0.970  0.020  1.090
 HW7  C12  H7   single    0.970  0.020  1.090
 HW7  C11  H8   single    0.970  0.020  1.090
 HW7  C11  H9   single    0.970  0.020  1.090
 HW7  C10  H10  single    0.970  0.020  1.090
 HW7  C10  H11  single    0.970  0.020  1.090
 HW7  C3'  H12  single    0.970  0.020  1.090
 HW7  C2'  H13  single    0.970  0.020  1.090
 HW7  C2'  H14  single    0.970  0.020  1.090
 HW7  C4'  H15  single    0.970  0.020  1.090
 HW7  C5'  H16  single    0.970  0.020  1.090
 HW7  C5'  H17  single    0.970  0.020  1.090
 HW7  N1'  H18  single    0.890  0.020  1.040
 HW7  C08  H20  single    0.970  0.020  1.090
 HW7  C08  H21  single    0.970  0.020  1.090
 HW7  C05  H22  single    0.930  0.020  1.080
 HW7  C07  H23  single    0.970  0.020  1.090
 HW7  C07  H24  single    0.970  0.020  1.090
 HW7  C07  H25  single    0.970  0.020  1.090
 HW7  C03  H26  single    0.930  0.020  1.080
 HW7  N02  H27  single    0.890  0.020  1.040
 HW7  N02  H28  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
 HW7  C26  C25  C24  122.89  3.000
 HW7  C26  C25  CL2  118.40  3.000
 HW7  C24  C25  CL2  118.71  3.000
 HW7  H1   C24  C23  121.35  3.000
 HW7  H1   C24  C25  122.16  3.000
 HW7  C23  C24  C25  116.48  3.000
 HW7  C22  C23  F23  118.48  3.000
 HW7  C22  C23  C24  123.39  3.000
 HW7  F23  C23  C24  118.13  3.000
 HW7  H2   C22  C21  120.56  3.000
 HW7  H2   C22  C23  120.91  3.000
 HW7  C21  C22  C23  118.53  3.000
 HW7  H3   C26  C21  121.79  3.000
 HW7  H3   C26  C25  119.66  3.000
 HW7  C21  C26  C25  118.55  3.000
 HW7  O14  C21  C26  123.97  3.000
 HW7  C26  C21  C22  120.16  3.000
 HW7  O14  C21  C22  115.87  3.000
 HW7  C13  O14  C21  119.42  3.000
 HW7  H5   C13  H4   107.78  3.000
 HW7  H5   C13  C12  110.72  3.000
 HW7  H4   C13  C12  110.20  3.000
 HW7  H5   C13  O14  110.03  3.000
 HW7  H4   C13  O14  110.21  3.000
 HW7  C12  C13  O14  107.91  3.000
 HW7  H7   C12  H6   107.15  3.000
 HW7  H7   C12  C11  109.66  3.000
 HW7  H6   C12  C11  109.91  3.000
 HW7  H7   C12  C13  109.14  3.000
 HW7  H6   C12  C13  109.53  3.000
 HW7  C11  C12  C13  111.35  3.000
 HW7  H9   C11  H8   107.05  3.000
 HW7  H9   C11  C10  109.38  3.000
 HW7  H8   C11  C10  109.35  3.000
 HW7  H9   C11  C12  110.00  3.000
 HW7  H8   C11  C12  109.75  3.000
 HW7  C10  C11  C12  111.21  3.000
 HW7  H11  C10  H10  106.58  3.000
 HW7  H11  C10  O09  111.30  3.000
 HW7  H10  C10  O09  110.38  3.000
 HW7  H11  C10  C11  109.43  3.000
 HW7  H10  C10  C11  109.90  3.000
 HW7  O09  C10  C11  109.22  3.000
 HW7  C3'  O09  C10  114.01  3.000
 HW7  H12  C3'  C4'  111.12  3.000
 HW7  H12  C3'  C2'  111.49  3.000
 HW7  C4'  C3'  C2'  103.30  3.000
 HW7  H12  C3'  O09  109.26  3.000
 HW7  C2'  C3'  O09  112.27  3.000
 HW7  C4'  C3'  O09  109.29  3.000
 HW7  H14  C2'  H13  106.81  3.000
 HW7  H14  C2'  N1'  110.22  3.000
 HW7  H13  C2'  N1'  110.27  3.000
 HW7  H14  C2'  C3'  109.26  3.000
 HW7  H13  C2'  C3'  112.20  3.000
 HW7  N1'  C2'  C3'  108.08  3.000
 HW7  H15  C4'  C08  108.13  3.000
 HW7  H15  C4'  C5'  107.30  3.000
 HW7  C08  C4'  C5'  115.59  3.000
 HW7  H15  C4'  C3'  107.02  3.000
 HW7  C5'  C4'  C3'  102.30  3.000
 HW7  C08  C4'  C3'  115.90  3.000
 HW7  H17  C5'  H16  107.36  3.000
 HW7  H17  C5'  N1'  110.68  3.000
 HW7  H16  C5'  N1'  110.06  3.000
 HW7  H17  C5'  C4'  113.40  3.000
 HW7  H16  C5'  C4'  110.25  3.000
 HW7  N1'  C5'  C4'  105.10  3.000
 HW7  H18  N1'  C5'  108.09  3.000
 HW7  H18  N1'  C2'  108.61  3.000
 HW7  C5'  N1'  C2'  105.94  3.000
 HW7  H21  C08  H20  107.11  3.000
 HW7  H21  C08  C06  108.93  3.000
 HW7  H20  C08  C06  109.51  3.000
 HW7  H21  C08  C4'  109.65  3.000
 HW7  H20  C08  C4'  110.37  3.000
 HW7  C06  C08  C4'  111.17  3.000
 HW7  C05  C06  N01  122.65  3.000
 HW7  C05  C06  C08  121.12  3.000
 HW7  N01  C06  C08  116.22  3.000
 HW7  C02  N01  C06  118.75  3.000
 HW7  H22  C05  C04  120.69  3.000
 HW7  H22  C05  C06  120.16  3.000
 HW7  C04  C05  C06  119.15  3.000
 HW7  C03  C04  C07  121.33  3.000
 HW7  C07  C04  C05  120.62  3.000
 HW7  C03  C04  C05  118.05  3.000
 HW7  H25  C07  H24  108.36  3.000
 HW7  H25  C07  H23  107.03  3.000
 HW7  H24  C07  H23  107.75  3.000
 HW7  H25  C07  C04  111.17  3.000
 HW7  H24  C07  C04  111.83  3.000
 HW7  H23  C07  C04  110.50  3.000
 HW7  H26  C03  C02  120.04  3.000
 HW7  H26  C03  C04  120.92  3.000
 HW7  C02  C03  C04  119.05  3.000
 HW7  N02  C02  C03  120.48  3.000
 HW7  C03  C02  N01  122.35  3.000
 HW7  N02  C02  N01  117.14  3.000
 HW7  H28  N02  H27  114.01  3.000
 HW7  H28  N02  C02  117.38  3.000
 HW7  H27  N02  C02  116.19  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
 HW7  CONST_01  C22  C23  C24  C25     0.00   0.0  0
 HW7  CONST_02  C22  C21  C26  C25     0.00   0.0  0
 HW7  CONST_03  C21  C22  C23  C24     0.00   0.0  0
 HW7  CONST_04  C21  C26  C25  C24     0.00   0.0  0
 HW7  CONST_05  C26  C21  C22  C23     0.00   0.0  0
 HW7  CONST_06  C26  C25  C24  C23     0.00   0.0  0
 HW7  CONST_07  C03  C02  N01  C06     0.00   0.0  0
 HW7  CONST_08  C03  C04  C05  C06     0.00   0.0  0
 HW7  CONST_09  C04  C05  C06  N01     0.00   0.0  0
 HW7  CONST_10  C04  C03  C02  N01     0.00   0.0  0
 HW7  CONST_11  C02  N01  C06  C05     0.00   0.0  0
 HW7  CONST_12  C02  C03  C04  C05     0.00   0.0  0
 HW7  CONST_13  C23  C24  C25  CL2   180.00   0.0  0
 HW7  CONST_14  C21  C26  C25  CL2   180.00   0.0  0
 HW7  CONST_15  F23  C23  C24  C25   180.00   0.0  0
 HW7  CONST_16  O14  C21  C26  C25   180.00   0.0  0
 HW7  CONST_17  O14  C21  C22  C23   180.00   0.0  0
 HW7  CONST_18  C21  C22  C23  F23   180.00   0.0  0
 HW7  CONST_19  C02  N01  C06  C08   180.00   0.0  0
 HW7  CONST_20  C04  C05  C06  C08   180.00   0.0  0
 HW7  CONST_21  N02  C02  N01  C06   180.00   0.0  0
 HW7  CONST_22  C07  C04  C05  C06   180.00   0.0  0
 HW7  CONST_23  N02  C02  C03  C04   180.00   0.0  0
 HW7  CONST_24  C02  C03  C04  C07   180.00   0.0  0
 HW7  CONST_25  H2   C22  C23  C24   180.00   0.0  0
 HW7  CONST_26  H3   C26  C25  C24   180.00   0.0  0
 HW7  CONST_27  H1   C24  C23  C22   180.00   0.0  0
 HW7  CONST_28  H22  C05  C06  N01   180.00   0.0  0
 HW7  CONST_29  H26  C03  C02  N01   180.00   0.0  0
 HW7  Var_01    C5'  N1'  C2'  C3'   -16.22  30.0  1
 HW7  Var_02    C4'  C5'  N1'  C2'    34.84  30.0  1
 HW7  Var_03    N01  C06  C08  C4'   -64.58  30.0  2
 HW7  Var_04    H23  C07  C04  C05    70.56  30.0  2
 HW7  Var_05    C12  C13  O14  C21  -179.03  30.0  3
 HW7  Var_06    H10  C10  O09  C3'    53.39  30.0  2
 HW7  Var_07    C11  C12  C13  O14   179.50  30.0  3
 HW7  Var_08    C10  C11  C12  C13  -179.15  30.0  1
 HW7  Var_09    O09  C10  C11  C12   177.74  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
 HW7  chir_01  C3'  O09  C4'  C2'  positiv
 HW7  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
 HW7  plan-1  CL2  0.020
 HW7  plan-1  C25  0.020
 HW7  plan-1  C24  0.020
 HW7  plan-1  C23  0.020
 HW7  plan-1  F23  0.020
 HW7  plan-1  C22  0.020
 HW7  plan-1  C26  0.020
 HW7  plan-1  C21  0.020
 HW7  plan-1  O14  0.020
 HW7  plan-1  H1   0.020
 HW7  plan-1  H2   0.020
 HW7  plan-1  H3   0.020
 HW7  plan-2  C08  0.020
 HW7  plan-2  C06  0.020
 HW7  plan-2  N01  0.020
 HW7  plan-2  C05  0.020
 HW7  plan-2  C04  0.020
 HW7  plan-2  C07  0.020
 HW7  plan-2  C03  0.020
 HW7  plan-2  C02  0.020
 HW7  plan-2  N02  0.020
 HW7  plan-2  H22  0.020
 HW7  plan-2  H26  0.020
 HW7  plan-3  C02  0.020
 HW7  plan-3  N02  0.020
 HW7  plan-3  H27  0.020
 HW7  plan-3  H28  0.020

