# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 13:44:24 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 6-{[(3R,4R)-4-(2-{[2-(3-chlorophenyl)-2,2-difluoroethyl]amino}ethoxy)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]2OCCNCC(F)(F)c3cccc(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
 8AX  8AX  6-{[(3R,4R)-4-(2-{[2-(3-chlorophenyl)-2,2-difluoroethyl]amino}ethoxy)pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine  ligand  56  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8AX
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
 8AX  N01   N   N     0  -0.485   5.6280   0.5904   1.1611
 8AX  C02   C   CR6   0   0.439   6.6766   1.3913   1.0103
 8AX  N02   N   NH2   0  -0.839   7.7715   1.1331   1.7842
 8AX  C03   C   CR16  0  -0.450   6.6621   2.4908   0.1339
 8AX  C04   C   CR6   0   0.205   5.5191   2.7526  -0.5926
 8AX  C05   C   CR16  0  -0.434   4.4175   1.9068  -0.4169
 8AX  C06   C   CR6   0   0.280   4.5190   0.8434   0.4619
 8AX  C07   C   CH3   0  -0.727   5.4554   3.8961  -1.5583
 8AX  C08   C   CH2   0  -0.486   3.3754  -0.1105   0.6685
 8AX  O09   O   O2    0  -0.491   1.3881  -2.0069   0.5841
 8AX  N1'   N   NH1   0  -0.588   3.7538  -2.9829  -1.7370
 8AX  C10   C   CH2   0  -0.162   0.4136  -2.8896   1.0845
 8AX  C11   C   CH2   0  -0.295  -0.8336  -2.0979   1.4026
 8AX  N12   N   NH1   0  -0.612  -1.4128  -1.5111   0.2073
 8AX  C13   C   CH2   0  -0.363  -2.5259  -0.6494   0.5221
 8AX  C14   C   CT    0   0.774  -3.2800  -0.2084  -0.7165
 8AX  F15   F   F     0  -0.346  -2.4164   0.3978  -1.5866
 8AX  F16   F   F     0  -0.340  -3.7623  -1.2960  -1.3829
 8AX  C2'   C   CH2   0  -0.303   3.8511  -1.5679  -1.4089
 8AX  C21   C   CR6   0  -0.098  -4.4118   0.7308  -0.3926
 8AX  C22   C   CR16  0  -0.252  -5.6584   0.2098  -0.0660
 8AX  C23   C   CR6   0  -0.018  -6.6804   1.0765   0.2847
 8AX  CL23  CL  CL    0  -0.121  -8.2334   0.4253   0.6927
 8AX  C24   C   CR16  0  -0.214  -6.4893   2.4486   0.3152
 8AX  C25   C   CR16  0  -0.243  -5.2395   2.9542  -0.0094
 8AX  C26   C   CR16  0  -0.282  -4.2012   2.1043  -0.3612
 8AX  C3'   C   CH1   0  -0.292   3.6997  -1.4943   0.1133
 8AX  C4'   C   CH1   0   0.049   2.6595  -2.5873   0.4107
 8AX  C5'   C   CH2   0  -0.334   2.7320  -3.5114  -0.8353
 8AX  HN02  H   HNH2  0   0.379   7.8347   0.2055   2.1708
 8AX  HN0A  H   HNH2  0   0.387   8.6528   1.5184   1.4893
 8AX  H03   H   HCR6  0   0.254   7.5401   3.1183   0.0362
 8AX  H05   H   HCR6  0   0.240   3.4985   2.0772  -0.9642
 8AX  H07   H   HCH3  0   0.253   5.3988   3.5279  -2.5841
 8AX  H07A  H   HCH3  0   0.249   4.5667   4.5053  -1.3902
 8AX  H07B  H   HCH3  0   0.246   6.3300   4.5398  -1.4816
 8AX  H08   H   HCH2  0   0.244   3.1658  -0.1825   1.7392
 8AX  H08A  H   HCH2  0   0.240   2.4770   0.2853   0.1930
 8AX  HN1'  H   HNH1  0   0.345   4.6396  -3.4175  -1.5090
 8AX  H10   H   HCH2  0   0.202   0.1782  -3.6817   0.3605
 8AX  H10A  H   HCH2  0   0.208   0.7679  -3.3817   2.0011
 8AX  H11   H   HCH2  0   0.233  -1.5623  -2.7775   1.8527
 8AX  H11A  H   HCH2  0   0.202  -0.5934  -1.3458   2.1706
 8AX  HN12  H   HNH1  0   0.349  -0.6965  -0.9743  -0.2661
 8AX  H13   H   HCH2  0   0.259  -3.2328  -1.1922   1.1565
 8AX  H13A  H   HCH2  0   0.237  -2.2435   0.2518   1.0877
 8AX  H2'   H   HCH2  0   0.240   4.7901  -1.1494  -1.7720
 8AX  H2'A  H   HCH2  0   0.216   3.0373  -1.0183  -1.8966
 8AX  H22   H   HCR6  0   0.286  -5.8374  -0.8569  -0.0745
 8AX  H24   H   HCR6  0   0.286  -7.2978   3.1125   0.5890
 8AX  H25   H   HCR6  0   0.276  -5.0762   4.0232   0.0124
 8AX  H26   H   HCR6  0   0.271  -3.2347   2.5228  -0.6063
 8AX  H3'   H   HCH1  0   0.246   4.6467  -1.8231   0.5548
 8AX  H4'   H   HCH1  0   0.215   2.9290  -3.1323   1.3256
 8AX  H5'   H   HCH2  0   0.226   1.7588  -3.5000  -1.3375
 8AX  H5'A  H   HCH2  0   0.240   2.9521  -4.5485  -0.5820

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
 8AX  N01   C06   aromatic  1.335  0.020  1.335
 8AX  N01   C02   aromatic  1.328  0.020  1.328
 8AX  N02   C02   single    1.365  0.020  1.365
 8AX  C02   C03   aromatic  1.406  0.020  1.406
 8AX  N02   HN02  single    0.890  0.020  1.040
 8AX  N02   HN0A  single    0.890  0.020  1.040
 8AX  C03   C04   aromatic  1.379  0.020  1.379
 8AX  C03   H03   single    0.930  0.020  1.080
 8AX  C05   C04   aromatic  1.400  0.020  1.400
 8AX  C04   C07   single    1.498  0.020  1.498
 8AX  C06   C05   aromatic  1.383  0.020  1.383
 8AX  C05   H05   single    0.930  0.020  1.080
 8AX  C08   C06   single    1.503  0.020  1.503
 8AX  C07   H07   single    0.970  0.020  1.090
 8AX  C07   H07A  single    0.970  0.020  1.090
 8AX  C07   H07B  single    0.970  0.020  1.090
 8AX  C08   C3'   single    1.526  0.020  1.526
 8AX  C08   H08   single    0.970  0.020  1.090
 8AX  C08   H08A  single    0.970  0.020  1.090
 8AX  C10   O09   single    1.407  0.020  1.407
 8AX  O09   C4'   single    1.408  0.020  1.408
 8AX  C5'   N1'   single    1.462  0.020  1.462
 8AX  C2'   N1'   single    1.456  0.020  1.456
 8AX  N1'   HN1'  single    0.890  0.020  1.040
 8AX  C11   C10   single    1.511  0.020  1.511
 8AX  C10   H10   single    0.970  0.020  1.090
 8AX  C10   H10A  single    0.970  0.020  1.090
 8AX  C11   N12   single    1.452  0.020  1.452
 8AX  C11   H11   single    0.970  0.020  1.090
 8AX  C11   H11A  single    0.970  0.020  1.090
 8AX  C13   N12   single    1.442  0.020  1.442
 8AX  N12   HN12  single    0.890  0.020  1.040
 8AX  C14   C13   single    1.516  0.020  1.516
 8AX  C13   H13   single    0.970  0.020  1.090
 8AX  C13   H13A  single    0.970  0.020  1.090
 8AX  F15   C14   single    1.368  0.020  1.368
 8AX  C21   C14   single    1.506  0.020  1.506
 8AX  C14   F16   single    1.364  0.020  1.364
 8AX  C3'   C2'   single    1.531  0.020  1.531
 8AX  C2'   H2'   single    0.970  0.020  1.090
 8AX  C2'   H2'A  single    0.970  0.020  1.090
 8AX  C22   C21   aromatic  1.390  0.020  1.390
 8AX  C21   C26   aromatic  1.390  0.020  1.390
 8AX  C23   C22   aromatic  1.385  0.020  1.385
 8AX  C22   H22   single    0.930  0.020  1.080
 8AX  CL23  C23   single    1.733  0.020  1.733
 8AX  C23   C24   aromatic  1.386  0.020  1.386
 8AX  C24   C25   aromatic  1.387  0.020  1.387
 8AX  C24   H24   single    0.930  0.020  1.080
 8AX  C25   C26   aromatic  1.387  0.020  1.387
 8AX  C25   H25   single    0.930  0.020  1.080
 8AX  C26   H26   single    0.930  0.020  1.080
 8AX  C4'   C3'   single    1.538  0.020  1.538
 8AX  C3'   H3'   single    0.970  0.020  1.090
 8AX  C4'   C5'   single    1.553  0.020  1.553
 8AX  C4'   H4'   single    0.970  0.020  1.090
 8AX  C5'   H5'   single    0.970  0.020  1.090
 8AX  C5'   H5'A  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
 8AX  C06   N01  C02   118.82  3.000
 8AX  C03   C02  N02   120.62  3.000
 8AX  C03   C02  N01   122.29  3.000
 8AX  N02   C02  N01   117.05  3.000
 8AX  HN0A  N02  HN02  114.23  3.000
 8AX  HN0A  N02  C02   117.64  3.000
 8AX  HN02  N02  C02   116.24  3.000
 8AX  H03   C03  C04   120.93  3.000
 8AX  H03   C03  C02   120.04  3.000
 8AX  C04   C03  C02   119.03  3.000
 8AX  C07   C04  C05   120.57  3.000
 8AX  C07   C04  C03   121.31  3.000
 8AX  C05   C04  C03   118.12  3.000
 8AX  H05   C05  C06   120.28  3.000
 8AX  H05   C05  C04   120.62  3.000
 8AX  C06   C05  C04   119.11  3.000
 8AX  C08   C06  C05   121.28  3.000
 8AX  C08   C06  N01   116.08  3.000
 8AX  C05   C06  N01   122.64  3.000
 8AX  H07B  C07  H07A  108.27  3.000
 8AX  H07B  C07  H07   107.90  3.000
 8AX  H07A  C07  H07   106.92  3.000
 8AX  H07B  C07  C04   111.83  3.000
 8AX  H07A  C07  C04   111.21  3.000
 8AX  H07   C07  C04   110.52  3.000
 8AX  H08A  C08  H08   107.03  3.000
 8AX  H08A  C08  C3'   110.21  3.000
 8AX  H08   C08  C3'   109.72  3.000
 8AX  H08A  C08  C06   109.65  3.000
 8AX  H08   C08  C06   108.79  3.000
 8AX  C3'   C08  C06   111.33  3.000
 8AX  C4'   O09  C10   114.24  3.000
 8AX  HN1'  N1'  C5'   108.51  3.000
 8AX  HN1'  N1'  C2'   107.94  3.000
 8AX  C5'   N1'  C2'   105.02  3.000
 8AX  H10A  C10  H10   107.21  3.000
 8AX  H10A  C10  C11   108.97  3.000
 8AX  H10   C10  C11   109.86  3.000
 8AX  H10A  C10  O09   110.75  3.000
 8AX  H10   C10  O09   111.49  3.000
 8AX  C11   C10  O09   108.53  3.000
 8AX  H11A  C11  H11   106.42  3.000
 8AX  H11A  C11  N12   112.65  3.000
 8AX  H11   C11  N12   108.92  3.000
 8AX  H11A  C11  C10   108.94  3.000
 8AX  H11   C11  C10   108.13  3.000
 8AX  N12   C11  C10   111.57  3.000
 8AX  HN12  N12  C13   109.34  3.000
 8AX  HN12  N12  C11   108.48  3.000
 8AX  C13   N12  C11   111.69  3.000
 8AX  H13A  C13  H13   105.91  3.000
 8AX  H13A  C13  C14   108.02  3.000
 8AX  H13   C13  C14   107.26  3.000
 8AX  H13A  C13  N12   113.78  3.000
 8AX  H13   C13  N12   109.19  3.000
 8AX  C14   C13  N12   112.30  3.000
 8AX  C21   C14  F16   109.68  3.000
 8AX  F16   C14  F15   105.42  3.000
 8AX  C21   C14  F15   109.57  3.000
 8AX  F16   C14  C13   110.08  3.000
 8AX  C21   C14  C13   112.31  3.000
 8AX  F15   C14  C13   109.55  3.000
 8AX  H2'A  C2'  H2'   107.37  3.000
 8AX  H2'A  C2'  C3'   110.16  3.000
 8AX  H2'   C2'  C3'   113.44  3.000
 8AX  H2'A  C2'  N1'   109.72  3.000
 8AX  H2'   C2'  N1'   110.83  3.000
 8AX  C3'   C2'  N1'   105.32  3.000
 8AX  C26   C21  C22   120.07  3.000
 8AX  C26   C21  C14   120.49  3.000
 8AX  C22   C21  C14   119.39  3.000
 8AX  H22   C22  C23   119.80  3.000
 8AX  H22   C22  C21   121.08  3.000
 8AX  C23   C22  C21   119.12  3.000
 8AX  C24   C23  CL23  119.38  3.000
 8AX  C24   C23  C22   121.56  3.000
 8AX  CL23  C23  C22   119.06  3.000
 8AX  H24   C24  C25   120.61  3.000
 8AX  H24   C24  C23   120.69  3.000
 8AX  C25   C24  C23   118.69  3.000
 8AX  H25   C25  C26   119.85  3.000
 8AX  H25   C25  C24   119.45  3.000
 8AX  C26   C25  C24   120.70  3.000
 8AX  H26   C26  C25   119.30  3.000
 8AX  H26   C26  C21   120.85  3.000
 8AX  C25   C26  C21   119.85  3.000
 8AX  H3'   C3'  C4'   107.07  3.000
 8AX  H3'   C3'  C2'   107.50  3.000
 8AX  C4'   C3'  C2'   103.00  3.000
 8AX  H3'   C3'  C08   108.01  3.000
 8AX  C4'   C3'  C08   115.49  3.000
 8AX  C2'   C3'  C08   115.23  3.000
 8AX  H4'   C4'  C5'   111.20  3.000
 8AX  H4'   C4'  C3'   110.35  3.000
 8AX  C5'   C4'  C3'   103.66  3.000
 8AX  H4'   C4'  O09   108.87  3.000
 8AX  C5'   C4'  O09   112.71  3.000
 8AX  C3'   C4'  O09   109.97  3.000
 8AX  H5'A  C5'  H5'   107.21  3.000
 8AX  H5'A  C5'  C4'   112.90  3.000
 8AX  H5'   C5'  C4'   108.68  3.000
 8AX  H5'A  C5'  N1'   110.26  3.000
 8AX  H5'   C5'  N1'   109.55  3.000
 8AX  C4'   C5'  N1'   108.20  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
 8AX  CONST_01  C04   C05  C06  N01      0.00   0.0  0
 8AX  CONST_02  C04   C03  C02  N01      0.00   0.0  0
 8AX  CONST_03  C05   C06  N01  C02      0.00   0.0  0
 8AX  CONST_04  C05   C04  C03  C02      0.00   0.0  0
 8AX  CONST_05  C06   N01  C02  C03      0.00   0.0  0
 8AX  CONST_06  C06   C05  C04  C03      0.00   0.0  0
 8AX  CONST_07  C24   C23  C22  C21      0.00   0.0  0
 8AX  CONST_08  C24   C25  C26  C21      0.00   0.0  0
 8AX  CONST_09  C25   C26  C21  C22      0.00   0.0  0
 8AX  CONST_10  C25   C24  C23  C22      0.00   0.0  0
 8AX  CONST_11  C26   C21  C22  C23      0.00   0.0  0
 8AX  CONST_12  C26   C25  C24  C23      0.00   0.0  0
 8AX  CONST_13  C08   C06  N01  C02    180.00   0.0  0
 8AX  CONST_14  C07   C04  C03  C02    180.00   0.0  0
 8AX  CONST_15  C06   N01  C02  N02    180.00   0.0  0
 8AX  CONST_16  C04   C03  C02  N02    180.00   0.0  0
 8AX  CONST_17  C08   C06  C05  C04    180.00   0.0  0
 8AX  CONST_18  C07   C04  C05  C06    180.00   0.0  0
 8AX  CONST_19  C23   C22  C21  C14    180.00   0.0  0
 8AX  CONST_20  C25   C26  C21  C14    180.00   0.0  0
 8AX  CONST_21  CL23  C23  C22  C21    180.00   0.0  0
 8AX  CONST_22  C25   C24  C23  CL23   180.00   0.0  0
 8AX  CONST_23  H05   C05  C06  N01    180.00   0.0  0
 8AX  CONST_24  H03   C03  C02  N01    180.00   0.0  0
 8AX  CONST_25  H25   C25  C26  C21    180.00   0.0  0
 8AX  CONST_26  H26   C26  C21  C22    180.00   0.0  0
 8AX  CONST_27  H24   C24  C23  C22    180.00   0.0  0
 8AX  CONST_28  H22   C22  C23  C24    180.00   0.0  0
 8AX  Var_01    C4'   C5'  N1'  C2'    -24.18  30.0  1
 8AX  Var_02    C5'   N1'  C2'  C3'     38.08  30.0  1
 8AX  Var_03    C3'   C08  C06  N01    -67.68  30.0  2
 8AX  Var_04    C22   C21  C14  C13    -87.08  30.0  3
 8AX  Var_05    H07   C07  C04  C03    111.39  30.0  2
 8AX  Var_06    C21   C14  C13  N12   -177.94  30.0  1
 8AX  Var_07    H10   C10  O09  C4'    -66.73  30.0  1
 8AX  Var_08    N12   C11  C10  O09     63.98  30.0  2
 8AX  Var_09    C13   N12  C11  C10   -174.37  30.0  3
 8AX  Var_10    C14   C13  N12  C11   -170.73  30.0  2

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
 8AX  chir_01  C3'  C08  C2'  C4'  positiv
 8AX  chir_02  C4'  O09  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
 8AX  plan-1  N01   0.020
 8AX  plan-1  C02   0.020
 8AX  plan-1  N02   0.020
 8AX  plan-1  C03   0.020
 8AX  plan-1  C04   0.020
 8AX  plan-1  C05   0.020
 8AX  plan-1  C06   0.020
 8AX  plan-1  C07   0.020
 8AX  plan-1  C08   0.020
 8AX  plan-1  H03   0.020
 8AX  plan-1  H05   0.020
 8AX  plan-2  C14   0.020
 8AX  plan-2  C21   0.020
 8AX  plan-2  C22   0.020
 8AX  plan-2  C23   0.020
 8AX  plan-2  CL23  0.020
 8AX  plan-2  C24   0.020
 8AX  plan-2  C25   0.020
 8AX  plan-2  C26   0.020
 8AX  plan-2  H22   0.020
 8AX  plan-2  H24   0.020
 8AX  plan-2  H25   0.020
 8AX  plan-2  H26   0.020
 8AX  plan-3  C02   0.020
 8AX  plan-3  N02   0.020
 8AX  plan-3  HN02  0.020
 8AX  plan-3  HN0A  0.020

