# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 16:56:10 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 6-{[(3R,4R)-4-(3-phenoxyphenoxy)pyrrolidin-3-yl]methyl}pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cccc(C[C@@H]2CNC[C@@H]2Oc3cccc(Oc4ccccc4)c3)n1
#
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
 XJH  XJH  6-{[(3R,4R)-4-(3-phenoxyphenoxy)pyrrolidin-3-yl]methyl}pyridin-2-amine  ligand  50  27  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_XJH
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
 XJH  N01   N  N     0  -0.477  -5.0840   0.8708  -0.8409
 XJH  C02   C  CR6   0   0.428  -6.3310   1.2760  -0.6264
 XJH  N02   N  NH2   0  -0.835  -7.2575   0.9682  -1.5817
 XJH  C03   C  CR16  0  -0.392  -6.7042   1.9531   0.5484
 XJH  C04   C  CR16  0  -0.146  -5.7338   2.1882   1.4951
 XJH  C05   C  CR16  0  -0.392  -4.4275   1.7560   1.2731
 XJH  C06   C  CR6   0   0.274  -4.1511   1.1000   0.0844
 XJH  C07   C  CH2   0  -0.492  -2.7698   0.5942  -0.2289
 XJH  N1'   N  NH1   0  -0.604  -2.3473  -2.9456   0.9206
 XJH  O10   O  O2    0  -0.486  -0.3909  -0.9322  -0.0075
 XJH  C11   C  CR6   0   0.412   0.8997  -1.1711  -0.2970
 XJH  C12   C  CR16  0  -0.386   1.3471  -1.9524  -1.3606
 XJH  C13   C  CR16  0  -0.236   2.7146  -2.1035  -1.5596
 XJH  C14   C  CR16  0  -0.342   3.6459  -1.5024  -0.7316
 XJH  C15   C  CR6   0   0.358   3.1807  -0.7215   0.3234
 XJH  C16   C  CR16  0  -0.446   1.8263  -0.5498   0.5429
 XJH  C2'   C  CH2   0  -0.255  -3.0665  -1.6647   0.9758
 XJH  O20   O  O2    0  -0.512   4.0291  -0.1376   1.2207
 XJH  C21   C  CR6   0   0.339   5.1743   0.4650   0.7802
 XJH  C22   C  CR16  0  -0.317   5.1984   1.2619  -0.3589
 XJH  C23   C  CR16  0  -0.248   6.3806   1.8921  -0.7205
 XJH  C24   C  CR16  0  -0.267   7.5288   1.7399   0.0462
 XJH  C25   C  CR16  0  -0.249   7.4883   0.9476   1.1854
 XJH  C26   C  CR16  0  -0.332   6.3155   0.3034   1.5539
 XJH  C3'   C  CH1   0  -0.295  -2.7449  -0.9263  -0.3360
 XJH  C4'   C  CH1   0  -0.020  -1.4225  -1.5454  -0.7703
 XJH  C5'   C  CH2   0  -0.329  -1.6377  -2.9979  -0.3534
 XJH  HN02  H  HNH2  0   0.379  -6.8936   0.7413  -2.4927
 XJH  HN0A  H  HNH2  0   0.388  -8.0989   1.5193  -1.6058
 XJH  H03   H  HCR6  0   0.263  -7.7261   2.2767   0.6967
 XJH  H04   H  HCR6  0   0.263  -5.9885   2.7099   2.4089
 XJH  H05   H  HCR6  0   0.250  -3.6490   1.9297   2.0035
 XJH  H07   H  HCH2  0   0.251  -2.4417   1.0308  -1.1772
 XJH  H07A  H  HCH2  0   0.245  -2.0737   0.9321   0.5400
 XJH  HN1'  H  HNH1  0   0.354  -1.6767  -2.9846   1.6740
 XJH  H12   H  HCR6  0   0.278   0.6625  -2.4486  -2.0337
 XJH  H13   H  HCR6  0   0.265   3.0580  -2.7155  -2.3834
 XJH  H14   H  HCR6  0   0.275   4.7048  -1.6461  -0.9002
 XJH  H16   H  HCR6  0   0.272   1.4812   0.0613   1.3679
 XJH  H2'   H  HCH2  0   0.220  -4.1439  -1.8148   1.0806
 XJH  H2'A  H  HCH2  0   0.223  -2.7423  -1.0779   1.8400
 XJH  H22   H  HCR6  0   0.278   4.3067   1.3974  -0.9580
 XJH  H23   H  HCR6  0   0.263   6.3982   2.5132  -1.6067
 XJH  H24   H  HCR6  0   0.258   8.4453   2.2383  -0.2402
 XJH  H25   H  HCR6  0   0.262   8.3761   0.8210   1.7912
 XJH  H26   H  HCR6  0   0.269   6.2821  -0.3182   2.4398
 XJH  H3'   H  HCH1  0   0.259  -3.4768  -1.2165  -1.0961
 XJH  H4'   H  HCH1  0   0.253  -1.2413  -1.4137  -1.8423
 XJH  H5'   H  HCH2  0   0.251  -0.7183  -3.5777  -0.2634
 XJH  H5'A  H  HCH2  0   0.230  -2.2491  -3.4862  -1.1194

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
 XJH  C02  N01   aromatic  1.329  0.020  1.329
 XJH  C06  N01   aromatic  1.334  0.020  1.334
 XJH  C03  C02   aromatic  1.406  0.020  1.406
 XJH  C02  N02   single    1.366  0.020  1.366
 XJH  N02  HN02  single    0.890  0.020  1.040
 XJH  N02  HN0A  single    0.890  0.020  1.040
 XJH  C04  C03   aromatic  1.376  0.020  1.376
 XJH  C03  H03   single    0.930  0.020  1.080
 XJH  C04  C05   aromatic  1.394  0.020  1.394
 XJH  C04  H04   single    0.930  0.020  1.080
 XJH  C05  C06   aromatic  1.386  0.020  1.386
 XJH  C05  H05   single    0.930  0.020  1.080
 XJH  C06  C07   single    1.504  0.020  1.504
 XJH  C07  C3'   single    1.525  0.020  1.525
 XJH  C07  H07   single    0.970  0.020  1.090
 XJH  C07  H07A  single    0.970  0.020  1.090
 XJH  C2'  N1'   single    1.470  0.020  1.470
 XJH  N1'  C5'   single    1.459  0.020  1.459
 XJH  N1'  HN1'  single    0.890  0.020  1.040
 XJH  O10  C4'   single    1.422  0.020  1.422
 XJH  O10  C11   single    1.344  0.020  1.344
 XJH  C12  C11   aromatic  1.393  0.020  1.393
 XJH  C11  C16   aromatic  1.396  0.020  1.396
 XJH  C12  C13   aromatic  1.390  0.020  1.390
 XJH  C12  H12   single    0.930  0.020  1.080
 XJH  C13  C14   aromatic  1.384  0.020  1.384
 XJH  C13  H13   single    0.930  0.020  1.080
 XJH  C14  C15   aromatic  1.393  0.020  1.393
 XJH  C14  H14   single    0.930  0.020  1.080
 XJH  C16  C15   aromatic  1.383  0.020  1.383
 XJH  C15  O20   single    1.366  0.020  1.366
 XJH  C16  H16   single    0.930  0.020  1.080
 XJH  C2'  C3'   single    1.539  0.020  1.539
 XJH  C2'  H2'   single    0.970  0.020  1.090
 XJH  C2'  H2'A  single    0.970  0.020  1.090
 XJH  O20  C21   single    1.367  0.020  1.367
 XJH  C26  C21   aromatic  1.388  0.020  1.388
 XJH  C21  C22   aromatic  1.390  0.020  1.390
 XJH  C23  C22   aromatic  1.388  0.020  1.388
 XJH  C22  H22   single    0.930  0.020  1.080
 XJH  C24  C23   aromatic  1.389  0.020  1.389
 XJH  C23  H23   single    0.930  0.020  1.080
 XJH  C25  C24   aromatic  1.388  0.020  1.388
 XJH  C24  H24   single    0.930  0.020  1.080
 XJH  C25  C26   aromatic  1.388  0.020  1.388
 XJH  C25  H25   single    0.930  0.020  1.080
 XJH  C26  H26   single    0.930  0.020  1.080
 XJH  C3'  C4'   single    1.523  0.020  1.523
 XJH  C3'  H3'   single    0.970  0.020  1.090
 XJH  C5'  C4'   single    1.526  0.020  1.526
 XJH  C4'  H4'   single    0.970  0.020  1.090
 XJH  C5'  H5'   single    0.970  0.020  1.090
 XJH  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
 XJH  C06   N01  C02   119.47  3.000
 XJH  C03   C02  N02   120.84  3.000
 XJH  N02   C02  N01   117.07  3.000
 XJH  C03   C02  N01   122.06  3.000
 XJH  HN0A  N02  HN02  113.83  3.000
 XJH  HN0A  N02  C02   117.43  3.000
 XJH  HN02  N02  C02   116.00  3.000
 XJH  H03   C03  C04   121.37  3.000
 XJH  H03   C03  C02   120.60  3.000
 XJH  C04   C03  C02   118.03  3.000
 XJH  H04   C04  C05   120.29  3.000
 XJH  H04   C04  C03   119.81  3.000
 XJH  C05   C04  C03   119.90  3.000
 XJH  H05   C05  C06   120.79  3.000
 XJH  H05   C05  C04   121.15  3.000
 XJH  C06   C05  C04   118.06  3.000
 XJH  C07   C06  C05   121.40  3.000
 XJH  C07   C06  N01   116.11  3.000
 XJH  C05   C06  N01   122.49  3.000
 XJH  H07A  C07  H07   107.21  3.000
 XJH  H07A  C07  C3'   110.36  3.000
 XJH  H07   C07  C3'   109.40  3.000
 XJH  H07A  C07  C06   109.58  3.000
 XJH  H07   C07  C06   108.77  3.000
 XJH  C3'   C07  C06   111.41  3.000
 XJH  HN1'  N1'  C5'   109.10  3.000
 XJH  HN1'  N1'  C2'   109.31  3.000
 XJH  C5'   N1'  C2'   107.57  3.000
 XJH  C4'   O10  C11   120.29  3.000
 XJH  C16   C11  C12   119.70  3.000
 XJH  C16   C11  O10   115.38  3.000
 XJH  C12   C11  O10   124.91  3.000
 XJH  H12   C12  C13   118.95  3.000
 XJH  H12   C12  C11   121.97  3.000
 XJH  C13   C12  C11   119.08  3.000
 XJH  H13   C13  C14   119.18  3.000
 XJH  H13   C13  C12   118.86  3.000
 XJH  C14   C13  C12   121.96  3.000
 XJH  H14   C14  C15   121.30  3.000
 XJH  H14   C14  C13   120.53  3.000
 XJH  C15   C14  C13   118.17  3.000
 XJH  O20   C15  C16   116.81  3.000
 XJH  O20   C15  C14   122.00  3.000
 XJH  C16   C15  C14   121.14  3.000
 XJH  H16   C16  C15   120.20  3.000
 XJH  H16   C16  C11   119.85  3.000
 XJH  C15   C16  C11   119.95  3.000
 XJH  H2'A  C2'  H2'   106.86  3.000
 XJH  H2'A  C2'  C3'   110.74  3.000
 XJH  H2'   C2'  C3'   110.71  3.000
 XJH  H2'A  C2'  N1'   110.62  3.000
 XJH  H2'   C2'  N1'   111.49  3.000
 XJH  C3'   C2'  N1'   106.49  3.000
 XJH  C21   O20  C15   119.80  3.000
 XJH  C26   C21  C22   120.60  3.000
 XJH  C22   C21  O20   122.09  3.000
 XJH  C26   C21  O20   117.24  3.000
 XJH  H22   C22  C23   120.04  3.000
 XJH  H22   C22  C21   120.71  3.000
 XJH  C23   C22  C21   119.25  3.000
 XJH  H23   C23  C24   120.09  3.000
 XJH  H23   C23  C22   119.20  3.000
 XJH  C24   C23  C22   120.71  3.000
 XJH  H24   C24  C25   120.32  3.000
 XJH  H24   C24  C23   120.24  3.000
 XJH  C25   C24  C23   119.43  3.000
 XJH  H25   C25  C26   119.35  3.000
 XJH  H25   C25  C24   120.15  3.000
 XJH  C26   C25  C24   120.49  3.000
 XJH  H26   C26  C25   120.65  3.000
 XJH  H26   C26  C21   119.84  3.000
 XJH  C25   C26  C21   119.51  3.000
 XJH  H3'   C3'  C4'   105.95  3.000
 XJH  H3'   C3'  C2'   108.97  3.000
 XJH  C4'   C3'  C2'   103.26  3.000
 XJH  H3'   C3'  C07   107.60  3.000
 XJH  C4'   C3'  C07   116.07  3.000
 XJH  C2'   C3'  C07   114.53  3.000
 XJH  H4'   C4'  C5'   113.90  3.000
 XJH  H4'   C4'  C3'   111.95  3.000
 XJH  C5'   C4'  C3'   100.75  3.000
 XJH  H4'   C4'  O10   110.68  3.000
 XJH  C5'   C4'  O10   111.48  3.000
 XJH  C3'   C4'  O10   107.55  3.000
 XJH  H5'A  C5'  H5'   106.94  3.000
 XJH  H5'A  C5'  C4'   108.18  3.000
 XJH  H5'   C5'  C4'   114.18  3.000
 XJH  H5'A  C5'  N1'   110.81  3.000
 XJH  H5'   C5'  N1'   110.91  3.000
 XJH  C4'   C5'  N1'   105.84  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
 XJH  CONST_01  C04  C03  C02  N01     0.00   0.0  0
 XJH  CONST_02  C04  C05  C06  N01     0.00   0.0  0
 XJH  CONST_03  C05  C06  N01  C02     0.00   0.0  0
 XJH  CONST_04  C05  C04  C03  C02     0.00   0.0  0
 XJH  CONST_05  C06  N01  C02  C03     0.00   0.0  0
 XJH  CONST_06  C06  C05  C04  C03     0.00   0.0  0
 XJH  CONST_07  C14  C13  C12  C11     0.00   0.0  0
 XJH  CONST_08  C14  C15  C16  C11     0.00   0.0  0
 XJH  CONST_09  C15  C16  C11  C12     0.00   0.0  0
 XJH  CONST_10  C15  C14  C13  C12     0.00   0.0  0
 XJH  CONST_11  C16  C11  C12  C13     0.00   0.0  0
 XJH  CONST_12  C16  C15  C14  C13     0.00   0.0  0
 XJH  CONST_13  C24  C25  C26  C21     0.00   0.0  0
 XJH  CONST_14  C24  C23  C22  C21     0.00   0.0  0
 XJH  CONST_15  C25  C26  C21  C22     0.00   0.0  0
 XJH  CONST_16  C25  C24  C23  C22     0.00   0.0  0
 XJH  CONST_17  C26  C21  C22  C23     0.00   0.0  0
 XJH  CONST_18  C26  C25  C24  C23     0.00   0.0  0
 XJH  CONST_19  C07  C06  N01  C02   180.00   0.0  0
 XJH  CONST_20  C06  N01  C02  N02   180.00   0.0  0
 XJH  CONST_21  C04  C03  C02  N02   180.00   0.0  0
 XJH  CONST_22  C07  C06  C05  C04   180.00   0.0  0
 XJH  CONST_23  C13  C12  C11  O10   180.00   0.0  0
 XJH  CONST_24  C15  C16  C11  O10   180.00   0.0  0
 XJH  CONST_25  O20  C15  C16  C11   180.00   0.0  0
 XJH  CONST_26  O20  C15  C14  C13   180.00   0.0  0
 XJH  CONST_27  C25  C26  C21  O20   180.00   0.0  0
 XJH  CONST_28  C23  C22  C21  O20   180.00   0.0  0
 XJH  CONST_29  H03  C03  C02  N01   180.00   0.0  0
 XJH  CONST_30  H05  C05  C06  N01   180.00   0.0  0
 XJH  CONST_31  H04  C04  C03  C02   180.00   0.0  0
 XJH  CONST_32  H13  C13  C12  C11   180.00   0.0  0
 XJH  CONST_33  H16  C16  C11  C12   180.00   0.0  0
 XJH  CONST_34  H14  C14  C13  C12   180.00   0.0  0
 XJH  CONST_35  H12  C12  C13  C14   180.00   0.0  0
 XJH  CONST_36  H25  C25  C26  C21   180.00   0.0  0
 XJH  CONST_37  H23  C23  C22  C21   180.00   0.0  0
 XJH  CONST_38  H26  C26  C21  C22   180.00   0.0  0
 XJH  CONST_39  H24  C24  C23  C22   180.00   0.0  0
 XJH  CONST_40  H22  C22  C23  C24   180.00   0.0  0
 XJH  Var_01    C4'  C5'  N1'  C2'    24.84  30.0  1
 XJH  Var_02    C5'  N1'  C2'  C3'    -0.55  30.0  1
 XJH  Var_03    C3'  C07  C06  N01   -63.78  30.0  2
 XJH  Var_04    C26  C21  O20  C15  -140.98  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
 XJH  chir_01  C3'  C07  C2'  C4'  positiv
 XJH  chir_02  C4'  O10  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
 XJH  plan-1  N01   0.020
 XJH  plan-1  C02   0.020
 XJH  plan-1  N02   0.020
 XJH  plan-1  C03   0.020
 XJH  plan-1  C04   0.020
 XJH  plan-1  C05   0.020
 XJH  plan-1  C06   0.020
 XJH  plan-1  C07   0.020
 XJH  plan-1  H03   0.020
 XJH  plan-1  H04   0.020
 XJH  plan-1  H05   0.020
 XJH  plan-2  O10   0.020
 XJH  plan-2  C11   0.020
 XJH  plan-2  C12   0.020
 XJH  plan-2  C13   0.020
 XJH  plan-2  C14   0.020
 XJH  plan-2  C15   0.020
 XJH  plan-2  C16   0.020
 XJH  plan-2  O20   0.020
 XJH  plan-2  H12   0.020
 XJH  plan-2  H13   0.020
 XJH  plan-2  H14   0.020
 XJH  plan-2  H16   0.020
 XJH  plan-3  O20   0.020
 XJH  plan-3  C21   0.020
 XJH  plan-3  C22   0.020
 XJH  plan-3  C23   0.020
 XJH  plan-3  C24   0.020
 XJH  plan-3  C25   0.020
 XJH  plan-3  C26   0.020
 XJH  plan-3  H22   0.020
 XJH  plan-3  H23   0.020
 XJH  plan-3  H24   0.020
 XJH  plan-3  H25   0.020
 XJH  plan-3  H26   0.020
 XJH  plan-4  C02   0.020
 XJH  plan-4  N02   0.020
 XJH  plan-4  HN02  0.020
 XJH  plan-4  HN0A  0.020

