# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 09:45:11 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 6-(2-{3-[2-(2-amino-6-methylpyridin-4-yl)ethyl]phenyl}ethyl)-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(CCc2cccc(CCc3cc(C)nc(N)c3)c2)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
 XFH  XFH  6-(2-{3-[2-(2-amino-6-methylpyridin-4-yl)ethyl]phenyl}ethyl)-4-methylpyridin-2-amine  ligand  52  26  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XFH
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
 XFH  N01   N  N     0  -0.484  -4.1343  -1.3549   0.1367
 XFH  C02   C  CR6   0   0.439  -5.2155  -2.1094   0.2958
 XFH  N02   N  NH2   0  -0.838  -5.0608  -3.2824   0.9790
 XFH  C03   C  CR16  0  -0.447  -6.4816  -1.7168  -0.1741
 XFH  C04   C  CR6   0   0.205  -6.6106  -0.5046  -0.8193
 XFH  C05   C  CR16  0  -0.432  -5.4638   0.2833  -0.9777
 XFH  C06   C  CR6   0   0.275  -4.2572  -0.1811  -0.4877
 XFH  C07   C  CH3   0  -0.727  -7.9359  -0.0275  -1.3291
 XFH  C08   C  CH2   0  -0.486  -3.0006   0.6331  -0.6097
 XFH  C09   C  CH2   0  -0.511  -2.5362   1.1690   0.7509
 XFH  C11   C  CR16  0  -0.224  -0.0088   3.9556   0.2425
 XFH  C12   C  CR16  0  -0.330  -1.2168   3.2830   0.3669
 XFH  C13   C  CR6   0   0.153  -1.2383   1.9183   0.6442
 XFH  C14   C  CR16  0  -0.376  -0.0252   1.2505   0.7873
 XFH  C15   C  CR6   0   0.154   1.1953   1.9095   0.6703
 XFH  C16   C  CR16  0  -0.330   1.1913   3.2742   0.3927
 XFH  C17   C  CH2   0  -0.511   2.4845   1.1493   0.8041
 XFH  C18   C  CH2   0  -0.509   2.9724   0.6129  -0.5495
 XFH  C21   C  CR16  0  -0.460   5.4676   0.3572  -0.6217
 XFH  C22   C  CR6   0   0.445   6.6119  -0.4346  -0.4225
 XFH  N22   N  NH2   0  -0.838   7.8605   0.0936  -0.5864
 XFH  N23   N  N     0  -0.487   6.5398  -1.7021  -0.0297
 XFH  C24   C  CR6   0   0.255   5.3382  -2.2400   0.1919
 XFH  C25   C  CR16  0  -0.436   4.1617  -1.5303   0.0253
 XFH  C26   C  CR6   0   0.240   4.2254  -0.1984  -0.3964
 XFH  HN02  H  HNH2  0   0.379  -4.1192  -3.6333   1.0438
 XFH  HN0A  H  HNH2  0   0.387  -5.7519  -3.9986   0.8308
 XFH  H03   H  HCR6  0   0.255  -7.3388  -2.3636  -0.0303
 XFH  H05   H  HCR6  0   0.242  -5.5172   1.2399  -1.4827
 XFH  H07   H  HCH3  0   0.253  -8.2776   0.8362  -0.7562
 XFH  H07A  H  HCH3  0   0.250  -7.8640   0.2894  -2.3700
 XFH  H07B  H  HCH3  0   0.247  -8.7003  -0.7994  -1.2584
 XFH  H08   H  HCH2  0   0.247  -2.2085   0.0124  -1.0376
 XFH  H08A  H  HCH2  0   0.246  -3.1598   1.4657  -1.2983
 XFH  H09   H  HCH2  0   0.247  -3.3118   1.8184   1.1646
 XFH  H09A  H  HCH2  0   0.247  -2.4255   0.3304   1.4420
 XFH  H11   H  HCR6  0   0.250  -0.0025   5.0184   0.0360
 XFH  H12   H  HCR6  0   0.243  -2.1489   3.8249   0.2551
 XFH  H14   H  HCR6  0   0.236  -0.0317   0.1868   1.0058
 XFH  H16   H  HCR6  0   0.244   2.1296   3.8090   0.3007
 XFH  H17   H  HCH2  0   0.252   3.2584   1.7892   1.2351
 XFH  H17A  H  HCH2  0   0.252   2.3500   0.3131   1.4952
 XFH  H18   H  HCH2  0   0.254   2.1856  -0.0011  -0.9950
 XFH  H18A  H  HCH2  0   0.253   3.1464   1.4490  -1.2306
 XFH  H21   H  HCR6  0   0.253   5.5658   1.3862  -0.9475
 XFH  HN22  H  HNH2  0   0.387   7.9486   0.9110  -1.1665
 XFH  HN2A  H  HNH2  0   0.378   8.6113  -0.5687  -0.6937
 XFH  H25   H  HCR6  0   0.243   3.2063  -2.0036   0.2160
 XFH  H27   H  HCH3  0   0.245   5.9662  -3.8274   1.4908
 XFH  H27A  H  HCH3  0   0.240   4.3207  -4.0126   0.8735
 XFH  H27B  H  HCH3  0   0.247   5.7066  -4.3195  -0.1736
 XFH  C27   C  CH3   0  -0.718   5.3249  -3.6762   0.6216

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
 XFH  C02  N01   aromatic  1.328  0.020  1.328
 XFH  C06  N01   aromatic  1.335  0.020  1.335
 XFH  C03  C02   aromatic  1.406  0.020  1.406
 XFH  C02  N02   single    1.366  0.020  1.366
 XFH  N02  HN02  single    0.890  0.020  1.040
 XFH  N02  HN0A  single    0.890  0.020  1.040
 XFH  C04  C03   aromatic  1.379  0.020  1.379
 XFH  C03  H03   single    0.930  0.020  1.080
 XFH  C07  C04   single    1.498  0.020  1.498
 XFH  C04  C05   aromatic  1.400  0.020  1.400
 XFH  C05  C06   aromatic  1.383  0.020  1.383
 XFH  C05  H05   single    0.930  0.020  1.080
 XFH  C06  C08   single    1.502  0.020  1.502
 XFH  C07  H07   single    0.970  0.020  1.090
 XFH  C07  H07A  single    0.970  0.020  1.090
 XFH  C07  H07B  single    0.970  0.020  1.090
 XFH  C08  C09   single    1.534  0.020  1.534
 XFH  C08  H08   single    0.970  0.020  1.090
 XFH  C08  H08A  single    0.970  0.020  1.090
 XFH  C09  C13   single    1.503  0.020  1.503
 XFH  C09  H09   single    0.970  0.020  1.090
 XFH  C09  H09A  single    0.970  0.020  1.090
 XFH  C12  C11   aromatic  1.388  0.020  1.388
 XFH  C11  C16   aromatic  1.388  0.020  1.388
 XFH  C11  H11   single    0.930  0.020  1.080
 XFH  C13  C12   aromatic  1.393  0.020  1.393
 XFH  C12  H12   single    0.930  0.020  1.080
 XFH  C13  C14   aromatic  1.392  0.020  1.392
 XFH  C14  C15   aromatic  1.392  0.020  1.392
 XFH  C14  H14   single    0.930  0.020  1.080
 XFH  C15  C17   single    1.503  0.020  1.503
 XFH  C15  C16   aromatic  1.393  0.020  1.393
 XFH  C16  H16   single    0.930  0.020  1.080
 XFH  C17  C18   single    1.536  0.020  1.536
 XFH  C17  H17   single    0.970  0.020  1.090
 XFH  C17  H17A  single    0.970  0.020  1.090
 XFH  C26  C18   single    1.501  0.020  1.501
 XFH  C18  H18   single    0.970  0.020  1.090
 XFH  C18  H18A  single    0.970  0.020  1.090
 XFH  C26  C21   aromatic  1.379  0.020  1.379
 XFH  C22  C21   aromatic  1.406  0.020  1.406
 XFH  C21  H21   single    0.930  0.020  1.080
 XFH  N23  C22   aromatic  1.329  0.020  1.329
 XFH  C22  N22   single    1.366  0.020  1.366
 XFH  N22  HN22  single    0.890  0.020  1.040
 XFH  N22  HN2A  single    0.890  0.020  1.040
 XFH  C24  N23   aromatic  1.335  0.020  1.335
 XFH  C27  C24   single    1.499  0.020  1.499
 XFH  C24  C25   aromatic  1.384  0.020  1.384
 XFH  C25  C26   aromatic  1.399  0.020  1.399
 XFH  C25  H25   single    0.930  0.020  1.080
 XFH  C27  H27   single    0.970  0.020  1.090
 XFH  C27  H27A  single    0.970  0.020  1.090
 XFH  C27  H27B  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
 XFH  C06   N01  C02   118.72  3.000
 XFH  C03   C02  N02   120.58  3.000
 XFH  N02   C02  N01   117.10  3.000
 XFH  C03   C02  N01   122.30  3.000
 XFH  HN0A  N02  HN02  113.81  3.000
 XFH  HN0A  N02  C02   117.36  3.000
 XFH  HN02  N02  C02   115.93  3.000
 XFH  H03   C03  C04   120.84  3.000
 XFH  H03   C03  C02   120.08  3.000
 XFH  C04   C03  C02   119.07  3.000
 XFH  C07   C04  C05   120.45  3.000
 XFH  C05   C04  C03   118.08  3.000
 XFH  C07   C04  C03   121.46  3.000
 XFH  H05   C05  C06   120.32  3.000
 XFH  H05   C05  C04   120.62  3.000
 XFH  C06   C05  C04   119.05  3.000
 XFH  C08   C06  C05   121.27  3.000
 XFH  C08   C06  N01   115.94  3.000
 XFH  C05   C06  N01   122.77  3.000
 XFH  H07B  C07  H07A  108.32  3.000
 XFH  H07B  C07  H07   107.90  3.000
 XFH  H07A  C07  H07   106.96  3.000
 XFH  H07B  C07  C04   111.92  3.000
 XFH  H07A  C07  C04   111.04  3.000
 XFH  H07   C07  C04   110.51  3.000
 XFH  H08A  C08  H08   106.95  3.000
 XFH  H08A  C08  C09   109.70  3.000
 XFH  H08   C08  C09   109.03  3.000
 XFH  H08A  C08  C06   110.03  3.000
 XFH  H08   C08  C06   109.27  3.000
 XFH  C09   C08  C06   111.74  3.000
 XFH  H09A  C09  H09   106.77  3.000
 XFH  H09A  C09  C13   109.89  3.000
 XFH  H09   C09  C13   110.09  3.000
 XFH  H09A  C09  C08   108.89  3.000
 XFH  H09   C09  C08   109.18  3.000
 XFH  C13   C09  C08   111.88  3.000
 XFH  H11   C11  C16   119.83  3.000
 XFH  H11   C11  C12   119.85  3.000
 XFH  C16   C11  C12   120.32  3.000
 XFH  H12   C12  C13   119.81  3.000
 XFH  H12   C12  C11   119.80  3.000
 XFH  C13   C12  C11   120.40  3.000
 XFH  C14   C13  C12   118.50  3.000
 XFH  C14   C13  C09   120.41  3.000
 XFH  C12   C13  C09   121.07  3.000
 XFH  H14   C14  C15   119.08  3.000
 XFH  H14   C14  C13   119.04  3.000
 XFH  C15   C14  C13   121.89  3.000
 XFH  C17   C15  C16   121.07  3.000
 XFH  C16   C15  C14   118.57  3.000
 XFH  C17   C15  C14   120.35  3.000
 XFH  H16   C16  C15   119.86  3.000
 XFH  H16   C16  C11   119.80  3.000
 XFH  C15   C16  C11   120.34  3.000
 XFH  H17A  C17  H17   106.60  3.000
 XFH  H17A  C17  C18   109.22  3.000
 XFH  H17   C17  C18   109.10  3.000
 XFH  H17A  C17  C15   109.74  3.000
 XFH  H17   C17  C15   110.27  3.000
 XFH  C18   C17  C15   111.77  3.000
 XFH  H18A  C18  H18   106.89  3.000
 XFH  H18A  C18  C26   110.14  3.000
 XFH  H18   C18  C26   109.82  3.000
 XFH  H18A  C18  C17   109.45  3.000
 XFH  H18   C18  C17   109.08  3.000
 XFH  C26   C18  C17   111.36  3.000
 XFH  H21   C21  C26   120.88  3.000
 XFH  H21   C21  C22   120.23  3.000
 XFH  C26   C21  C22   118.89  3.000
 XFH  N23   C22  N22   117.00  3.000
 XFH  N22   C22  C21   120.63  3.000
 XFH  N23   C22  C21   122.34  3.000
 XFH  HN2A  N22  HN22  114.05  3.000
 XFH  HN2A  N22  C22   116.11  3.000
 XFH  HN22  N22  C22   117.61  3.000
 XFH  C24   N23  C22   118.83  3.000
 XFH  C27   C24  C25   121.21  3.000
 XFH  C25   C24  N23   122.58  3.000
 XFH  C27   C24  N23   116.20  3.000
 XFH  H25   C25  C26   120.63  3.000
 XFH  H25   C25  C24   120.30  3.000
 XFH  C26   C25  C24   119.07  3.000
 XFH  C25   C26  C21   118.29  3.000
 XFH  C25   C26  C18   120.50  3.000
 XFH  C21   C26  C18   121.17  3.000
 XFH  H27B  C27  H27A  107.99  3.000
 XFH  H27B  C27  H27   107.05  3.000
 XFH  H27A  C27  H27   108.37  3.000
 XFH  H27B  C27  C24   110.65  3.000
 XFH  H27A  C27  C24   111.75  3.000
 XFH  H27   C27  C24   110.86  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
 XFH  CONST_01  C04  C03  C02  N01     0.00   0.0  0
 XFH  CONST_02  C04  C05  C06  N01     0.00   0.0  0
 XFH  CONST_03  C05  C06  N01  C02     0.00   0.0  0
 XFH  CONST_04  C05  C04  C03  C02     0.00   0.0  0
 XFH  CONST_05  C06  N01  C02  C03     0.00   0.0  0
 XFH  CONST_06  C06  C05  C04  C03     0.00   0.0  0
 XFH  CONST_07  C14  C13  C12  C11     0.00   0.0  0
 XFH  CONST_08  C14  C15  C16  C11     0.00   0.0  0
 XFH  CONST_09  C15  C16  C11  C12     0.00   0.0  0
 XFH  CONST_10  C15  C14  C13  C12     0.00   0.0  0
 XFH  CONST_11  C16  C11  C12  C13     0.00   0.0  0
 XFH  CONST_12  C16  C15  C14  C13     0.00   0.0  0
 XFH  CONST_13  C24  C25  C26  C21     0.00   0.0  0
 XFH  CONST_14  C24  N23  C22  C21     0.00   0.0  0
 XFH  CONST_15  C25  C26  C21  C22     0.00   0.0  0
 XFH  CONST_16  C25  C24  N23  C22     0.00   0.0  0
 XFH  CONST_17  C26  C21  C22  N23     0.00   0.0  0
 XFH  CONST_18  C26  C25  C24  N23     0.00   0.0  0
 XFH  CONST_19  C08  C06  N01  C02   180.00   0.0  0
 XFH  CONST_20  C07  C04  C03  C02   180.00   0.0  0
 XFH  CONST_21  C06  N01  C02  N02   180.00   0.0  0
 XFH  CONST_22  C04  C03  C02  N02   180.00   0.0  0
 XFH  CONST_23  C08  C06  C05  C04   180.00   0.0  0
 XFH  CONST_24  C07  C04  C05  C06   180.00   0.0  0
 XFH  CONST_25  C11  C12  C13  C09   180.00   0.0  0
 XFH  CONST_26  C15  C14  C13  C09   180.00   0.0  0
 XFH  CONST_27  C17  C15  C16  C11   180.00   0.0  0
 XFH  CONST_28  C17  C15  C14  C13   180.00   0.0  0
 XFH  CONST_29  C22  C21  C26  C18   180.00   0.0  0
 XFH  CONST_30  C24  C25  C26  C18   180.00   0.0  0
 XFH  CONST_31  C27  C24  N23  C22   180.00   0.0  0
 XFH  CONST_32  C26  C21  C22  N22   180.00   0.0  0
 XFH  CONST_33  C24  N23  C22  N22   180.00   0.0  0
 XFH  CONST_34  C27  C24  C25  C26   180.00   0.0  0
 XFH  CONST_35  H03  C03  C02  N01   180.00   0.0  0
 XFH  CONST_36  H05  C05  C06  N01   180.00   0.0  0
 XFH  CONST_37  H16  C16  C11  C12   180.00   0.0  0
 XFH  CONST_38  H14  C14  C13  C12   180.00   0.0  0
 XFH  CONST_39  H11  C11  C12  C13   180.00   0.0  0
 XFH  CONST_40  H12  C12  C13  C14   180.00   0.0  0
 XFH  CONST_41  H25  C25  C26  C21   180.00   0.0  0
 XFH  CONST_42  H21  C21  C22  N23   180.00   0.0  0
 XFH  Var_01    C09  C08  C06  N01   -69.13  30.0  2
 XFH  Var_02    C13  C09  C08  C06   176.78  30.0  3
 XFH  Var_03    C12  C13  C09  C08    88.41  30.0  2
 XFH  Var_04    C18  C17  C15  C14    90.00  30.0  2
 XFH  Var_05    C26  C18  C17  C15  -177.35  30.0  3
 XFH  Var_06    C21  C26  C18  C17   -97.28  30.0  3
 XFH  Var_07    H07  C07  C04  C03   111.78  30.0  2
 XFH  Var_08    H27  C27  C24  N23    53.54  30.0  2

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
 XFH  plan-1  N01   0.020
 XFH  plan-1  C02   0.020
 XFH  plan-1  N02   0.020
 XFH  plan-1  C03   0.020
 XFH  plan-1  C04   0.020
 XFH  plan-1  C05   0.020
 XFH  plan-1  C06   0.020
 XFH  plan-1  C07   0.020
 XFH  plan-1  C08   0.020
 XFH  plan-1  H03   0.020
 XFH  plan-1  H05   0.020
 XFH  plan-2  C09   0.020
 XFH  plan-2  C11   0.020
 XFH  plan-2  C12   0.020
 XFH  plan-2  C13   0.020
 XFH  plan-2  C14   0.020
 XFH  plan-2  C15   0.020
 XFH  plan-2  C16   0.020
 XFH  plan-2  C17   0.020
 XFH  plan-2  H11   0.020
 XFH  plan-2  H12   0.020
 XFH  plan-2  H14   0.020
 XFH  plan-2  H16   0.020
 XFH  plan-3  C18   0.020
 XFH  plan-3  C21   0.020
 XFH  plan-3  C22   0.020
 XFH  plan-3  N22   0.020
 XFH  plan-3  N23   0.020
 XFH  plan-3  C24   0.020
 XFH  plan-3  C25   0.020
 XFH  plan-3  C26   0.020
 XFH  plan-3  H21   0.020
 XFH  plan-3  H25   0.020
 XFH  plan-3  C27   0.020
 XFH  plan-4  C02   0.020
 XFH  plan-4  N02   0.020
 XFH  plan-4  HN02  0.020
 XFH  plan-4  HN0A  0.020
 XFH  plan-5  C22   0.020
 XFH  plan-5  N22   0.020
 XFH  plan-5  HN22  0.020
 XFH  plan-5  HN2A  0.020

