# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 22:05:56 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 6-(2-{3-fluoro-5-[3-(methylamino)prop-1-yn-1-yl]phenyl}ethyl)-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCC#Cc1cc(F)cc(CCc2cc(C)cc(N)n2)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
 KLY  KLY  6-(2-{3-fluoro-5-[3-(methylamino)prop-1-yn-1-yl]phenyl}ethyl)-4-methylpyridin-2-amine  ligand  42  22  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KLY
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
 KLY  C15  C  CR6   0  -0.074   2.6956   0.8694  -0.0492
 KLY  C14  C  CR16  0  -0.474   2.8466   2.2571  -0.0986
 KLY  C11  C  CR6   0   0.157   0.3430   1.1280   0.4760
 KLY  C12  C  CR16  0  -0.469   0.4952   2.5112   0.4242
 KLY  C19  C  CH2   0  -0.459   5.9367  -1.5206  -0.7674
 KLY  C21  C  CH3   0  -0.525   7.2338  -3.3961  -0.0231
 KLY  N20  N  NH1   0  -0.592   6.0555  -2.5845   0.2129
 KLY  C18  C  CSP   0   0.037   4.7777  -0.6735  -0.5051
 KLY  C17  C  CSP   0   0.171   3.8212   0.0279  -0.2937
 KLY  C16  C  CR16  0  -0.366   1.4459   0.3157   0.2376
 KLY  C13  C  CR6   0   0.557   1.7382   3.0412   0.1395
 KLY  F13  F  F     0  -0.313   1.8749   4.3756   0.0928
 KLY  C09  C  CH2   0  -0.515  -1.0104   0.5287   0.7296
 KLY  C08  C  CH2   0  -0.490  -1.7836   0.3252  -0.5804
 KLY  C06  C  CR6   0   0.284  -3.1603  -0.2305  -0.3492
 KLY  C05  C  CR16  0  -0.436  -4.2863   0.4759  -0.7300
 KLY  C04  C  CR6   0   0.207  -5.5496  -0.0789  -0.4910
 KLY  C07  C  CH3   0  -0.726  -6.7910   0.6436  -0.9164
 KLY  C03  C  CR16  0  -0.449  -5.6120  -1.3089   0.1293
 KLY  C02  C  CR6   0   0.444  -4.4149  -1.9543   0.4894
 KLY  N02  N  NH2   0  -0.840  -4.4413  -3.1464   1.1506
 KLY  N01  N  N     0  -0.488  -3.2216  -1.4236   0.2461
 KLY  H1   H  HCR6  0   0.279   3.8060   2.7060  -0.3176
 KLY  H2   H  HCR6  0   0.275  -0.3472   3.1679   0.6054
 KLY  H3   H  HCH2  0   0.263   6.8371  -0.9009  -0.7182
 KLY  H4   H  HCH2  0   0.240   5.8810  -1.8873  -1.8044
 KLY  H5   H  HCH3  0   0.239   7.2624  -4.2145   0.6952
 KLY  H6   H  HCH3  0   0.200   7.2889  -3.8283  -1.0315
 KLY  H7   H  HCH3  0   0.227   8.1329  -2.7947   0.1244
 KLY  H8   H  HNH1  0   0.353   5.2326  -3.1715   0.1597
 KLY  H10  H  HCR6  0   0.256   1.3386  -0.7610   0.2757
 KLY  H11  H  HCH2  0   0.255  -0.9082  -0.4318   1.2372
 KLY  H12  H  HCH2  0   0.254  -1.5851   1.1817   1.3906
 KLY  H13  H  HCH2  0   0.251  -1.8540   1.2748  -1.1149
 KLY  H14  H  HCH2  0   0.251  -1.2208  -0.3578  -1.2237
 KLY  H15  H  HCR6  0   0.243  -4.1898   1.4416  -1.2104
 KLY  H16  H  HCH3  0   0.254  -6.8928   0.6213  -2.0029
 KLY  H17  H  HCH3  0   0.247  -7.6867   0.1961  -0.4889
 KLY  H18  H  HCH3  0   0.249  -6.7567   1.6925  -0.6215
 KLY  H19  H  HCR6  0   0.255  -6.5663  -1.7766   0.3405
 KLY  H20  H  HNH2  0   0.389  -5.2796  -3.6994   1.0966
 KLY  H21  H  HNH2  0   0.380  -3.5872  -3.6788   1.1561

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
 KLY  N20  C21  single    1.450  0.020  1.450
 KLY  N20  C19  single    1.452  0.020  1.452
 KLY  C19  C18  single    1.459  0.020  1.459
 KLY  C18  C17  triple    1.205  0.020  1.205
 KLY  C17  C15  single    1.427  0.020  1.427
 KLY  C15  C16  aromatic  1.397  0.020  1.397
 KLY  C15  C14  aromatic  1.397  0.020  1.397
 KLY  C16  C11  aromatic  1.390  0.020  1.390
 KLY  N02  C02  single    1.363  0.020  1.363
 KLY  C08  C06  single    1.502  0.020  1.502
 KLY  C08  C09  single    1.535  0.020  1.535
 KLY  N01  C02  aromatic  1.329  0.020  1.329
 KLY  N01  C06  aromatic  1.335  0.020  1.335
 KLY  C14  C13  aromatic  1.378  0.020  1.378
 KLY  C02  C03  aromatic  1.407  0.020  1.407
 KLY  C06  C05  aromatic  1.383  0.020  1.383
 KLY  C11  C09  single    1.502  0.020  1.502
 KLY  C11  C12  aromatic  1.393  0.020  1.393
 KLY  C13  C12  aromatic  1.381  0.020  1.381
 KLY  C13  F13  single    1.342  0.020  1.342
 KLY  C03  C04  aromatic  1.379  0.020  1.379
 KLY  C05  C04  aromatic  1.400  0.020  1.400
 KLY  C04  C07  single    1.498  0.020  1.498
 KLY  C14  H1   single    0.930  0.020  1.080
 KLY  C12  H2   single    0.930  0.020  1.080
 KLY  C19  H3   single    0.970  0.020  1.090
 KLY  C19  H4   single    0.970  0.020  1.090
 KLY  C21  H5   single    0.970  0.020  1.090
 KLY  C21  H6   single    0.970  0.020  1.090
 KLY  C21  H7   single    0.970  0.020  1.090
 KLY  N20  H8   single    0.890  0.020  1.040
 KLY  C16  H10  single    0.930  0.020  1.080
 KLY  C09  H11  single    0.970  0.020  1.090
 KLY  C09  H12  single    0.970  0.020  1.090
 KLY  C08  H13  single    0.970  0.020  1.090
 KLY  C08  H14  single    0.970  0.020  1.090
 KLY  C05  H15  single    0.930  0.020  1.080
 KLY  C07  H16  single    0.970  0.020  1.090
 KLY  C07  H17  single    0.970  0.020  1.090
 KLY  C07  H18  single    0.970  0.020  1.090
 KLY  C03  H19  single    0.930  0.020  1.080
 KLY  N02  H20  single    0.890  0.020  1.040
 KLY  N02  H21  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
 KLY  C16  C15  C17  120.49  3.000
 KLY  C16  C15  C14  119.86  3.000
 KLY  C17  C15  C14  119.65  3.000
 KLY  H1   C14  C13  120.80  3.000
 KLY  H1   C14  C15  121.02  3.000
 KLY  C13  C14  C15  118.17  3.000
 KLY  C09  C11  C16  120.72  3.000
 KLY  C09  C11  C12  120.07  3.000
 KLY  C16  C11  C12  119.16  3.000
 KLY  H2   C12  C13  120.11  3.000
 KLY  H2   C12  C11  120.73  3.000
 KLY  C13  C12  C11  119.16  3.000
 KLY  H4   C19  H3   105.82  3.000
 KLY  H4   C19  C18  108.80  3.000
 KLY  H3   C19  C18  108.46  3.000
 KLY  H4   C19  N20  113.33  3.000
 KLY  H3   C19  N20  108.51  3.000
 KLY  C18  C19  N20  111.66  3.000
 KLY  H7   C21  H6   107.42  3.000
 KLY  H7   C21  H5   107.65  3.000
 KLY  H6   C21  H5   107.96  3.000
 KLY  H7   C21  N20  109.81  3.000
 KLY  H6   C21  N20  114.23  3.000
 KLY  H5   C21  N20  109.55  3.000
 KLY  H8   N20  C21  109.12  3.000
 KLY  H8   N20  C19  108.84  3.000
 KLY  C21  N20  C19  111.52  3.000
 KLY  C17  C18  C19  180.00  3.000
 KLY  C18  C17  C15  180.00  3.000
 KLY  H10  C16  C11  119.75  3.000
 KLY  H10  C16  C15  119.35  3.000
 KLY  C11  C16  C15  120.89  3.000
 KLY  F13  C13  C12  118.71  3.000
 KLY  F13  C13  C14  118.54  3.000
 KLY  C12  C13  C14  122.75  3.000
 KLY  H12  C09  H11  107.09  3.000
 KLY  H12  C09  C08  109.31  3.000
 KLY  H11  C09  C08  109.12  3.000
 KLY  H12  C09  C11  109.74  3.000
 KLY  H11  C09  C11  110.21  3.000
 KLY  C08  C09  C11  111.28  3.000
 KLY  H14  C08  H13  106.76  3.000
 KLY  H14  C08  C06  109.32  3.000
 KLY  H13  C08  C06  109.75  3.000
 KLY  H14  C08  C09  109.00  3.000
 KLY  H13  C08  C09  109.57  3.000
 KLY  C06  C08  C09  112.29  3.000
 KLY  N01  C06  C05  122.82  3.000
 KLY  C05  C06  C08  120.99  3.000
 KLY  N01  C06  C08  116.19  3.000
 KLY  H15  C05  C04  120.63  3.000
 KLY  H15  C05  C06  120.34  3.000
 KLY  C04  C05  C06  119.03  3.000
 KLY  C03  C04  C07  121.36  3.000
 KLY  C07  C04  C05  120.54  3.000
 KLY  C03  C04  C05  118.10  3.000
 KLY  H18  C07  H17  108.37  3.000
 KLY  H18  C07  H16  106.97  3.000
 KLY  H17  C07  H16  107.80  3.000
 KLY  H18  C07  C04  111.17  3.000
 KLY  H17  C07  C04  111.85  3.000
 KLY  H16  C07  C04  110.49  3.000
 KLY  H19  C03  C02  120.09  3.000
 KLY  H19  C03  C04  120.84  3.000
 KLY  C02  C03  C04  119.07  3.000
 KLY  N01  C02  N02  117.09  3.000
 KLY  N01  C02  C03  122.29  3.000
 KLY  N02  C02  C03  120.59  3.000
 KLY  H21  N02  H20  114.62  3.000
 KLY  H21  N02  C02  116.67  3.000
 KLY  H20  N02  C02  118.09  3.000
 KLY  C02  N01  C06  118.69  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
 KLY  CONST_01  C12  C11  C16  C15     0.00   0.0  0
 KLY  CONST_02  C12  C13  C14  C15     0.00   0.0  0
 KLY  CONST_03  C11  C16  C15  C14     0.00   0.0  0
 KLY  CONST_04  C11  C12  C13  C14     0.00   0.0  0
 KLY  CONST_05  C13  C14  C15  C16     0.00   0.0  0
 KLY  CONST_06  C13  C12  C11  C16     0.00   0.0  0
 KLY  CONST_07  C03  C02  N01  C06     0.00   0.0  0
 KLY  CONST_08  C03  C04  C05  C06     0.00   0.0  0
 KLY  CONST_09  C02  N01  C06  C05     0.00   0.0  0
 KLY  CONST_10  C02  C03  C04  C05     0.00   0.0  0
 KLY  CONST_11  N01  C02  C03  C04     0.00   0.0  0
 KLY  CONST_12  N01  C06  C05  C04     0.00   0.0  0
 KLY  CONST_13  C09  C11  C16  C15   180.00   0.0  0
 KLY  CONST_14  F13  C13  C14  C15   180.00   0.0  0
 KLY  CONST_15  C17  C15  C16  C11   180.00   0.0  0
 KLY  CONST_16  F13  C13  C12  C11   180.00   0.0  0
 KLY  CONST_17  C13  C14  C15  C17   180.00   0.0  0
 KLY  CONST_18  C09  C11  C12  C13   180.00   0.0  0
 KLY  CONST_19  C02  N01  C06  C08   180.00   0.0  0
 KLY  CONST_20  C04  C05  C06  C08   180.00   0.0  0
 KLY  CONST_21  N02  C02  N01  C06   180.00   0.0  0
 KLY  CONST_22  C07  C04  C05  C06   180.00   0.0  0
 KLY  CONST_23  N02  C02  C03  C04   180.00   0.0  0
 KLY  CONST_24  C02  C03  C04  C07   180.00   0.0  0
 KLY  CONST_25  H10  C16  C15  C14   180.00   0.0  0
 KLY  CONST_26  H2   C12  C13  C14   180.00   0.0  0
 KLY  CONST_27  H1   C14  C13  C12   180.00   0.0  0
 KLY  CONST_28  H19  C03  C04  C05   180.00   0.0  0
 KLY  CONST_29  H15  C05  C04  C03   180.00   0.0  0
 KLY  Var_01    C06  C08  C09  C11  -178.06  30.0  2
 KLY  Var_02    C08  C09  C11  C12    88.10  30.0  2
 KLY  Var_03    N01  C06  C08  C09   -60.69  30.0  2
 KLY  Var_04    H16  C07  C04  C05    71.54  30.0  2
 KLY  Var_05    C18  C19  N20  C21  -178.00  30.0  3
 KLY  Var_06    H5   C21  N20  C19  -176.94  30.0  3

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
 KLY  plan-1  C15  0.020
 KLY  plan-1  C14  0.020
 KLY  plan-1  C11  0.020
 KLY  plan-1  C12  0.020
 KLY  plan-1  C18  0.020
 KLY  plan-1  C17  0.020
 KLY  plan-1  C16  0.020
 KLY  plan-1  C13  0.020
 KLY  plan-1  F13  0.020
 KLY  plan-1  C09  0.020
 KLY  plan-1  H1   0.020
 KLY  plan-1  H2   0.020
 KLY  plan-1  H10  0.020
 KLY  plan-2  C08  0.020
 KLY  plan-2  C06  0.020
 KLY  plan-2  C05  0.020
 KLY  plan-2  C04  0.020
 KLY  plan-2  C07  0.020
 KLY  plan-2  C03  0.020
 KLY  plan-2  C02  0.020
 KLY  plan-2  N02  0.020
 KLY  plan-2  N01  0.020
 KLY  plan-2  H15  0.020
 KLY  plan-2  H19  0.020
 KLY  plan-3  C02  0.020
 KLY  plan-3  N02  0.020
 KLY  plan-3  H20  0.020
 KLY  plan-3  H21  0.020

