# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 20:09:05 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 6-(2-{3-[3-(dimethylamino)prop-1-yn-1-yl]-5-fluorophenyl}ethyl)-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CC#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
 KM7  KM7  6-(2-{3-[3-(dimethylamino)prop-1-yn-1-yl]-5-fluorophenyl}ethyl)-4-methylpyridin-2-amine  ligand  45  23  .  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_KM7
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
 KM7  C02  C  CR6   0   0.440  -4.5267  -2.0053   0.5652
 KM7  C03  C  CR16  0  -0.446  -5.7221  -1.5125   0.0124
 KM7  C04  C  CR6   0   0.204  -5.6806  -0.3794  -0.7728
 KM7  C05  C  CR16  0  -0.434  -4.4372   0.2265  -0.9913
 KM7  C06  C  CR6   0   0.279  -3.3106  -0.3268  -0.4116
 KM7  C07  C  CH3   0  -0.725  -6.9269   0.2056  -1.3633
 KM7  C08  C  CH2   0  -0.489  -1.9536   0.2919  -0.5964
 KM7  C09  C  CH2   0  -0.516  -1.3967   0.8464   0.7215
 KM7  C11  C  CR6   0   0.158  -0.0150   1.4075   0.5442
 KM7  C12  C  CR16  0  -0.471   0.1689   2.7597   0.2698
 KM7  C13  C  CR6   0   0.557   1.4497   3.2384   0.0700
 KM7  C14  C  CR16  0  -0.474   2.5651   2.4310   0.1258
 KM7  C15  C  CR6   0  -0.081   2.3827   1.0734   0.4007
 KM7  C16  C  CR16  0  -0.368   1.0961   0.5735   0.6082
 KM7  C17  C  CSP   0   0.161   3.5111   0.2031   0.4689
 KM7  C18  C  CSP   0   0.058   4.4596  -0.5376   0.5236
 KM7  C19  C  CH2   0  -0.461   5.6085  -1.4362   0.5924
 KM7  C21  C  CH3   0  -0.527   5.8786  -1.6908  -1.7790
 KM7  C22  C  CH3   0  -0.526   6.6352  -3.3975  -0.2870
 KM7  F13  F  F     0  -0.313   1.6154   4.5451  -0.1874
 KM7  N01  N  N     0  -0.485  -3.3537  -1.4194   0.3540
 KM7  N02  N  NH2   0  -0.838  -4.5247  -3.1493   1.3113
 KM7  N20  N  NT    0  -0.406   5.6436  -2.3683  -0.5207
 KM7  H1   H  HCR6  0   0.255  -6.6599  -2.0202   0.2039
 KM7  H2   H  HCR6  0   0.244  -4.3573   1.1143  -1.6062
 KM7  H3   H  HCH3  0   0.254  -7.1991   1.1263  -0.8441
 KM7  H4   H  HCH3  0   0.249  -6.7832   0.4617  -2.4131
 KM7  H5   H  HCH3  0   0.247  -7.7700  -0.4793  -1.2895
 KM7  H6   H  HCH2  0   0.251  -1.2656  -0.4640  -0.9856
 KM7  H7   H  HCH2  0   0.250  -2.0040   1.0900  -1.3399
 KM7  H8   H  HCH2  0   0.255  -2.0667   1.6217   1.0999
 KM7  H9   H  HCH2  0   0.257  -1.3816   0.0458   1.4631
 KM7  H10  H  HCR6  0   0.276  -0.6762   3.4353   0.2183
 KM7  H11  H  HCR6  0   0.279   3.5536   2.8384  -0.0374
 KM7  H12  H  HCR6  0   0.256   0.9653  -0.4796   0.8240
 KM7  H13  H  HCH2  0   0.238   6.5290  -0.8319   0.6627
 KM7  H14  H  HCH2  0   0.275   5.5464  -2.0065   1.5238
 KM7  H15  H  HCH3  0   0.238   5.8595  -2.4124  -2.5960
 KM7  H16  H  HCH3  0   0.240   5.0959  -0.9552  -1.9686
 KM7  H17  H  HCH3  0   0.196   6.8475  -1.1684  -1.8100
 KM7  H18  H  HCH3  0   0.197   7.6617  -3.0057  -0.2157
 KM7  H19  H  HCH3  0   0.237   6.4154  -3.9287   0.6400
 KM7  H20  H  HCH3  0   0.240   6.6123  -4.1216  -1.1015
 KM7  H21  H  HNH2  0   0.387  -5.3927  -3.4256   1.7391
 KM7  H22  H  HNH2  0   0.379  -3.7183  -3.2917   1.8975

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
 KM7  C21  N20  single    1.448  0.020  1.448
 KM7  C22  N20  single    1.448  0.020  1.448
 KM7  N20  C19  single    1.452  0.020  1.452
 KM7  C19  C18  single    1.460  0.020  1.460
 KM7  C18  C17  triple    1.205  0.020  1.205
 KM7  C17  C15  single    1.427  0.020  1.427
 KM7  C15  C16  aromatic  1.396  0.020  1.396
 KM7  C15  C14  aromatic  1.397  0.020  1.397
 KM7  C16  C11  aromatic  1.391  0.020  1.391
 KM7  N02  C02  single    1.366  0.020  1.366
 KM7  C08  C06  single    1.503  0.020  1.503
 KM7  C08  C09  single    1.534  0.020  1.534
 KM7  N01  C02  aromatic  1.328  0.020  1.328
 KM7  N01  C06  aromatic  1.335  0.020  1.335
 KM7  C14  C13  aromatic  1.378  0.020  1.378
 KM7  C02  C03  aromatic  1.406  0.020  1.406
 KM7  C06  C05  aromatic  1.383  0.020  1.383
 KM7  C11  C09  single    1.502  0.020  1.502
 KM7  C11  C12  aromatic  1.392  0.020  1.392
 KM7  C13  C12  aromatic  1.382  0.020  1.382
 KM7  C13  F13  single    1.342  0.020  1.342
 KM7  C03  C04  aromatic  1.379  0.020  1.379
 KM7  C05  C04  aromatic  1.400  0.020  1.400
 KM7  C04  C07  single    1.498  0.020  1.498
 KM7  C03  H1   single    0.930  0.020  1.080
 KM7  C05  H2   single    0.930  0.020  1.080
 KM7  C07  H3   single    0.970  0.020  1.090
 KM7  C07  H4   single    0.970  0.020  1.090
 KM7  C07  H5   single    0.970  0.020  1.090
 KM7  C08  H6   single    0.970  0.020  1.090
 KM7  C08  H7   single    0.970  0.020  1.090
 KM7  C09  H8   single    0.970  0.020  1.090
 KM7  C09  H9   single    0.970  0.020  1.090
 KM7  C12  H10  single    0.930  0.020  1.080
 KM7  C14  H11  single    0.930  0.020  1.080
 KM7  C16  H12  single    0.930  0.020  1.080
 KM7  C19  H13  single    0.970  0.020  1.090
 KM7  C19  H14  single    0.970  0.020  1.090
 KM7  C21  H15  single    0.970  0.020  1.090
 KM7  C21  H16  single    0.970  0.020  1.090
 KM7  C21  H17  single    0.970  0.020  1.090
 KM7  C22  H18  single    0.970  0.020  1.090
 KM7  C22  H19  single    0.970  0.020  1.090
 KM7  C22  H20  single    0.970  0.020  1.090
 KM7  N02  H21  single    0.890  0.020  1.040
 KM7  N02  H22  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
 KM7  N02  C02  N01  117.07  3.000
 KM7  N01  C02  C03  122.26  3.000
 KM7  N02  C02  C03  120.63  3.000
 KM7  H1   C03  C04  120.77  3.000
 KM7  H1   C03  C02  120.14  3.000
 KM7  C04  C03  C02  119.08  3.000
 KM7  C07  C04  C05  120.55  3.000
 KM7  C07  C04  C03  121.34  3.000
 KM7  C05  C04  C03  118.10  3.000
 KM7  H2   C05  C06  120.40  3.000
 KM7  H2   C05  C04  120.59  3.000
 KM7  C06  C05  C04  119.01  3.000
 KM7  N01  C06  C08  115.89  3.000
 KM7  N01  C06  C05  122.80  3.000
 KM7  C08  C06  C05  121.30  3.000
 KM7  H5   C07  H4   108.36  3.000
 KM7  H5   C07  H3   107.78  3.000
 KM7  H4   C07  H3   107.02  3.000
 KM7  H5   C07  C04  111.84  3.000
 KM7  H4   C07  C04  111.21  3.000
 KM7  H3   C07  C04  110.45  3.000
 KM7  H7   C08  H6   106.97  3.000
 KM7  H7   C08  C09  109.73  3.000
 KM7  H6   C08  C09  109.09  3.000
 KM7  H7   C08  C06  110.06  3.000
 KM7  H6   C08  C06  109.10  3.000
 KM7  C09  C08  C06  111.77  3.000
 KM7  H9   C09  H8   107.08  3.000
 KM7  H9   C09  C11  109.97  3.000
 KM7  H8   C09  C11  109.88  3.000
 KM7  H9   C09  C08  108.88  3.000
 KM7  H8   C09  C08  109.35  3.000
 KM7  C11  C09  C08  111.56  3.000
 KM7  C16  C11  C12  119.09  3.000
 KM7  C12  C11  C09  120.51  3.000
 KM7  C16  C11  C09  120.36  3.000
 KM7  H10  C12  C13  120.01  3.000
 KM7  H10  C12  C11  120.82  3.000
 KM7  C13  C12  C11  119.17  3.000
 KM7  F13  C13  C14  118.57  3.000
 KM7  F13  C13  C12  118.65  3.000
 KM7  C14  C13  C12  122.78  3.000
 KM7  H11  C14  C15  121.00  3.000
 KM7  H11  C14  C13  120.86  3.000
 KM7  C15  C14  C13  118.14  3.000
 KM7  C17  C15  C16  120.23  3.000
 KM7  C16  C15  C14  119.84  3.000
 KM7  C17  C15  C14  119.93  3.000
 KM7  H12  C16  C15  119.29  3.000
 KM7  H12  C16  C11  119.73  3.000
 KM7  C15  C16  C11  120.98  3.000
 KM7  C18  C17  C15  180.00  3.000
 KM7  C19  C18  C17  180.00  3.000
 KM7  H14  C19  H13  106.18  3.000
 KM7  H14  C19  N20  108.63  3.000
 KM7  H13  C19  N20  112.35  3.000
 KM7  H14  C19  C18  108.44  3.000
 KM7  H13  C19  C18  108.80  3.000
 KM7  N20  C19  C18  112.20  3.000
 KM7  H17  C21  H16  107.85  3.000
 KM7  H17  C21  H15  107.95  3.000
 KM7  H16  C21  H15  107.67  3.000
 KM7  H17  C21  N20  112.91  3.000
 KM7  H16  C21  N20  110.49  3.000
 KM7  H15  C21  N20  109.80  3.000
 KM7  H20  C22  H19  107.90  3.000
 KM7  H20  C22  H18  107.72  3.000
 KM7  H19  C22  H18  107.82  3.000
 KM7  H20  C22  N20  109.70  3.000
 KM7  H19  C22  N20  110.19  3.000
 KM7  H18  C22  N20  113.33  3.000
 KM7  C06  N01  C02  118.74  3.000
 KM7  H22  N02  H21  113.86  3.000
 KM7  H22  N02  C02  115.95  3.000
 KM7  H21  N02  C02  117.45  3.000
 KM7  C22  N20  C21  111.19  3.000
 KM7  C22  N20  C19  110.43  3.000
 KM7  C21  N20  C19  111.69  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
 KM7  CONST_01  C05  C06  N01  C02     0.00   0.0  0
 KM7  CONST_02  C05  C04  C03  C02     0.00   0.0  0
 KM7  CONST_03  C06  N01  C02  C03     0.00   0.0  0
 KM7  CONST_04  C06  C05  C04  C03     0.00   0.0  0
 KM7  CONST_05  N01  C02  C03  C04     0.00   0.0  0
 KM7  CONST_06  N01  C06  C05  C04     0.00   0.0  0
 KM7  CONST_07  C14  C15  C16  C11     0.00   0.0  0
 KM7  CONST_08  C14  C13  C12  C11     0.00   0.0  0
 KM7  CONST_09  C15  C16  C11  C12     0.00   0.0  0
 KM7  CONST_10  C15  C14  C13  C12     0.00   0.0  0
 KM7  CONST_11  C16  C15  C14  C13     0.00   0.0  0
 KM7  CONST_12  C16  C11  C12  C13     0.00   0.0  0
 KM7  CONST_13  C08  C06  N01  C02   180.00   0.0  0
 KM7  CONST_14  C07  C04  C03  C02   180.00   0.0  0
 KM7  CONST_15  N02  C02  C03  C04   180.00   0.0  0
 KM7  CONST_16  C08  C06  C05  C04   180.00   0.0  0
 KM7  CONST_17  N02  C02  N01  C06   180.00   0.0  0
 KM7  CONST_18  C07  C04  C05  C06   180.00   0.0  0
 KM7  CONST_19  C15  C16  C11  C09   180.00   0.0  0
 KM7  CONST_20  C13  C12  C11  C09   180.00   0.0  0
 KM7  CONST_21  C17  C15  C16  C11   180.00   0.0  0
 KM7  CONST_22  F13  C13  C12  C11   180.00   0.0  0
 KM7  CONST_23  C17  C15  C14  C13   180.00   0.0  0
 KM7  CONST_24  F13  C13  C14  C15   180.00   0.0  0
 KM7  CONST_25  H2   C05  C04  C03   180.00   0.0  0
 KM7  CONST_26  H1   C03  C04  C05   180.00   0.0  0
 KM7  CONST_27  H12  C16  C11  C12   180.00   0.0  0
 KM7  CONST_28  H11  C14  C13  C12   180.00   0.0  0
 KM7  CONST_29  H10  C12  C13  C14   180.00   0.0  0
 KM7  Var_01    C09  C08  C06  C05   113.67  30.0  1
 KM7  Var_02    C11  C09  C08  C06   177.42  30.0  3
 KM7  Var_03    C16  C11  C09  C08   -84.78  30.0  3
 KM7  Var_04    H3   C07  C04  C03   106.92  30.0  2
 KM7  Var_05    N20  C19  C18  C17   123.69  30.0  2
 KM7  Var_06    C21  N20  C19  C18    66.66  30.0  2
 KM7  Var_07    H15  C21  N20  C19  -177.76  30.0  3
 KM7  Var_08    H18  C22  N20  C19   -62.77  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
 KM7  plan-1  C09  0.020
 KM7  plan-1  C11  0.020
 KM7  plan-1  C12  0.020
 KM7  plan-1  C13  0.020
 KM7  plan-1  C14  0.020
 KM7  plan-1  C15  0.020
 KM7  plan-1  C16  0.020
 KM7  plan-1  C17  0.020
 KM7  plan-1  C18  0.020
 KM7  plan-1  F13  0.020
 KM7  plan-1  H10  0.020
 KM7  plan-1  H11  0.020
 KM7  plan-1  H12  0.020
 KM7  plan-2  C02  0.020
 KM7  plan-2  C03  0.020
 KM7  plan-2  C04  0.020
 KM7  plan-2  C05  0.020
 KM7  plan-2  C06  0.020
 KM7  plan-2  C07  0.020
 KM7  plan-2  C08  0.020
 KM7  plan-2  N01  0.020
 KM7  plan-2  N02  0.020
 KM7  plan-2  H1   0.020
 KM7  plan-2  H2   0.020
 KM7  plan-3  C02  0.020
 KM7  plan-3  N02  0.020
 KM7  plan-3  H21  0.020
 KM7  plan-3  H22  0.020

