# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 20:00:32 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 6-(2-{5-[3-(dimethylamino)propyl]-2,3,4-trifluorophenyl}ethyl)-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CCCc1cc(CCc2cc(C)cc(N)n2)c(F)c(F)c1F
#
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
 KMS  KMS  6-(2-{5-[3-(dimethylamino)propyl]-2,3,4-trifluorophenyl}ethyl)-4-methylpyridin-2-amine  ligand  49  25  .  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_KMS
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
 KMS  C02  C  CR6   0   0.438  -5.7533  -0.2205  -0.8607
 KMS  C04  C  CR6   0   0.204  -5.5794  -1.8836   0.8626
 KMS  C05  C  CR16  0  -0.440  -4.3164  -1.3574   1.1515
 KMS  C06  C  CR6   0   0.279  -3.8497  -0.2848   0.4113
 KMS  C09  C  CH2   0  -0.503  -1.5468   0.1048  -0.5249
 KMS  C11  C  CR6   0  -0.069  -0.1830   0.6717  -0.2550
 KMS  C12  C  CR6   0   0.378   0.0784   2.0222  -0.4105
 KMS  C03  C  CR16  0  -0.441  -6.3050  -1.3052  -0.1601
 KMS  C07  C  CH3   0  -0.725  -6.1391  -3.0245   1.6563
 KMS  C08  C  CH2   0  -0.490  -2.4912   0.3029   0.6688
 KMS  C13  C  CR6   0   0.290   1.3186   2.5560  -0.1151
 KMS  C14  C  CR6   0   0.378   2.3235   1.7292   0.3495
 KMS  C15  C  CR6   0  -0.061   2.1190   0.3708   0.5250
 KMS  C16  C  CR16  0  -0.358   0.8572  -0.1261   0.2132
 KMS  C17  C  CH2   0  -0.502   3.2245  -0.5261   1.0029
 KMS  C18  C  CH2   0  -0.444   4.2236  -0.8751  -0.1029
 KMS  C19  C  CH2   0  -0.254   5.2831  -1.8429   0.4054
 KMS  C21  C  CH3   0  -0.519   7.4621  -2.7698   0.1194
 KMS  C22  C  CH3   0  -0.526   5.9952  -2.6549  -1.7527
 KMS  F12  F  F     0  -0.301  -0.8735   2.8532  -0.8509
 KMS  F13  F  F     0  -0.300   1.5418   3.8610  -0.2744
 KMS  F14  F  F     0  -0.300   3.5104   2.2791   0.6317
 KMS  N01  N  N     0  -0.483  -4.5520   0.2724  -0.5755
 KMS  N02  N  NH2   0  -0.838  -6.4619   0.4044  -1.8483
 KMS  N20  N  NT    0  -0.408   6.3926  -2.0267  -0.5111
 KMS  H1   H  HCR6  0   0.245  -3.7058  -1.7846   1.9370
 KMS  H2   H  HCH2  0   0.259  -1.9900   0.5552  -1.4142
 KMS  H3   H  HCH2  0   0.260  -1.4486  -0.9627  -0.7310
 KMS  H4   H  HCR6  0   0.255  -7.2871  -1.6797  -0.4236
 KMS  H5   H  HCH3  0   0.256  -6.7597  -2.6506   2.4731
 KMS  H6   H  HCH3  0   0.248  -6.7653  -3.6719   1.0435
 KMS  H7   H  HCH3  0   0.247  -5.3490  -3.6289   2.0998
 KMS  H8   H  HCH2  0   0.252  -2.5967   1.3710   0.8760
 KMS  H9   H  HCH2  0   0.252  -2.0508  -0.1526   1.5578
 KMS  H10  H  HCR6  0   0.265   0.6753  -1.1862   0.3459
 KMS  H11  H  HCH2  0   0.251   3.7524  -0.0636   1.8405
 KMS  H12  H  HCH2  0   0.254   2.7804  -1.4457   1.3910
 KMS  H13  H  HCH2  0   0.236   3.6775  -1.3044  -0.9463
 KMS  H14  H  HCH2  0   0.230   4.7130   0.0310  -0.4695
 KMS  H15  H  HCH2  0   0.225   5.6926  -1.4476   1.3406
 KMS  H16  H  HCH2  0   0.187   4.8031  -2.8047   0.6641
 KMS  H17  H  HCH3  0   0.231   8.3138  -2.8482  -0.5581
 KMS  H18  H  HCH3  0   0.231   7.7975  -2.2524   1.0196
 KMS  H19  H  HCH3  0   0.189   7.1710  -3.7921   0.4090
 KMS  H20  H  HCH3  0   0.188   5.5693  -3.6620  -1.6127
 KMS  H21  H  HCH3  0   0.236   5.2555  -2.0503  -2.2769
 KMS  H22  H  HCH3  0   0.233   6.8603  -2.7509  -2.4101
 KMS  H23  H  HNH2  0   0.387  -7.1934  -0.1235  -2.2948
 KMS  H24  H  HNH2  0   0.378  -5.9247   0.9718  -2.4834

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
 KMS  C21  N20  single    1.447  0.020  1.447
 KMS  C22  N20  single    1.447  0.020  1.447
 KMS  N20  C19  single    1.451  0.020  1.451
 KMS  C19  C18  single    1.522  0.020  1.522
 KMS  C17  C18  single    1.531  0.020  1.531
 KMS  C17  C15  single    1.502  0.020  1.502
 KMS  C15  C16  aromatic  1.392  0.020  1.392
 KMS  C15  C14  aromatic  1.385  0.020  1.385
 KMS  F14  C14  single    1.338  0.020  1.338
 KMS  C16  C11  aromatic  1.392  0.020  1.392
 KMS  C14  C13  aromatic  1.382  0.020  1.382
 KMS  N02  C02  single    1.367  0.020  1.367
 KMS  C08  C06  single    1.502  0.020  1.502
 KMS  C08  C09  single    1.535  0.020  1.535
 KMS  N01  C02  aromatic  1.329  0.020  1.329
 KMS  N01  C06  aromatic  1.333  0.020  1.333
 KMS  C11  C09  single    1.501  0.020  1.501
 KMS  C11  C12  aromatic  1.384  0.020  1.384
 KMS  C02  C03  aromatic  1.404  0.020  1.404
 KMS  C06  C05  aromatic  1.384  0.020  1.384
 KMS  C13  C12  aromatic  1.382  0.020  1.382
 KMS  C13  F13  single    1.334  0.020  1.334
 KMS  C12  F12  single    1.338  0.020  1.338
 KMS  C03  C04  aromatic  1.381  0.020  1.381
 KMS  C05  C04  aromatic  1.398  0.020  1.398
 KMS  C04  C07  single    1.498  0.020  1.498
 KMS  C05  H1   single    0.930  0.020  1.080
 KMS  C09  H2   single    0.970  0.020  1.090
 KMS  C09  H3   single    0.970  0.020  1.090
 KMS  C03  H4   single    0.930  0.020  1.080
 KMS  C07  H5   single    0.970  0.020  1.090
 KMS  C07  H6   single    0.970  0.020  1.090
 KMS  C07  H7   single    0.970  0.020  1.090
 KMS  C08  H8   single    0.970  0.020  1.090
 KMS  C08  H9   single    0.970  0.020  1.090
 KMS  C16  H10  single    0.930  0.020  1.080
 KMS  C17  H11  single    0.970  0.020  1.090
 KMS  C17  H12  single    0.970  0.020  1.090
 KMS  C18  H13  single    0.970  0.020  1.090
 KMS  C18  H14  single    0.970  0.020  1.090
 KMS  C19  H15  single    0.970  0.020  1.090
 KMS  C19  H16  single    0.970  0.020  1.090
 KMS  C21  H17  single    0.970  0.020  1.090
 KMS  C21  H18  single    0.970  0.020  1.090
 KMS  C21  H19  single    0.970  0.020  1.090
 KMS  C22  H20  single    0.970  0.020  1.090
 KMS  C22  H21  single    0.970  0.020  1.090
 KMS  C22  H22  single    0.970  0.020  1.090
 KMS  N02  H23  single    0.890  0.020  1.040
 KMS  N02  H24  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
 KMS  N02  C02  N01  117.00  3.000
 KMS  N01  C02  C03  122.30  3.000
 KMS  N02  C02  C03  120.66  3.000
 KMS  C07  C04  C03  121.00  3.000
 KMS  C07  C04  C05  120.96  3.000
 KMS  C03  C04  C05  118.04  3.000
 KMS  H1   C05  C06  120.23  3.000
 KMS  H1   C05  C04  120.72  3.000
 KMS  C06  C05  C04  119.05  3.000
 KMS  N01  C06  C08  116.08  3.000
 KMS  N01  C06  C05  122.82  3.000
 KMS  C08  C06  C05  121.08  3.000
 KMS  H3   C09  H2   106.64  3.000
 KMS  H3   C09  C08  109.18  3.000
 KMS  H2   C09  C08  109.31  3.000
 KMS  H3   C09  C11  108.75  3.000
 KMS  H2   C09  C11  111.08  3.000
 KMS  C08  C09  C11  111.74  3.000
 KMS  C16  C11  C12  117.12  3.000
 KMS  C12  C11  C09  121.31  3.000
 KMS  C16  C11  C09  121.52  3.000
 KMS  F12  C12  C13  117.96  3.000
 KMS  F12  C12  C11  120.56  3.000
 KMS  C13  C12  C11  121.48  3.000
 KMS  H4   C03  C04  120.77  3.000
 KMS  H4   C03  C02  120.11  3.000
 KMS  C04  C03  C02  119.12  3.000
 KMS  H7   C07  H6   108.44  3.000
 KMS  H7   C07  H5   107.32  3.000
 KMS  H6   C07  H5   107.31  3.000
 KMS  H7   C07  C04  111.55  3.000
 KMS  H6   C07  C04  111.67  3.000
 KMS  H5   C07  C04  110.36  3.000
 KMS  H9   C08  H8   106.99  3.000
 KMS  H9   C08  C09  109.34  3.000
 KMS  H8   C08  C09  109.45  3.000
 KMS  H9   C08  C06  109.94  3.000
 KMS  H8   C08  C06  109.11  3.000
 KMS  C09  C08  C06  111.88  3.000
 KMS  F13  C13  C14  120.27  3.000
 KMS  F13  C13  C12  120.17  3.000
 KMS  C14  C13  C12  119.56  3.000
 KMS  F14  C14  C15  120.49  3.000
 KMS  F14  C14  C13  118.04  3.000
 KMS  C15  C14  C13  121.47  3.000
 KMS  C17  C15  C16  121.71  3.000
 KMS  C16  C15  C14  117.12  3.000
 KMS  C17  C15  C14  121.16  3.000
 KMS  H10  C16  C15  118.30  3.000
 KMS  H10  C16  C11  118.45  3.000
 KMS  C15  C16  C11  123.25  3.000
 KMS  H12  C17  H11  106.28  3.000
 KMS  H12  C17  C18  109.27  3.000
 KMS  H11  C17  C18  109.57  3.000
 KMS  H12  C17  C15  108.45  3.000
 KMS  H11  C17  C15  110.30  3.000
 KMS  C18  C17  C15  112.75  3.000
 KMS  H14  C18  H13  106.89  3.000
 KMS  H14  C18  C19  109.11  3.000
 KMS  H13  C18  C19  110.84  3.000
 KMS  H14  C18  C17  110.22  3.000
 KMS  H13  C18  C17  108.73  3.000
 KMS  C19  C18  C17  110.98  3.000
 KMS  H16  C19  H15  106.06  3.000
 KMS  H16  C19  N20  111.69  3.000
 KMS  H15  C19  N20  107.42  3.000
 KMS  H16  C19  C18  109.21  3.000
 KMS  H15  C19  C18  108.42  3.000
 KMS  N20  C19  C18  113.69  3.000
 KMS  H19  C21  H18  107.72  3.000
 KMS  H19  C21  H17  107.62  3.000
 KMS  H18  C21  H17  107.84  3.000
 KMS  H19  C21  N20  113.32  3.000
 KMS  H18  C21  N20  110.07  3.000
 KMS  H17  C21  N20  110.08  3.000
 KMS  H22  C22  H21  107.29  3.000
 KMS  H22  C22  H20  107.61  3.000
 KMS  H21  C22  H20  107.80  3.000
 KMS  H22  C22  N20  109.73  3.000
 KMS  H21  C22  N20  110.99  3.000
 KMS  H20  C22  N20  113.19  3.000
 KMS  C06  N01  C02  118.67  3.000
 KMS  H24  N02  H23  113.79  3.000
 KMS  H24  N02  C02  115.90  3.000
 KMS  H23  N02  C02  117.23  3.000
 KMS  C22  N20  C21  110.72  3.000
 KMS  C22  N20  C19  112.77  3.000
 KMS  C21  N20  C19  110.80  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
 KMS  CONST_01  C05  C06  N01  C02     0.00   0.0  0
 KMS  CONST_02  C05  C04  C03  C02     0.00   0.0  0
 KMS  CONST_03  N01  C02  C03  C04     0.00   0.0  0
 KMS  CONST_04  N01  C06  C05  C04     0.00   0.0  0
 KMS  CONST_05  C03  C02  N01  C06     0.00   0.0  0
 KMS  CONST_06  C03  C04  C05  C06     0.00   0.0  0
 KMS  CONST_07  C14  C15  C16  C11     0.00   0.0  0
 KMS  CONST_08  C14  C13  C12  C11     0.00   0.0  0
 KMS  CONST_09  C15  C16  C11  C12     0.00   0.0  0
 KMS  CONST_10  C15  C14  C13  C12     0.00   0.0  0
 KMS  CONST_11  C16  C15  C14  C13     0.00   0.0  0
 KMS  CONST_12  C16  C11  C12  C13     0.00   0.0  0
 KMS  CONST_13  C08  C06  N01  C02   180.00   0.0  0
 KMS  CONST_14  C07  C04  C03  C02   180.00   0.0  0
 KMS  CONST_15  N02  C02  C03  C04   180.00   0.0  0
 KMS  CONST_16  C08  C06  C05  C04   180.00   0.0  0
 KMS  CONST_17  N02  C02  N01  C06   180.00   0.0  0
 KMS  CONST_18  C07  C04  C05  C06   180.00   0.0  0
 KMS  CONST_19  C15  C16  C11  C09   180.00   0.0  0
 KMS  CONST_20  C13  C12  C11  C09   180.00   0.0  0
 KMS  CONST_21  C17  C15  C16  C11   180.00   0.0  0
 KMS  CONST_22  F13  C13  C12  C11   180.00   0.0  0
 KMS  CONST_23  F14  C14  C13  C12   180.00   0.0  0
 KMS  CONST_24  C17  C15  C14  C13   180.00   0.0  0
 KMS  CONST_25  F12  C12  C13  C14   180.00   0.0  0
 KMS  CONST_26  F13  C13  C14  C15   180.00   0.0  0
 KMS  CONST_27  F14  C14  C15  C16   180.00   0.0  0
 KMS  CONST_28  F12  C12  C11  C16   180.00   0.0  0
 KMS  CONST_29  H4   C03  C04  C05   180.00   0.0  0
 KMS  CONST_30  H10  C16  C11  C12   180.00   0.0  0
 KMS  CONST_31  H1   C05  C04  C03   180.00   0.0  0
 KMS  Var_01    C09  C08  C06  C05   114.60  30.0  1
 KMS  Var_02    C11  C09  C08  C06  -179.00  30.0  3
 KMS  Var_03    C08  C09  C11  C12   -81.67  30.0  2
 KMS  Var_04    C18  C17  C15  C14   -77.97  30.0  3
 KMS  Var_05    H5   C07  C04  C05    93.64  30.0  2
 KMS  Var_06    C19  C18  C17  C15  -176.99  30.0  3
 KMS  Var_07    N20  C19  C18  C17  -169.46  30.0  2
 KMS  Var_08    C21  N20  C19  C18   170.27  30.0  1
 KMS  Var_09    H17  C21  N20  C19  -176.54  30.0  3
 KMS  Var_10    H20  C22  N20  C19   -60.89  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
 KMS  plan-1  C09  0.020
 KMS  plan-1  C11  0.020
 KMS  plan-1  C12  0.020
 KMS  plan-1  C13  0.020
 KMS  plan-1  C14  0.020
 KMS  plan-1  C15  0.020
 KMS  plan-1  C16  0.020
 KMS  plan-1  C17  0.020
 KMS  plan-1  F12  0.020
 KMS  plan-1  F13  0.020
 KMS  plan-1  F14  0.020
 KMS  plan-1  H10  0.020
 KMS  plan-2  C02  0.020
 KMS  plan-2  C04  0.020
 KMS  plan-2  C05  0.020
 KMS  plan-2  C06  0.020
 KMS  plan-2  C03  0.020
 KMS  plan-2  C07  0.020
 KMS  plan-2  C08  0.020
 KMS  plan-2  N01  0.020
 KMS  plan-2  N02  0.020
 KMS  plan-2  H1   0.020
 KMS  plan-2  H4   0.020
 KMS  plan-3  C02  0.020
 KMS  plan-3  N02  0.020
 KMS  plan-3  H23  0.020
 KMS  plan-3  H24  0.020

