# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 13:26:25 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 1-[4-methyl-6-(methylamino)-1,3,5-triazin-2-yl]-N-[2-(trifluoromethyl)benzyl]piperidine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1nc(C)nc(n1)N2CCC(CC2)C(=O)NCc3ccccc3C(F)(F)F
#
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
 1LF  1LF  1-[4-methyl-6-(methylamino)-1,3,5-triazin-2-yl]-N-[2-(trifluoromethyl)benzyl]piperidine-4-carboxamide  ligand  52  29  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1LF
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
 1LF  N1   N  NH1   0  -0.628   2.3907  -1.9183   0.0624
 1LF  C10  C  CH2   0  -0.323  -0.9678   0.2862   0.4003
 1LF  C13  C  CR6   0   0.107   4.6237  -0.9544   0.1323
 1LF  C15  C  CR16  0  -0.230   6.3824  -0.6692  -1.5155
 1LF  C17  C  CR16  0  -0.279   5.6114   1.2204  -0.2600
 1LF  C01  C  CH3   0  -0.509  -6.0579   3.3042  -1.7384
 1LF  C02  C  CR6   0   0.590  -4.7004   1.5941  -0.6181
 1LF  N02  N  N     0  -0.499  -5.8224   0.9031  -0.3809
 1LF  C03  C  CR6   0   0.369  -5.6339  -0.2440   0.2598
 1LF  C04  C  CH3   0  -0.729  -6.8527  -1.0631   0.5420
 1LF  N03  N  N     0  -0.505  -4.4708  -0.7230   0.6586
 1LF  C05  C  CR6   0   0.641  -3.4016   0.0461   0.3728
 1LF  N04  N  N     0  -0.527  -3.4724   1.2099  -0.2664
 1LF  N05  N  NT    0  -0.483  -2.1945  -0.3883   0.7810
 1LF  C06  C  CH2   0  -0.316  -1.9786  -1.7269   1.3009
 1LF  C07  C  CH2   0  -0.431  -1.2578  -2.5931   0.2709
 1LF  C08  C  CH1   0  -0.416   0.0095  -1.9504  -0.2976
 1LF  C09  C  CH2   0  -0.432  -0.2675  -0.4924  -0.7059
 1LF  C11  C  C     0   0.582   1.1893  -2.0282   0.6604
 1LF  O1   O  O     0  -0.490   1.0691  -2.1690   1.8692
 1LF  C12  C  CH2   0  -0.371   3.6482  -1.9115   0.7767
 1LF  C14  C  CR16  0  -0.284   5.4770  -1.4714  -0.8359
 1LF  C16  C  CR16  0  -0.250   6.4489   0.6824  -1.2262
 1LF  C18  C  CR6   0  -0.248   4.7000   0.4169   0.4156
 1LF  C1   C  CT    0   1.058   3.8336   1.0375   1.4723
 1LF  F01  F  F     0  -0.315   4.0919   0.5330   2.6900
 1LF  F02  F  F     0  -0.299   4.0074   2.3588   1.5674
 1LF  F    F  F     0  -0.310   2.5276   0.8419   1.2438
 1LF  H1   H  HNH1  0   0.402   2.4324  -1.8820  -0.9440
 1LF  H2   H  HCH2  0   0.272  -1.1923   1.2977   0.0756
 1LF  H3   H  HCH2  0   0.242  -0.3295   0.3597   1.2852
 1LF  H4   H  HCR6  0   0.270   7.0329  -1.1036  -2.2631
 1LF  H5   H  HCR6  0   0.274   5.6852   2.2760  -0.0402
 1LF  H6   H  HCH3  0   0.250  -5.8529   4.2671  -2.1982
 1LF  H7   H  HCH3  0   0.233  -6.5247   2.6608  -2.4856
 1LF  H8   H  HCH3  0   0.235  -6.7727   3.4579  -0.9295
 1LF  H9   H  HNH1  0   0.396  -3.9580   3.2581  -1.4497
 1LF  H10  H  HCH3  0   0.256  -7.3131  -1.3843  -0.3937
 1LF  H11  H  HCH3  0   0.246  -6.6081  -1.9427   1.1318
 1LF  H12  H  HCH3  0   0.254  -7.5952  -0.4693   1.0752
 1LF  H13  H  HCH2  0   0.246  -1.3900  -1.6502   2.2158
 1LF  H14  H  HCH2  0   0.267  -2.9351  -2.1700   1.5597
 1LF  H15  H  HCH2  0   0.245  -1.0354  -3.5675   0.7096
 1LF  H16  H  HCH2  0   0.239  -1.9418  -2.7752  -0.5629
 1LF  H17  H  HCH1  0   0.278   0.2908  -2.4971  -1.2032
 1LF  H18  H  HCH2  0   0.246  -0.9097  -0.4970  -1.5908
 1LF  H19  H  HCH2  0   0.247   0.6559   0.0149  -0.9930
 1LF  H20  H  HCH2  0   0.267   3.4521  -1.6752   1.8192
 1LF  H21  H  HCH2  0   0.267   4.0936  -2.9101   0.7713
 1LF  H22  H  HCR6  0   0.267   5.4321  -2.5305  -1.0595
 1LF  H23  H  HCR6  0   0.271   7.1524   1.3223  -1.7411
 1LF  N01  N  NH1   0  -0.642  -4.8120   2.7622  -1.2587

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
 1LF  C04  C03  single    1.495  0.020  1.495
 1LF  C03  N02  aromatic  1.327  0.020  1.327
 1LF  C03  N03  aromatic  1.320  0.020  1.320
 1LF  N02  C02  aromatic  1.339  0.020  1.339
 1LF  N03  C05  aromatic  1.348  0.020  1.348
 1LF  C02  N01  single    1.337  0.020  1.337
 1LF  C02  N04  aromatic  1.334  0.020  1.334
 1LF  C05  N04  aromatic  1.330  0.020  1.330
 1LF  C05  N05  single    1.346  0.020  1.346
 1LF  C01  N01  single    1.441  0.020  1.441
 1LF  C06  N05  single    1.452  0.020  1.452
 1LF  C06  C07  single    1.527  0.020  1.527
 1LF  N05  C10  single    1.451  0.020  1.451
 1LF  C07  C08  single    1.530  0.020  1.530
 1LF  C10  C09  single    1.523  0.020  1.523
 1LF  C15  C14  aromatic  1.387  0.020  1.387
 1LF  C15  C16  aromatic  1.384  0.020  1.384
 1LF  C08  C09  single    1.539  0.020  1.539
 1LF  C08  C11  single    1.522  0.020  1.522
 1LF  C14  C13  aromatic  1.390  0.020  1.390
 1LF  C16  C17  aromatic  1.387  0.020  1.387
 1LF  C11  N1   single    1.346  0.020  1.346
 1LF  C11  O1   double    1.223  0.020  1.223
 1LF  N1   C12  single    1.446  0.020  1.446
 1LF  C13  C12  single    1.511  0.020  1.511
 1LF  C13  C18  aromatic  1.402  0.020  1.402
 1LF  C17  C18  aromatic  1.390  0.020  1.390
 1LF  C18  C1   single    1.501  0.020  1.501
 1LF  C1   F02  single    1.336  0.020  1.336
 1LF  C1   F01  single    1.343  0.020  1.343
 1LF  C1   F    single    1.340  0.020  1.340
 1LF  N1   H1   single    0.860  0.020  1.020
 1LF  C10  H2   single    0.970  0.020  1.090
 1LF  C10  H3   single    0.970  0.020  1.090
 1LF  C15  H4   single    0.930  0.020  1.080
 1LF  C17  H5   single    0.930  0.020  1.080
 1LF  C01  H6   single    0.970  0.020  1.090
 1LF  C01  H7   single    0.970  0.020  1.090
 1LF  C01  H8   single    0.970  0.020  1.090
 1LF  N01  H9   single    0.860  0.020  1.020
 1LF  C04  H10  single    0.970  0.020  1.090
 1LF  C04  H11  single    0.970  0.020  1.090
 1LF  C04  H12  single    0.970  0.020  1.090
 1LF  C06  H13  single    0.970  0.020  1.090
 1LF  C06  H14  single    0.970  0.020  1.090
 1LF  C07  H15  single    0.970  0.020  1.090
 1LF  C07  H16  single    0.970  0.020  1.090
 1LF  C08  H17  single    0.970  0.020  1.090
 1LF  C09  H18  single    0.970  0.020  1.090
 1LF  C09  H19  single    0.970  0.020  1.090
 1LF  C12  H20  single    0.970  0.020  1.090
 1LF  C12  H21  single    0.970  0.020  1.090
 1LF  C14  H22  single    0.930  0.020  1.080
 1LF  C16  H23  single    0.930  0.020  1.080

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
 1LF  H1   N1   C12  117.20  3.000
 1LF  H1   N1   C11  118.90  3.000
 1LF  C12  N1   C11  123.84  3.000
 1LF  H3   C10  H2   107.46  3.000
 1LF  H3   C10  C09  110.71  3.000
 1LF  H2   C10  C09  110.73  3.000
 1LF  H3   C10  N05  108.21  3.000
 1LF  H2   C10  N05  109.68  3.000
 1LF  C09  C10  N05  109.98  3.000
 1LF  C18  C13  C14  118.09  3.000
 1LF  C18  C13  C12  124.64  3.000
 1LF  C14  C13  C12  117.24  3.000
 1LF  H4   C15  C16  120.51  3.000
 1LF  H4   C15  C14  119.91  3.000
 1LF  C16  C15  C14  119.58  3.000
 1LF  H5   C17  C18  120.70  3.000
 1LF  H5   C17  C16  118.64  3.000
 1LF  C18  C17  C16  120.67  3.000
 1LF  H8   C01  H7   108.10  3.000
 1LF  H8   C01  H6   108.23  3.000
 1LF  H7   C01  H6   108.27  3.000
 1LF  H8   C01  N01  111.89  3.000
 1LF  H7   C01  N01  112.09  3.000
 1LF  H6   C01  N01  108.13  3.000
 1LF  N04  C02  N02  125.18  3.000
 1LF  N04  C02  N01  117.06  3.000
 1LF  N02  C02  N01  117.76  3.000
 1LF  C03  N02  C02  114.36  3.000
 1LF  N03  C03  C04  117.55  3.000
 1LF  N03  C03  N02  125.79  3.000
 1LF  C04  C03  N02  116.66  3.000
 1LF  H12  C04  H11  109.19  3.000
 1LF  H12  C04  H10  107.00  3.000
 1LF  H11  C04  H10  108.79  3.000
 1LF  H12  C04  C03  110.43  3.000
 1LF  H11  C04  C03  111.24  3.000
 1LF  H10  C04  C03  110.08  3.000
 1LF  C05  N03  C03  115.34  3.000
 1LF  N05  C05  N04  118.42  3.000
 1LF  N05  C05  N03  117.58  3.000
 1LF  N04  C05  N03  124.00  3.000
 1LF  C05  N04  C02  115.33  3.000
 1LF  C06  N05  C05  122.63  3.000
 1LF  C06  N05  C10  113.38  3.000
 1LF  C05  N05  C10  121.91  3.000
 1LF  H14  C06  H13  107.71  3.000
 1LF  H14  C06  C07  110.20  3.000
 1LF  H13  C06  C07  110.55  3.000
 1LF  H14  C06  N05  109.31  3.000
 1LF  H13  C06  N05  108.41  3.000
 1LF  C07  C06  N05  110.59  3.000
 1LF  H16  C07  H15  106.57  3.000
 1LF  H16  C07  C08  107.74  3.000
 1LF  H15  C07  C08  110.82  3.000
 1LF  H16  C07  C06  108.27  3.000
 1LF  H15  C07  C06  109.36  3.000
 1LF  C08  C07  C06  113.79  3.000
 1LF  H17  C08  C11  107.22  3.000
 1LF  H17  C08  C09  107.45  3.000
 1LF  C11  C08  C09  110.79  3.000
 1LF  H17  C08  C07  108.08  3.000
 1LF  C11  C08  C07  112.75  3.000
 1LF  C09  C08  C07  110.32  3.000
 1LF  H19  C09  H18  106.61  3.000
 1LF  H19  C09  C08  110.95  3.000
 1LF  H18  C09  C08  108.44  3.000
 1LF  H19  C09  C10  110.02  3.000
 1LF  H18  C09  C10  108.65  3.000
 1LF  C08  C09  C10  111.97  3.000
 1LF  O1   C11  C08  123.50  3.000
 1LF  O1   C11  N1   122.42  3.000
 1LF  C08  C11  N1   114.09  3.000
 1LF  H21  C12  H20  106.07  3.000
 1LF  H21  C12  C13  108.27  3.000
 1LF  H20  C12  C13  112.83  3.000
 1LF  H21  C12  N1   110.33  3.000
 1LF  H20  C12  N1   108.53  3.000
 1LF  C13  C12  N1   110.71  3.000
 1LF  H22  C14  C15  119.42  3.000
 1LF  H22  C14  C13  118.80  3.000
 1LF  C15  C14  C13  121.77  3.000
 1LF  H23  C16  C17  119.66  3.000
 1LF  H23  C16  C15  120.64  3.000
 1LF  C17  C16  C15  119.70  3.000
 1LF  C1   C18  C17  118.79  3.000
 1LF  C1   C18  C13  121.01  3.000
 1LF  C17  C18  C13  120.18  3.000
 1LF  F    C1   F02  106.46  3.000
 1LF  F    C1   F01  106.69  3.000
 1LF  F02  C1   F01  106.38  3.000
 1LF  F    C1   C18  112.46  3.000
 1LF  F01  C1   C18  111.84  3.000
 1LF  F02  C1   C18  112.58  3.000
 1LF  H9   N01  C02  116.80  3.000
 1LF  H9   N01  C01  119.04  3.000
 1LF  C02  N01  C01  124.09  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
 1LF  CONST_01  C16  C15  C14  C13     0.00   0.0  0
 1LF  CONST_02  C16  C17  C18  C13     0.00   0.0  0
 1LF  CONST_03  C18  C13  C14  C15     0.00   0.0  0
 1LF  CONST_04  C18  C17  C16  C15     0.00   0.0  0
 1LF  CONST_05  C14  C15  C16  C17     0.00   0.0  0
 1LF  CONST_06  C14  C13  C18  C17     0.00   0.0  0
 1LF  CONST_07  N03  C03  N02  C02     0.00   0.0  0
 1LF  CONST_08  N03  C05  N04  C02     0.00   0.0  0
 1LF  CONST_09  C05  N03  C03  N02     0.00   0.0  0
 1LF  CONST_10  C05  N04  C02  N02     0.00   0.0  0
 1LF  CONST_11  N04  C02  N02  C03     0.00   0.0  0
 1LF  CONST_12  N04  C05  N03  C03     0.00   0.0  0
 1LF  CONST_13  N05  C05  N04  C02   180.00   0.0  0
 1LF  CONST_14  N05  C05  N03  C03   180.00   0.0  0
 1LF  CONST_15  C12  C13  C14  C15   180.00   0.0  0
 1LF  CONST_16  C12  C13  C18  C17   180.00   0.0  0
 1LF  CONST_17  C03  N02  C02  N01   180.00   0.0  0
 1LF  CONST_18  C05  N04  C02  N01   180.00   0.0  0
 1LF  CONST_19  C04  C03  N02  C02   180.00   0.0  0
 1LF  CONST_20  C05  N03  C03  C04   180.00   0.0  0
 1LF  CONST_21  C1   C18  C13  C14   180.00   0.0  0
 1LF  CONST_22  C1   C18  C17  C16   180.00   0.0  0
 1LF  CONST_23  H4   C15  C14  C13   180.00   0.0  0
 1LF  CONST_24  H5   C17  C18  C13   180.00   0.0  0
 1LF  CONST_25  H23  C16  C15  C14   180.00   0.0  0
 1LF  CONST_26  H22  C14  C15  C16   180.00   0.0  0
 1LF  CONST_27  N02  C02  N01  C01     0.00   0.0  0
 1LF  CONST_28  N04  C02  N01  C01   180.00   0.0  0
 1LF  CONST_29  H9   N01  C02  N02   180.00   0.0  0
 1LF  CONST_30  C12  N1   C11  C08   180.00   0.0  0
 1LF  CONST_31  H1   N1   C11  C08     0.00   0.0  0
 1LF  CONST_32  C12  N1   C11  O1      0.00   0.0  0
 1LF  Var_01    N03  C05  N05  C10   173.16  30.0  2
 1LF  Var_02    C07  C06  N05  C10   -58.26  30.0  1
 1LF  Var_03    C09  C10  N05  C05  -102.77  30.0  1
 1LF  Var_04    C08  C07  C06  N05    51.02  30.0  1
 1LF  Var_05    C08  C09  C10  N05   -56.12  30.0  1
 1LF  Var_06    C14  C13  C12  N1    -91.80  30.0  3
 1LF  Var_07    F02  C1   C18  C13  -177.63  30.0  2
 1LF  Var_08    H10  C04  C03  N02    63.57  30.0  2
 1LF  Var_09    C11  N1   C12  C13  -142.97  30.0  2
 1LF  Var_10    H6   C01  N01  C02   178.89  30.0  3

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
 1LF  chir_01  C08  C07  C09  C11  negativ

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
 1LF  plan-1  C13  0.020
 1LF  plan-1  C15  0.020
 1LF  plan-1  C17  0.020
 1LF  plan-1  C12  0.020
 1LF  plan-1  C14  0.020
 1LF  plan-1  C16  0.020
 1LF  plan-1  C18  0.020
 1LF  plan-1  C1   0.020
 1LF  plan-1  H4   0.020
 1LF  plan-1  H5   0.020
 1LF  plan-1  H22  0.020
 1LF  plan-1  H23  0.020
 1LF  plan-2  C02  0.020
 1LF  plan-2  N02  0.020
 1LF  plan-2  C03  0.020
 1LF  plan-2  C04  0.020
 1LF  plan-2  N03  0.020
 1LF  plan-2  C05  0.020
 1LF  plan-2  N04  0.020
 1LF  plan-2  N05  0.020
 1LF  plan-2  N01  0.020
 1LF  plan-3  N1   0.020
 1LF  plan-3  C08  0.020
 1LF  plan-3  C11  0.020
 1LF  plan-3  O1   0.020
 1LF  plan-3  C12  0.020
 1LF  plan-3  H1   0.020
 1LF  plan-4  C01  0.020
 1LF  plan-4  C02  0.020
 1LF  plan-4  H9   0.020
 1LF  plan-4  N01  0.020

