# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 04:50:22 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 6-[2-(3-fluoro-5-{2-[(2R,4S)-4-fluoro-1-methylpyrrolidin-2-yl]ethyl}phenyl)ethyl]-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C[C@@H](F)C[C@H]1CCc2cc(F)cc(CCc3cc(C)cc(N)n3)c2
#
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
 KLD  KLD  6-[2-(3-fluoro-5-{2-[(2R,4S)-4-fluoro-1-methylpyrrolidin-2-yl]ethyl}phenyl)ethyl]-4-methylpyridin-2-amine  ligand  53  26  .  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_KLD
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
 KLD  C13  C  CR6   0   0.561  -0.4005   3.3691   0.2996
 KLD  C15  C  CR6   0   0.182  -1.4052   1.4353  -0.6723
 KLD  C12  C  CR16  0  -0.487   0.8680   2.8502   0.1415
 KLD  C16  C  CR16  0  -0.395  -0.1299   0.8981  -0.8329
 KLD  C14  C  CR16  0  -0.493  -1.5396   2.6927  -0.0919
 KLD  C11  C  CR6   0   0.170   1.0095   1.5895  -0.4348
 KLD  C02  C  CR6   0   0.441   5.2799  -2.1238  -0.3935
 KLD  C03  C  CR16  0  -0.447   6.5111  -1.6919   0.1310
 KLD  C04  C  CR6   0   0.204   6.5503  -0.5380   0.8857
 KLD  C05  C  CR16  0  -0.434   5.3500   0.1496   1.1031
 KLD  C06  C  CR6   0   0.275   4.1836  -0.3464   0.5503
 KLD  C09  C  CH2   0  -0.512   2.3725   0.9757  -0.5867
 KLD  C17  C  CH2   0  -0.521  -2.6193   0.6519  -1.0830
 KLD  C18  C  CH2   0  -0.440  -3.1288  -0.2489   0.0434
 KLD  C22  C  CH2   0  -0.324  -6.1183  -2.3506   0.3365
 KLD  C23  C  CH1   0   0.192  -6.7061  -1.0077  -0.0228
 KLD  C24  C  CH2   0  -0.540  -5.5652  -0.3142  -0.7568
 KLD  C25  C  CH1   0  -0.024  -4.2965  -1.1173  -0.4017
 KLD  F13  F  F     0  -0.320  -0.5338   4.5882   0.8527
 KLD  N01  N  N     0  -0.484   4.1487  -1.4590  -0.1862
 KLD  N02  N  NH2   0  -0.839   5.1949  -3.2860  -1.1049
 KLD  N21  N  NT    0  -0.433  -4.7395  -2.0332   0.6443
 KLD  H1   H  HCR6  0   0.266   1.7352   3.4197   0.4551
 KLD  H2   H  HCR6  0   0.241  -0.0227  -0.0807  -1.2884
 KLD  H3   H  HCR6  0   0.266  -2.5164   3.1404   0.0472
 KLD  H4   H  HCR6  0   0.254   7.4129  -2.2618  -0.0589
 KLD  H5   H  HCR6  0   0.243   5.3331   1.0560   1.6955
 KLD  H6   H  HCH3  0   0.254   8.1587   0.8717   0.8940
 KLD  H7   H  HCH3  0   0.249   7.7263   0.2790   2.4872
 KLD  H8   H  HCH3  0   0.247   8.6372  -0.7526   1.3789
 KLD  H11  H  HCH2  0   0.252   2.3448   0.1989  -1.3530
 KLD  H12  H  HCH2  0   0.251   3.0869   1.7319  -0.9220
 KLD  H13  H  HCH2  0   0.250  -3.4111   1.3374  -1.3943
 KLD  H14  H  HCH2  0   0.245  -2.3773   0.0360  -1.9537
 KLD  H15  H  HCH2  0   0.238  -2.3038  -0.8779   0.3892
 KLD  H16  H  HCH2  0   0.228  -3.4396   0.3596   0.8982
 KLD  H20  H  HCH2  0   0.250  -6.6246  -2.8337   1.1753
 KLD  H21  H  HCH2  0   0.202  -6.2117  -3.0189  -0.5377
 KLD  H22  H  HCH1  0   0.222  -7.6235  -1.0809  -0.6074
 KLD  H23  H  HCH2  0   0.256  -5.7434  -0.3228  -1.8314
 KLD  H24  H  HCH2  0   0.255  -5.4967   0.7324  -0.4532
 KLD  H25  H  HCH1  0   0.201  -3.9808  -1.6854  -1.2950
 KLD  H26  H  HNH2  0   0.379   4.3757  -3.3958  -1.6798
 KLD  H27  H  HNH2  0   0.387   6.0393  -3.6411  -1.5211
 KLD  F23  F  F     0  -0.390  -7.0206  -0.3063   1.1479
 KLD  C08  C  CH2   0  -0.488   2.8704   0.3620   0.7285
 KLD  C21  C  CH3   0  -0.527  -3.9098  -3.2012   0.8114
 KLD  C07  C  CH3   0  -0.726   7.8387  -0.0154   1.4436
 KLD  H9   H  HCH2  0   0.249   2.1264  -0.3505   1.0950
 KLD  H10  H  HCH2  0   0.248   2.9655   1.1425   1.4863
 KLD  H17  H  HCH3  0   0.235  -2.8844  -2.9175   1.0487
 KLD  H18  H  HCH3  0   0.235  -4.2793  -3.8064   1.6405
 KLD  H19  H  HCH3  0   0.193  -3.8849  -3.8384  -0.0865

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
 KLD  C07  C04  single    1.498  0.020  1.498
 KLD  C04  C03  aromatic  1.379  0.020  1.379
 KLD  C04  C05  aromatic  1.400  0.020  1.400
 KLD  C03  C02  aromatic  1.406  0.020  1.406
 KLD  C05  C06  aromatic  1.383  0.020  1.383
 KLD  C06  N01  aromatic  1.335  0.020  1.335
 KLD  C06  C08  single    1.503  0.020  1.503
 KLD  C02  N01  aromatic  1.328  0.020  1.328
 KLD  C02  N02  single    1.365  0.020  1.365
 KLD  F13  C13  single    1.345  0.020  1.345
 KLD  C08  C09  single    1.534  0.020  1.534
 KLD  C13  C14  aromatic  1.381  0.020  1.381
 KLD  C13  C12  aromatic  1.380  0.020  1.380
 KLD  C14  C15  aromatic  1.391  0.020  1.391
 KLD  C12  C11  aromatic  1.393  0.020  1.393
 KLD  C15  C16  aromatic  1.393  0.020  1.393
 KLD  C15  C17  single    1.502  0.020  1.502
 KLD  C11  C16  aromatic  1.391  0.020  1.391
 KLD  C11  C09  single    1.502  0.020  1.502
 KLD  C17  C18  single    1.530  0.020  1.530
 KLD  C24  C25  single    1.543  0.020  1.543
 KLD  C24  C23  single    1.524  0.020  1.524
 KLD  C18  C25  single    1.522  0.020  1.522
 KLD  C25  N21  single    1.459  0.020  1.459
 KLD  C23  F23  single    1.400  0.020  1.400
 KLD  C23  C22  single    1.509  0.020  1.509
 KLD  N21  C21  single    1.442  0.020  1.442
 KLD  N21  C22  single    1.448  0.020  1.448
 KLD  C12  H1   single    0.930  0.020  1.080
 KLD  C16  H2   single    0.930  0.020  1.080
 KLD  C14  H3   single    0.930  0.020  1.080
 KLD  C03  H4   single    0.930  0.020  1.080
 KLD  C05  H5   single    0.930  0.020  1.080
 KLD  C07  H6   single    0.970  0.020  1.090
 KLD  C07  H7   single    0.970  0.020  1.090
 KLD  C07  H8   single    0.970  0.020  1.090
 KLD  C08  H9   single    0.970  0.020  1.090
 KLD  C08  H10  single    0.970  0.020  1.090
 KLD  C09  H11  single    0.970  0.020  1.090
 KLD  C09  H12  single    0.970  0.020  1.090
 KLD  C17  H13  single    0.970  0.020  1.090
 KLD  C17  H14  single    0.970  0.020  1.090
 KLD  C18  H15  single    0.970  0.020  1.090
 KLD  C18  H16  single    0.970  0.020  1.090
 KLD  C21  H17  single    0.970  0.020  1.090
 KLD  C21  H18  single    0.970  0.020  1.090
 KLD  C21  H19  single    0.970  0.020  1.090
 KLD  C22  H20  single    0.970  0.020  1.090
 KLD  C22  H21  single    0.970  0.020  1.090
 KLD  C23  H22  single    0.970  0.020  1.090
 KLD  C24  H23  single    0.970  0.020  1.090
 KLD  C24  H24  single    0.970  0.020  1.090
 KLD  C25  H25  single    0.970  0.020  1.090
 KLD  N02  H26  single    0.890  0.020  1.040
 KLD  N02  H27  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
 KLD  F13  C13  C14  118.59  3.000
 KLD  C14  C13  C12  122.79  3.000
 KLD  F13  C13  C12  118.63  3.000
 KLD  C17  C15  C14  120.48  3.000
 KLD  C17  C15  C16  120.48  3.000
 KLD  C14  C15  C16  119.01  3.000
 KLD  H1   C12  C11  120.92  3.000
 KLD  H1   C12  C13  120.32  3.000
 KLD  C11  C12  C13  118.76  3.000
 KLD  H2   C16  C11  119.19  3.000
 KLD  H2   C16  C15  119.13  3.000
 KLD  C11  C16  C15  121.68  3.000
 KLD  H3   C14  C15  120.93  3.000
 KLD  H3   C14  C13  120.31  3.000
 KLD  C15  C14  C13  118.76  3.000
 KLD  C09  C11  C16  120.74  3.000
 KLD  C09  C11  C12  120.24  3.000
 KLD  C16  C11  C12  119.01  3.000
 KLD  N02  C02  N01  117.02  3.000
 KLD  N02  C02  C03  120.68  3.000
 KLD  N01  C02  C03  122.25  3.000
 KLD  H4   C03  C04  120.81  3.000
 KLD  H4   C03  C02  120.12  3.000
 KLD  C04  C03  C02  119.07  3.000
 KLD  C07  C04  C05  120.54  3.000
 KLD  C05  C04  C03  118.12  3.000
 KLD  C07  C04  C03  121.33  3.000
 KLD  H5   C05  C06  120.38  3.000
 KLD  H5   C05  C04  120.62  3.000
 KLD  C06  C05  C04  119.01  3.000
 KLD  N01  C06  C08  115.82  3.000
 KLD  C08  C06  C05  121.38  3.000
 KLD  N01  C06  C05  122.80  3.000
 KLD  H12  C09  H11  107.07  3.000
 KLD  H12  C09  C08  109.12  3.000
 KLD  H11  C09  C08  108.99  3.000
 KLD  H12  C09  C11  109.96  3.000
 KLD  H11  C09  C11  109.80  3.000
 KLD  C08  C09  C11  111.79  3.000
 KLD  H14  C17  H13  106.67  3.000
 KLD  H14  C17  C18  109.17  3.000
 KLD  H13  C17  C18  109.75  3.000
 KLD  H14  C17  C15  109.43  3.000
 KLD  H13  C17  C15  109.66  3.000
 KLD  C18  C17  C15  112.03  3.000
 KLD  H16  C18  H15  106.68  3.000
 KLD  H16  C18  C25  109.14  3.000
 KLD  H15  C18  C25  110.07  3.000
 KLD  H16  C18  C17  110.02  3.000
 KLD  H15  C18  C17  108.68  3.000
 KLD  C25  C18  C17  112.10  3.000
 KLD  H21  C22  H20  107.52  3.000
 KLD  H21  C22  N21  112.42  3.000
 KLD  H20  C22  N21  112.03  3.000
 KLD  H21  C22  C23  108.49  3.000
 KLD  H20  C22  C23  113.31  3.000
 KLD  N21  C22  C23  103.09  3.000
 KLD  H22  C23  F23  107.03  3.000
 KLD  H22  C23  C24  113.72  3.000
 KLD  F23  C23  C24  110.05  3.000
 KLD  H22  C23  C22  113.30  3.000
 KLD  F23  C23  C22  109.52  3.000
 KLD  C24  C23  C22  103.18  3.000
 KLD  H24  C24  H23  106.98  3.000
 KLD  H24  C24  C25  112.54  3.000
 KLD  H23  C24  C25  110.94  3.000
 KLD  H24  C24  C23  110.45  3.000
 KLD  H23  C24  C23  110.44  3.000
 KLD  C25  C24  C23  105.54  3.000
 KLD  H25  C25  N21  110.10  3.000
 KLD  H25  C25  C24  108.46  3.000
 KLD  N21  C25  C24  104.01  3.000
 KLD  H25  C25  C18  108.10  3.000
 KLD  N21  C25  C18  112.43  3.000
 KLD  C24  C25  C18  113.65  3.000
 KLD  C06  N01  C02  118.75  3.000
 KLD  H27  N02  H26  114.09  3.000
 KLD  H27  N02  C02  117.63  3.000
 KLD  H26  N02  C02  116.16  3.000
 KLD  C25  N21  C22  105.92  3.000
 KLD  C22  N21  C21  113.26  3.000
 KLD  C25  N21  C21  114.63  3.000
 KLD  H10  C08  H9   107.00  3.000
 KLD  H10  C08  C09  109.71  3.000
 KLD  H9   C08  C09  109.09  3.000
 KLD  H10  C08  C06  110.07  3.000
 KLD  H9   C08  C06  109.10  3.000
 KLD  C09  C08  C06  111.75  3.000
 KLD  H19  C21  H18  107.83  3.000
 KLD  H19  C21  H17  107.86  3.000
 KLD  H18  C21  H17  107.31  3.000
 KLD  H19  C21  N21  112.77  3.000
 KLD  H18  C21  N21  110.03  3.000
 KLD  H17  C21  N21  110.83  3.000
 KLD  H8   C07  H7   108.38  3.000
 KLD  H8   C07  H6   107.78  3.000
 KLD  H7   C07  H6   107.02  3.000
 KLD  H8   C07  C04  111.87  3.000
 KLD  H7   C07  C04  111.22  3.000
 KLD  H6   C07  C04  110.38  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
 KLD  CONST_01  C16  C15  C14  C13     0.00   0.0  0
 KLD  CONST_02  C16  C11  C12  C13     0.00   0.0  0
 KLD  CONST_03  C12  C13  C14  C15     0.00   0.0  0
 KLD  CONST_04  C12  C11  C16  C15     0.00   0.0  0
 KLD  CONST_05  C11  C12  C13  C14     0.00   0.0  0
 KLD  CONST_06  C11  C16  C15  C14     0.00   0.0  0
 KLD  CONST_07  C05  C04  C03  C02     0.00   0.0  0
 KLD  CONST_08  C05  C06  N01  C02     0.00   0.0  0
 KLD  CONST_09  C06  C05  C04  C03     0.00   0.0  0
 KLD  CONST_10  C06  N01  C02  C03     0.00   0.0  0
 KLD  CONST_11  N01  C02  C03  C04     0.00   0.0  0
 KLD  CONST_12  N01  C06  C05  C04     0.00   0.0  0
 KLD  CONST_13  C17  C15  C14  C13   180.00   0.0  0
 KLD  CONST_14  C09  C11  C12  C13   180.00   0.0  0
 KLD  CONST_15  F13  C13  C14  C15   180.00   0.0  0
 KLD  CONST_16  C09  C11  C16  C15   180.00   0.0  0
 KLD  CONST_17  F13  C13  C12  C11   180.00   0.0  0
 KLD  CONST_18  C17  C15  C16  C11   180.00   0.0  0
 KLD  CONST_19  C07  C04  C03  C02   180.00   0.0  0
 KLD  CONST_20  C08  C06  N01  C02   180.00   0.0  0
 KLD  CONST_21  N02  C02  C03  C04   180.00   0.0  0
 KLD  CONST_22  C08  C06  C05  C04   180.00   0.0  0
 KLD  CONST_23  C07  C04  C05  C06   180.00   0.0  0
 KLD  CONST_24  N02  C02  N01  C06   180.00   0.0  0
 KLD  CONST_25  H3   C14  C13  C12   180.00   0.0  0
 KLD  CONST_26  H2   C16  C11  C12   180.00   0.0  0
 KLD  CONST_27  H1   C12  C11  C16   180.00   0.0  0
 KLD  CONST_28  H5   C05  C04  C03   180.00   0.0  0
 KLD  CONST_29  H4   C03  C04  C05   180.00   0.0  0
 KLD  Var_01    C25  N21  C22  C23   -44.07  30.0  1
 KLD  Var_02    C25  C18  C17  C15  -175.88  30.0  3
 KLD  Var_03    C08  C09  C11  C12    79.47  30.0  2
 KLD  Var_04    C18  C17  C15  C16    88.02  30.0  2
 KLD  Var_05    C06  C08  C09  C11   175.48  30.0  2
 KLD  Var_06    C09  C08  C06  C05   110.68  30.0  2
 KLD  Var_07    H6   C07  C04  C03   106.81  30.0  2
 KLD  Var_08    H17  C21  N21  C22  -179.57  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
 KLD  chir_01  C23  C24  F23  C22  positiv
 KLD  chir_02  C25  N21  C18  C24  positiv

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
 KLD  plan-1  C13  0.020
 KLD  plan-1  C15  0.020
 KLD  plan-1  C12  0.020
 KLD  plan-1  C16  0.020
 KLD  plan-1  C14  0.020
 KLD  plan-1  C11  0.020
 KLD  plan-1  C09  0.020
 KLD  plan-1  C17  0.020
 KLD  plan-1  F13  0.020
 KLD  plan-1  H1   0.020
 KLD  plan-1  H2   0.020
 KLD  plan-1  H3   0.020
 KLD  plan-2  C02  0.020
 KLD  plan-2  C03  0.020
 KLD  plan-2  C04  0.020
 KLD  plan-2  C05  0.020
 KLD  plan-2  C06  0.020
 KLD  plan-2  N01  0.020
 KLD  plan-2  N02  0.020
 KLD  plan-2  H4   0.020
 KLD  plan-2  H5   0.020
 KLD  plan-2  C08  0.020
 KLD  plan-2  C07  0.020
 KLD  plan-3  C02  0.020
 KLD  plan-3  N02  0.020
 KLD  plan-3  H26  0.020
 KLD  plan-3  H27  0.020

