# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 20:05:08 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 6-[2-(3-fluoro-5-{2-[(2R)-1-methylpyrrolidin-2-yl]ethyl}phenyl)ethyl]-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCC[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
 KMD  KMD  6-[2-(3-fluoro-5-{2-[(2R)-1-methylpyrrolidin-2-yl]ethyl}phenyl)ethyl]-4-methylpyridin-2-amine  ligand  53  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_KMD
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
 KMD  C02  C  CR6   0   0.441  -5.1494   1.8941  -0.6532
 KMD  C03  C  CR16  0  -0.447  -6.3517   1.3810  -0.1356
 KMD  C04  C  CR6   0   0.204  -6.3098   0.2702   0.6815
 KMD  C05  C  CR16  0  -0.435  -5.0602  -0.2958   0.9615
 KMD  C06  C  CR6   0   0.274  -3.9264   0.2774   0.4155
 KMD  C07  C  CH3   0  -0.725  -7.5620  -0.3295   1.2440
 KMD  C08  C  CH2   0  -0.488  -2.5610  -0.2995   0.6630
 KMD  C09  C  CH2   0  -0.512  -1.9915  -0.9563  -0.6013
 KMD  C11  C  CR6   0   0.172  -0.5905  -1.4585  -0.3957
 KMD  C12  C  CR16  0  -0.489  -0.3650  -2.6723   0.2479
 KMD  C13  C  CR6   0   0.561   0.9373  -3.0898   0.4375
 KMD  C14  C  CR16  0  -0.490   2.0277  -2.3583   0.0121
 KMD  C15  C  CR6   0   0.188   1.8098  -1.1419  -0.6310
 KMD  C16  C  CR16  0  -0.404   0.5014  -0.7071  -0.8214
 KMD  C17  C  CH2   0  -0.515   2.9688  -0.3033  -1.0897
 KMD  C18  C  CH2   0  -0.454   3.6631   0.4219   0.0640
 KMD  C22  C  CH1   0  -0.030   4.7153   1.4096  -0.4505
 KMD  C23  C  CH2   0  -0.484   5.8825   0.6815  -1.1555
 KMD  C24  C  CH2   0  -0.451   7.1559   1.2235  -0.5011
 KMD  C25  C  CH2   0  -0.264   6.6604   1.6314   0.8757
 KMD  F13  F  F     0  -0.320   1.1526  -4.2644   1.0574
 KMD  N01  N  N     0  -0.484  -3.9691   1.3516  -0.3758
 KMD  N02  N  NH2   0  -0.839  -5.1577   2.9617  -1.5044
 KMD  N21  N  NT    0  -0.431   5.3748   2.2192   0.5742
 KMD  H1   H  HCR6  0   0.255  -7.2942   1.8594  -0.3744
 KMD  H2   H  HCR6  0   0.243  -4.9799  -1.1634   1.6047
 KMD  H3   H  HCH3  0   0.254  -7.8116  -1.2541   0.7201
 KMD  H4   H  HCH3  0   0.248  -7.4403  -0.5821   2.2974
 KMD  H5   H  HCH3  0   0.246  -8.4115   0.3449   1.1487
 KMD  H6   H  HCH2  0   0.249  -1.8879   0.4990   0.9871
 KMD  H7   H  HCH2  0   0.248  -2.6038  -1.0332   1.4705
 KMD  H8   H  HCH2  0   0.252  -2.6425  -1.7824  -0.8997
 KMD  H9   H  HCH2  0   0.252  -2.0052  -0.2289  -1.4152
 KMD  H10  H  HCR6  0   0.266  -1.1910  -3.2858   0.5889
 KMD  H11  H  HCR6  0   0.266   3.0316  -2.7323   0.1747
 KMD  H12  H  HCR6  0   0.242   0.3261   0.2365  -1.3265
 KMD  H13  H  HCH2  0   0.249   3.6881  -0.9302  -1.6230
 KMD  H14  H  HCH2  0   0.241   2.6108   0.4391  -1.8082
 KMD  H15  H  HCH2  0   0.238   2.9049   0.9508   0.6478
 KMD  H16  H  HCH2  0   0.225   4.1302  -0.3059   0.7360
 KMD  H17  H  HCH1  0   0.213   4.2023   2.0847  -1.1494
 KMD  H18  H  HCH2  0   0.230   5.8101  -0.3945  -0.9757
 KMD  H19  H  HCH2  0   0.242   5.8686   0.8222  -2.2363
 KMD  H20  H  HCH2  0   0.231   7.9573   0.4856  -0.4667
 KMD  H21  H  HCH2  0   0.226   7.5292   2.0987  -1.0362
 KMD  H22  H  HCH2  0   0.184   6.5934   0.7525   1.5408
 KMD  H23  H  HCH2  0   0.225   7.3093   2.3583   1.3720
 KMD  H24  H  HCH3  0   0.232   5.1546   3.3856   2.2778
 KMD  H25  H  HCH3  0   0.230   3.6665   3.1032   1.3845
 KMD  H26  H  HCH3  0   0.192   4.3402   1.8248   2.4065
 KMD  H27  H  HNH2  0   0.388  -5.9691   3.5563  -1.4968
 KMD  H28  H  HNH2  0   0.379  -4.2861   3.4555  -1.6066
 KMD  C26  C  CH3   0  -0.525   4.5982   2.6365   1.7099

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
 KMD  C25  N21  single    1.445  0.020  1.445
 KMD  C25  C24  single    1.519  0.020  1.519
 KMD  C26  N21  single    1.438  0.020  1.438
 KMD  N21  C22  single    1.463  0.020  1.463
 KMD  C24  C23  single    1.531  0.020  1.531
 KMD  C22  C23  single    1.546  0.020  1.546
 KMD  C22  C18  single    1.532  0.020  1.532
 KMD  C18  C17  single    1.529  0.020  1.529
 KMD  C17  C15  single    1.502  0.020  1.502
 KMD  C15  C16  aromatic  1.392  0.020  1.392
 KMD  C15  C14  aromatic  1.393  0.020  1.393
 KMD  C16  C11  aromatic  1.392  0.020  1.392
 KMD  C08  C06  single    1.503  0.020  1.503
 KMD  C08  C09  single    1.534  0.020  1.534
 KMD  N02  C02  single    1.365  0.020  1.365
 KMD  N01  C06  aromatic  1.335  0.020  1.335
 KMD  N01  C02  aromatic  1.328  0.020  1.328
 KMD  C14  C13  aromatic  1.380  0.020  1.380
 KMD  C06  C05  aromatic  1.383  0.020  1.383
 KMD  C11  C09  single    1.502  0.020  1.502
 KMD  C11  C12  aromatic  1.392  0.020  1.392
 KMD  C02  C03  aromatic  1.406  0.020  1.406
 KMD  C13  C12  aromatic  1.381  0.020  1.381
 KMD  C13  F13  single    1.346  0.020  1.346
 KMD  C05  C04  aromatic  1.400  0.020  1.400
 KMD  C03  C04  aromatic  1.380  0.020  1.380
 KMD  C04  C07  single    1.498  0.020  1.498
 KMD  C03  H1   single    0.930  0.020  1.080
 KMD  C05  H2   single    0.930  0.020  1.080
 KMD  C07  H3   single    0.970  0.020  1.090
 KMD  C07  H4   single    0.970  0.020  1.090
 KMD  C07  H5   single    0.970  0.020  1.090
 KMD  C08  H6   single    0.970  0.020  1.090
 KMD  C08  H7   single    0.970  0.020  1.090
 KMD  C09  H8   single    0.970  0.020  1.090
 KMD  C09  H9   single    0.970  0.020  1.090
 KMD  C12  H10  single    0.930  0.020  1.080
 KMD  C14  H11  single    0.930  0.020  1.080
 KMD  C16  H12  single    0.930  0.020  1.080
 KMD  C17  H13  single    0.970  0.020  1.090
 KMD  C17  H14  single    0.970  0.020  1.090
 KMD  C18  H15  single    0.970  0.020  1.090
 KMD  C18  H16  single    0.970  0.020  1.090
 KMD  C22  H17  single    0.970  0.020  1.090
 KMD  C23  H18  single    0.970  0.020  1.090
 KMD  C23  H19  single    0.970  0.020  1.090
 KMD  C24  H20  single    0.970  0.020  1.090
 KMD  C24  H21  single    0.970  0.020  1.090
 KMD  C25  H22  single    0.970  0.020  1.090
 KMD  C25  H23  single    0.970  0.020  1.090
 KMD  C26  H24  single    0.970  0.020  1.090
 KMD  C26  H25  single    0.970  0.020  1.090
 KMD  C26  H26  single    0.970  0.020  1.090
 KMD  N02  H27  single    0.890  0.020  1.040
 KMD  N02  H28  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
 KMD  N02  C02  N01  117.06  3.000
 KMD  N01  C02  C03  122.27  3.000
 KMD  N02  C02  C03  120.64  3.000
 KMD  H1   C03  C04  120.82  3.000
 KMD  H1   C03  C02  120.10  3.000
 KMD  C04  C03  C02  119.07  3.000
 KMD  C07  C04  C05  120.61  3.000
 KMD  C07  C04  C03  121.29  3.000
 KMD  C05  C04  C03  118.10  3.000
 KMD  H2   C05  C06  120.39  3.000
 KMD  H2   C05  C04  120.59  3.000
 KMD  C06  C05  C04  119.03  3.000
 KMD  N01  C06  C08  115.83  3.000
 KMD  N01  C06  C05  122.78  3.000
 KMD  C08  C06  C05  121.38  3.000
 KMD  H5   C07  H4   108.37  3.000
 KMD  H5   C07  H3   107.71  3.000
 KMD  H4   C07  H3   107.04  3.000
 KMD  H5   C07  C04  111.80  3.000
 KMD  H4   C07  C04  111.24  3.000
 KMD  H3   C07  C04  110.49  3.000
 KMD  H7   C08  H6   107.20  3.000
 KMD  H7   C08  C09  109.65  3.000
 KMD  H6   C08  C09  109.17  3.000
 KMD  H7   C08  C06  110.13  3.000
 KMD  H6   C08  C06  109.13  3.000
 KMD  C09  C08  C06  111.46  3.000
 KMD  H9   C09  H8   107.01  3.000
 KMD  H9   C09  C11  109.66  3.000
 KMD  H8   C09  C11  109.88  3.000
 KMD  H9   C09  C08  108.93  3.000
 KMD  H8   C09  C08  109.11  3.000
 KMD  C11  C09  C08  112.11  3.000
 KMD  C16  C11  C12  119.01  3.000
 KMD  C12  C11  C09  120.38  3.000
 KMD  C16  C11  C09  120.60  3.000
 KMD  H10  C12  C13  120.29  3.000
 KMD  H10  C12  C11  121.03  3.000
 KMD  C13  C12  C11  118.68  3.000
 KMD  F13  C13  C14  118.57  3.000
 KMD  F13  C13  C12  118.57  3.000
 KMD  C14  C13  C12  122.86  3.000
 KMD  H11  C14  C15  121.03  3.000
 KMD  H11  C14  C13  120.18  3.000
 KMD  C15  C14  C13  118.78  3.000
 KMD  C17  C15  C16  120.60  3.000
 KMD  C16  C15  C14  118.88  3.000
 KMD  C17  C15  C14  120.51  3.000
 KMD  H12  C16  C15  119.17  3.000
 KMD  H12  C16  C11  119.03  3.000
 KMD  C15  C16  C11  121.79  3.000
 KMD  H14  C17  H13  106.51  3.000
 KMD  H14  C17  C18  108.81  3.000
 KMD  H13  C17  C18  109.96  3.000
 KMD  H14  C17  C15  109.09  3.000
 KMD  H13  C17  C15  109.66  3.000
 KMD  C18  C17  C15  112.62  3.000
 KMD  H16  C18  H15  106.83  3.000
 KMD  H16  C18  C22  109.98  3.000
 KMD  H15  C18  C22  110.10  3.000
 KMD  H16  C18  C17  109.96  3.000
 KMD  H15  C18  C17  108.50  3.000
 KMD  C22  C18  C17  111.35  3.000
 KMD  H17  C22  N21  108.42  3.000
 KMD  H17  C22  C23  110.60  3.000
 KMD  N21  C22  C23  103.87  3.000
 KMD  H17  C22  C18  106.80  3.000
 KMD  C23  C22  C18  111.59  3.000
 KMD  N21  C22  C18  115.53  3.000
 KMD  H19  C23  H18  106.82  3.000
 KMD  H19  C23  C24  112.88  3.000
 KMD  H18  C23  C24  109.46  3.000
 KMD  H19  C23  C22  112.45  3.000
 KMD  H18  C23  C22  109.79  3.000
 KMD  C24  C23  C22  105.45  3.000
 KMD  H21  C24  H20  107.87  3.000
 KMD  H21  C24  C25  109.91  3.000
 KMD  H20  C24  C25  113.15  3.000
 KMD  H21  C24  C23  111.02  3.000
 KMD  H20  C24  C23  112.67  3.000
 KMD  C25  C24  C23  102.19  3.000
 KMD  H23  C25  H22  106.96  3.000
 KMD  H23  C25  N21  110.62  3.000
 KMD  H22  C25  N21  113.29  3.000
 KMD  H23  C25  C24  113.35  3.000
 KMD  H22  C25  C24  110.61  3.000
 KMD  N21  C25  C24  102.14  3.000
 KMD  C06  N01  C02  118.75  3.000
 KMD  H28  N02  H27  114.15  3.000
 KMD  H28  N02  C02  116.19  3.000
 KMD  H27  N02  C02  117.54  3.000
 KMD  C26  N21  C25  115.70  3.000
 KMD  C26  N21  C22  118.06  3.000
 KMD  C25  N21  C22  108.78  3.000
 KMD  H26  C26  H25  107.70  3.000
 KMD  H26  C26  H24  107.23  3.000
 KMD  H25  C26  H24  107.24  3.000
 KMD  H26  C26  N21  114.37  3.000
 KMD  H25  C26  N21  110.46  3.000
 KMD  H24  C26  N21  109.55  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
 KMD  CONST_01  C05  C06  N01  C02     0.00   0.0  0
 KMD  CONST_02  C05  C04  C03  C02     0.00   0.0  0
 KMD  CONST_03  C06  N01  C02  C03     0.00   0.0  0
 KMD  CONST_04  C06  C05  C04  C03     0.00   0.0  0
 KMD  CONST_05  N01  C06  C05  C04     0.00   0.0  0
 KMD  CONST_06  N01  C02  C03  C04     0.00   0.0  0
 KMD  CONST_07  C14  C15  C16  C11     0.00   0.0  0
 KMD  CONST_08  C14  C13  C12  C11     0.00   0.0  0
 KMD  CONST_09  C15  C16  C11  C12     0.00   0.0  0
 KMD  CONST_10  C15  C14  C13  C12     0.00   0.0  0
 KMD  CONST_11  C16  C15  C14  C13     0.00   0.0  0
 KMD  CONST_12  C16  C11  C12  C13     0.00   0.0  0
 KMD  CONST_13  C08  C06  N01  C02   180.00   0.0  0
 KMD  CONST_14  C07  C04  C03  C02   180.00   0.0  0
 KMD  CONST_15  C08  C06  C05  C04   180.00   0.0  0
 KMD  CONST_16  N02  C02  C03  C04   180.00   0.0  0
 KMD  CONST_17  N02  C02  N01  C06   180.00   0.0  0
 KMD  CONST_18  C07  C04  C05  C06   180.00   0.0  0
 KMD  CONST_19  C15  C16  C11  C09   180.00   0.0  0
 KMD  CONST_20  C13  C12  C11  C09   180.00   0.0  0
 KMD  CONST_21  C17  C15  C16  C11   180.00   0.0  0
 KMD  CONST_22  F13  C13  C12  C11   180.00   0.0  0
 KMD  CONST_23  C17  C15  C14  C13   180.00   0.0  0
 KMD  CONST_24  F13  C13  C14  C15   180.00   0.0  0
 KMD  CONST_25  H2   C05  C04  C03   180.00   0.0  0
 KMD  CONST_26  H1   C03  C04  C05   180.00   0.0  0
 KMD  CONST_27  H12  C16  C11  C12   180.00   0.0  0
 KMD  CONST_28  H11  C14  C13  C12   180.00   0.0  0
 KMD  CONST_29  H10  C12  C13  C14   180.00   0.0  0
 KMD  Var_01    C24  C25  N21  C22    40.47  30.0  1
 KMD  Var_02    C25  C24  C23  C22    26.60  30.0  1
 KMD  Var_03    N21  C25  C24  C23   -40.23  30.0  1
 KMD  Var_04    C09  C08  C06  C05   109.23  30.0  1
 KMD  Var_05    C11  C09  C08  C06   176.26  30.0  3
 KMD  Var_06    C16  C11  C09  C08   -98.69  30.0  2
 KMD  Var_07    C18  C17  C15  C14   -75.40  30.0  3
 KMD  Var_08    C22  C18  C17  C15  -172.40  30.0  1
 KMD  Var_09    H3   C07  C04  C03   105.14  30.0  2
 KMD  Var_10    H24  C26  N21  C22  -168.82  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
 KMD  chir_01  C22  N21  C23  C18  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
 KMD  plan-1  C09  0.020
 KMD  plan-1  C11  0.020
 KMD  plan-1  C12  0.020
 KMD  plan-1  C13  0.020
 KMD  plan-1  C14  0.020
 KMD  plan-1  C15  0.020
 KMD  plan-1  C16  0.020
 KMD  plan-1  C17  0.020
 KMD  plan-1  F13  0.020
 KMD  plan-1  H10  0.020
 KMD  plan-1  H11  0.020
 KMD  plan-1  H12  0.020
 KMD  plan-2  C02  0.020
 KMD  plan-2  C03  0.020
 KMD  plan-2  C04  0.020
 KMD  plan-2  C05  0.020
 KMD  plan-2  C06  0.020
 KMD  plan-2  C07  0.020
 KMD  plan-2  C08  0.020
 KMD  plan-2  N01  0.020
 KMD  plan-2  N02  0.020
 KMD  plan-2  H1   0.020
 KMD  plan-2  H2   0.020
 KMD  plan-3  C02  0.020
 KMD  plan-3  N02  0.020
 KMD  plan-3  H27  0.020
 KMD  plan-3  H28  0.020

