# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 00:35:46 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 6-[2-(3-fluoro-5-{2-[(2R)-pyrrolidin-2-yl]ethyl}phenyl)ethyl]-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(CCc2cc(F)cc(CC[C@@H]3CCCN3)c2)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
 KMA  KMA  6-[2-(3-fluoro-5-{2-[(2R)-pyrrolidin-2-yl]ethyl}phenyl)ethyl]-4-methylpyridin-2-amine  ligand  50  24  .  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_KMA
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
 KMA  F13  F  F     0  -0.320   1.1412   4.5658  -0.0281
 KMA  C13  C  CR6   0   0.561   1.0479   3.2250   0.0345
 KMA  C12  C  CR16  0  -0.493  -0.1513   2.6291  -0.3022
 KMA  C14  C  CR16  0  -0.492   2.1556   2.5033   0.4308
 KMA  C15  C  CR6   0   0.174   2.0649   1.1149   0.4953
 KMA  C17  C  CH2   0  -0.506   3.2638   0.2906   0.8688
 KMA  C18  C  CH2   0  -0.436   4.1401  -0.0184  -0.3467
 KMA  C22  C  CH1   0  -0.093   5.3488  -0.8759  -0.0188
 KMA  C23  C  CH2   0  -0.443   6.2568  -1.1694  -1.2258
 KMA  C24  C  CH2   0  -0.471   6.9257  -2.5120  -0.8802
 KMA  C25  C  CH2   0  -0.319   6.1918  -2.9808   0.3986
 KMA  N21  N  NH1   0  -0.584   4.9784  -2.1818   0.5200
 KMA  C16  C  CR16  0  -0.390   0.8614   0.5025   0.1573
 KMA  C11  C  CR6   0   0.169  -0.2487   1.2417  -0.2419
 KMA  C09  C  CH2   0  -0.512  -1.5505   0.5589  -0.5515
 KMA  C08  C  CH2   0  -0.487  -2.4042   0.3678   0.7106
 KMA  C06  C  CR6   0   0.275  -3.7201  -0.2834   0.3934
 KMA  C05  C  CR16  0  -0.434  -3.9904  -1.5834   0.7803
 KMA  N01  N  N     0  -0.484  -4.5846   0.4585  -0.3026
 KMA  C02  C  CR6   0   0.440  -5.7524  -0.0742  -0.6437
 KMA  N02  N  NH2   0  -0.839  -6.5917   0.6972  -1.3959
 KMA  C03  C  CR16  0  -0.447  -6.1089  -1.3887  -0.2945
 KMA  C04  C  CR6   0   0.205  -5.2197  -2.1549   0.4302
 KMA  C07  C  CH3   0  -0.726  -5.5577  -3.5533   0.8482
 KMA  H1   H  HCR6  0   0.266  -0.9975   3.2335  -0.6070
 KMA  H2   H  HCR6  0   0.265   3.0764   3.0135   0.6876
 KMA  H3   H  HCH2  0   0.241   3.8620   0.8186   1.6164
 KMA  H4   H  HCH2  0   0.246   2.9371  -0.6433   1.3297
 KMA  H5   H  HCH2  0   0.224   3.5400  -0.5220  -1.1138
 KMA  H6   H  HCH2  0   0.238   4.4828   0.9187  -0.7948
 KMA  H7   H  HCH1  0   0.220   5.9467  -0.3647   0.7480
 KMA  H8   H  HCH2  0   0.220   5.6459  -1.2611  -2.1282
 KMA  H9   H  HCH2  0   0.231   6.9761  -0.3686  -1.4040
 KMA  H10  H  HCH2  0   0.230   6.8043  -3.2317  -1.6902
 KMA  H11  H  HCH2  0   0.230   7.9973  -2.4069  -0.7068
 KMA  H12  H  HCH2  0   0.234   5.9489  -4.0435   0.3886
 KMA  H13  H  HCH2  0   0.220   6.8219  -2.8033   1.2745
 KMA  H14  H  HNH1  0   0.334   4.2710  -2.5802  -0.0908
 KMA  H16  H  HCR6  0   0.240   0.7854  -0.5787   0.2062
 KMA  H17  H  HCH2  0   0.252  -2.1184   1.1437  -1.2778
 KMA  H18  H  HCH2  0   0.251  -1.3585  -0.4168  -1.0047
 KMA  H19  H  HCH2  0   0.248  -1.8532  -0.2342   1.4359
 KMA  H20  H  HCH2  0   0.249  -2.5840   1.3432   1.1710
 KMA  H21  H  HCR6  0   0.244  -3.2610  -2.1475   1.3480
 KMA  H22  H  HNH2  0   0.379  -6.4115   1.6877  -1.3824
 KMA  H23  H  HNH2  0   0.388  -7.5694   0.4591  -1.3919
 KMA  H24  H  HCR6  0   0.255  -7.0703  -1.7881  -0.5949
 KMA  H25  H  HCH3  0   0.254  -5.7508  -3.5966   1.9216
 KMA  H26  H  HCH3  0   0.247  -6.4427  -3.9253   0.3345
 KMA  H27  H  HCH3  0   0.249  -4.7320  -4.2355   0.6446

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
 KMA  C25  N21  single    1.458  0.020  1.458
 KMA  C25  C24  single    1.547  0.020  1.547
 KMA  N21  C22  single    1.460  0.020  1.460
 KMA  C24  C23  single    1.539  0.020  1.539
 KMA  C22  C23  single    1.539  0.020  1.539
 KMA  C22  C18  single    1.518  0.020  1.518
 KMA  C18  C17  single    1.530  0.020  1.530
 KMA  C17  C15  single    1.502  0.020  1.502
 KMA  C15  C16  aromatic  1.392  0.020  1.392
 KMA  C15  C14  aromatic  1.393  0.020  1.393
 KMA  C16  C11  aromatic  1.392  0.020  1.392
 KMA  C08  C06  single    1.502  0.020  1.502
 KMA  C08  C09  single    1.536  0.020  1.536
 KMA  C14  C13  aromatic  1.380  0.020  1.380
 KMA  N02  C02  single    1.366  0.020  1.366
 KMA  N01  C06  aromatic  1.335  0.020  1.335
 KMA  N01  C02  aromatic  1.328  0.020  1.328
 KMA  C06  C05  aromatic  1.383  0.020  1.383
 KMA  C02  C03  aromatic  1.406  0.020  1.406
 KMA  C11  C09  single    1.502  0.020  1.502
 KMA  C11  C12  aromatic  1.392  0.020  1.392
 KMA  C13  C12  aromatic  1.381  0.020  1.381
 KMA  C13  F13  single    1.345  0.020  1.345
 KMA  C05  C04  aromatic  1.400  0.020  1.400
 KMA  C03  C04  aromatic  1.379  0.020  1.379
 KMA  C04  C07  single    1.498  0.020  1.498
 KMA  C12  H1   single    0.930  0.020  1.080
 KMA  C14  H2   single    0.930  0.020  1.080
 KMA  C17  H3   single    0.970  0.020  1.090
 KMA  C17  H4   single    0.970  0.020  1.090
 KMA  C18  H5   single    0.970  0.020  1.090
 KMA  C18  H6   single    0.970  0.020  1.090
 KMA  C22  H7   single    0.970  0.020  1.090
 KMA  C23  H8   single    0.970  0.020  1.090
 KMA  C23  H9   single    0.970  0.020  1.090
 KMA  C24  H10  single    0.970  0.020  1.090
 KMA  C24  H11  single    0.970  0.020  1.090
 KMA  C25  H12  single    0.970  0.020  1.090
 KMA  C25  H13  single    0.970  0.020  1.090
 KMA  N21  H14  single    0.890  0.020  1.040
 KMA  C16  H16  single    0.930  0.020  1.080
 KMA  C09  H17  single    0.970  0.020  1.090
 KMA  C09  H18  single    0.970  0.020  1.090
 KMA  C08  H19  single    0.970  0.020  1.090
 KMA  C08  H20  single    0.970  0.020  1.090
 KMA  C05  H21  single    0.930  0.020  1.080
 KMA  N02  H22  single    0.890  0.020  1.040
 KMA  N02  H23  single    0.890  0.020  1.040
 KMA  C03  H24  single    0.930  0.020  1.080
 KMA  C07  H25  single    0.970  0.020  1.090
 KMA  C07  H26  single    0.970  0.020  1.090
 KMA  C07  H27  single    0.970  0.020  1.090

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
 KMA  C14  C13  C12  122.78  3.000
 KMA  C12  C13  F13  118.62  3.000
 KMA  C14  C13  F13  118.61  3.000
 KMA  H1   C12  C11  120.89  3.000
 KMA  H1   C12  C13  120.40  3.000
 KMA  C11  C12  C13  118.71  3.000
 KMA  H2   C14  C15  120.91  3.000
 KMA  H2   C14  C13  120.25  3.000
 KMA  C15  C14  C13  118.84  3.000
 KMA  C16  C15  C17  120.60  3.000
 KMA  C16  C15  C14  118.92  3.000
 KMA  C17  C15  C14  120.43  3.000
 KMA  H4   C17  H3   106.75  3.000
 KMA  H4   C17  C18  109.52  3.000
 KMA  H3   C17  C18  109.11  3.000
 KMA  H4   C17  C15  109.61  3.000
 KMA  H3   C17  C15  109.97  3.000
 KMA  C18  C17  C15  111.74  3.000
 KMA  H6   C18  H5   106.16  3.000
 KMA  H6   C18  C22  108.84  3.000
 KMA  H5   C18  C22  109.12  3.000
 KMA  H6   C18  C17  109.39  3.000
 KMA  H5   C18  C17  109.58  3.000
 KMA  C22  C18  C17  113.49  3.000
 KMA  H7   C22  N21  107.25  3.000
 KMA  H7   C22  C23  108.37  3.000
 KMA  N21  C22  C23  105.58  3.000
 KMA  H7   C22  C18  108.74  3.000
 KMA  C23  C22  C18  114.09  3.000
 KMA  N21  C22  C18  112.51  3.000
 KMA  H9   C23  H8   107.16  3.000
 KMA  H9   C23  C24  112.98  3.000
 KMA  H8   C23  C24  110.78  3.000
 KMA  H9   C23  C22  112.16  3.000
 KMA  H8   C23  C22  109.49  3.000
 KMA  C24  C23  C22  104.28  3.000
 KMA  H11  C24  H10  106.92  3.000
 KMA  H11  C24  C25  111.33  3.000
 KMA  H10  C24  C25  111.18  3.000
 KMA  H11  C24  C23  112.25  3.000
 KMA  H10  C24  C23  111.14  3.000
 KMA  C25  C24  C23  104.11  3.000
 KMA  H13  C25  H12  107.09  3.000
 KMA  H13  C25  N21  108.90  3.000
 KMA  H12  C25  N21  110.46  3.000
 KMA  H13  C25  C24  109.85  3.000
 KMA  H12  C25  C24  113.17  3.000
 KMA  N21  C25  C24  107.31  3.000
 KMA  H14  N21  C25  108.33  3.000
 KMA  H14  N21  C22  107.79  3.000
 KMA  C25  N21  C22  104.37  3.000
 KMA  H16  C16  C11  119.09  3.000
 KMA  H16  C16  C15  119.21  3.000
 KMA  C11  C16  C15  121.70  3.000
 KMA  C09  C11  C16  120.58  3.000
 KMA  C09  C11  C12  120.31  3.000
 KMA  C16  C11  C12  119.07  3.000
 KMA  H18  C09  H17  107.08  3.000
 KMA  H18  C09  C08  109.11  3.000
 KMA  H17  C09  C08  108.92  3.000
 KMA  H18  C09  C11  109.82  3.000
 KMA  H17  C09  C11  110.14  3.000
 KMA  C08  C09  C11  111.65  3.000
 KMA  H20  C08  H19  107.16  3.000
 KMA  H20  C08  C06  109.37  3.000
 KMA  H19  C08  C06  110.08  3.000
 KMA  H20  C08  C09  109.05  3.000
 KMA  H19  C08  C09  109.52  3.000
 KMA  C06  C08  C09  111.56  3.000
 KMA  N01  C06  C05  122.80  3.000
 KMA  C05  C06  C08  121.31  3.000
 KMA  N01  C06  C08  115.88  3.000
 KMA  H21  C05  C04  120.65  3.000
 KMA  H21  C05  C06  120.32  3.000
 KMA  C04  C05  C06  119.03  3.000
 KMA  C02  N01  C06  118.71  3.000
 KMA  C03  C02  N02  120.59  3.000
 KMA  C03  C02  N01  122.29  3.000
 KMA  N02  C02  N01  117.09  3.000
 KMA  H23  N02  H22  114.00  3.000
 KMA  H23  N02  C02  117.47  3.000
 KMA  H22  N02  C02  115.99  3.000
 KMA  H24  C03  C04  120.86  3.000
 KMA  H24  C03  C02  120.05  3.000
 KMA  C04  C03  C02  119.09  3.000
 KMA  C07  C04  C03  121.30  3.000
 KMA  C07  C04  C05  120.61  3.000
 KMA  C03  C04  C05  118.08  3.000
 KMA  H27  C07  H26  108.28  3.000
 KMA  H27  C07  H25  107.03  3.000
 KMA  H26  C07  H25  107.86  3.000
 KMA  H27  C07  C04  111.17  3.000
 KMA  H26  C07  C04  111.75  3.000
 KMA  H25  C07  C04  110.57  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
 KMA  CONST_01  C16  C15  C14  C13     0.00   0.0  0
 KMA  CONST_02  C16  C11  C12  C13     0.00   0.0  0
 KMA  CONST_03  C15  C16  C11  C12     0.00   0.0  0
 KMA  CONST_04  C15  C14  C13  C12     0.00   0.0  0
 KMA  CONST_05  C11  C16  C15  C14     0.00   0.0  0
 KMA  CONST_06  C11  C12  C13  C14     0.00   0.0  0
 KMA  CONST_07  C03  C02  N01  C06     0.00   0.0  0
 KMA  CONST_08  C03  C04  C05  C06     0.00   0.0  0
 KMA  CONST_09  C02  N01  C06  C05     0.00   0.0  0
 KMA  CONST_10  C02  C03  C04  C05     0.00   0.0  0
 KMA  CONST_11  C04  C05  C06  N01     0.00   0.0  0
 KMA  CONST_12  C04  C03  C02  N01     0.00   0.0  0
 KMA  CONST_13  C15  C14  C13  F13   180.00   0.0  0
 KMA  CONST_14  C11  C12  C13  F13   180.00   0.0  0
 KMA  CONST_15  C17  C15  C14  C13   180.00   0.0  0
 KMA  CONST_16  C09  C11  C12  C13   180.00   0.0  0
 KMA  CONST_17  C09  C11  C16  C15   180.00   0.0  0
 KMA  CONST_18  C11  C16  C15  C17   180.00   0.0  0
 KMA  CONST_19  C02  N01  C06  C08   180.00   0.0  0
 KMA  CONST_20  C04  C05  C06  C08   180.00   0.0  0
 KMA  CONST_21  N02  C02  N01  C06   180.00   0.0  0
 KMA  CONST_22  C07  C04  C05  C06   180.00   0.0  0
 KMA  CONST_23  C07  C04  C03  C02   180.00   0.0  0
 KMA  CONST_24  C04  C03  C02  N02   180.00   0.0  0
 KMA  CONST_25  H16  C16  C11  C12   180.00   0.0  0
 KMA  CONST_26  H2   C14  C13  C12   180.00   0.0  0
 KMA  CONST_27  H1   C12  C13  C14   180.00   0.0  0
 KMA  CONST_28  H24  C03  C04  C05   180.00   0.0  0
 KMA  CONST_29  H21  C05  C06  N01   180.00   0.0  0
 KMA  Var_01    C24  C25  N21  C22   -33.63  30.0  1
 KMA  Var_02    C25  C24  C23  C22     8.03  30.0  1
 KMA  Var_03    N21  C25  C24  C23    15.20  30.0  1
 KMA  Var_04    C08  C09  C11  C12   -90.88  30.0  2
 KMA  Var_05    C18  C17  C15  C14   -85.67  30.0  2
 KMA  Var_06    C22  C18  C17  C15  -178.76  30.0  1
 KMA  Var_07    C06  C08  C09  C11   178.55  30.0  1
 KMA  Var_08    N01  C06  C08  C09   -69.14  30.0  2
 KMA  Var_09    H25  C07  C04  C05    71.67  30.0  2

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
 KMA  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
 KMA  plan-1  F13  0.020
 KMA  plan-1  C13  0.020
 KMA  plan-1  C12  0.020
 KMA  plan-1  C14  0.020
 KMA  plan-1  C15  0.020
 KMA  plan-1  C17  0.020
 KMA  plan-1  C16  0.020
 KMA  plan-1  C11  0.020
 KMA  plan-1  C09  0.020
 KMA  plan-1  H1   0.020
 KMA  plan-1  H2   0.020
 KMA  plan-1  H16  0.020
 KMA  plan-2  C08  0.020
 KMA  plan-2  C06  0.020
 KMA  plan-2  C05  0.020
 KMA  plan-2  N01  0.020
 KMA  plan-2  C02  0.020
 KMA  plan-2  N02  0.020
 KMA  plan-2  C03  0.020
 KMA  plan-2  C04  0.020
 KMA  plan-2  C07  0.020
 KMA  plan-2  H21  0.020
 KMA  plan-2  H24  0.020
 KMA  plan-3  C02  0.020
 KMA  plan-3  N02  0.020
 KMA  plan-3  H22  0.020
 KMA  plan-3  H23  0.020

