# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 01:45:09 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: (1S,2S)-2-(3-fluorobenzyl)-N-{2-[2-(1H-imidazol-1-yl)pyrimidin-4-yl]ethyl}cyclopropanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cccc(C[C@H]2C[C@@H]2NCCc3ccnc(n3)n4ccnc4)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
 K9L  K9L  (1S,2S)-2-(3-fluorobenzyl)-N-{2-[2-(1H-imidazol-1-yl)pyrimidin-4-yl]ethyl}cyclopropanamine  ligand  45  25  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_K9L
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
 K9L  N01   N  N     0  -0.444   6.5615  -2.3612  -0.5289
 K9L  C02   C  CR15  0   0.115   5.5647  -1.6605  -0.0773
 K9L  N03   N  NR5   0  -0.528   5.5123  -0.4292  -0.6632
 K9L  C04   C  CR15  0  -0.094   6.5629  -0.3619  -1.5503
 K9L  C05   C  CR15  0  -0.209   7.1925  -1.5610  -1.4497
 K9L  C1'   C  CR6   0   0.170  -4.6592  -0.7085  -0.5961
 K9L  N11   N  N     0  -0.452   3.6397   0.2798   0.4802
 K9L  C12   C  CR6   0   0.635   4.5671   0.5697  -0.4097
 K9L  N13   N  N     0  -0.440   4.7076   1.6926  -1.0864
 K9L  C14   C  CR16  0   0.004   3.8020   2.6296  -0.8323
 K9L  C15   C  CR16  0  -0.384   2.7784   2.4438   0.0776
 K9L  C16   C  CR6   0   0.315   2.7307   1.2183   0.7334
 K9L  C17   C  CH2   0  -0.523   1.6502   0.8797   1.7082
 K9L  C18   C  CH2   0  -0.257   0.6215  -0.0628   1.0815
 K9L  N19   N  NH1   0  -0.607  -0.4267  -0.3666   2.0350
 K9L  C2'   C  CR16  0  -0.467  -5.0153   0.4794  -1.2298
 K9L  C21   C  CH1   0  -0.082  -1.4688  -1.1729   1.4816
 K9L  C22   C  CH2   0  -0.502  -2.8212  -1.0986   2.1205
 K9L  C23   C  CH1   0  -0.222  -2.5901  -0.4767   0.7765
 K9L  C24   C  CH2   0  -0.546  -3.2099  -1.0864  -0.4607
 K9L  C3'   C  CR6   0   0.538  -6.3482   0.8333  -1.3039
 K9L  C4'   C  CR16  0  -0.427  -7.3560   0.0531  -0.7716
 K9L  C5'   C  CR16  0  -0.225  -6.9953  -1.1313  -0.1427
 K9L  C6'   C  CR16  0  -0.322  -5.6628  -1.5094  -0.0549
 K9L  F7'   F  F     0  -0.319  -6.6750   1.9816  -1.9230
 K9L  H02   H  HCR5  0   0.294   4.8472  -1.9728   0.6640
 K9L  H04   H  HCR5  0   0.300   6.7552   0.5086  -2.1513
 K9L  H05   H  HCR5  0   0.261   8.0654  -1.8936  -1.9892
 K9L  H14   H  HCR6  0   0.287   3.9012   3.5606  -1.3775
 K9L  H15   H  HCR6  0   0.284   2.0498   3.2177   0.2708
 K9L  H17   H  HCH2  0   0.261   2.0971   0.4014   2.5839
 K9L  H17A  H  HCH2  0   0.256   1.1497   1.7889   2.0435
 K9L  H18   H  HCH2  0   0.233   0.1651   0.4262   0.2164
 K9L  H18A  H  HCH2  0   0.209   1.1337  -0.9590   0.7014
 K9L  HN19  H  HNH1  0   0.347  -0.0278  -0.8390   2.8383
 K9L  H2'   H  HCR6  0   0.269  -4.2594   1.1218  -1.6660
 K9L  H21   H  HCH1  0   0.227  -1.1842  -2.1436   1.0688
 K9L  H22   H  HCH2  0   0.244  -3.4141  -2.0039   2.1740
 K9L  H22A  H  HCH2  0   0.249  -2.9318  -0.4377   2.9710
 K9L  H23   H  HCH1  0   0.256  -2.5270   0.6074   0.7660
 K9L  H24   H  HCH2  0   0.249  -3.1163  -2.1745  -0.4175
 K9L  H24A  H  HCH2  0   0.254  -2.6561  -0.7570  -1.3435
 K9L  H4'   H  HCR6  0   0.276  -8.3913   0.3573  -0.8495
 K9L  H5'   H  HCR6  0   0.265  -7.7654  -1.7649   0.2776
 K9L  H6'   H  HCR6  0   0.250  -5.3993  -2.4396   0.4335

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
 K9L  N01  C02   aromatic  1.299  0.020  1.299
 K9L  N01  C05   aromatic  1.373  0.020  1.373
 K9L  C02  N03   aromatic  1.365  0.020  1.365
 K9L  N03  C04   aromatic  1.377  0.020  1.377
 K9L  N03  C12   single    1.398  0.020  1.398
 K9L  C04  C05   aromatic  1.358  0.020  1.358
 K9L  C1'  C2'   aromatic  1.393  0.020  1.393
 K9L  C1'  C24   single    1.504  0.020  1.504
 K9L  C1'  C6'   aromatic  1.393  0.020  1.393
 K9L  N11  C12   aromatic  1.318  0.020  1.318
 K9L  N11  C16   aromatic  1.331  0.020  1.331
 K9L  C12  N13   aromatic  1.319  0.020  1.319
 K9L  N13  C14   aromatic  1.328  0.020  1.328
 K9L  C14  C15   aromatic  1.382  0.020  1.382
 K9L  C15  C16   aromatic  1.391  0.020  1.391
 K9L  C16  C17   single    1.494  0.020  1.494
 K9L  C17  C18   single    1.529  0.020  1.529
 K9L  C18  N19   single    1.449  0.020  1.449
 K9L  N19  C21   single    1.429  0.020  1.429
 K9L  C2'  C3'   aromatic  1.381  0.020  1.381
 K9L  C21  C22   single    1.498  0.020  1.498
 K9L  C21  C23   single    1.496  0.020  1.496
 K9L  C22  C23   single    1.499  0.020  1.499
 K9L  C23  C24   single    1.512  0.020  1.512
 K9L  C3'  C4'   aromatic  1.381  0.020  1.381
 K9L  C3'  F7'   single    1.345  0.020  1.345
 K9L  C4'  C5'   aromatic  1.389  0.020  1.389
 K9L  C5'  C6'   aromatic  1.388  0.020  1.388
 K9L  C02  H02   single    0.930  0.020  1.080
 K9L  C04  H04   single    0.930  0.020  1.080
 K9L  C05  H05   single    0.930  0.020  1.080
 K9L  C14  H14   single    0.930  0.020  1.080
 K9L  C15  H15   single    0.930  0.020  1.080
 K9L  C17  H17   single    0.970  0.020  1.090
 K9L  C17  H17A  single    0.970  0.020  1.090
 K9L  C18  H18   single    0.970  0.020  1.090
 K9L  C18  H18A  single    0.970  0.020  1.090
 K9L  N19  HN19  single    0.890  0.020  1.040
 K9L  C2'  H2'   single    0.930  0.020  1.080
 K9L  C21  H21   single    0.970  0.020  1.090
 K9L  C22  H22   single    0.970  0.020  1.090
 K9L  C22  H22A  single    0.970  0.020  1.090
 K9L  C23  H23   single    0.970  0.020  1.090
 K9L  C24  H24   single    0.970  0.020  1.090
 K9L  C24  H24A  single    0.970  0.020  1.090
 K9L  C4'  H4'   single    0.930  0.020  1.080
 K9L  C5'  H5'   single    0.930  0.020  1.080
 K9L  C6'  H6'   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
 K9L  C05   N01  C02  105.74  3.000
 K9L  H02   C02  N03  122.08  3.000
 K9L  H02   C02  N01  126.40  3.000
 K9L  N03   C02  N01  111.52  3.000
 K9L  C12   N03  C04  126.71  3.000
 K9L  C12   N03  C02  126.35  3.000
 K9L  C04   N03  C02  106.95  3.000
 K9L  H04   C04  C05  132.33  3.000
 K9L  H04   C04  N03  122.43  3.000
 K9L  C05   C04  N03  105.24  3.000
 K9L  H05   C05  C04  127.62  3.000
 K9L  H05   C05  N01  121.83  3.000
 K9L  C04   C05  N01  110.55  3.000
 K9L  C6'   C1'  C24  120.98  3.000
 K9L  C6'   C1'  C2'  118.87  3.000
 K9L  C24   C1'  C2'  120.12  3.000
 K9L  C16   N11  C12  117.01  3.000
 K9L  N13   C12  N11  127.52  3.000
 K9L  N13   C12  N03  116.31  3.000
 K9L  N11   C12  N03  116.17  3.000
 K9L  C14   N13  C12  115.47  3.000
 K9L  H14   C14  C15  120.97  3.000
 K9L  H14   C14  N13  116.59  3.000
 K9L  C15   C14  N13  122.44  3.000
 K9L  H15   C15  C16  121.58  3.000
 K9L  H15   C15  C14  121.40  3.000
 K9L  C16   C15  C14  117.02  3.000
 K9L  C17   C16  C15  122.15  3.000
 K9L  C17   C16  N11  117.28  3.000
 K9L  C15   C16  N11  120.55  3.000
 K9L  H17A  C17  H17  107.82  3.000
 K9L  H17A  C17  C18  109.33  3.000
 K9L  H17   C17  C18  109.49  3.000
 K9L  H17A  C17  C16  110.09  3.000
 K9L  H17   C17  C16  109.03  3.000
 K9L  C18   C17  C16  111.02  3.000
 K9L  H18A  C18  H18  106.57  3.000
 K9L  H18A  C18  N19  113.16  3.000
 K9L  H18   C18  N19  108.20  3.000
 K9L  H18A  C18  C17  109.30  3.000
 K9L  H18   C18  C17  109.23  3.000
 K9L  N19   C18  C17  110.25  3.000
 K9L  HN19  N19  C21  109.32  3.000
 K9L  HN19  N19  C18  109.54  3.000
 K9L  C21   N19  C18  113.01  3.000
 K9L  H2'   C2'  C3'  119.98  3.000
 K9L  H2'   C2'  C1'  120.69  3.000
 K9L  C3'   C2'  C1'  119.33  3.000
 K9L  H21   C21  C23  115.50  3.000
 K9L  H21   C21  C22  116.14  3.000
 K9L  C23   C21  C22   60.08  3.000
 K9L  H21   C21  N19  117.24  3.000
 K9L  C23   C21  N19  117.80  3.000
 K9L  C22   C21  N19  117.73  3.000
 K9L  H22A  C22  H22  114.54  3.000
 K9L  H22A  C22  C23  117.83  3.000
 K9L  H22   C22  C23  118.38  3.000
 K9L  H22A  C22  C21  117.24  3.000
 K9L  H22   C22  C21  118.28  3.000
 K9L  C23   C22  C21   59.92  3.000
 K9L  H23   C23  C24  114.73  3.000
 K9L  H23   C23  C22  115.58  3.000
 K9L  C24   C23  C22  120.21  3.000
 K9L  H23   C23  C21  115.18  3.000
 K9L  C24   C23  C21  120.34  3.000
 K9L  C22   C23  C21   60.00  3.000
 K9L  H24A  C24  H24  106.77  3.000
 K9L  H24A  C24  C23  109.38  3.000
 K9L  H24   C24  C23  109.51  3.000
 K9L  H24A  C24  C1'  109.87  3.000
 K9L  H24   C24  C1'  109.65  3.000
 K9L  C23   C24  C1'  111.55  3.000
 K9L  F7'   C3'  C4'  118.84  3.000
 K9L  F7'   C3'  C2'  118.55  3.000
 K9L  C4'   C3'  C2'  122.60  3.000
 K9L  H4'   C4'  C5'  121.40  3.000
 K9L  H4'   C4'  C3'  120.77  3.000
 K9L  C5'   C4'  C3'  117.82  3.000
 K9L  H5'   C5'  C6'  119.94  3.000
 K9L  H5'   C5'  C4'  119.37  3.000
 K9L  C6'   C5'  C4'  120.69  3.000
 K9L  H6'   C6'  C5'  119.74  3.000
 K9L  H6'   C6'  C1'  119.57  3.000
 K9L  C5'   C6'  C1'  120.69  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
 K9L  CONST_01  C04  N03  C02  N01     0.00   0.0  0
 K9L  CONST_02  C12  N03  C02  N01   180.00   0.0  0
 K9L  CONST_03  N03  C04  C05  N01     0.00   0.0  0
 K9L  CONST_04  C04  C05  N01  C02     0.00   0.0  0
 K9L  CONST_05  C05  C04  N03  C02     0.00   0.0  0
 K9L  CONST_06  N11  C12  N03  C02     0.00   0.0  0
 K9L  CONST_07  N13  C12  N03  C02   180.00   0.0  0
 K9L  CONST_08  C05  N01  C02  N03     0.00   0.0  0
 K9L  CONST_09  C16  N11  C12  N03   180.00   0.0  0
 K9L  CONST_10  C14  N13  C12  N03   180.00   0.0  0
 K9L  CONST_11  N11  C12  N03  C04   180.00   0.0  0
 K9L  CONST_12  N13  C12  N03  C04     0.00   0.0  0
 K9L  CONST_13  C12  N03  C04  C05   180.00   0.0  0
 K9L  CONST_14  C4'  C3'  C2'  C1'     0.00   0.0  0
 K9L  CONST_15  C4'  C5'  C6'  C1'     0.00   0.0  0
 K9L  CONST_16  C14  N13  C12  N11     0.00   0.0  0
 K9L  CONST_17  C14  C15  C16  N11     0.00   0.0  0
 K9L  CONST_18  C15  C16  N11  C12     0.00   0.0  0
 K9L  CONST_19  C15  C14  N13  C12     0.00   0.0  0
 K9L  CONST_20  C16  N11  C12  N13     0.00   0.0  0
 K9L  CONST_21  C16  C15  C14  N13     0.00   0.0  0
 K9L  CONST_22  C5'  C6'  C1'  C2'     0.00   0.0  0
 K9L  CONST_23  C5'  C4'  C3'  C2'     0.00   0.0  0
 K9L  CONST_24  C6'  C1'  C2'  C3'     0.00   0.0  0
 K9L  CONST_25  C6'  C5'  C4'  C3'     0.00   0.0  0
 K9L  CONST_26  F7'  C3'  C2'  C1'   180.00   0.0  0
 K9L  CONST_27  C17  C16  N11  C12   180.00   0.0  0
 K9L  CONST_28  C17  C16  C15  C14   180.00   0.0  0
 K9L  CONST_29  C3'  C2'  C1'  C24   180.00   0.0  0
 K9L  CONST_30  C5'  C6'  C1'  C24   180.00   0.0  0
 K9L  CONST_31  F7'  C3'  C4'  C5'   180.00   0.0  0
 K9L  CONST_32  H04  C04  C05  N01   180.00   0.0  0
 K9L  CONST_33  H05  C05  N01  C02   180.00   0.0  0
 K9L  CONST_34  H02  C02  N03  C04   180.00   0.0  0
 K9L  CONST_35  H5'  C5'  C6'  C1'   180.00   0.0  0
 K9L  CONST_36  H15  C15  C16  N11   180.00   0.0  0
 K9L  CONST_37  H14  C14  N13  C12   180.00   0.0  0
 K9L  CONST_38  H6'  C6'  C1'  C2'   180.00   0.0  0
 K9L  CONST_39  H4'  C4'  C3'  C2'   180.00   0.0  0
 K9L  CONST_40  H2'  C2'  C3'  C4'   180.00   0.0  0
 K9L  Var_01    C21  C23  C24  C1'   150.11  30.0  1
 K9L  Var_02    C23  C22  C21  N19   107.78  30.0  1
 K9L  Var_03    C23  C24  C1'  C2'    86.36  30.0  2
 K9L  Var_04    C24  C23  C22  C21   109.80  30.0  1
 K9L  Var_05    C18  C17  C16  N11   -74.81  30.0  2
 K9L  Var_06    C22  C21  N19  C18  -155.54  30.0  3
 K9L  Var_07    N19  C18  C17  C16  -179.28  30.0  3
 K9L  Var_08    C21  N19  C18  C17   176.06  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
 K9L  chir_01  C21  N19  C22  C23  both
 K9L  chir_02  C23  C21  C22  C24  both

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
 K9L  plan-1  N01  0.020
 K9L  plan-1  C02  0.020
 K9L  plan-1  N03  0.020
 K9L  plan-1  C04  0.020
 K9L  plan-1  C05  0.020
 K9L  plan-1  C12  0.020
 K9L  plan-1  H02  0.020
 K9L  plan-1  H04  0.020
 K9L  plan-1  H05  0.020
 K9L  plan-2  C1'  0.020
 K9L  plan-2  C2'  0.020
 K9L  plan-2  C24  0.020
 K9L  plan-2  C3'  0.020
 K9L  plan-2  C4'  0.020
 K9L  plan-2  C5'  0.020
 K9L  plan-2  C6'  0.020
 K9L  plan-2  F7'  0.020
 K9L  plan-2  H2'  0.020
 K9L  plan-2  H4'  0.020
 K9L  plan-2  H5'  0.020
 K9L  plan-2  H6'  0.020
 K9L  plan-3  N03  0.020
 K9L  plan-3  N11  0.020
 K9L  plan-3  C12  0.020
 K9L  plan-3  N13  0.020
 K9L  plan-3  C14  0.020
 K9L  plan-3  C15  0.020
 K9L  plan-3  C16  0.020
 K9L  plan-3  C17  0.020
 K9L  plan-3  H14  0.020
 K9L  plan-3  H15  0.020

