# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 07:11:41 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: (1R,2R)-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
 L5Z  L5Z  (1R,2R)-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_L5Z
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
 L5Z  N01   N  N     0  -0.443   6.4914   2.6428   0.9739
 L5Z  C02   C  CR15  0   0.115   5.5535   1.8766   0.5033
 L5Z  N03   N  NR5   0  -0.528   5.8671   0.5564   0.6463
 L5Z  C04   C  CR15  0  -0.094   7.1003   0.5003   1.2558
 L5Z  C05   C  CR15  0  -0.210   7.4635   1.7949   1.4459
 L5Z  C1'   C  CR6   0   0.169  -5.2309   0.6117  -0.0970
 L5Z  N11   N  N     0  -0.452   3.9479  -0.2373  -0.3555
 L5Z  C12   C  CR6   0   0.634   5.0790  -0.5299   0.2537
 L5Z  N13   N  N     0  -0.440   5.5538  -1.7281   0.5323
 L5Z  C14   C  CR16  0   0.004   4.7906  -2.7465   0.1543
 L5Z  C15   C  CR16  0  -0.384   3.5786  -2.5680  -0.4856
 L5Z  C16   C  CR6   0   0.316   3.1819  -1.2580  -0.7326
 L5Z  C17   C  CH2   0  -0.523   1.8839  -0.9287  -1.3953
 L5Z  C18   C  CH2   0  -0.256   0.8628  -0.3994  -0.3871
 L5Z  N19   N  NH1   0  -0.609  -0.3764  -0.0696  -1.0613
 L5Z  C2'   C  CR16  0  -0.469  -5.6982   0.2217   1.1551
 L5Z  C21   C  CH1   0  -0.075  -1.4072   0.3541  -0.1675
 L5Z  C22   C  CH2   0  -0.486  -2.2577  -0.7085   0.4636
 L5Z  C23   C  CH1   0  -0.242  -2.8281   0.1824  -0.5978
 L5Z  C24   C  CH2   0  -0.544  -3.8650   1.2240  -0.2409
 L5Z  C3'   C  CR6   0   0.538  -6.9351  -0.3853   1.2572
 L5Z  C4'   C  CR16  0  -0.427  -7.7388  -0.6250   0.1603
 L5Z  C5'   C  CR16  0  -0.225  -7.2684  -0.2321  -1.0864
 L5Z  C6'   C  CR16  0  -0.321  -6.0296   0.3792  -1.2155
 L5Z  F7'   F  F     0  -0.319  -7.3711  -0.7542   2.4748
 L5Z  H02   H  HCR5  0   0.294   4.6303   2.2003   0.0516
 L5Z  H04   H  HCR5  0   0.300   7.5880  -0.4301   1.4850
 L5Z  H05   H  HCR5  0   0.261   8.3716   2.1641   1.8961
 L5Z  H14   H  HCR6  0   0.287   5.1649  -3.7397   0.3715
 L5Z  H15   H  HCR6  0   0.283   2.9722  -3.4109  -0.7833
 L5Z  H17   H  HCH2  0   0.261   2.0618  -0.1691  -2.1615
 L5Z  H17A  H  HCH2  0   0.256   1.4806  -1.8126  -1.8909
 L5Z  H18   H  HCH2  0   0.233   0.6544  -1.1720   0.3578
 L5Z  H18A  H  HCH2  0   0.208   1.2985   0.4516   0.1567
 L5Z  HN19  H  HNH1  0   0.347  -0.2048   0.6565  -1.7471
 L5Z  H2'   H  HCR6  0   0.267  -5.1055   0.3939   2.0453
 L5Z  H21   H  HCH1  0   0.228  -1.2014   1.2260   0.4586
 L5Z  H22   H  HCH2  0   0.249  -2.0418  -1.7368   0.2010
 L5Z  H22A  H  HCH2  0   0.243  -2.5814  -0.5649   1.4878
 L5Z  H23   H  HCH1  0   0.256  -2.9667  -0.2772  -1.5714
 L5Z  H24   H  HCH2  0   0.255  -3.8844   1.9987  -1.0119
 L5Z  H24A  H  HCH2  0   0.249  -3.5807   1.7164   0.6923
 L5Z  H4'   H  HCR6  0   0.276  -8.7039  -1.1012   0.2742
 L5Z  H5'   H  HCR6  0   0.265  -7.8793  -0.4044  -1.9627
 L5Z  H6'   H  HCR6  0   0.253  -5.6791   0.6804  -2.1954

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
 L5Z  N01  C02   aromatic  1.299  0.020  1.299
 L5Z  N01  C05   aromatic  1.374  0.020  1.374
 L5Z  C02  N03   aromatic  1.364  0.020  1.364
 L5Z  N03  C04   aromatic  1.377  0.020  1.377
 L5Z  N03  C12   single    1.398  0.020  1.398
 L5Z  C04  C05   aromatic  1.358  0.020  1.358
 L5Z  C1'  C2'   aromatic  1.392  0.020  1.392
 L5Z  C1'  C24   single    1.504  0.020  1.504
 L5Z  C1'  C6'   aromatic  1.394  0.020  1.394
 L5Z  N11  C12   aromatic  1.318  0.020  1.318
 L5Z  N11  C16   aromatic  1.331  0.020  1.331
 L5Z  C12  N13   aromatic  1.319  0.020  1.319
 L5Z  N13  C14   aromatic  1.328  0.020  1.328
 L5Z  C14  C15   aromatic  1.382  0.020  1.382
 L5Z  C15  C16   aromatic  1.391  0.020  1.391
 L5Z  C16  C17   single    1.494  0.020  1.494
 L5Z  C17  C18   single    1.529  0.020  1.529
 L5Z  C18  N19   single    1.449  0.020  1.449
 L5Z  N19  C21   single    1.429  0.020  1.429
 L5Z  C2'  C3'   aromatic  1.382  0.020  1.382
 L5Z  C21  C22   single    1.500  0.020  1.500
 L5Z  C21  C23   single    1.494  0.020  1.494
 L5Z  C22  C23   single    1.499  0.020  1.499
 L5Z  C23  C24   single    1.513  0.020  1.513
 L5Z  C3'  C4'   aromatic  1.381  0.020  1.381
 L5Z  C3'  F7'   single    1.345  0.020  1.345
 L5Z  C4'  C5'   aromatic  1.389  0.020  1.389
 L5Z  C5'  C6'   aromatic  1.387  0.020  1.387
 L5Z  C02  H02   single    0.930  0.020  1.080
 L5Z  C04  H04   single    0.930  0.020  1.080
 L5Z  C05  H05   single    0.930  0.020  1.080
 L5Z  C14  H14   single    0.930  0.020  1.080
 L5Z  C15  H15   single    0.930  0.020  1.080
 L5Z  C17  H17   single    0.970  0.020  1.090
 L5Z  C17  H17A  single    0.970  0.020  1.090
 L5Z  C18  H18   single    0.970  0.020  1.090
 L5Z  C18  H18A  single    0.970  0.020  1.090
 L5Z  N19  HN19  single    0.890  0.020  1.040
 L5Z  C2'  H2'   single    0.930  0.020  1.080
 L5Z  C21  H21   single    0.970  0.020  1.090
 L5Z  C22  H22   single    0.970  0.020  1.090
 L5Z  C22  H22A  single    0.970  0.020  1.090
 L5Z  C23  H23   single    0.970  0.020  1.090
 L5Z  C24  H24   single    0.970  0.020  1.090
 L5Z  C24  H24A  single    0.970  0.020  1.090
 L5Z  C4'  H4'   single    0.930  0.020  1.080
 L5Z  C5'  H5'   single    0.930  0.020  1.080
 L5Z  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
 L5Z  C05   N01  C02  105.74  3.000
 L5Z  H02   C02  N03  122.11  3.000
 L5Z  H02   C02  N01  126.37  3.000
 L5Z  N03   C02  N01  111.52  3.000
 L5Z  C12   N03  C04  126.69  3.000
 L5Z  C12   N03  C02  126.35  3.000
 L5Z  C04   N03  C02  106.96  3.000
 L5Z  H04   C04  C05  132.36  3.000
 L5Z  H04   C04  N03  122.41  3.000
 L5Z  C05   C04  N03  105.23  3.000
 L5Z  H05   C05  C04  127.58  3.000
 L5Z  H05   C05  N01  121.87  3.000
 L5Z  C04   C05  N01  110.55  3.000
 L5Z  C6'   C1'  C24  120.77  3.000
 L5Z  C6'   C1'  C2'  118.85  3.000
 L5Z  C24   C1'  C2'  120.34  3.000
 L5Z  C16   N11  C12  117.06  3.000
 L5Z  N13   C12  N11  127.49  3.000
 L5Z  N13   C12  N03  116.34  3.000
 L5Z  N11   C12  N03  116.18  3.000
 L5Z  C14   N13  C12  115.46  3.000
 L5Z  H14   C14  C15  120.95  3.000
 L5Z  H14   C14  N13  116.59  3.000
 L5Z  C15   C14  N13  122.47  3.000
 L5Z  H15   C15  C16  121.73  3.000
 L5Z  H15   C15  C14  121.27  3.000
 L5Z  C16   C15  C14  117.00  3.000
 L5Z  C17   C16  C15  122.29  3.000
 L5Z  C17   C16  N11  117.17  3.000
 L5Z  C15   C16  N11  120.52  3.000
 L5Z  H17A  C17  H17  107.74  3.000
 L5Z  H17A  C17  C18  109.46  3.000
 L5Z  H17   C17  C18  109.27  3.000
 L5Z  H17A  C17  C16  110.13  3.000
 L5Z  H17   C17  C16  108.82  3.000
 L5Z  C18   C17  C16  111.34  3.000
 L5Z  H18A  C18  H18  106.58  3.000
 L5Z  H18A  C18  N19  113.13  3.000
 L5Z  H18   C18  N19  108.35  3.000
 L5Z  H18A  C18  C17  109.22  3.000
 L5Z  H18   C18  C17  109.38  3.000
 L5Z  N19   C18  C17  110.06  3.000
 L5Z  HN19  N19  C21  109.46  3.000
 L5Z  HN19  N19  C18  109.46  3.000
 L5Z  C21   N19  C18  113.17  3.000
 L5Z  H2'   C2'  C3'  119.93  3.000
 L5Z  H2'   C2'  C1'  120.72  3.000
 L5Z  C3'   C2'  C1'  119.34  3.000
 L5Z  H21   C21  C23  115.83  3.000
 L5Z  H21   C21  C22  115.52  3.000
 L5Z  C23   C21  C22   60.05  3.000
 L5Z  H21   C21  N19  117.33  3.000
 L5Z  C23   C21  N19  118.15  3.000
 L5Z  C22   C21  N19  117.53  3.000
 L5Z  H22A  C22  H22  114.49  3.000
 L5Z  H22A  C22  C23  118.49  3.000
 L5Z  H22   C22  C23  117.94  3.000
 L5Z  H22A  C22  C21  118.23  3.000
 L5Z  H22   C22  C21  117.22  3.000
 L5Z  C23   C22  C21   59.78  3.000
 L5Z  H23   C23  C24  114.56  3.000
 L5Z  H23   C23  C22  115.61  3.000
 L5Z  C24   C23  C22  120.21  3.000
 L5Z  H23   C23  C21  115.37  3.000
 L5Z  C24   C23  C21  120.31  3.000
 L5Z  C22   C23  C21   60.17  3.000
 L5Z  H24A  C24  H24  106.72  3.000
 L5Z  H24A  C24  C23  109.48  3.000
 L5Z  H24   C24  C23  109.50  3.000
 L5Z  H24A  C24  C1'  109.76  3.000
 L5Z  H24   C24  C1'  109.88  3.000
 L5Z  C23   C24  C1'  111.40  3.000
 L5Z  F7'   C3'  C4'  118.88  3.000
 L5Z  F7'   C3'  C2'  118.53  3.000
 L5Z  C4'   C3'  C2'  122.59  3.000
 L5Z  H4'   C4'  C5'  121.39  3.000
 L5Z  H4'   C4'  C3'  120.78  3.000
 L5Z  C5'   C4'  C3'  117.82  3.000
 L5Z  H5'   C5'  C6'  119.93  3.000
 L5Z  H5'   C5'  C4'  119.38  3.000
 L5Z  C6'   C5'  C4'  120.69  3.000
 L5Z  H6'   C6'  C5'  119.70  3.000
 L5Z  H6'   C6'  C1'  119.61  3.000
 L5Z  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
 L5Z  CONST_01  C04  N03  C02  N01     0.00   0.0  0
 L5Z  CONST_02  C12  N03  C02  N01   180.00   0.0  0
 L5Z  CONST_03  N03  C04  C05  N01     0.00   0.0  0
 L5Z  CONST_04  C04  C05  N01  C02     0.00   0.0  0
 L5Z  CONST_05  C05  C04  N03  C02     0.00   0.0  0
 L5Z  CONST_06  N11  C12  N03  C02     0.00   0.0  0
 L5Z  CONST_07  N13  C12  N03  C02   180.00   0.0  0
 L5Z  CONST_08  C05  N01  C02  N03     0.00   0.0  0
 L5Z  CONST_09  C16  N11  C12  N03   180.00   0.0  0
 L5Z  CONST_10  C14  N13  C12  N03   180.00   0.0  0
 L5Z  CONST_11  N11  C12  N03  C04   180.00   0.0  0
 L5Z  CONST_12  N13  C12  N03  C04     0.00   0.0  0
 L5Z  CONST_13  C12  N03  C04  C05   180.00   0.0  0
 L5Z  CONST_14  C4'  C3'  C2'  C1'     0.00   0.0  0
 L5Z  CONST_15  C4'  C5'  C6'  C1'     0.00   0.0  0
 L5Z  CONST_16  C14  N13  C12  N11     0.00   0.0  0
 L5Z  CONST_17  C14  C15  C16  N11     0.00   0.0  0
 L5Z  CONST_18  C15  C16  N11  C12     0.00   0.0  0
 L5Z  CONST_19  C15  C14  N13  C12     0.00   0.0  0
 L5Z  CONST_20  C16  N11  C12  N13     0.00   0.0  0
 L5Z  CONST_21  C16  C15  C14  N13     0.00   0.0  0
 L5Z  CONST_22  C5'  C6'  C1'  C2'     0.00   0.0  0
 L5Z  CONST_23  C5'  C4'  C3'  C2'     0.00   0.0  0
 L5Z  CONST_24  C6'  C1'  C2'  C3'     0.00   0.0  0
 L5Z  CONST_25  C6'  C5'  C4'  C3'     0.00   0.0  0
 L5Z  CONST_26  F7'  C3'  C2'  C1'   180.00   0.0  0
 L5Z  CONST_27  C17  C16  N11  C12   180.00   0.0  0
 L5Z  CONST_28  C17  C16  C15  C14   180.00   0.0  0
 L5Z  CONST_29  C3'  C2'  C1'  C24   180.00   0.0  0
 L5Z  CONST_30  C5'  C6'  C1'  C24   180.00   0.0  0
 L5Z  CONST_31  F7'  C3'  C4'  C5'   180.00   0.0  0
 L5Z  CONST_32  H04  C04  C05  N01   180.00   0.0  0
 L5Z  CONST_33  H05  C05  N01  C02   180.00   0.0  0
 L5Z  CONST_34  H02  C02  N03  C04   180.00   0.0  0
 L5Z  CONST_35  H5'  C5'  C6'  C1'   180.00   0.0  0
 L5Z  CONST_36  H15  C15  C16  N11   180.00   0.0  0
 L5Z  CONST_37  H14  C14  N13  C12   180.00   0.0  0
 L5Z  CONST_38  H6'  C6'  C1'  C2'   180.00   0.0  0
 L5Z  CONST_39  H4'  C4'  C3'  C2'   180.00   0.0  0
 L5Z  CONST_40  H2'  C2'  C3'  C4'   180.00   0.0  0
 L5Z  Var_01    C21  C23  C24  C1'  -150.37  30.0  1
 L5Z  Var_02    C23  C22  C21  N19  -108.28  30.0  1
 L5Z  Var_03    C23  C24  C1'  C2'    94.65  30.0  2
 L5Z  Var_04    C24  C23  C22  C21  -109.83  30.0  1
 L5Z  Var_05    C18  C17  C16  N11   -73.59  30.0  2
 L5Z  Var_06    C22  C21  N19  C18   -86.21  30.0  3
 L5Z  Var_07    N19  C18  C17  C16   179.11  30.0  3
 L5Z  Var_08    C21  N19  C18  C17   176.33  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
 L5Z  chir_01  C21  N19  C22  C23  both
 L5Z  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
 L5Z  plan-1  N01  0.020
 L5Z  plan-1  C02  0.020
 L5Z  plan-1  N03  0.020
 L5Z  plan-1  C04  0.020
 L5Z  plan-1  C05  0.020
 L5Z  plan-1  C12  0.020
 L5Z  plan-1  H02  0.020
 L5Z  plan-1  H04  0.020
 L5Z  plan-1  H05  0.020
 L5Z  plan-2  C1'  0.020
 L5Z  plan-2  C2'  0.020
 L5Z  plan-2  C24  0.020
 L5Z  plan-2  C3'  0.020
 L5Z  plan-2  C4'  0.020
 L5Z  plan-2  C5'  0.020
 L5Z  plan-2  C6'  0.020
 L5Z  plan-2  F7'  0.020
 L5Z  plan-2  H2'  0.020
 L5Z  plan-2  H4'  0.020
 L5Z  plan-2  H5'  0.020
 L5Z  plan-2  H6'  0.020
 L5Z  plan-3  N03  0.020
 L5Z  plan-3  N11  0.020
 L5Z  plan-3  C12  0.020
 L5Z  plan-3  N13  0.020
 L5Z  plan-3  C14  0.020
 L5Z  plan-3  C15  0.020
 L5Z  plan-3  C16  0.020
 L5Z  plan-3  C17  0.020
 L5Z  plan-3  H14  0.020
 L5Z  plan-3  H15  0.020

