# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 19:14:24 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: N-{[(1R,2R)-2-(3-fluorophenyl)cyclopropyl]methyl}-2-[2-(1H-imidazol-1-yl)pyrimidin-4-yl]ethanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cccc(c1)[C@@H]2C[C@H]2CNCCc3ccnc(n3)n4ccnc4
#
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
 9HL  9HL  N-{[(1R,2R)-2-(3-fluorophenyl)cyclopropyl]methyl}-2-[2-(1H-imidazol-1-yl)pyrimidin-4-yl]ethanamine  ligand  45  25  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_9HL
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
 9HL  N01   N  N     0  -0.443   6.1167  -2.9356  -0.6397
 9HL  C02   C  CR15  0   0.115   5.2637  -2.0444  -0.2318
 9HL  N03   N  NR5   0  -0.528   5.7386  -0.7780  -0.4117
 9HL  C04   C  CR15  0  -0.093   6.9884  -0.8944  -0.9774
 9HL  C05   C  CR15  0  -0.209   7.1984  -2.2298  -1.1070
 9HL  C1'   C  CR6   0   0.257  -5.2293  -0.6225   0.1105
 9HL  N11   N  N     0  -0.452   3.8903   0.2781   0.4738
 9HL  C12   C  CR6   0   0.634   5.0755   0.4094  -0.0863
 9HL  N13   N  N     0  -0.440   5.7083   1.5301  -0.3736
 9HL  C14   C  CR16  0   0.004   5.0617   2.6466  -0.0608
 9HL  C15   C  CR16  0  -0.385   3.8088   2.6394   0.5228
 9HL  C16   C  CR6   0   0.318   3.2403   1.3975   0.7841
 9HL  C17   C  CH2   0  -0.522   1.8806   1.2528   1.3874
 9HL  C18   C  CH2   0  -0.253   0.8663   0.7534   0.3583
 9HL  N19   N  NH1   0  -0.603  -0.4392   0.6064   0.9670
 9HL  C2'   C  CR16  0  -0.490  -5.9897  -1.0530  -0.9754
 9HL  C20   C  CH2   0  -0.261  -1.4504   0.1644   0.0252
 9HL  C21   C  CH1   0  -0.249  -2.7785   0.0088   0.7130
 9HL  C22   C  CH2   0  -0.471  -3.0892  -1.2448   1.4598
 9HL  C23   C  CH1   0  -0.390  -3.7875  -0.9582   0.1556
 9HL  C3'   C  CR6   0   0.541  -7.3349  -0.7431  -1.0318
 9HL  C4'   C  CR16  0  -0.433  -7.9727  -0.0144  -0.0487
 9HL  C5'   C  CR16  0  -0.221  -7.2105   0.4132   1.0315
 9HL  C6'   C  CR16  0  -0.367  -5.8591   0.1162   1.1146
 9HL  F7'   F  F     0  -0.319  -8.0460  -1.1704  -2.0899
 9HL  H02   H  HCR5  0   0.294   4.2938  -2.2368   0.1968
 9HL  H04   H  HCR5  0   0.300   7.5909  -0.0387  -1.2246
 9HL  H05   H  HCR5  0   0.261   8.0683  -2.7233  -1.5111
 9HL  H14   H  HCR6  0   0.287   5.5657   3.5788  -0.2861
 9HL  H15   H  HCR6  0   0.284   3.2988   3.5597   0.7664
 9HL  H17   H  HCH2  0   0.262   1.9374   0.5409   2.2157
 9HL  H17A  H  HCH2  0   0.256   1.5473   2.2089   1.7930
 9HL  H18   H  HCH2  0   0.231   0.7892   1.4817  -0.4543
 9HL  H18A  H  HCH2  0   0.207   1.2367  -0.1794  -0.0931
 9HL  HN19  H  HNH1  0   0.342  -0.3764  -0.0759   1.7146
 9HL  H2'   H  HCR6  0   0.271  -5.5340  -1.6247  -1.7746
 9HL  H20   H  HCH2  0   0.233  -1.5334   0.9138  -0.7678
 9HL  H20A  H  HCH2  0   0.197  -1.1838  -0.7834  -0.4716
 9HL  H21   H  HCH1  0   0.263  -3.1854   0.9275   1.1255
 9HL  H22   H  HCH2  0   0.260  -2.3544  -2.0414   1.4605
 9HL  H22A  H  HCH2  0   0.258  -3.6707  -1.1767   2.3711
 9HL  H23   H  HCH1  0   0.261  -3.4479  -1.5450  -0.6917
 9HL  H4'   H  HCR6  0   0.276  -9.0280   0.2131  -0.1215
 9HL  H5'   H  HCR6  0   0.267  -7.6823   0.9860   1.8188
 9HL  H6'   H  HCR6  0   0.254  -5.2974   0.4672   1.9715

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
 9HL  N01  C02   aromatic  1.299  0.020  1.299
 9HL  N01  C05   aromatic  1.374  0.020  1.374
 9HL  C02  N03   aromatic  1.364  0.020  1.364
 9HL  N03  C04   aromatic  1.377  0.020  1.377
 9HL  N03  C12   single    1.398  0.020  1.398
 9HL  C04  C05   aromatic  1.358  0.020  1.358
 9HL  C1'  C2'   aromatic  1.394  0.020  1.394
 9HL  C1'  C23   single    1.481  0.020  1.481
 9HL  C1'  C6'   aromatic  1.397  0.020  1.397
 9HL  N11  C12   aromatic  1.317  0.020  1.317
 9HL  N11  C16   aromatic  1.331  0.020  1.331
 9HL  C12  N13   aromatic  1.319  0.020  1.319
 9HL  N13  C14   aromatic  1.328  0.020  1.328
 9HL  C14  C15   aromatic  1.382  0.020  1.382
 9HL  C15  C16   aromatic  1.391  0.020  1.391
 9HL  C16  C17   single    1.495  0.020  1.495
 9HL  C17  C18   single    1.529  0.020  1.529
 9HL  C18  N19   single    1.448  0.020  1.448
 9HL  N19  C20   single    1.451  0.020  1.451
 9HL  C2'  C3'   aromatic  1.382  0.020  1.382
 9HL  C20  C21   single    1.504  0.020  1.504
 9HL  C21  C22   single    1.492  0.020  1.492
 9HL  C21  C23   single    1.505  0.020  1.505
 9HL  C22  C23   single    1.507  0.020  1.507
 9HL  C3'  C4'   aromatic  1.380  0.020  1.380
 9HL  C3'  F7'   single    1.345  0.020  1.345
 9HL  C4'  C5'   aromatic  1.390  0.020  1.390
 9HL  C5'  C6'   aromatic  1.386  0.020  1.386
 9HL  C02  H02   single    0.930  0.020  1.080
 9HL  C04  H04   single    0.930  0.020  1.080
 9HL  C05  H05   single    0.930  0.020  1.080
 9HL  C14  H14   single    0.930  0.020  1.080
 9HL  C15  H15   single    0.930  0.020  1.080
 9HL  C17  H17   single    0.970  0.020  1.090
 9HL  C17  H17A  single    0.970  0.020  1.090
 9HL  C18  H18   single    0.970  0.020  1.090
 9HL  C18  H18A  single    0.970  0.020  1.090
 9HL  N19  HN19  single    0.890  0.020  1.040
 9HL  C2'  H2'   single    0.930  0.020  1.080
 9HL  C20  H20   single    0.970  0.020  1.090
 9HL  C20  H20A  single    0.970  0.020  1.090
 9HL  C21  H21   single    0.970  0.020  1.090
 9HL  C22  H22   single    0.970  0.020  1.090
 9HL  C22  H22A  single    0.970  0.020  1.090
 9HL  C23  H23   single    0.970  0.020  1.090
 9HL  C4'  H4'   single    0.930  0.020  1.080
 9HL  C5'  H5'   single    0.930  0.020  1.080
 9HL  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
 9HL  C05   N01  C02  105.74  3.000
 9HL  H02   C02  N03  122.09  3.000
 9HL  H02   C02  N01  126.39  3.000
 9HL  N03   C02  N01  111.52  3.000
 9HL  C12   N03  C04  126.72  3.000
 9HL  C12   N03  C02  126.33  3.000
 9HL  C04   N03  C02  106.96  3.000
 9HL  H04   C04  C05  132.37  3.000
 9HL  H04   C04  N03  122.40  3.000
 9HL  C05   C04  N03  105.23  3.000
 9HL  H05   C05  C04  127.62  3.000
 9HL  H05   C05  N01  121.83  3.000
 9HL  C04   C05  N01  110.55  3.000
 9HL  C6'   C1'  C23  122.48  3.000
 9HL  C6'   C1'  C2'  118.52  3.000
 9HL  C23   C1'  C2'  119.00  3.000
 9HL  C16   N11  C12  117.04  3.000
 9HL  N13   C12  N11  127.52  3.000
 9HL  N13   C12  N03  116.32  3.000
 9HL  N11   C12  N03  116.16  3.000
 9HL  C14   N13  C12  115.45  3.000
 9HL  H14   C14  C15  120.93  3.000
 9HL  H14   C14  N13  116.62  3.000
 9HL  C15   C14  N13  122.45  3.000
 9HL  H15   C15  C16  121.70  3.000
 9HL  H15   C15  C14  121.26  3.000
 9HL  C16   C15  C14  117.04  3.000
 9HL  C17   C16  C15  122.29  3.000
 9HL  C17   C16  N11  117.19  3.000
 9HL  C15   C16  N11  120.50  3.000
 9HL  H17A  C17  H17  107.74  3.000
 9HL  H17A  C17  C18  109.51  3.000
 9HL  H17   C17  C18  109.37  3.000
 9HL  H17A  C17  C16  110.08  3.000
 9HL  H17   C17  C16  108.75  3.000
 9HL  C18   C17  C16  111.32  3.000
 9HL  H18A  C18  H18  106.46  3.000
 9HL  H18A  C18  N19  112.95  3.000
 9HL  H18   C18  N19  108.44  3.000
 9HL  H18A  C18  C17  109.25  3.000
 9HL  H18   C18  C17  109.22  3.000
 9HL  N19   C18  C17  110.39  3.000
 9HL  HN19  N19  C20  108.47  3.000
 9HL  HN19  N19  C18  108.81  3.000
 9HL  C20   N19  C18  112.73  3.000
 9HL  H2'   C2'  C3'  119.86  3.000
 9HL  H2'   C2'  C1'  120.55  3.000
 9HL  C3'   C2'  C1'  119.59  3.000
 9HL  H20A  C20  H20  106.29  3.000
 9HL  H20A  C20  C21  109.31  3.000
 9HL  H20   C20  C21  109.59  3.000
 9HL  H20A  C20  N19  112.69  3.000
 9HL  H20   C20  N19  108.34  3.000
 9HL  C21   C20  N19  110.50  3.000
 9HL  H21   C21  C23  115.66  3.000
 9HL  H21   C21  C22  116.27  3.000
 9HL  C23   C21  C22   60.38  3.000
 9HL  H21   C21  C20  114.65  3.000
 9HL  C23   C21  C20  119.30  3.000
 9HL  C22   C21  C20  119.99  3.000
 9HL  H22A  C22  H22  114.19  3.000
 9HL  H22A  C22  C23  117.86  3.000
 9HL  H22   C22  C23  117.04  3.000
 9HL  H22A  C22  C21  118.69  3.000
 9HL  H22   C22  C21  118.47  3.000
 9HL  C23   C22  C21   60.23  3.000
 9HL  H23   C23  C22  115.33  3.000
 9HL  H23   C23  C21  115.27  3.000
 9HL  C22   C23  C21   59.39  3.000
 9HL  H23   C23  C1'  113.80  3.000
 9HL  C22   C23  C1'  121.37  3.000
 9HL  C21   C23  C1'  121.23  3.000
 9HL  F7'   C3'  C4'  118.95  3.000
 9HL  F7'   C3'  C2'  118.41  3.000
 9HL  C4'   C3'  C2'  122.64  3.000
 9HL  H4'   C4'  C5'  121.51  3.000
 9HL  H4'   C4'  C3'  120.93  3.000
 9HL  C5'   C4'  C3'  117.57  3.000
 9HL  H5'   C5'  C6'  119.67  3.000
 9HL  H5'   C5'  C4'  119.30  3.000
 9HL  C6'   C5'  C4'  121.03  3.000
 9HL  H6'   C6'  C5'  118.92  3.000
 9HL  H6'   C6'  C1'  120.43  3.000
 9HL  C5'   C6'  C1'  120.65  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
 9HL  CONST_01  C04  N03  C02  N01     0.00   0.0  0
 9HL  CONST_02  C12  N03  C02  N01   180.00   0.0  0
 9HL  CONST_03  N03  C04  C05  N01     0.00   0.0  0
 9HL  CONST_04  C04  C05  N01  C02     0.00   0.0  0
 9HL  CONST_05  C05  C04  N03  C02     0.00   0.0  0
 9HL  CONST_06  N11  C12  N03  C02     0.00   0.0  0
 9HL  CONST_07  N13  C12  N03  C02   180.00   0.0  0
 9HL  CONST_08  C05  N01  C02  N03     0.00   0.0  0
 9HL  CONST_09  C16  N11  C12  N03   180.00   0.0  0
 9HL  CONST_10  C14  N13  C12  N03   180.00   0.0  0
 9HL  CONST_11  N11  C12  N03  C04   180.00   0.0  0
 9HL  CONST_12  N13  C12  N03  C04     0.00   0.0  0
 9HL  CONST_13  C12  N03  C04  C05   180.00   0.0  0
 9HL  CONST_14  C4'  C3'  C2'  C1'     0.00   0.0  0
 9HL  CONST_15  C4'  C5'  C6'  C1'     0.00   0.0  0
 9HL  CONST_16  C14  N13  C12  N11     0.00   0.0  0
 9HL  CONST_17  C14  C15  C16  N11     0.00   0.0  0
 9HL  CONST_18  C15  C16  N11  C12     0.00   0.0  0
 9HL  CONST_19  C15  C14  N13  C12     0.00   0.0  0
 9HL  CONST_20  C16  N11  C12  N13     0.00   0.0  0
 9HL  CONST_21  C16  C15  C14  N13     0.00   0.0  0
 9HL  CONST_22  C5'  C6'  C1'  C2'     0.00   0.0  0
 9HL  CONST_23  C5'  C4'  C3'  C2'     0.00   0.0  0
 9HL  CONST_24  C6'  C1'  C2'  C3'     0.00   0.0  0
 9HL  CONST_25  C6'  C5'  C4'  C3'     0.00   0.0  0
 9HL  CONST_26  C3'  C2'  C1'  C23   180.00   0.0  0
 9HL  CONST_27  C5'  C6'  C1'  C23   180.00   0.0  0
 9HL  CONST_28  F7'  C3'  C2'  C1'   180.00   0.0  0
 9HL  CONST_29  C17  C16  N11  C12   180.00   0.0  0
 9HL  CONST_30  C17  C16  C15  C14   180.00   0.0  0
 9HL  CONST_31  F7'  C3'  C4'  C5'   180.00   0.0  0
 9HL  CONST_32  H04  C04  C05  N01   180.00   0.0  0
 9HL  CONST_33  H05  C05  N01  C02   180.00   0.0  0
 9HL  CONST_34  H02  C02  N03  C04   180.00   0.0  0
 9HL  CONST_35  H5'  C5'  C6'  C1'   180.00   0.0  0
 9HL  CONST_36  H15  C15  C16  N11   180.00   0.0  0
 9HL  CONST_37  H14  C14  N13  C12   180.00   0.0  0
 9HL  CONST_38  H6'  C6'  C1'  C2'   180.00   0.0  0
 9HL  CONST_39  H4'  C4'  C3'  C2'   180.00   0.0  0
 9HL  CONST_40  H2'  C2'  C1'  C23     0.00   0.0  0
 9HL  Var_01    C22  C21  C23  C1'   110.41  30.0  1
 9HL  Var_02    C21  C23  C1'  C2'   143.55  30.0  2
 9HL  Var_03    C23  C22  C21  C20  -108.78  30.0  1
 9HL  Var_04    C18  C17  C16  N11   -70.71  30.0  2
 9HL  Var_05    N19  C18  C17  C16   179.36  30.0  3
 9HL  Var_06    C21  C20  N19  C18   179.15  30.0  3
 9HL  Var_07    C20  N19  C18  C17   178.61  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
 9HL  chir_01  C21  C20  C22  C23  both
 9HL  chir_02  C23  C22  C21  C1'  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
 9HL  plan-1  N01  0.020
 9HL  plan-1  C02  0.020
 9HL  plan-1  N03  0.020
 9HL  plan-1  C04  0.020
 9HL  plan-1  C05  0.020
 9HL  plan-1  C12  0.020
 9HL  plan-1  H02  0.020
 9HL  plan-1  H04  0.020
 9HL  plan-1  H05  0.020
 9HL  plan-2  C1'  0.020
 9HL  plan-2  C2'  0.020
 9HL  plan-2  C23  0.020
 9HL  plan-2  C3'  0.020
 9HL  plan-2  C4'  0.020
 9HL  plan-2  C5'  0.020
 9HL  plan-2  C6'  0.020
 9HL  plan-2  F7'  0.020
 9HL  plan-2  H2'  0.020
 9HL  plan-2  H4'  0.020
 9HL  plan-2  H5'  0.020
 9HL  plan-2  H6'  0.020
 9HL  plan-3  N03  0.020
 9HL  plan-3  N11  0.020
 9HL  plan-3  C12  0.020
 9HL  plan-3  N13  0.020
 9HL  plan-3  C14  0.020
 9HL  plan-3  C15  0.020
 9HL  plan-3  C16  0.020
 9HL  plan-3  C17  0.020
 9HL  plan-3  H14  0.020
 9HL  plan-3  H15  0.020

