# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 15:52:47 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 2-{[(1r,3s,5R,7S)-3-hydroxytricyclo[3.3.1.1~3,7~]decan-1-yl]amino}-1-{(2S)-2-[(E)-iminomethyl]pyrrolidin-1-yl}ethan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC12C[C@H]3C[C@@H](C1)CC(C3)(C2)NCC(=O)N4CCC[C@H]4C=N
#
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
 LF7  LF7  2-{[(1r,3s,5R,7S)-3-hydroxytricyclo[3.3.1.1~3,7~]decan-1-yl]amino}-1-{(2S)-2-[(E)-iminomethyl]pyrrolidin-1-yl}ethan-1-one  ligand  49  22  .  2021-08-12  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LF7
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
 LF7  O20  O  O     0  -0.496   2.1787  -1.7414  -0.2382
 LF7  C14  C  C     0   0.547   2.1166  -0.5207  -0.1827
 LF7  N15  N  NT    0  -0.486   3.2203   0.2471  -0.2155
 LF7  C19  C  CH2   0  -0.275   3.2544   1.7043  -0.1376
 LF7  C18  C  CH2   0  -0.478   4.7171   1.9991   0.1642
 LF7  C17  C  CH2   0  -0.482   5.4498   0.8745  -0.5584
 LF7  C16  C  CH1   0  -0.129   4.5433  -0.3499  -0.3561
 LF7  C20  C  C1    0  -0.004   4.9233  -1.1291   0.8728
 LF7  N2   N  N     0  -0.549   5.5619  -2.2139   0.7872
 LF7  C13  C  CH2   0  -0.407   0.7985   0.2196  -0.0450
 LF7  N12  N  NH1   0  -0.622  -0.3126  -0.6792  -0.2302
 LF7  C7   C  CT    0   0.119  -1.6478  -0.1195  -0.0384
 LF7  C8   C  CH2   0  -0.428  -1.8930   0.4511   1.3689
 LF7  C1   C  CH1   0  -0.256  -3.3330   0.9532   1.4975
 LF7  C2   C  CH2   0  -0.419  -3.5863   2.0482   0.4607
 LF7  C10  C  CH1   0  -0.257  -3.3676   1.4751  -0.9402
 LF7  C9   C  CH2   0  -0.431  -1.9268   0.9782  -1.0708
 LF7  C5   C  CH2   0  -0.450  -4.3345   0.3129  -1.1736
 LF7  C21  C  CH2   0  -0.452  -4.2961  -0.2119   1.2609
 LF7  C3   C  CT    0   0.245  -4.0824  -0.7873  -0.1404
 LF7  O4   O  OH1   0  -0.687  -4.9111  -1.9132  -0.3697
 LF7  C6   C  CH2   0  -0.444  -2.6396  -1.2665  -0.2745
 LF7  H1   H  HCH2  0   0.246   2.9501   2.1527  -1.0884
 LF7  H2   H  HCH2  0   0.258   2.5897   2.0805   0.6403
 LF7  H3   H  HCH2  0   0.259   5.0137   2.9893  -0.1775
 LF7  H4   H  HCH2  0   0.246   4.8962   1.9497   1.2401
 LF7  H5   H  HCH2  0   0.258   5.5197   1.0939  -1.6256
 LF7  H6   H  HCH2  0   0.264   6.4619   0.7069  -0.1917
 LF7  H7   H  HCH1  0   0.269   4.5862  -1.0214  -1.2159
 LF7  H8   H  H     0   0.225   4.6386  -0.6664   1.8232
 LF7  H9   H  H     0   0.345   5.7699  -2.5789   1.7123
 LF7  H10  H  HCH2  0   0.237   0.8138   0.7364   0.9283
 LF7  H11  H  HCH2  0   0.262   0.7649   1.0133  -0.7961
 LF7  H12  H  HNH1  0   0.338  -0.2016  -1.4731   0.3900
 LF7  H14  H  HCH2  0   0.222  -1.6992  -0.3272   2.1161
 LF7  H15  H  HCH2  0   0.230  -1.1983   1.2705   1.5777
 LF7  H16  H  HCH1  0   0.230  -3.4900   1.3518   2.5037
 LF7  H17  H  HCH2  0   0.226  -4.6077   2.4300   0.5560
 LF7  H18  H  HCH2  0   0.226  -2.9131   2.8938   0.6333
 LF7  H19  H  HCH1  0   0.232  -3.5466   2.2513  -1.6892
 LF7  H20  H  HCH2  0   0.232  -1.2441   1.8221  -0.9323
 LF7  H21  H  HCH2  0   0.228  -1.7444   0.5860  -2.0769
 LF7  H22  H  HCH2  0   0.226  -5.3700   0.6658  -1.0972
 LF7  H23  H  HCH2  0   0.229  -4.2053  -0.0929  -2.1826
 LF7  H24  H  HCH2  0   0.229  -4.1342  -0.9940   2.0099
 LF7  H25  H  HCH2  0   0.226  -5.3333   0.1265   1.3705
 LF7  H26  H  HOH1  0   0.439  -5.8283  -1.6284  -0.2948
 LF7  H27  H  HCH2  0   0.233  -2.4755  -1.6809  -1.2749
 LF7  H28  H  HCH2  0   0.229  -2.4480  -2.0691   0.4482

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
 LF7  O4   C3   single  1.417  0.020  1.417
 LF7  C6   C3   single  1.526  0.020  1.526
 LF7  C6   C7   single  1.535  0.020  1.535
 LF7  C3   C5   single  1.530  0.020  1.530
 LF7  C3   C21  single  1.530  0.020  1.530
 LF7  C5   C10  single  1.530  0.020  1.530
 LF7  N12  C7   single  1.460  0.020  1.460
 LF7  N12  C13  single  1.441  0.020  1.441
 LF7  C7   C9   single  1.532  0.020  1.532
 LF7  C7   C8   single  1.538  0.020  1.538
 LF7  C21  C1   single  1.530  0.020  1.530
 LF7  C9   C10  single  1.530  0.020  1.530
 LF7  C10  C2   single  1.529  0.020  1.529
 LF7  C13  C14  single  1.518  0.020  1.518
 LF7  O20  C14  double  1.224  0.020  1.224
 LF7  C8   C1   single  1.530  0.020  1.530
 LF7  C1   C2   single  1.529  0.020  1.529
 LF7  C14  N15  single  1.345  0.020  1.345
 LF7  N15  C16  single  1.458  0.020  1.458
 LF7  N15  C19  single  1.460  0.020  1.460
 LF7  C16  C20  single  1.504  0.020  1.504
 LF7  C16  C17  single  1.537  0.020  1.537
 LF7  C19  C18  single  1.522  0.020  1.522
 LF7  C20  N2   double  1.262  0.020  1.262
 LF7  C17  C18  single  1.524  0.020  1.524
 LF7  C19  H1   single  0.970  0.020  1.090
 LF7  C19  H2   single  0.970  0.020  1.090
 LF7  C18  H3   single  0.970  0.020  1.090
 LF7  C18  H4   single  0.970  0.020  1.090
 LF7  C17  H5   single  0.970  0.020  1.090
 LF7  C17  H6   single  0.970  0.020  1.090
 LF7  C16  H7   single  0.970  0.020  1.090
 LF7  C20  H8   single  0.930  0.020  1.080
 LF7  N2   H9   single  0.890  0.020  1.040
 LF7  C13  H10  single  0.970  0.020  1.090
 LF7  C13  H11  single  0.970  0.020  1.090
 LF7  N12  H12  single  0.890  0.020  1.040
 LF7  C8   H14  single  0.970  0.020  1.090
 LF7  C8   H15  single  0.970  0.020  1.090
 LF7  C1   H16  single  0.970  0.020  1.090
 LF7  C2   H17  single  0.970  0.020  1.090
 LF7  C2   H18  single  0.970  0.020  1.090
 LF7  C10  H19  single  0.970  0.020  1.090
 LF7  C9   H20  single  0.970  0.020  1.090
 LF7  C9   H21  single  0.970  0.020  1.090
 LF7  C5   H22  single  0.970  0.020  1.090
 LF7  C5   H23  single  0.970  0.020  1.090
 LF7  C21  H24  single  0.970  0.020  1.090
 LF7  C21  H25  single  0.970  0.020  1.090
 LF7  O4   H26  single  0.850  0.020  0.980
 LF7  C6   H27  single  0.970  0.020  1.090
 LF7  C6   H28  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
 LF7  C13  C14  N15  115.87  3.000
 LF7  N15  C14  O20  121.79  3.000
 LF7  C13  C14  O20  122.33  3.000
 LF7  C16  N15  C19  113.12  3.000
 LF7  C19  N15  C14  126.00  3.000
 LF7  C16  N15  C14  120.88  3.000
 LF7  H2   C19  H1   108.00  3.000
 LF7  H2   C19  C18  112.18  3.000
 LF7  H1   C19  C18  111.11  3.000
 LF7  H2   C19  N15  111.61  3.000
 LF7  H1   C19  N15  110.86  3.000
 LF7  C18  C19  N15  103.08  3.000
 LF7  H4   C18  H3   107.80  3.000
 LF7  H4   C18  C17  110.79  3.000
 LF7  H3   C18  C17  113.03  3.000
 LF7  H4   C18  C19  110.14  3.000
 LF7  H3   C18  C19  112.07  3.000
 LF7  C17  C18  C19  103.01  3.000
 LF7  H6   C17  H5   107.48  3.000
 LF7  H6   C17  C16  112.40  3.000
 LF7  H5   C17  C16  109.06  3.000
 LF7  H6   C17  C18  113.61  3.000
 LF7  H5   C17  C18  110.24  3.000
 LF7  C16  C17  C18  103.99  3.000
 LF7  H7   C16  C20  108.35  3.000
 LF7  H7   C16  C17  111.30  3.000
 LF7  C20  C16  C17  111.80  3.000
 LF7  H7   C16  N15  111.30  3.000
 LF7  C17  C16  N15  102.81  3.000
 LF7  C20  C16  N15  111.26  3.000
 LF7  H8   C20  N2   123.64  3.000
 LF7  H8   C20  C16  115.13  3.000
 LF7  N2   C20  C16  121.19  3.000
 LF7  H9   N2   C20  110.53  3.000
 LF7  H11  C13  H10  105.47  3.000
 LF7  H11  C13  N12  109.93  3.000
 LF7  H10  C13  N12  114.62  3.000
 LF7  H11  C13  C14  108.56  3.000
 LF7  H10  C13  C14  107.26  3.000
 LF7  N12  C13  C14  110.71  3.000
 LF7  H12  N12  C7   108.66  3.000
 LF7  H12  N12  C13  109.00  3.000
 LF7  C7   N12  C13  116.68  3.000
 LF7  C6   C7   C9   108.30  3.000
 LF7  C9   C7   C8   108.76  3.000
 LF7  C6   C7   C8   108.36  3.000
 LF7  C8   C7   N12  114.09  3.000
 LF7  C9   C7   N12  110.64  3.000
 LF7  C6   C7   N12  106.51  3.000
 LF7  H15  C8   H14  106.82  3.000
 LF7  H15  C8   C1   109.61  3.000
 LF7  H14  C8   C1   110.00  3.000
 LF7  H15  C8   C7   110.55  3.000
 LF7  H14  C8   C7   109.39  3.000
 LF7  C1   C8   C7   110.40  3.000
 LF7  H16  C1   C21  109.24  3.000
 LF7  H16  C1   C2   109.82  3.000
 LF7  C21  C1   C2   109.65  3.000
 LF7  H16  C1   C8   109.39  3.000
 LF7  C2   C1   C8   109.50  3.000
 LF7  C21  C1   C8   109.23  3.000
 LF7  H18  C2   H17  106.90  3.000
 LF7  H18  C2   C10  110.24  3.000
 LF7  H17  C2   C10  110.12  3.000
 LF7  H18  C2   C1   110.15  3.000
 LF7  H17  C2   C1   110.20  3.000
 LF7  C10  C2   C1   109.21  3.000
 LF7  H19  C10  C5   109.35  3.000
 LF7  H19  C10  C9   109.04  3.000
 LF7  C5   C10  C9   109.61  3.000
 LF7  H19  C10  C2   109.76  3.000
 LF7  C9   C10  C2   109.55  3.000
 LF7  C5   C10  C2   109.52  3.000
 LF7  H21  C9   H20  106.77  3.000
 LF7  H21  C9   C10  110.59  3.000
 LF7  H20  C9   C10  109.05  3.000
 LF7  H21  C9   C7   109.40  3.000
 LF7  H20  C9   C7   110.70  3.000
 LF7  C10  C9   C7   110.28  3.000
 LF7  H23  C5   H22  107.16  3.000
 LF7  H23  C5   C3   109.64  3.000
 LF7  H22  C5   C3   109.87  3.000
 LF7  H23  C5   C10  110.34  3.000
 LF7  H22  C5   C10  109.98  3.000
 LF7  C3   C5   C10  109.82  3.000
 LF7  H25  C21  H24  106.97  3.000
 LF7  H25  C21  C3   109.86  3.000
 LF7  H24  C21  C3   109.71  3.000
 LF7  H25  C21  C1   110.17  3.000
 LF7  H24  C21  C1   110.19  3.000
 LF7  C3   C21  C1   109.89  3.000
 LF7  C6   C3   O4   106.81  3.000
 LF7  C6   C3   C21  109.30  3.000
 LF7  O4   C3   C21  111.44  3.000
 LF7  C21  C3   C5   108.97  3.000
 LF7  C6   C3   C5   108.80  3.000
 LF7  O4   C3   C5   111.45  3.000
 LF7  H26  O4   C3   108.03  3.000
 LF7  H28  C6   H27  107.39  3.000
 LF7  H28  C6   C3   109.70  3.000
 LF7  H27  C6   C3   109.92  3.000
 LF7  H28  C6   C7   109.43  3.000
 LF7  H27  C6   C7   109.05  3.000
 LF7  C3   C6   C7   111.27  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
 LF7  CONST_01  C16  N15  C14  O20    0.00   0.0  0
 LF7  CONST_02  C19  N15  C14  O20  180.00   0.0  0
 LF7  CONST_03  C13  C14  N15  C19    0.00   0.0  0
 LF7  CONST_04  C13  C14  N15  C16  180.00   0.0  0
 LF7  Var_01    C17  C18  C19  N15   32.39  30.0  1
 LF7  Var_02    C16  C17  C18  C19  -37.58  30.0  1
 LF7  Var_03    C16  N15  C19  C18  -15.75  30.0  1
 LF7  Var_04    C7   N12  C13  C14  176.12  30.0  2
 LF7  Var_05    N12  C13  C14  N15  171.04  30.0  1

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
 LF7  chir_01  C16  N15  C20  C17  positiv
 LF7  chir_02  C7   C6   C9   C8   negativ
 LF7  chir_03  C1   C21  C8   C2   negativ
 LF7  chir_04  C10  C5   C9   C2   positiv
 LF7  chir_05  C3   C6   C5   C21  positiv

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
 LF7  plan-1  O20  0.020
 LF7  plan-1  C14  0.020
 LF7  plan-1  N15  0.020
 LF7  plan-1  C19  0.020
 LF7  plan-1  C16  0.020
 LF7  plan-1  C13  0.020
 LF7  plan-2  C16  0.020
 LF7  plan-2  C20  0.020
 LF7  plan-2  N2   0.020
 LF7  plan-2  H8   0.020
 LF7  plan-2  H9   0.020

