# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 22:10:32 2021
#   Inital geometry file: a 65 line input string
#   Ligand name: (2~{S})-2-azanyl-3-[(3~{S})-2-oxidanylidenepiperidin-3-yl]propanal
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](C[C@@H]1CCCNC1=O)C=O
#
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
 ELF  ELF  (2~{S})-2-azanyl-3-[(3~{S})-2-oxidanylidenepiperidin-3-yl]propanal  ligand  26  12  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_ELF
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
 ELF  C6   C  CH2   0  -0.468  -21.6738  24.9204  -0.1274
 ELF  C11  C  CH1   0  -0.218  -21.4007  21.0821   2.1680
 ELF  C13  C  CH2   0  -0.449  -21.5392  23.4789   0.3295
 ELF  C15  C  C     0   0.563  -19.2339  24.1448   1.1833
 ELF  C17  C  CH2   0  -0.443  -20.1736  21.9158   1.7992
 ELF  C24  C  C1    0   0.190  -20.9320  19.7026   2.5698
 ELF  C25  C  CH1   0  -0.367  -20.5140  23.3668   1.4538
 ELF  C27  C  CH2   0  -0.260  -20.3508  25.4086  -0.6766
 ELF  N3   N  NH2   0  -0.784  -22.1435  21.7072   3.2467
 ELF  N4   N  NH1   0  -0.630  -19.2638  25.0910   0.2309
 ELF  O3   O  O     0  -0.377  -21.1172  18.6876   1.9459
 ELF  O4   O  O     0  -0.514  -18.2184  23.9416   1.8423
 ELF  H1   H  HCH2  0   0.233  -21.9864  25.5478   0.7125
 ELF  H2   H  HCH2  0   0.250  -22.4370  25.0175  -0.9007
 ELF  H3   H  HCH1  0   0.259  -22.0589  20.9773   1.3020
 ELF  H4   H  HCH2  0   0.253  -22.5024  23.1051   0.6792
 ELF  H5   H  HCH2  0   0.227  -21.2417  22.8475  -0.5150
 ELF  H6   H  HCH2  0   0.249  -19.6726  21.4433   0.9489
 ELF  H7   H  HCH2  0   0.244  -19.4655  21.8942   2.6318
 ELF  H8   H  H     0   0.179  -20.3957  19.6875   3.5403
 ELF  H9   H  HCH1  0   0.275  -20.9496  23.8342   2.3453
 ELF  H10  H  HCH2  0   0.231  -20.1623  24.9538  -1.6545
 ELF  H11  H  HCH2  0   0.251  -20.3663  26.4889  -0.8263
 ELF  H12  H  HNH2  0   0.362  -22.9563  21.1581   3.4953
 ELF  H14  H  HNH2  0   0.351  -21.5731  21.7899   4.0803
 ELF  H15  H  HNH1  0   0.391  -18.3930  25.5802   0.0810

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
 ELF  C27  C6   single  1.513  0.020  1.513
 ELF  C27  N4   single  1.451  0.020  1.451
 ELF  C6   C13  single  1.518  0.020  1.518
 ELF  N4   C15  single  1.343  0.020  1.343
 ELF  C13  C25  single  1.526  0.020  1.526
 ELF  C15  C25  single  1.522  0.020  1.522
 ELF  C15  O4   double  1.228  0.020  1.228
 ELF  C25  C17  single  1.530  0.020  1.530
 ELF  O3   C24  double  1.206  0.020  1.206
 ELF  C17  C11  single  1.529  0.020  1.529
 ELF  C11  C24  single  1.511  0.020  1.511
 ELF  C11  N3   single  1.451  0.020  1.451
 ELF  C6   H1   single  0.970  0.020  1.090
 ELF  C6   H2   single  0.970  0.020  1.090
 ELF  C11  H3   single  0.970  0.020  1.090
 ELF  C13  H4   single  0.970  0.020  1.090
 ELF  C13  H5   single  0.970  0.020  1.090
 ELF  C17  H6   single  0.970  0.020  1.090
 ELF  C17  H7   single  0.970  0.020  1.090
 ELF  C24  H8   single  0.930  0.020  1.080
 ELF  C25  H9   single  0.970  0.020  1.090
 ELF  C27  H10  single  0.970  0.020  1.090
 ELF  C27  H11  single  0.970  0.020  1.090
 ELF  N3   H12  single  0.890  0.020  1.040
 ELF  N3   H14  single  0.890  0.020  1.040
 ELF  N4   H15  single  0.860  0.020  1.020

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
 ELF  H2   C6   H1   107.06  3.000
 ELF  H2   C6   C27  109.00  3.000
 ELF  H1   C6   C27  110.09  3.000
 ELF  H2   C6   C13  111.09  3.000
 ELF  H1   C6   C13  109.81  3.000
 ELF  C27  C6   C13  109.76  3.000
 ELF  H3   C11  N3   108.79  3.000
 ELF  H3   C11  C24  108.06  3.000
 ELF  N3   C11  C24  110.75  3.000
 ELF  H3   C11  C17  110.16  3.000
 ELF  N3   C11  C17  110.81  3.000
 ELF  C24  C11  C17  108.24  3.000
 ELF  H5   C13  H4   106.82  3.000
 ELF  H5   C13  C25  110.07  3.000
 ELF  H4   C13  C25  109.39  3.000
 ELF  H5   C13  C6   109.83  3.000
 ELF  H4   C13  C6   110.10  3.000
 ELF  C25  C13  C6   110.56  3.000
 ELF  O4   C15  N4   121.05  3.000
 ELF  O4   C15  C25  121.04  3.000
 ELF  N4   C15  C25  117.87  3.000
 ELF  H7   C17  H6   106.67  3.000
 ELF  H7   C17  C25  109.56  3.000
 ELF  H6   C17  C25  109.63  3.000
 ELF  H7   C17  C11  108.99  3.000
 ELF  H6   C17  C11  108.63  3.000
 ELF  C25  C17  C11  113.15  3.000
 ELF  H8   C24  O3   121.04  3.000
 ELF  H8   C24  C11  113.27  3.000
 ELF  O3   C24  C11  125.67  3.000
 ELF  H9   C25  C17  108.00  3.000
 ELF  H9   C25  C15  105.11  3.000
 ELF  C17  C25  C15  109.74  3.000
 ELF  H9   C25  C13  107.50  3.000
 ELF  C17  C25  C13  112.68  3.000
 ELF  C15  C25  C13  113.37  3.000
 ELF  H11  C27  H10  106.94  3.000
 ELF  H11  C27  N4   108.25  3.000
 ELF  H10  C27  N4   109.80  3.000
 ELF  H11  C27  C6   110.91  3.000
 ELF  H10  C27  C6   109.92  3.000
 ELF  N4   C27  C6   110.93  3.000
 ELF  H14  N3   H12  107.11  3.000
 ELF  H14  N3   C11  111.00  3.000
 ELF  H12  N3   C11  111.10  3.000
 ELF  H15  N4   C27  116.55  3.000
 ELF  H15  N4   C15  115.30  3.000
 ELF  C27  N4   C15  127.91  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
 ELF  CONST_01  C27  N4   C15  C25    0.00   0.0  0
 ELF  CONST_02  O4   C15  N4   C27  180.00   0.0  0
 ELF  CONST_03  H15  N4   C15  C25  180.00   0.0  0
 ELF  Var_01    C15  N4   C27  C6    21.69  30.0  1
 ELF  Var_02    N4   C27  C6   C13  -48.44  30.0  1
 ELF  Var_03    C27  C6   C13  C25   61.90  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
 ELF  chir_01  C11  C17  C24  N3   negativ
 ELF  chir_02  C25  C13  C15  C17  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
 ELF  plan-1  C15  0.020
 ELF  plan-1  C25  0.020
 ELF  plan-1  C27  0.020
 ELF  plan-1  N4   0.020
 ELF  plan-1  O4   0.020
 ELF  plan-1  H15  0.020
 ELF  plan-2  C11  0.020
 ELF  plan-2  C24  0.020
 ELF  plan-2  O3   0.020
 ELF  plan-2  H8   0.020

