# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 22:07:40 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: ~{N}'-cyclopentyl-~{N}-(pyridin-2-ylmethyl)ethanediamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCc1ccccn1)C(=O)NC2CCCC2
#
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
 JW2  JW2  ~{N}'-cyclopentyl-~{N}-(pyridin-2-ylmethyl)ethanediamide  ligand  35  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JW2
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
 JW2  C2   C  C     0   0.446   1.2036   0.0263  -0.1688
 JW2  C4   C  CH1   0  -0.065   3.6217  -0.4125  -0.2011
 JW2  C5   C  CH2   0  -0.446   4.5399   0.6681  -0.8180
 JW2  C6   C  CH2   0  -0.450   5.9816   0.2256  -0.4948
 JW2  C7   C  CH2   0  -0.452   5.8507  -1.1796   0.1066
 JW2  C8   C  CH2   0  -0.448   4.5040  -1.1345   0.8161
 JW2  C12  C  CH2   0  -0.299  -2.2990   1.0474   0.7998
 JW2  C15  C  CR16  0  -0.144  -5.7718  -0.4286   0.6281
 JW2  C16  C  CR16  0  -0.333  -5.6951  -1.0356  -0.6179
 JW2  C17  C  CR16  0  -0.064  -4.5052  -0.9375  -1.3196
 JW2  O1   O  O     0  -0.482   0.9331  -0.5088  -1.2347
 JW2  N3   N  NH1   0  -0.627   2.4093   0.1141   0.3807
 JW2  C9   C  C     0   0.448   0.1073   0.6789   0.6910
 JW2  O10  O  O     0  -0.483   0.3733   1.2675   1.7291
 JW2  N11  N  NH1   0  -0.631  -1.1090   0.5181   0.1860
 JW2  C13  C  CR6   0   0.233  -3.5157   0.2922   0.3312
 JW2  C14  C  CR16  0  -0.331  -4.6639   0.2454   1.1136
 JW2  N18  N  N     0  -0.447  -3.4416  -0.2881  -0.8595
 JW2  H1   H  HCH1  0   0.258   3.3268  -1.1211  -0.9755
 JW2  H2   H  HCH2  0   0.240   4.3627   0.7582  -1.8901
 JW2  H3   H  HCH2  0   0.237   4.3183   1.6427  -0.3798
 JW2  H4   H  HCH2  0   0.235   6.6333   0.2432  -1.3685
 JW2  H5   H  HCH2  0   0.229   6.4217   0.8988   0.2431
 JW2  H6   H  HCH2  0   0.224   5.8234  -1.9309  -0.6872
 JW2  H7   H  HCH2  0   0.237   6.6774  -1.4347   0.7707
 JW2  H8   H  HCH2  0   0.226   4.5824  -0.5359   1.7302
 JW2  H9   H  HCH2  0   0.245   4.1111  -2.1138   1.0922
 JW2  H10  H  HCH2  0   0.268  -2.2143   0.9917   1.8853
 JW2  H11  H  HCH2  0   0.275  -2.4219   2.1072   0.5482
 JW2  H13  H  HCR6  0   0.273  -6.5327  -1.5778  -1.0339
 JW2  H14  H  HCR6  0   0.268  -4.4025  -1.4015  -2.2939
 JW2  H15  H  HNH1  0   0.404   2.4797   0.6074   1.2599
 JW2  H16  H  HNH1  0   0.407  -1.2145   0.0543  -0.7064
 JW2  H17  H  HCR6  0   0.271  -4.6848   0.7242   2.0839
 JW2  H12  H  HCR6  0   0.278  -6.6784  -0.4850   1.2159

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
 JW2  O10  C9   double    1.223  0.020  1.223
 JW2  C7   C6   single    1.534  0.020  1.534
 JW2  C7   C8   single    1.523  0.020  1.523
 JW2  C6   C5   single    1.542  0.020  1.542
 JW2  C12  N11  single    1.440  0.020  1.440
 JW2  C12  C13  single    1.507  0.020  1.507
 JW2  C9   N11  single    1.327  0.020  1.327
 JW2  C9   C2   single    1.539  0.020  1.539
 JW2  C5   C4   single    1.546  0.020  1.546
 JW2  N3   C2   single    1.328  0.020  1.328
 JW2  N3   C4   single    1.444  0.020  1.444
 JW2  N18  C13  aromatic  1.327  0.020  1.327
 JW2  N18  C17  aromatic  1.328  0.020  1.328
 JW2  C2   O1   double    1.223  0.020  1.223
 JW2  C8   C4   single    1.528  0.020  1.528
 JW2  C13  C14  aromatic  1.390  0.020  1.390
 JW2  C17  C16  aromatic  1.385  0.020  1.385
 JW2  C14  C15  aromatic  1.385  0.020  1.385
 JW2  C16  C15  aromatic  1.388  0.020  1.388
 JW2  C4   H1   single    0.970  0.020  1.090
 JW2  C5   H2   single    0.970  0.020  1.090
 JW2  C5   H3   single    0.970  0.020  1.090
 JW2  C6   H4   single    0.970  0.020  1.090
 JW2  C6   H5   single    0.970  0.020  1.090
 JW2  C7   H6   single    0.970  0.020  1.090
 JW2  C7   H7   single    0.970  0.020  1.090
 JW2  C8   H8   single    0.970  0.020  1.090
 JW2  C8   H9   single    0.970  0.020  1.090
 JW2  C12  H10  single    0.970  0.020  1.090
 JW2  C12  H11  single    0.970  0.020  1.090
 JW2  C15  H12  single    0.930  0.020  1.080
 JW2  C16  H13  single    0.930  0.020  1.080
 JW2  C17  H14  single    0.930  0.020  1.080
 JW2  N3   H15  single    0.860  0.020  1.020
 JW2  N11  H16  single    0.860  0.020  1.020
 JW2  C14  H17  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
 JW2  C9   C2   N3   112.81  3.000
 JW2  N3   C2   O1   126.18  3.000
 JW2  C9   C2   O1   121.00  3.000
 JW2  H1   C4   N3   107.22  3.000
 JW2  H1   C4   C8   108.78  3.000
 JW2  N3   C4   C8   112.89  3.000
 JW2  H1   C4   C5   109.35  3.000
 JW2  C8   C4   C5   104.65  3.000
 JW2  N3   C4   C5   113.85  3.000
 JW2  H3   C5   H2   106.74  3.000
 JW2  H3   C5   C6   111.21  3.000
 JW2  H2   C5   C6   112.43  3.000
 JW2  H3   C5   C4   110.08  3.000
 JW2  H2   C5   C4   110.70  3.000
 JW2  C6   C5   C4   105.72  3.000
 JW2  H5   C6   H4   106.91  3.000
 JW2  H5   C6   C7   109.53  3.000
 JW2  H4   C6   C7   112.34  3.000
 JW2  H5   C6   C5   109.97  3.000
 JW2  H4   C6   C5   112.72  3.000
 JW2  C7   C6   C5   105.38  3.000
 JW2  H7   C7   H6   107.47  3.000
 JW2  H7   C7   C8   113.17  3.000
 JW2  H6   C7   C8   109.66  3.000
 JW2  H7   C7   C6   112.85  3.000
 JW2  H6   C7   C6   110.30  3.000
 JW2  C8   C7   C6   103.36  3.000
 JW2  H9   C8   H8   107.76  3.000
 JW2  H9   C8   C7   114.21  3.000
 JW2  H8   C8   C7   109.98  3.000
 JW2  H9   C8   C4   112.63  3.000
 JW2  H8   C8   C4   109.79  3.000
 JW2  C7   C8   C4   102.39  3.000
 JW2  H11  C12  H10  106.65  3.000
 JW2  H11  C12  C13  108.82  3.000
 JW2  H10  C12  C13  110.29  3.000
 JW2  H11  C12  N11  110.51  3.000
 JW2  H10  C12  N11  109.97  3.000
 JW2  C13  C12  N11  110.52  3.000
 JW2  H12  C15  C14  120.35  3.000
 JW2  H12  C15  C16  120.74  3.000
 JW2  C14  C15  C16  118.91  3.000
 JW2  H13  C16  C17  120.41  3.000
 JW2  H13  C16  C15  121.46  3.000
 JW2  C17  C16  C15  118.12  3.000
 JW2  H14  C17  N18  116.40  3.000
 JW2  H14  C17  C16  120.44  3.000
 JW2  N18  C17  C16  123.16  3.000
 JW2  H15  N3   C4   118.03  3.000
 JW2  H15  N3   C2   117.10  3.000
 JW2  C4   N3   C2   124.85  3.000
 JW2  N11  C9   O10  125.51  3.000
 JW2  N11  C9   C2   112.90  3.000
 JW2  O10  C9   C2   121.58  3.000
 JW2  H16  N11  C9   119.15  3.000
 JW2  H16  N11  C12  117.30  3.000
 JW2  C9   N11  C12  123.43  3.000
 JW2  N18  C13  C14  122.45  3.000
 JW2  C14  C13  C12  120.58  3.000
 JW2  N18  C13  C12  116.96  3.000
 JW2  H17  C14  C13  120.38  3.000
 JW2  H17  C14  C15  120.95  3.000
 JW2  C13  C14  C15  118.68  3.000
 JW2  C13  N18  C17  118.69  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
 JW2  CONST_01  N18  C13  C14  C15     0.00   0.0  0
 JW2  CONST_02  N18  C17  C16  C15     0.00   0.0  0
 JW2  CONST_03  C13  N18  C17  C16     0.00   0.0  0
 JW2  CONST_04  C13  C14  C15  C16     0.00   0.0  0
 JW2  CONST_05  C14  C13  N18  C17     0.00   0.0  0
 JW2  CONST_06  C14  C15  C16  C17     0.00   0.0  0
 JW2  CONST_07  C17  N18  C13  C12   180.00   0.0  0
 JW2  CONST_08  C15  C14  C13  C12   180.00   0.0  0
 JW2  CONST_09  H14  C17  C16  C15   180.00   0.0  0
 JW2  CONST_10  H17  C14  C15  C16   180.00   0.0  0
 JW2  CONST_11  H12  C15  C16  C17   180.00   0.0  0
 JW2  CONST_12  H13  C16  C15  C14   180.00   0.0  0
 JW2  CONST_13  C9   C2   N3   C4    180.00   0.0  0
 JW2  CONST_14  O1   C2   N3   C4      0.00   0.0  0
 JW2  CONST_15  C12  N11  C9   C2    180.00   0.0  0
 JW2  CONST_16  O10  C9   N11  C12     0.00   0.0  0
 JW2  CONST_17  N11  C9   C2   O1      0.00   0.0  0
 JW2  CONST_18  N11  C9   C2   N3    180.00   0.0  0
 JW2  CONST_19  H16  N11  C9   C2      0.00   0.0  0
 JW2  CONST_20  H15  N3   C2   O1    180.00   0.0  0
 JW2  Var_01    C7   C6   C5   C4      8.04  30.0  1
 JW2  Var_02    C6   C7   C8   C4     43.08  30.0  1
 JW2  Var_03    C8   C7   C6   C5    -31.63  30.0  1
 JW2  Var_04    N18  C13  C12  N11   -26.29  30.0  2
 JW2  Var_05    C13  C12  N11  C9   -158.31  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
 JW2  chir_01  C4  C5  N3  C8  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
 JW2  plan-1  C12  0.020
 JW2  plan-1  C15  0.020
 JW2  plan-1  C16  0.020
 JW2  plan-1  C17  0.020
 JW2  plan-1  C13  0.020
 JW2  plan-1  C14  0.020
 JW2  plan-1  N18  0.020
 JW2  plan-1  H13  0.020
 JW2  plan-1  H14  0.020
 JW2  plan-1  H17  0.020
 JW2  plan-1  H12  0.020
 JW2  plan-2  C2   0.020
 JW2  plan-2  C4   0.020
 JW2  plan-2  C12  0.020
 JW2  plan-2  O1   0.020
 JW2  plan-2  N3   0.020
 JW2  plan-2  C9   0.020
 JW2  plan-2  O10  0.020
 JW2  plan-2  N11  0.020
 JW2  plan-2  H15  0.020
 JW2  plan-2  H16  0.020

