# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 08:43:34 2021
#   Inital geometry file: a 69 line input string
#   Ligand name: N-(cyclopentanecarbonyl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(=O)C1CCCC1)C(O)=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
 W21  W21  N-(cyclopentanecarbonyl)-L-alanine  ligand  28  13  .  2022-03-29  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_W21
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
 W21  C4   C  CH2   0  -0.445  -1.0073  10.3235  -7.8512
 W21  C5   C  CH2   0  -0.444  -1.9238   9.1110  -7.7070
 W21  C6   C  CH2   0  -0.447  -1.4692   8.4918  -6.3901
 W21  C7   C  CH2   0  -0.478   0.0577   8.5836  -6.4652
 W21  C8   C  C     0   0.549   1.0291  11.9081  -3.0936
 W21  O1   O  O     0  -0.434   0.3846  10.9694  -2.7002
 W21  O2   O  OH1   0  -0.587   1.6881  12.7376  -2.3014
 W21  C1   C  CH1   0  -0.199   1.1677  12.3053  -4.5499
 W21  C    C  CH3   0  -0.652   0.4873  13.6519  -4.8135
 W21  N    N  NH1   0  -0.628   0.6297  11.2519  -5.3695
 W21  C2   C  C     0   0.548   1.1029  10.9506  -6.5950
 W21  O    O  O     0  -0.499   2.0466  11.5469  -7.0962
 W21  C3   C  CH1   0  -0.361   0.3678   9.8426  -7.3196
 W21  H1   H  HCH2  0   0.250  -0.9390  10.6972  -8.8729
 W21  H2   H  HCH2  0   0.231  -1.3928  11.1425  -7.2379
 W21  H3   H  HCH2  0   0.237  -2.9807   9.3805  -7.7182
 W21  H4   H  HCH2  0   0.224  -1.7543   8.4073  -8.5267
 W21  H5   H  HCH2  0   0.220  -1.8534   9.0824  -5.5522
 W21  H6   H  HCH2  0   0.241  -1.8181   7.4689  -6.2445
 W21  H7   H  HCH2  0   0.252   0.4522   7.7060  -6.9789
 W21  H8   H  HCH2  0   0.243   0.5316   8.6034  -5.4826
 W21  H9   H  HOH1  0   0.488   1.5607  12.4895  -1.3730
 W21  H10  H  HCH1  0   0.293   2.2331  12.4035  -4.7713
 W21  H12  H  HCH3  0   0.252   0.5921  13.9061  -5.8671
 W21  H13  H  HCH3  0   0.238  -0.5758  13.6060  -4.5767
 W21  H14  H  HNH1  0   0.396  -0.1724  10.7549  -5.0146
 W21  H15  H  HCH1  0   0.268   1.0000   9.5622  -8.1625
 W21  H11  H  HCH3  0   0.246   0.9402  14.4512  -4.2296

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
 W21  C4  C5   single  1.527  0.020  1.527
 W21  C4  C3   single  1.551  0.020  1.551
 W21  C5  C6   single  1.525  0.020  1.525
 W21  C3  C2   single  1.514  0.020  1.514
 W21  C3  C7   single  1.553  0.020  1.553
 W21  O   C2   double  1.224  0.020  1.224
 W21  C2  N    single  1.348  0.020  1.348
 W21  C7  C6   single  1.531  0.020  1.531
 W21  N   C1   single  1.439  0.020  1.439
 W21  C   C1   single  1.532  0.020  1.532
 W21  C1  C8   single  1.516  0.020  1.516
 W21  C8  O1   double  1.205  0.020  1.205
 W21  C8  O2   single  1.323  0.020  1.323
 W21  C4  H1   single  0.970  0.020  1.090
 W21  C4  H2   single  0.970  0.020  1.090
 W21  C5  H3   single  0.970  0.020  1.090
 W21  C5  H4   single  0.970  0.020  1.090
 W21  C6  H5   single  0.970  0.020  1.090
 W21  C6  H6   single  0.970  0.020  1.090
 W21  C7  H7   single  0.970  0.020  1.090
 W21  C7  H8   single  0.970  0.020  1.090
 W21  O2  H9   single  0.850  0.020  0.980
 W21  C1  H10  single  0.970  0.020  1.090
 W21  C   H11  single  0.970  0.020  1.090
 W21  C   H12  single  0.970  0.020  1.090
 W21  C   H13  single  0.970  0.020  1.090
 W21  N   H14  single  0.860  0.020  1.020
 W21  C3  H15  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
 W21  H2   C4  H1   106.92  3.000
 W21  H2   C4  C3   110.64  3.000
 W21  H1   C4  C3   111.85  3.000
 W21  H2   C4  C5   109.28  3.000
 W21  H1   C4  C5   113.48  3.000
 W21  C3   C4  C5   104.69  3.000
 W21  H4   C5  H3   107.54  3.000
 W21  H4   C5  C6   109.87  3.000
 W21  H3   C5  C6   113.46  3.000
 W21  H4   C5  C4   110.32  3.000
 W21  H3   C5  C4   112.61  3.000
 W21  C6   C5  C4   103.01  3.000
 W21  H6   C6  H5   106.95  3.000
 W21  H6   C6  C7   112.44  3.000
 W21  H5   C6  C7   110.80  3.000
 W21  H6   C6  C5   113.63  3.000
 W21  H5   C6  C5   109.72  3.000
 W21  C7   C6  C5   103.33  3.000
 W21  H8   C7  H7   106.36  3.000
 W21  H8   C7  C3   113.21  3.000
 W21  H7   C7  C3   108.72  3.000
 W21  H8   C7  C6   112.95  3.000
 W21  H7   C7  C6   109.60  3.000
 W21  C3   C7  C6   105.94  3.000
 W21  C1   C8  O2   111.44  3.000
 W21  O2   C8  O1   124.03  3.000
 W21  C1   C8  O1   124.53  3.000
 W21  H9   O2  C8   110.34  3.000
 W21  H10  C1  N    108.36  3.000
 W21  H10  C1  C    108.63  3.000
 W21  N    C1  C    112.30  3.000
 W21  H10  C1  C8   107.90  3.000
 W21  C    C1  C8   110.80  3.000
 W21  N    C1  C8   108.73  3.000
 W21  H13  C   H12  108.29  3.000
 W21  H13  C   H11  108.68  3.000
 W21  H12  C   H11  107.90  3.000
 W21  H13  C   C1   111.03  3.000
 W21  H12  C   C1   109.21  3.000
 W21  H11  C   C1   111.62  3.000
 W21  H14  N   C2   119.29  3.000
 W21  H14  N   C1   117.25  3.000
 W21  C2   N   C1   123.38  3.000
 W21  C3   C2  O    122.34  3.000
 W21  O    C2  N    122.29  3.000
 W21  C3   C2  N    115.36  3.000
 W21  H15  C3  C2   106.06  3.000
 W21  H15  C3  C7   109.43  3.000
 W21  C2   C3  C7   115.27  3.000
 W21  H15  C3  C4   109.20  3.000
 W21  C7   C3  C4   105.25  3.000
 W21  C2   C3  C4   111.57  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
 W21  CONST_01  C3   C2  N   C1  180.00   0.0  0
 W21  CONST_02  H14  N   C2  C3    0.00   0.0  0
 W21  CONST_03  O    C2  N   C1    0.00   0.0  0
 W21  CONST_04  H9   O2  C8  O1    0.00   0.0  0
 W21  Var_01    C7   C6  C5  C4  -42.17  30.0  1
 W21  Var_02    C3   C7  C6  C5   30.23  30.0  1
 W21  Var_03    C3   C4  C5  C6   37.91  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
 W21  chir_01  C1  N   C   C8  negativ
 W21  chir_02  C3  C7  C2  C4  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
 W21  plan-1  C1   0.020
 W21  plan-1  N    0.020
 W21  plan-1  C2   0.020
 W21  plan-1  O    0.020
 W21  plan-1  C3   0.020
 W21  plan-1  H14  0.020
 W21  plan-2  C8   0.020
 W21  plan-2  O1   0.020
 W21  plan-2  O2   0.020
 W21  plan-2  C1   0.020
 W21  plan-2  H9   0.020

