# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 09:46:15 2022
#   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  27  13  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.441  -1.1120  10.3499  -7.8654
 W21  C5   C  CH2    0  -0.443  -1.9957   9.1216  -7.6609
 W21  C6   C  CH2    0  -0.442  -1.4613   8.5245  -6.3639
 W21  C7   C  CH2    0  -0.480   0.0551   8.6381  -6.5325
 W21  C8   C  C      0   0.415   0.8942  11.9114  -3.0516
 W21  O1   O  O      0  -0.593   0.2294  10.8748  -2.8507
 W21  O2   O  OC    -1  -0.596   1.3532  12.6915  -2.2002
 W21  C1   C  CH1    0  -0.202   1.1797  12.2931  -4.5283
 W21  C    C  CH3    0  -0.653   0.6185  13.6787  -4.8394
 W21  N    N  NH1    0  -0.632   0.6324  11.2736  -5.3945
 W21  C2   C  C      0   0.524   0.9902  11.0687  -6.6681
 W21  O    O  O      0  -0.514   1.7914  11.7859  -7.2614
 W21  C3   C  CR15   0  -0.342   0.2959   9.9174  -7.3736
 W21  H1   H  HCH2   0   0.242  -1.0934  10.7008  -8.8972
 W21  H2   H  HCH2   0   0.229  -1.4912  11.1729  -7.2541
 W21  H3   H  HCH2   0   0.232  -3.0575   9.3697  -7.6213
 W21  H4   H  HCH2   0   0.220  -1.8542   8.4123  -8.4811
 W21  H5   H  HCH2   0   0.222  -1.8031   9.1210  -5.5123
 W21  H6   H  HCH2   0   0.234  -1.7889   7.4987  -6.1901
 W21  H7   H  HCH2   0   0.245   0.4215   7.7758  -7.0925
 W21  H8   H  HCH2   0   0.238   0.5949   8.6344  -5.5842
 W21  H10  H  HCH1   0   0.229   2.2671  12.3243  -4.6585
 W21  H13  H  HCH3   0   0.213  -0.4626  13.7040  -4.6891
 W21  H14  H  HNH1   0   0.391   0.0392  10.6126  -4.9116
 W21  H15  H  HCR5   0   0.255   0.9180   9.6722  -8.2353
 W21  H11  H  HCH3   0   0.223   1.0689  14.4250  -4.1873
 W21  H12  H  HCH3   0   0.225   0.8233  13.9655  -5.8703

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  1.553  0.020  1.553
 W21  C5  C6   single  1.525  0.020  1.525
 W21  C3  C2   single  1.518  0.020  1.518
 W21  C3  C7   single  1.550  0.020  1.550
 W21  O   C2   double  1.228  0.020  1.228
 W21  C2  N    single  1.339  0.020  1.339
 W21  C7  C6   single  1.530  0.020  1.530
 W21  N   C1   single  1.445  0.020  1.445
 W21  C   C1   single  1.527  0.020  1.527
 W21  C1  C8   single  1.552  0.020  1.552
 W21  C8  O1   deloc   1.248  0.020  1.248
 W21  C8  O2   deloc   1.243  0.020  1.243
 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  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   107.03  3.000
 W21  H2   C4  C3   110.31  3.000
 W21  H1   C4  C3   111.97  3.000
 W21  H2   C4  C5   109.26  3.000
 W21  H1   C4  C5   113.31  3.000
 W21  C3   C4  C5   104.97  3.000
 W21  H4   C5  H3   107.49  3.000
 W21  H4   C5  C6   109.79  3.000
 W21  H3   C5  C6   113.54  3.000
 W21  H4   C5  C4   110.27  3.000
 W21  H3   C5  C4   112.66  3.000
 W21  C6   C5  C4   103.07  3.000
 W21  H6   C6  H5   107.14  3.000
 W21  H6   C6  C7   112.65  3.000
 W21  H5   C6  C7   110.78  3.000
 W21  H6   C6  C5   113.49  3.000
 W21  H5   C6  C5   109.81  3.000
 W21  C7   C6  C5   102.98  3.000
 W21  H8   C7  H7   106.09  3.000
 W21  H8   C7  C3   113.43  3.000
 W21  H7   C7  C3   108.75  3.000
 W21  H8   C7  C6   113.22  3.000
 W21  H7   C7  C6   109.30  3.000
 W21  C3   C7  C6   105.97  3.000
 W21  C1   C8  O2   115.45  3.000
 W21  O2   C8  O1   127.44  3.000
 W21  C1   C8  O1   117.10  3.000
 W21  H10  C1  N    108.95  3.000
 W21  H10  C1  C    108.34  3.000
 W21  N    C1  C    112.26  3.000
 W21  H10  C1  C8   107.62  3.000
 W21  C    C1  C8   110.45  3.000
 W21  N    C1  C8   109.10  3.000
 W21  H13  C   H12  108.08  3.000
 W21  H13  C   H11  108.15  3.000
 W21  H12  C   H11  107.97  3.000
 W21  H13  C   C1   110.91  3.000
 W21  H12  C   C1   111.25  3.000
 W21  H11  C   C1   110.36  3.000
 W21  H14  N   C2   120.74  3.000
 W21  H14  N   C1   113.40  3.000
 W21  C2   N   C1   125.23  3.000
 W21  C3   C2  O    121.11  3.000
 W21  O    C2  N    123.00  3.000
 W21  C3   C2  N    115.84  3.000
 W21  H15  C3  C2   106.07  3.000
 W21  H15  C3  C7   109.38  3.000
 W21  C2   C3  C7   116.41  3.000
 W21  H15  C3  C4   109.24  3.000
 W21  C7   C3  C4   105.13  3.000
 W21  C2   C3  C4   110.52  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  Var_01    C7   C6  C5  C4  -42.58  30.0  1
 W21  Var_02    C3   C7  C6  C5   32.25  30.0  1
 W21  Var_03    C3   C4  C5  C6   36.67  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

