# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 22:52:23 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 1-methylcyclopentanecarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(CCCC1)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
 CCM  CCM  '1-methylcyclopentanecarboxylic acid'  ligand  20  9  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CCM
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
 CCM  CH2   C  CH3    0  -0.665   1.1533   1.4952   0.1929
 CCM  CA    C  CT     0  -0.151   0.2034   0.3039   0.0115
 CCM  CB1   C  CH2    0  -0.423  -0.9476   0.6916  -0.9389
 CCM  CB2   C  CH2    0  -0.434   0.9426  -0.8492  -0.7253
 CCM  CG1   C  CH2    0  -0.440  -0.4964   0.2305  -2.3208
 CCM  CG2   C  CH2    0  -0.441   0.1612  -1.1117  -2.0170
 CCM  C     C  C      0   0.419  -0.2742  -0.0934   1.4269
 CCM  O     O  O      0  -0.609  -1.4002   0.3042   1.7910
 CCM  OXT   O  OC    -1  -0.619   0.5291  -0.7468   2.1262
 CCM  HH21  H  HCH3   0   0.217   0.6643   2.3186   0.7186
 CCM  HH22  H  HCH3   0   0.220   2.0373   1.2079   0.7647
 CCM  HH23  H  HCH3   0   0.217   1.4977   1.8768  -0.7715
 CCM  HB11  H  HCH2   0   0.213  -1.8593   0.1575  -0.6622
 CCM  HB12  H  HCH2   0   0.211  -1.1847   1.7574  -0.8971
 CCM  HB21  H  HCH2   0   0.210   1.9655  -0.5473  -0.9690
 CCM  HB22  H  HCH2   0   0.223   1.0279  -1.7409  -0.1054
 CCM  HG11  H  HCH2   0   0.220  -1.3163   0.1587  -3.0386
 CCM  HG12  H  HCH2   0   0.206   0.2394   0.9219  -2.7434
 CCM  HG21  H  HCH2   0   0.209  -0.6154  -1.8635  -1.8462
 CCM  HG22  H  HCH2   0   0.220   0.7904  -1.4836  -2.8281

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
 CCM  CH2  CA    single  1.534  0.020  1.534
 CCM  CH2  HH21  single  0.970  0.020  1.090
 CCM  CH2  HH22  single  0.970  0.020  1.090
 CCM  CH2  HH23  single  0.970  0.020  1.090
 CCM  CA   CB1   single  1.542  0.020  1.542
 CCM  CA   CB2   single  1.555  0.020  1.555
 CCM  CA   C     single  1.546  0.020  1.546
 CCM  CB1  CG1   single  1.525  0.020  1.525
 CCM  CB1  HB11  single  0.970  0.020  1.090
 CCM  CB1  HB12  single  0.970  0.020  1.090
 CCM  CB2  CG2   single  1.532  0.020  1.532
 CCM  CB2  HB21  single  0.970  0.020  1.090
 CCM  CB2  HB22  single  0.970  0.020  1.090
 CCM  CG1  CG2   single  1.525  0.020  1.525
 CCM  CG1  HG11  single  0.970  0.020  1.090
 CCM  CG1  HG12  single  0.970  0.020  1.090
 CCM  CG2  HG21  single  0.970  0.020  1.090
 CCM  CG2  HG22  single  0.970  0.020  1.090
 CCM  C    O     deloc   1.248  0.020  1.248
 CCM  C    OXT   deloc   1.250  0.020  1.250

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
 CCM  HH23  CH2  HH22  107.40  3.000
 CCM  HH23  CH2  HH21  107.61  3.000
 CCM  HH22  CH2  HH21  107.99  3.000
 CCM  HH23  CH2  CA    111.22  3.000
 CCM  HH22  CH2  CA    111.04  3.000
 CCM  HH21  CH2  CA    111.41  3.000
 CCM  C     CA   CB2   112.96  3.000
 CCM  C     CA   CB1   113.47  3.000
 CCM  CB2   CA   CB1   104.43  3.000
 CCM  C     CA   CH2   106.42  3.000
 CCM  CB2   CA   CH2   109.72  3.000
 CCM  CB1   CA   CH2   109.86  3.000
 CCM  HB12  CB1  HB11  106.63  3.000
 CCM  HB12  CB1  CG1   113.18  3.000
 CCM  HB11  CB1  CG1   109.19  3.000
 CCM  HB12  CB1  CA    112.55  3.000
 CCM  HB11  CB1  CA    110.12  3.000
 CCM  CG1   CB1  CA    105.17  3.000
 CCM  HB22  CB2  HB21  106.23  3.000
 CCM  HB22  CB2  CG2   112.30  3.000
 CCM  HB21  CB2  CG2   109.65  3.000
 CCM  HB22  CB2  CA    112.00  3.000
 CCM  HB21  CB2  CA    110.20  3.000
 CCM  CG2   CB2  CA    106.49  3.000
 CCM  HG12  CG1  HG11  107.01  3.000
 CCM  HG12  CG1  CG2   110.05  3.000
 CCM  HG11  CG1  CG2   113.37  3.000
 CCM  HG12  CG1  CB1   110.97  3.000
 CCM  HG11  CG1  CB1   113.16  3.000
 CCM  CG2   CG1  CB1   102.30  3.000
 CCM  HG22  CG2  HG21  106.91  3.000
 CCM  HG22  CG2  CG1   113.60  3.000
 CCM  HG21  CG2  CG1   109.25  3.000
 CCM  HG22  CG2  CB2   113.00  3.000
 CCM  HG21  CG2  CB2   110.37  3.000
 CCM  CG1   CG2  CB2   103.71  3.000
 CCM  OXT   C    O     125.68  3.000
 CCM  OXT   C    CA    116.63  3.000
 CCM  O     C    CA    117.64  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
 CCM  Var_01  CG2  CG1  CB1  CA    40.09  30.0  1
 CCM  Var_02  CG1  CG2  CB2  CA    26.95  30.0  1
 CCM  Var_03  CB2  CG2  CG1  CB1  -41.10  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
 CCM  chir_01  CA  CB1  CB2  C  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
 CCM  plan-1  CA   0.020
 CCM  plan-1  C    0.020
 CCM  plan-1  O    0.020
 CCM  plan-1  OXT  0.020

