# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 16:19:42 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  21  9  .  2021-08-08  2021-08-08  
;
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  -0.662   1.1841   1.4729   0.2187
 CCM  CA    C  CR5   0  -0.186   0.2137   0.3005   0.0103
 CCM  CB1   C  CH2   0  -0.427  -0.9282   0.7158  -0.9376
 CCM  CB2   C  CH2   0  -0.440   0.9322  -0.8776  -0.7252
 CCM  CG1   C  CH2   0  -0.446  -0.4616   0.2695  -2.3187
 CCM  CG2   C  CH2   0  -0.439   0.1599  -1.0923  -2.0304
 CCM  C     C  C     0   0.567  -0.3071  -0.1261   1.3663
 CCM  O     O  O     0  -0.441  -1.4586  -0.0830   1.7258
 CCM  OXT   O  OH1   0  -0.595   0.6688  -0.5536   2.1632
 CCM  HH21  H  HCH3  0   0.238   0.7119   2.2932   0.7620
 CCM  HH22  H  HCH3  0   0.242   2.0787   1.1705   0.7622
 CCM  HH23  H  HCH3  0   0.241   1.5047   1.8587  -0.7497
 CCM  HB11  H  HCH2  0   0.236  -1.8490   0.1867  -0.6853
 CCM  HB12  H  HCH2  0   0.237  -1.1456   1.7836  -0.8731
 CCM  HB21  H  HCH2  0   0.240   1.9642  -0.5902  -0.9369
 CCM  HB22  H  HCH2  0   0.245   0.9838  -1.7883  -0.1281
 CCM  HG11  H  HCH2  0   0.235  -1.2755   0.2280  -3.0436
 CCM  HG12  H  HCH2  0   0.219   0.2925   0.9534  -2.7181
 CCM  HG21  H  HCH2  0   0.222  -0.6325  -1.8308  -1.8833
 CCM  HG22  H  HCH2  0   0.235   0.7981  -1.4592  -2.8354
 CCM  HXT   H  HOH1  0   0.478   0.3041  -0.8122   3.0226

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  1.536  0.020  1.536
 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  1.541  0.020  1.541
 CCM  CA   CB2   single  1.564  0.020  1.564
 CCM  CA   C     single  1.514  0.020  1.514
 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  1.524  0.020  1.524
 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     double  1.207  0.020  1.207
 CCM  C    OXT   single  1.331  0.020  1.331
 CCM  OXT  HXT   single  0.850  0.020  0.980

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  107.44  3.000
 CCM  HH23  CH2  HH21  107.66  3.000
 CCM  HH22  CH2  HH21  108.39  3.000
 CCM  HH23  CH2  CA    109.59  3.000
 CCM  HH22  CH2  CA    111.99  3.000
 CCM  HH21  CH2  CA    111.59  3.000
 CCM  C     CA   CB2   111.54  3.000
 CCM  C     CA   CB1   111.84  3.000
 CCM  CB2   CA   CB1   104.72  3.000
 CCM  C     CA   CH2   108.11  3.000
 CCM  CB2   CA   CH2   110.40  3.000
 CCM  CB1   CA   CH2   110.23  3.000
 CCM  HB12  CB1  HB11  107.00  3.000
 CCM  HB12  CB1  CG1   113.63  3.000
 CCM  HB11  CB1  CG1   109.00  3.000
 CCM  HB12  CB1  CA    112.02  3.000
 CCM  HB11  CB1  CA    110.63  3.000
 CCM  CG1   CB1  CA    104.57  3.000
 CCM  HB22  CB2  HB21  106.34  3.000
 CCM  HB22  CB2  CG2   111.93  3.000
 CCM  HB21  CB2  CG2   110.38  3.000
 CCM  HB22  CB2  CA    113.17  3.000
 CCM  HB21  CB2  CA    109.10  3.000
 CCM  CG2   CB2  CA    105.95  3.000
 CCM  HG12  CG1  HG11  107.19  3.000
 CCM  HG12  CG1  CG2   110.28  3.000
 CCM  HG11  CG1  CG2   113.33  3.000
 CCM  HG12  CG1  CB1   111.03  3.000
 CCM  HG11  CG1  CB1   112.64  3.000
 CCM  CG2   CG1  CB1   102.41  3.000
 CCM  HG22  CG2  HG21  107.23  3.000
 CCM  HG22  CG2  CG1   113.54  3.000
 CCM  HG21  CG2  CG1   109.47  3.000
 CCM  HG22  CG2  CB2   112.40  3.000
 CCM  HG21  CG2  CB2   110.21  3.000
 CCM  CG1   CG2  CB2   103.98  3.000
 CCM  OXT   C    O     122.19  3.000
 CCM  OXT   C    CA    112.00  3.000
 CCM  O     C    CA    125.80  3.000
 CCM  HXT   OXT  C     109.93  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  CONST_01  HXT  OXT  C    CA   180.00   0.0  0
 CCM  Var_01    CG2  CG1  CB1  CA    41.01  30.0  1
 CCM  Var_02    CG1  CG2  CB2  CA    26.12  30.0  1
 CCM  Var_03    CB2  CG2  CG1  CB1  -41.42  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
 CCM  plan-1  HXT  0.020

