# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 13:21:28 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: N-[(1S)-2-methyl-1-(pyridin-4-ylcarbamoyl)propyl]cyclohexanecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](NC(=O)C1CCCCC1)C(=O)Nc2ccncc2
#
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
 CII  CII  N-[(1S)-2-methyl-1-(pyridin-4-ylcarbamoyl)propyl]cyclohexanecarboxamide  ligand  47  22  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CII
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
 CII  O1    O  O     0  -0.467  -18.0571   0.3439  68.7015
 CII  C8    C  C     0   0.551  -17.8258  -0.2729  69.7282
 CII  C9    C  CH1   0  -0.389  -18.9026  -0.6831  70.7087
 CII  C10   C  CH2   0  -0.461  -18.5676  -0.3381  72.1614
 CII  C11   C  CH2   0  -0.428  -19.8054  -0.5308  73.0464
 CII  C12   C  CH2   0  -0.449  -20.6662  -1.7219  72.5947
 CII  C13   C  CH2   0  -0.447  -19.8219  -2.7617  71.8690
 CII  C14   C  CH2   0  -0.428  -19.2331  -2.1888  70.5743
 CII  N3    N  NH1   0  -0.674  -16.5639  -0.6677  70.0405
 CII  C7    C  CH1   0  -0.156  -15.4158  -0.2196  69.2909
 CII  C15   C  CH1   0  -0.291  -14.1363  -0.2595  70.1486
 CII  C16   C  CH3   0  -0.669  -13.7376  -1.6708  70.5707
 CII  C17   C  CH3   0  -0.649  -14.2655   0.6671  71.3542
 CII  C6    C  C     0   0.535  -15.1956  -0.9900  67.9900
 CII  O2    O  O     0  -0.450  -14.4650  -0.5417  67.1291
 CII  N2    N  NH1   0  -0.740  -15.8331  -2.1861  67.9127
 CII  C5    C  CR6   0   0.474  -15.8153  -3.1278  66.8944
 CII  C1    C  CR16  0  -0.374  -15.0765  -3.0216  65.7163
 CII  C2    C  CR16  0  -0.069  -15.1647  -4.0542  64.7953
 CII  N1    N  N     0  -0.416  -15.9044  -5.1452  64.9475
 CII  C3    C  CR16  0  -0.062  -16.6049  -5.2355  66.0740
 CII  C4    C  CR16  0  -0.420  -16.5974  -4.2725  67.0636
 CII  H9    H  HCH1  0   0.268  -19.7873  -0.1072  70.4246
 CII  H3    H  HNH1  0   0.401  -16.4061  -1.1122  70.9315
 CII  H101  H  HCH2  0   0.221  -17.7564  -0.9765  72.5268
 CII  H102  H  HCH2  0   0.254  -18.2085   0.6899  72.2440
 CII  H141  H  HCH2  0   0.246  -19.9352  -2.3220  69.7491
 CII  H142  H  HCH2  0   0.222  -18.3365  -2.7578  70.3120
 CII  H111  H  HCH2  0   0.231  -19.4796  -0.6727  74.0786
 CII  H112  H  HCH2  0   0.231  -20.4053   0.3818  73.0342
 CII  H121  H  HCH2  0   0.236  -21.1661  -2.1704  73.4550
 CII  H122  H  HCH2  0   0.222  -21.4637  -1.3809  71.9279
 CII  H131  H  HCH2  0   0.224  -19.0151  -3.0962  72.5276
 CII  H132  H  HCH2  0   0.239  -20.4132  -3.6498  71.6390
 CII  H7    H  HCH1  0   0.295  -15.5745   0.8193  68.9878
 CII  H15   H  HCH1  0   0.264  -13.3443   0.1406  69.5112
 CII  H161  H  HCH3  0   0.241  -13.5391  -2.3215  69.7182
 CII  H162  H  HCH3  0   0.249  -12.8253  -1.6364  71.1667
 CII  H163  H  HCH3  0   0.222  -14.4994  -2.1549  71.1866
 CII  H171  H  HCH3  0   0.215  -14.9902   0.3024  72.0851
 CII  H172  H  HCH3  0   0.243  -13.3068   0.7454  71.8674
 CII  H173  H  HCH3  0   0.238  -14.5675   1.6718  71.0552
 CII  H1    H  HCR6  0   0.291  -14.4470  -2.1747  65.5030
 CII  H4    H  HCR6  0   0.277  -17.1941  -4.4162  67.9562
 CII  H2    H  HCR6  0   0.266  -14.5936  -3.9822  63.8762
 CII  HA    H  HNH1  0   0.412  -16.4059  -2.4216  68.7108
 CII  HB    H  HCR6  0   0.269  -17.2102  -6.1257  66.2029

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
 CII  O1   C8    double    1.220  0.020  1.220
 CII  C8   C9    single    1.513  0.020  1.513
 CII  C8   N3    single    1.359  0.020  1.359
 CII  C9   C10   single    1.530  0.020  1.530
 CII  C9   C14   single    1.547  0.020  1.547
 CII  C10  C11   single    1.534  0.020  1.534
 CII  C11  C12   single    1.537  0.020  1.537
 CII  C12  C13   single    1.523  0.020  1.523
 CII  C13  C14   single    1.533  0.020  1.533
 CII  N3   C7    single    1.443  0.020  1.443
 CII  C7   C15   single    1.541  0.020  1.541
 CII  C7   C6    single    1.528  0.020  1.528
 CII  C15  C16   single    1.526  0.020  1.526
 CII  C15  C17   single    1.526  0.020  1.526
 CII  C6   O2    double    1.215  0.020  1.215
 CII  C6   N2    single    1.358  0.020  1.358
 CII  N2   C5    single    1.387  0.020  1.387
 CII  C5   C1    aromatic  1.395  0.020  1.395
 CII  C5   C4    aromatic  1.397  0.020  1.397
 CII  C1   C2    aromatic  1.386  0.020  1.386
 CII  C2   N1    aromatic  1.327  0.020  1.327
 CII  N1   C3    aromatic  1.330  0.020  1.330
 CII  C3   C4    aromatic  1.381  0.020  1.381
 CII  C9   H9    single    0.970  0.020  1.090
 CII  N3   H3    single    0.860  0.020  1.020
 CII  C10  H101  single    0.970  0.020  1.090
 CII  C10  H102  single    0.970  0.020  1.090
 CII  C14  H141  single    0.970  0.020  1.090
 CII  C14  H142  single    0.970  0.020  1.090
 CII  C11  H111  single    0.970  0.020  1.090
 CII  C11  H112  single    0.970  0.020  1.090
 CII  C12  H121  single    0.970  0.020  1.090
 CII  C12  H122  single    0.970  0.020  1.090
 CII  C13  H131  single    0.970  0.020  1.090
 CII  C13  H132  single    0.970  0.020  1.090
 CII  C7   H7    single    0.970  0.020  1.090
 CII  C15  H15   single    0.970  0.020  1.090
 CII  C16  H161  single    0.970  0.020  1.090
 CII  C16  H162  single    0.970  0.020  1.090
 CII  C16  H163  single    0.970  0.020  1.090
 CII  C17  H171  single    0.970  0.020  1.090
 CII  C17  H172  single    0.970  0.020  1.090
 CII  C17  H173  single    0.970  0.020  1.090
 CII  C1   H1    single    0.930  0.020  1.080
 CII  C4   H4    single    0.930  0.020  1.080
 CII  C2   H2    single    0.930  0.020  1.080
 CII  N2   HA    single    0.860  0.020  1.020
 CII  C3   HB    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
 CII  N3    C8   C9    115.67  3.000
 CII  N3    C8   O1    121.10  3.000
 CII  C9    C8   O1    123.20  3.000
 CII  H9    C9   C14   108.49  3.000
 CII  H9    C9   C10   107.77  3.000
 CII  C14   C9   C10   110.40  3.000
 CII  H9    C9   C8    105.35  3.000
 CII  C14   C9   C8    111.07  3.000
 CII  C10   C9   C8    113.48  3.000
 CII  H102  C10  H101  106.26  3.000
 CII  H102  C10  C11   109.88  3.000
 CII  H101  C10  C11   109.40  3.000
 CII  H102  C10  C9    110.85  3.000
 CII  H101  C10  C9    110.33  3.000
 CII  C11   C10  C9    110.04  3.000
 CII  H112  C11  H111  106.44  3.000
 CII  H112  C11  C12   109.67  3.000
 CII  H111  C11  C12   110.13  3.000
 CII  H112  C11  C10   109.38  3.000
 CII  H111  C11  C10   108.72  3.000
 CII  C12   C11  C10   112.31  3.000
 CII  H122  C12  H121  105.94  3.000
 CII  H122  C12  C13   109.05  3.000
 CII  H121  C12  C13   110.42  3.000
 CII  H122  C12  C11   110.22  3.000
 CII  H121  C12  C11   110.07  3.000
 CII  C13   C12  C11   111.00  3.000
 CII  H132  C13  H131  106.12  3.000
 CII  H132  C13  C14   109.52  3.000
 CII  H131  C13  C14   109.85  3.000
 CII  H132  C13  C12   110.82  3.000
 CII  H131  C13  C12   109.31  3.000
 CII  C14   C13  C12   111.10  3.000
 CII  H142  C14  H141  106.41  3.000
 CII  H142  C14  C13   108.83  3.000
 CII  H141  C14  C13   110.23  3.000
 CII  H142  C14  C9    110.61  3.000
 CII  H141  C14  C9    108.77  3.000
 CII  C13   C14  C9    111.85  3.000
 CII  H3    N3   C7    118.14  3.000
 CII  H3    N3   C8    118.47  3.000
 CII  C7    N3   C8    121.97  3.000
 CII  H7    C7   C6    105.30  3.000
 CII  H7    C7   C15   107.42  3.000
 CII  C6    C7   C15   109.96  3.000
 CII  H7    C7   N3    108.88  3.000
 CII  C6    C7   N3    113.61  3.000
 CII  C15   C7   N3    111.32  3.000
 CII  H15   C15  C17   107.45  3.000
 CII  H15   C15  C16   108.10  3.000
 CII  C17   C15  C16   111.42  3.000
 CII  H15   C15  C7    105.53  3.000
 CII  C17   C15  C7    110.72  3.000
 CII  C16   C15  C7    113.25  3.000
 CII  H163  C16  H162  106.81  3.000
 CII  H163  C16  H161  107.65  3.000
 CII  H162  C16  H161  107.09  3.000
 CII  H163  C16  C15   112.55  3.000
 CII  H162  C16  C15   109.91  3.000
 CII  H161  C16  C15   112.53  3.000
 CII  H173  C17  H172  107.84  3.000
 CII  H173  C17  H171  107.90  3.000
 CII  H172  C17  H171  107.01  3.000
 CII  H173  C17  C15   111.48  3.000
 CII  H172  C17  C15   109.94  3.000
 CII  H171  C17  C15   112.46  3.000
 CII  N2    C6   O2    124.55  3.000
 CII  N2    C6   C7    115.15  3.000
 CII  O2    C6   C7    120.27  3.000
 CII  HA    N2   C5    115.40  3.000
 CII  HA    N2   C6    115.26  3.000
 CII  C5    N2   C6    129.34  3.000
 CII  C4    C5   C1    117.48  3.000
 CII  C4    C5   N2    117.41  3.000
 CII  C1    C5   N2    125.11  3.000
 CII  H1    C1   C2    119.43  3.000
 CII  H1    C1   C5    122.49  3.000
 CII  C2    C1   C5    118.08  3.000
 CII  H2    C2   N1    116.45  3.000
 CII  H2    C2   C1    118.69  3.000
 CII  N1    C2   C1    124.87  3.000
 CII  C3    N1   C2    116.53  3.000
 CII  HB    C3   C4    119.37  3.000
 CII  HB    C3   N1    116.78  3.000
 CII  C4    C3   N1    123.84  3.000
 CII  H4    C4   C3    119.67  3.000
 CII  H4    C4   C5    121.13  3.000
 CII  C3    C4   C5    119.20  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
 CII  CONST_01  N1    C2   C1   C5     0.00   0.0  0
 CII  CONST_02  N1    C3   C4   C5     0.00   0.0  0
 CII  CONST_03  C3    C4   C5   C1     0.00   0.0  0
 CII  CONST_04  C3    N1   C2   C1     0.00   0.0  0
 CII  CONST_05  C4    C5   C1   C2     0.00   0.0  0
 CII  CONST_06  C4    C3   N1   C2     0.00   0.0  0
 CII  CONST_07  C2    C1   C5   N2   180.00   0.0  0
 CII  CONST_08  C3    C4   C5   N2   180.00   0.0  0
 CII  CONST_09  H2    C2   C1   C5   180.00   0.0  0
 CII  CONST_10  HB    C3   C4   C5   180.00   0.0  0
 CII  CONST_11  H4    C4   C5   C1   180.00   0.0  0
 CII  CONST_12  H1    C1   C2   N1   180.00   0.0  0
 CII  CONST_13  C1    C5   N2   C6     0.00   0.0  0
 CII  CONST_14  C4    C5   N2   C6   180.00   0.0  0
 CII  CONST_15  HA    N2   C5   C1   180.00   0.0  0
 CII  CONST_16  C7    N3   C8   C9   180.00   0.0  0
 CII  CONST_17  C5    N2   C6   C7   180.00   0.0  0
 CII  CONST_18  C5    N2   C6   O2     0.00   0.0  0
 CII  CONST_19  H3    N3   C8   C9     0.00   0.0  0
 CII  CONST_20  C7    N3   C8   O1     0.00   0.0  0
 CII  Var_01    C12   C11  C10  C9    35.65  30.0  1
 CII  Var_02    C12   C13  C14  C9    33.61  30.0  1
 CII  Var_03    C13   C12  C11  C10   26.56  30.0  1
 CII  Var_04    C14   C13  C12  C11  -63.73  30.0  1
 CII  Var_05    H161  C16  C15  C7    60.35  30.0  3
 CII  Var_06    H171  C17  C15  C7    69.34  30.0  3

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
 CII  chir_01  C9  C8  C10  C14  positiv
 CII  chir_02  C7  N3  C6   C15  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
 CII  plan-1  N2  0.020
 CII  plan-1  C5  0.020
 CII  plan-1  C1  0.020
 CII  plan-1  C2  0.020
 CII  plan-1  N1  0.020
 CII  plan-1  C3  0.020
 CII  plan-1  C4  0.020
 CII  plan-1  H1  0.020
 CII  plan-1  H4  0.020
 CII  plan-1  H2  0.020
 CII  plan-1  HB  0.020
 CII  plan-2  C7  0.020
 CII  plan-2  C6  0.020
 CII  plan-2  O2  0.020
 CII  plan-2  N2  0.020
 CII  plan-2  C5  0.020
 CII  plan-2  HA  0.020
 CII  plan-3  O1  0.020
 CII  plan-3  C8  0.020
 CII  plan-3  C9  0.020
 CII  plan-3  N3  0.020
 CII  plan-3  C7  0.020
 CII  plan-3  H3  0.020

