# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 18:15:43 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 2,2,4,4,6,6,8-heptamethylnonane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CC(C)(C)CC(C)(C)CC(C)(C)C
#
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
 PUN  PUN  2,2,4,4,6,6,8-heptamethylnonane  ligand  50  16  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PUN
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
 PUN  C     C  CH1   0  -0.234   4.1486   0.1027  -0.3755
 PUN  C1    C  CH3   0  -0.656   4.7038  -1.1068  -1.1248
 PUN  C2    C  CH3   0  -0.656   4.9390   1.3544  -0.7487
 PUN  C3    C  CH2   0  -0.396   2.6438   0.3087  -0.6360
 PUN  C4    C  CT    0  -0.079   1.6527  -0.1884   0.4465
 PUN  C5    C  CH3   0  -0.657   1.9296  -1.6624   0.7552
 PUN  C6    C  CH3   0  -0.661   1.8633   0.6458   1.7111
 PUN  C7    C  CH2   0  -0.375   0.2524  -0.0060  -0.1952
 PUN  C8    C  CT    0  -0.062  -1.1030  -0.0387   0.5679
 PUN  C9    C  CH3   0  -0.665  -1.1913  -1.2209   1.5367
 PUN  C10   C  CH3   0  -0.664  -1.3099   1.2608   1.3487
 PUN  C11   C  CH2   0  -0.365  -2.1490  -0.2055  -0.5716
 PUN  C12   C  CT    0  -0.090  -3.6650   0.0789  -0.4339
 PUN  C13   C  CH3   0  -0.640  -3.9753   1.5803  -0.4213
 PUN  C14   C  CH3   0  -0.641  -4.3093  -0.5032  -1.7002
 PUN  C15   C  CH3   0  -0.651  -4.3226  -0.5881   0.7740
 PUN  H     H  HCH1  0   0.217   4.3068  -0.0712   0.6945
 PUN  H1    H  HCH3  0   0.211   4.5957  -0.9760  -2.2045
 PUN  H1A   H  HCH3  0   0.219   5.7662  -1.2465  -0.9142
 PUN  H1B   H  HCH3  0   0.229   4.1895  -2.0292  -0.8539
 PUN  H2    H  HCH3  0   0.212   4.8206   1.5901  -1.8093
 PUN  H2A   H  HCH3  0   0.222   4.6012   2.2216  -0.1782
 PUN  H2B   H  HCH3  0   0.220   6.0061   1.2243  -0.5570
 PUN  H3    H  HCH2  0   0.218   2.4495   1.3778  -0.7779
 PUN  H3A   H  HCH2  0   0.215   2.3820  -0.1628  -1.5910
 PUN  H5    H  HCH3  0   0.225   2.9549  -1.8093   1.0994
 PUN  H5A   H  HCH3  0   0.234   1.2783  -2.0507   1.5359
 PUN  H5B   H  HCH3  0   0.215   1.7887  -2.2823  -0.1331
 PUN  H6    H  HCH3  0   0.219   1.6568   1.7032   1.5337
 PUN  H6A   H  HCH3  0   0.226   1.2283   0.3170   2.5342
 PUN  H6B   H  HCH3  0   0.228   2.8945   0.5685   2.0618
 PUN  H7    H  HCH2  0   0.211   0.2650   0.9522  -0.7289
 PUN  H7A   H  HCH2  0   0.212   0.1958  -0.7667  -0.9836
 PUN  H9    H  HCH3  0   0.223  -0.4706  -1.1294   2.3500
 PUN  H9A   H  HCH3  0   0.237  -2.1758  -1.2861   1.9978
 PUN  H9B   H  HCH3  0   0.216  -1.0050  -2.1689   1.0283
 PUN  H10   H  HCH3  0   0.217  -1.2749   2.1340   0.6946
 PUN  H10A  H  HCH3  0   0.222  -2.2711   1.2706   1.8636
 PUN  H10B  H  HCH3  0   0.237  -0.5478   1.3921   2.1143
 PUN  H11   H  HCH2  0   0.211  -1.8150   0.4101  -1.4159
 PUN  H11A  H  HCH2  0   0.210  -2.0444  -1.2416  -0.9174
 PUN  H13   H  HCH3  0   0.215  -3.5015   2.0853  -1.2667
 PUN  H13A  H  HCH3  0   0.218  -5.0525   1.7436  -0.5053
 PUN  H13B  H  HCH3  0   0.227  -3.6439   2.0774   0.4886
 PUN  H14   H  HCH3  0   0.220  -4.1652  -1.5842  -1.7593
 PUN  H14A  H  HCH3  0   0.221  -5.3845  -0.3107  -1.7169
 PUN  H14B  H  HCH3  0   0.219  -3.8785  -0.0609  -2.6018
 PUN  H15   H  HCH3  0   0.223  -3.9866  -0.1642   1.7208
 PUN  H15A  H  HCH3  0   0.223  -5.4068  -0.4566   0.7302
 PUN  H15B  H  HCH3  0   0.220  -4.1255  -1.6618   0.7990

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
 PUN  C    C1    single  1.527  0.020  1.527
 PUN  C    C2    single  1.527  0.020  1.527
 PUN  C    C3    single  1.541  0.020  1.541
 PUN  C    H     single  0.970  0.020  1.090
 PUN  C1   H1    single  0.970  0.020  1.090
 PUN  C1   H1A   single  0.970  0.020  1.090
 PUN  C1   H1B   single  0.970  0.020  1.090
 PUN  C2   H2    single  0.970  0.020  1.090
 PUN  C2   H2A   single  0.970  0.020  1.090
 PUN  C2   H2B   single  0.970  0.020  1.090
 PUN  C3   C4    single  1.550  0.020  1.550
 PUN  C3   H3    single  0.970  0.020  1.090
 PUN  C3   H3A   single  0.970  0.020  1.090
 PUN  C4   C5    single  1.531  0.020  1.531
 PUN  C4   C6    single  1.530  0.020  1.530
 PUN  C4   C7    single  1.551  0.020  1.551
 PUN  C5   H5    single  0.970  0.020  1.090
 PUN  C5   H5A   single  0.970  0.020  1.090
 PUN  C5   H5B   single  0.970  0.020  1.090
 PUN  C6   H6    single  0.970  0.020  1.090
 PUN  C6   H6A   single  0.970  0.020  1.090
 PUN  C6   H6B   single  0.970  0.020  1.090
 PUN  C7   C8    single  1.556  0.020  1.556
 PUN  C7   H7    single  0.970  0.020  1.090
 PUN  C7   H7A   single  0.970  0.020  1.090
 PUN  C8   C9    single  1.531  0.020  1.531
 PUN  C8   C10   single  1.530  0.020  1.530
 PUN  C8   C11   single  1.556  0.020  1.556
 PUN  C9   H9    single  0.970  0.020  1.090
 PUN  C9   H9A   single  0.970  0.020  1.090
 PUN  C9   H9B   single  0.970  0.020  1.090
 PUN  C10  H10   single  0.970  0.020  1.090
 PUN  C10  H10A  single  0.970  0.020  1.090
 PUN  C10  H10B  single  0.970  0.020  1.090
 PUN  C11  C12   single  1.549  0.020  1.549
 PUN  C11  H11   single  0.970  0.020  1.090
 PUN  C11  H11A  single  0.970  0.020  1.090
 PUN  C12  C13   single  1.533  0.020  1.533
 PUN  C12  C14   single  1.535  0.020  1.535
 PUN  C12  C15   single  1.529  0.020  1.529
 PUN  C13  H13   single  0.970  0.020  1.090
 PUN  C13  H13A  single  0.970  0.020  1.090
 PUN  C13  H13B  single  0.970  0.020  1.090
 PUN  C14  H14   single  0.970  0.020  1.090
 PUN  C14  H14A  single  0.970  0.020  1.090
 PUN  C14  H14B  single  0.970  0.020  1.090
 PUN  C15  H15   single  0.970  0.020  1.090
 PUN  C15  H15A  single  0.970  0.020  1.090
 PUN  C15  H15B  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
 PUN  H     C    C3    109.10  3.000
 PUN  H     C    C2    107.10  3.000
 PUN  C3    C    C2    110.77  3.000
 PUN  H     C    C1    107.52  3.000
 PUN  C3    C    C1    112.21  3.000
 PUN  C2    C    C1    109.95  3.000
 PUN  H1B   C1   H1A   107.62  3.000
 PUN  H1B   C1   H1    107.46  3.000
 PUN  H1A   C1   H1    107.58  3.000
 PUN  H1B   C1   C     112.12  3.000
 PUN  H1A   C1   C     111.13  3.000
 PUN  H1    C1   C     110.73  3.000
 PUN  H2B   C2   H2A   107.78  3.000
 PUN  H2B   C2   H2    107.57  3.000
 PUN  H2A   C2   H2    107.60  3.000
 PUN  H2B   C2   C     111.43  3.000
 PUN  H2A   C2   C     111.31  3.000
 PUN  H2    C2   C     110.97  3.000
 PUN  H3A   C3   H3    105.32  3.000
 PUN  H3A   C3   C4    108.53  3.000
 PUN  H3    C3   C4    106.86  3.000
 PUN  H3A   C3   C     108.83  3.000
 PUN  H3    C3   C     108.99  3.000
 PUN  C4    C3   C     117.62  3.000
 PUN  C7    C4   C6    113.72  3.000
 PUN  C7    C4   C5    111.09  3.000
 PUN  C6    C4   C5    109.47  3.000
 PUN  C7    C4   C3    104.52  3.000
 PUN  C6    C4   C3    108.33  3.000
 PUN  C5    C4   C3    109.51  3.000
 PUN  H5B   C5   H5A   107.68  3.000
 PUN  H5B   C5   H5    107.53  3.000
 PUN  H5A   C5   H5    106.73  3.000
 PUN  H5B   C5   C4    111.04  3.000
 PUN  H5A   C5   C4    112.32  3.000
 PUN  H5    C5   C4    111.29  3.000
 PUN  H6B   C6   H6A   106.63  3.000
 PUN  H6B   C6   H6    107.42  3.000
 PUN  H6A   C6   H6    107.74  3.000
 PUN  H6B   C6   C4    110.91  3.000
 PUN  H6A   C6   C4    112.30  3.000
 PUN  H6    C6   C4    111.58  3.000
 PUN  H7A   C7   H7    104.87  3.000
 PUN  H7A   C7   C8    107.04  3.000
 PUN  H7    C7   C8    105.48  3.000
 PUN  H7A   C7   C4    105.21  3.000
 PUN  H7    C7   C4    107.07  3.000
 PUN  C8    C7   C4    125.53  3.000
 PUN  C11   C8   C10   111.96  3.000
 PUN  C11   C8   C9    109.99  3.000
 PUN  C10   C8   C9    108.97  3.000
 PUN  C11   C8   C7    103.22  3.000
 PUN  C10   C8   C7    110.51  3.000
 PUN  C9    C8   C7    112.14  3.000
 PUN  H9B   C9   H9A   107.42  3.000
 PUN  H9B   C9   H9    107.90  3.000
 PUN  H9A   C9   H9    106.66  3.000
 PUN  H9B   C9   C8    111.47  3.000
 PUN  H9A   C9   C8    111.49  3.000
 PUN  H9    C9   C8    111.65  3.000
 PUN  H10B  C10  H10A  106.50  3.000
 PUN  H10B  C10  H10   107.61  3.000
 PUN  H10A  C10  H10   107.70  3.000
 PUN  H10B  C10  C8    111.52  3.000
 PUN  H10A  C10  C8    111.58  3.000
 PUN  H10   C10  C8    111.67  3.000
 PUN  H11A  C11  H11   104.97  3.000
 PUN  H11A  C11  C12   107.14  3.000
 PUN  H11   C11  C12   105.28  3.000
 PUN  H11A  C11  C8    105.54  3.000
 PUN  H11   C11  C8    107.39  3.000
 PUN  C12   C11  C8    124.98  3.000
 PUN  C15   C12  C14   107.80  3.000
 PUN  C15   C12  C13   109.50  3.000
 PUN  C14   C12  C13   107.04  3.000
 PUN  C15   C12  C11   114.29  3.000
 PUN  C14   C12  C11   105.54  3.000
 PUN  C13   C12  C11   112.25  3.000
 PUN  H13B  C13  H13A  107.23  3.000
 PUN  H13B  C13  H13   107.68  3.000
 PUN  H13A  C13  H13   107.39  3.000
 PUN  H13B  C13  C12   113.10  3.000
 PUN  H13A  C13  C12   110.19  3.000
 PUN  H13   C13  C12   111.00  3.000
 PUN  H14B  C14  H14A  107.71  3.000
 PUN  H14B  C14  H14   107.69  3.000
 PUN  H14A  C14  H14   107.66  3.000
 PUN  H14B  C14  C12   111.20  3.000
 PUN  H14A  C14  C12   111.03  3.000
 PUN  H14   C14  C12   111.37  3.000
 PUN  H15B  C15  H15A  107.36  3.000
 PUN  H15B  C15  H15   107.87  3.000
 PUN  H15A  C15  H15   107.08  3.000
 PUN  H15B  C15  C12   111.69  3.000
 PUN  H15A  C15  C12   110.03  3.000
 PUN  H15   C15  C12   112.58  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
 PUN  Var_01  C5   C4   C3   C     -53.72  30.0  3
 PUN  Var_02  C4   C3   C    C1    100.25  30.0  3
 PUN  Var_03  C8   C7   C4   C3   -164.98  30.0  3
 PUN  Var_04  C9   C8   C7   C4    -46.44  30.0  3
 PUN  Var_05  C12  C11  C8   C7   -162.70  30.0  3
 PUN  Var_06  C13  C12  C11  C8     75.33  30.0  3
 PUN  Var_07  H2   C2   C    C1     63.76  30.0  3
 PUN  Var_08  H1   C1   C    C2    -62.27  30.0  3
 PUN  Var_09  H5   C5   C4   C3     58.52  30.0  3
 PUN  Var_10  H6   C6   C4   C3     61.67  30.0  3
 PUN  Var_11  H9   C9   C8   C7     65.95  30.0  3
 PUN  Var_12  H10  C10  C8   C7     57.47  30.0  3
 PUN  Var_13  H13  C13  C12  C11    50.97  30.0  3
 PUN  Var_14  H14  C14  C12  C11    62.57  30.0  3
 PUN  Var_15  H15  C15  C12  C11    68.32  30.0  3

