# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 22:28:19 2022
#   Inital geometry file: a 75 line input string
#   Ligand name: N-pentylpentan-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCNCCCCC
#
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
 DIP  DIP  'N-pentylpentan-1-amine   '  ligand  34  11  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DIP
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
 DIP  N     N  NH1   0  -0.593  42.3110   -8.3662  44.1158
 DIP  C1    C  CH2   0  -0.289  43.4927   -9.1692  44.3787
 DIP  C2    C  CH2   0  -0.441  43.4295  -10.6477  43.9978
 DIP  C3    C  CH2   0  -0.416  44.7475  -11.3625  44.2712
 DIP  C4    C  CH2   0  -0.422  44.7498  -12.8399  43.8874
 DIP  C5    C  CH3   0  -0.665  43.7910  -13.6903  44.7111
 DIP  C1'   C  CH2   0  -0.291  41.0695   -8.8547  44.6951
 DIP  C2'   C  CH2   0  -0.447  41.1007   -8.9217  46.2169
 DIP  C3'   C  CH2   0  -0.398  41.4403   -7.6061  46.9040
 DIP  C4'   C  CH2   0  -0.416  41.3917   -7.7066  48.4245
 DIP  C5'   C  CH3   0  -0.659  41.7301   -6.3949  49.1190
 DIP  HN    H  HNH1  0   0.340  42.1882   -8.2799  43.1150
 DIP  H11   H  HCH2  0   0.220  44.3257   -8.7020  43.8449
 DIP  H12   H  HCH2  0   0.211  43.7441   -9.0882  45.4417
 DIP  H21   H  HCH2  0   0.219  42.6229  -11.1374  44.5500
 DIP  H22   H  HCH2  0   0.205  43.1764  -10.7402  42.9353
 DIP  H31   H  HCH2  0   0.215  45.5487  -10.8515  43.7278
 DIP  H32   H  HCH2  0   0.206  44.9972  -11.2685  45.3343
 DIP  H41   H  HCH2  0   0.209  44.5074  -12.9386  42.8247
 DIP  H42   H  HCH2  0   0.218  45.7634  -13.2330  44.0032
 DIP  H51   H  HCH3  0   0.226  43.8683  -14.7448  44.4436
 DIP  H52   H  HCH3  0   0.214  44.0087  -13.6035  45.7776
 DIP  H53   H  HCH3  0   0.219  42.7519  -13.3937  44.5630
 DIP  H1'1  H  HCH2  0   0.218  40.2779   -8.1637  44.3905
 DIP  H1'2  H  HCH2  0   0.198  40.7733   -9.8431  44.3137
 DIP  H2'1  H  HCH2  0   0.222  40.1149   -9.2608  46.5503
 DIP  H2'2  H  HCH2  0   0.214  41.8014   -9.6974  46.5446
 DIP  H3'1  H  HCH2  0   0.212  42.4348   -7.2680  46.5978
 DIP  H3'2  H  HCH2  0   0.202  40.7423   -6.8306  46.5688
 DIP  H4'1  H  HCH2  0   0.207  40.3962   -8.0397  48.7342
 DIP  H4'2  H  HCH2  0   0.208  42.0859   -8.4851  48.7563
 DIP  H5'1  H  HCH3  0   0.224  41.6966   -6.4950  50.2045
 DIP  H5'2  H  HCH3  0   0.214  42.7316   -6.0531  48.8509
 DIP  H5'3  H  HCH3  0   0.214  41.0292   -5.6064  48.8387

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
 DIP  N    C1    single  1.453  0.020  1.453
 DIP  N    C1'   single  1.454  0.020  1.454
 DIP  N    HN    single  0.890  0.020  1.040
 DIP  C1   C2    single  1.528  0.020  1.528
 DIP  C1   H11   single  0.970  0.020  1.090
 DIP  C1   H12   single  0.970  0.020  1.090
 DIP  C2   C3    single  1.524  0.020  1.524
 DIP  C2   H21   single  0.970  0.020  1.090
 DIP  C2   H22   single  0.970  0.020  1.090
 DIP  C3   C4    single  1.526  0.020  1.526
 DIP  C3   H31   single  0.970  0.020  1.090
 DIP  C3   H32   single  0.970  0.020  1.090
 DIP  C4   C5    single  1.523  0.020  1.523
 DIP  C4   H41   single  0.970  0.020  1.090
 DIP  C4   H42   single  0.970  0.020  1.090
 DIP  C5   H51   single  0.970  0.020  1.090
 DIP  C5   H52   single  0.970  0.020  1.090
 DIP  C5   H53   single  0.970  0.020  1.090
 DIP  C1'  C2'   single  1.524  0.020  1.524
 DIP  C1'  H1'1  single  0.970  0.020  1.090
 DIP  C1'  H1'2  single  0.970  0.020  1.090
 DIP  C2'  C3'   single  1.523  0.020  1.523
 DIP  C2'  H2'1  single  0.970  0.020  1.090
 DIP  C2'  H2'2  single  0.970  0.020  1.090
 DIP  C3'  C4'   single  1.525  0.020  1.525
 DIP  C3'  H3'1  single  0.970  0.020  1.090
 DIP  C3'  H3'2  single  0.970  0.020  1.090
 DIP  C4'  C5'   single  1.522  0.020  1.522
 DIP  C4'  H4'1  single  0.970  0.020  1.090
 DIP  C4'  H4'2  single  0.970  0.020  1.090
 DIP  C5'  H5'1  single  0.970  0.020  1.090
 DIP  C5'  H5'2  single  0.970  0.020  1.090
 DIP  C5'  H5'3  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
 DIP  HN    N    C1'   108.60  3.000
 DIP  HN    N    C1    108.96  3.000
 DIP  C1'   N    C1    115.89  3.000
 DIP  H12   C1   H11   105.50  3.000
 DIP  H12   C1   C2    108.85  3.000
 DIP  H11   C1   C2    108.84  3.000
 DIP  H12   C1   N     108.76  3.000
 DIP  H11   C1   N     107.16  3.000
 DIP  C2    C1   N     117.13  3.000
 DIP  H22   C2   H21   106.35  3.000
 DIP  H22   C2   C3    109.51  3.000
 DIP  H21   C2   C3    109.71  3.000
 DIP  H22   C2   C1    109.44  3.000
 DIP  H21   C2   C1    109.75  3.000
 DIP  C3    C2   C1    111.92  3.000
 DIP  H32   C3   H31   105.95  3.000
 DIP  H32   C3   C4    109.06  3.000
 DIP  H31   C3   C4    109.02  3.000
 DIP  H32   C3   C2    109.32  3.000
 DIP  H31   C3   C2    108.96  3.000
 DIP  C4    C3   C2    114.22  3.000
 DIP  H42   C4   H41   106.01  3.000
 DIP  H42   C4   C5    109.00  3.000
 DIP  H41   C4   C5    109.59  3.000
 DIP  H42   C4   C3    108.83  3.000
 DIP  H41   C4   C3    109.33  3.000
 DIP  C5    C4   C3    113.79  3.000
 DIP  H53   C5   H52   107.51  3.000
 DIP  H53   C5   H51   107.29  3.000
 DIP  H52   C5   H51   107.59  3.000
 DIP  H53   C5   C4    111.99  3.000
 DIP  H52   C5   C4    110.99  3.000
 DIP  H51   C5   C4    111.25  3.000
 DIP  H1'2  C1'  H1'1  106.03  3.000
 DIP  H1'2  C1'  C2'   108.20  3.000
 DIP  H1'1  C1'  C2'   108.70  3.000
 DIP  H1'2  C1'  N     113.17  3.000
 DIP  H1'1  C1'  N     107.13  3.000
 DIP  C2'   C1'  N     113.27  3.000
 DIP  H2'2  C2'  H2'1  105.40  3.000
 DIP  H2'2  C2'  C3'   109.53  3.000
 DIP  H2'1  C2'  C3'   109.33  3.000
 DIP  H2'2  C2'  C1'   110.06  3.000
 DIP  H2'1  C2'  C1'   107.42  3.000
 DIP  C3'   C2'  C1'   114.67  3.000
 DIP  H3'2  C3'  H3'1  105.95  3.000
 DIP  H3'2  C3'  C4'   109.35  3.000
 DIP  H3'1  C3'  C4'   109.18  3.000
 DIP  H3'2  C3'  C2'   109.35  3.000
 DIP  H3'1  C3'  C2'   110.08  3.000
 DIP  C4'   C3'  C2'   112.70  3.000
 DIP  H4'2  C4'  H4'1  105.94  3.000
 DIP  H4'2  C4'  C5'   109.49  3.000
 DIP  H4'1  C4'  C5'   109.59  3.000
 DIP  H4'2  C4'  C3'   109.21  3.000
 DIP  H4'1  C4'  C3'   109.35  3.000
 DIP  C5'   C4'  C3'   113.02  3.000
 DIP  H5'3  C5'  H5'2  107.44  3.000
 DIP  H5'3  C5'  H5'1  107.58  3.000
 DIP  H5'2  C5'  H5'1  107.54  3.000
 DIP  H5'3  C5'  C4'   111.26  3.000
 DIP  H5'2  C5'  C4'   111.21  3.000
 DIP  H5'1  C5'  C4'   111.61  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
 DIP  Var_01  C3    C2   C1   N     177.66  30.0  3
 DIP  Var_02  C3'   C2'  C1'  N      56.09  30.0  3
 DIP  Var_03  C2'   C1'  N    C1     61.51  30.0  3
 DIP  Var_04  C4    C3   C2   C1   -179.04  30.0  3
 DIP  Var_05  C1'   N    C1   C2     54.93  30.0  1
 DIP  Var_06  C5    C4   C3   C2    -65.14  30.0  3
 DIP  Var_07  C4'   C3'  C2'  C1'   177.16  30.0  3
 DIP  Var_08  C5'   C4'  C3'  C2'  -180.00  30.0  3
 DIP  Var_09  H51   C5   C4   C3   -176.66  30.0  3
 DIP  Var_10  H5'1  C5'  C4'  C3'  -179.52  30.0  3

