# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 11:44:21 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: 3-cyclopentyl-N-methylpropan-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCCCC1CCCC1
#
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
 DIX  DIX  3-cyclopentyl-N-methylpropan-1-amine  ligand  29  10  .  2021-08-08  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DIX
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
 DIX  N     N  NH1   0  -0.593   0.4243  -0.1994   3.5689
 DIX  CM    C  CH3   0  -0.516  -0.0315   0.3432   4.8314
 DIX  C3    C  CH2   0  -0.248  -0.3986   0.2149   2.4492
 DIX  C2    C  CH2   0  -0.443   0.1156  -0.3560   1.1371
 DIX  C1    C  CH2   0  -0.428  -0.7529   0.0289  -0.0535
 DIX  C1'   C  CH1   0  -0.210  -0.2571  -0.5359  -1.3802
 DIX  C2'   C  CH2   0  -0.444  -1.1757  -0.1713  -2.5761
 DIX  C5'   C  CH2   0  -0.441   1.1408  -0.0226  -1.7766
 DIX  C4'   C  CH2   0  -0.441   1.1054   0.0813  -3.2985
 DIX  C3'   C  CH2   0  -0.440  -0.3016   0.6076  -3.5662
 DIX  HN    H  HNH1  0   0.338   1.3753   0.1075   3.4046
 DIX  HM1   H  HCH3  0   0.228   0.6501   0.0491   5.6301
 DIX  HM2   H  HCH3  0   0.190  -0.1166   1.4393   4.8488
 DIX  HM3   H  HCH3  0   0.219  -1.0157  -0.0618   5.0749
 DIX  H31   H  HCH2  0   0.209  -1.4191  -0.1434   2.6247
 DIX  H32   H  HCH2  0   0.180  -0.4732   1.3126   2.3641
 DIX  H21   H  HCH2  0   0.221   1.1432  -0.0125   0.9747
 DIX  H22   H  HCH2  0   0.212   0.1638  -1.4465   1.2181
 DIX  H11   H  HCH2  0   0.217  -1.7778  -0.3147   0.1249
 DIX  H12   H  HCH2  0   0.207  -0.8071   1.1217  -0.1343
 DIX  H1'   H  HCH1  0   0.219  -0.2161  -1.6264  -1.2875
 DIX  H2'1  H  HCH2  0   0.223  -1.5584  -1.0792  -3.0469
 DIX  H2'2  H  HCH2  0   0.224  -2.0480   0.4037  -2.2567
 DIX  H5'1  H  HCH2  0   0.212   1.3049   0.9740  -1.3505
 DIX  H5'2  H  HCH2  0   0.228   1.9455  -0.6604  -1.4068
 DIX  H4'1  H  HCH2  0   0.213   1.2275  -0.9092  -3.7480
 DIX  H4'2  H  HCH2  0   0.225   1.8918   0.7203  -3.7043
 DIX  H3'1  H  HCH2  0   0.226  -0.6212   0.4853  -4.6026
 DIX  H3'2  H  HCH2  0   0.215  -0.3376   1.6777  -3.3425

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
 DIX  N    CM    single  1.448  0.020  1.448
 DIX  N    C3    single  1.450  0.020  1.450
 DIX  N    HN    single  0.890  0.020  1.040
 DIX  CM   HM1   single  0.970  0.020  1.090
 DIX  CM   HM2   single  0.970  0.020  1.090
 DIX  CM   HM3   single  0.970  0.020  1.090
 DIX  C3   C2    single  1.521  0.020  1.521
 DIX  C3   H31   single  0.970  0.020  1.090
 DIX  C3   H32   single  0.970  0.020  1.090
 DIX  C2   C1    single  1.523  0.020  1.523
 DIX  C2   H21   single  0.970  0.020  1.090
 DIX  C2   H22   single  0.970  0.020  1.090
 DIX  C1   C1'   single  1.525  0.020  1.525
 DIX  C1   H11   single  0.970  0.020  1.090
 DIX  C1   H12   single  0.970  0.020  1.090
 DIX  C1'  C2'   single  1.551  0.020  1.551
 DIX  C1'  C5'   single  1.541  0.020  1.541
 DIX  C1'  H1'   single  0.970  0.020  1.090
 DIX  C2'  C3'   single  1.533  0.020  1.533
 DIX  C2'  H2'1  single  0.970  0.020  1.090
 DIX  C2'  H2'2  single  0.970  0.020  1.090
 DIX  C5'  C4'   single  1.526  0.020  1.526
 DIX  C5'  H5'1  single  0.970  0.020  1.090
 DIX  C5'  H5'2  single  0.970  0.020  1.090
 DIX  C4'  C3'   single  1.526  0.020  1.526
 DIX  C4'  H4'1  single  0.970  0.020  1.090
 DIX  C4'  H4'2  single  0.970  0.020  1.090
 DIX  C3'  H3'1  single  0.970  0.020  1.090
 DIX  C3'  H3'2  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
 DIX  HN    N    C3    108.73  3.000
 DIX  HN    N    CM    108.88  3.000
 DIX  C3    N    CM    112.81  3.000
 DIX  HM3   CM   HM2   107.24  3.000
 DIX  HM3   CM   HM1   107.46  3.000
 DIX  HM2   CM   HM1   107.79  3.000
 DIX  HM3   CM   N     109.83  3.000
 DIX  HM2   CM   N     114.32  3.000
 DIX  HM1   CM   N     109.93  3.000
 DIX  H32   C3   H31   105.94  3.000
 DIX  H32   C3   C2    109.25  3.000
 DIX  H31   C3   C2    109.30  3.000
 DIX  H32   C3   N     112.46  3.000
 DIX  H31   C3   N     108.15  3.000
 DIX  C2    C3   N     111.54  3.000
 DIX  H22   C2   H21   106.37  3.000
 DIX  H22   C2   C1    109.56  3.000
 DIX  H21   C2   C1    109.86  3.000
 DIX  H22   C2   C3    108.97  3.000
 DIX  H21   C2   C3    109.11  3.000
 DIX  C1    C2   C3    112.76  3.000
 DIX  H12   C1   H11   106.15  3.000
 DIX  H12   C1   C1'   108.73  3.000
 DIX  H11   C1   C1'   109.25  3.000
 DIX  H12   C1   C2    109.72  3.000
 DIX  H11   C1   C2    109.08  3.000
 DIX  C1'   C1   C2    113.65  3.000
 DIX  H1'   C1'  C5'   108.63  3.000
 DIX  H1'   C1'  C2'   108.75  3.000
 DIX  C5'   C1'  C2'   105.10  3.000
 DIX  H1'   C1'  C1    107.90  3.000
 DIX  C5'   C1'  C1    113.29  3.000
 DIX  C2'   C1'  C1    113.02  3.000
 DIX  H2'2  C2'  H2'1  106.49  3.000
 DIX  H2'2  C2'  C3'   112.12  3.000
 DIX  H2'1  C2'  C3'   110.10  3.000
 DIX  H2'2  C2'  C1'   111.78  3.000
 DIX  H2'1  C2'  C1'   110.15  3.000
 DIX  C3'   C2'  C1'   106.23  3.000
 DIX  H5'2  C5'  H5'1  106.81  3.000
 DIX  H5'2  C5'  C4'   113.26  3.000
 DIX  H5'1  C5'  C4'   109.22  3.000
 DIX  H5'2  C5'  C1'   112.77  3.000
 DIX  H5'1  C5'  C1'   109.79  3.000
 DIX  C4'   C5'  C1'   104.97  3.000
 DIX  H4'2  C4'  H4'1  107.27  3.000
 DIX  H4'2  C4'  C3'   113.40  3.000
 DIX  H4'1  C4'  C3'   110.05  3.000
 DIX  H4'2  C4'  C5'   113.20  3.000
 DIX  H4'1  C4'  C5'   110.21  3.000
 DIX  C3'   C4'  C5'   102.70  3.000
 DIX  H3'2  C3'  H3'1  107.11  3.000
 DIX  H3'2  C3'  C4'   109.38  3.000
 DIX  H3'1  C3'  C4'   113.45  3.000
 DIX  H3'2  C3'  C2'   110.26  3.000
 DIX  H3'1  C3'  C2'   112.91  3.000
 DIX  C4'   C3'  C2'   103.72  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
 DIX  Var_01  C4'  C3'  C2'  C1'    27.34  30.0  1
 DIX  Var_02  C3'  C4'  C5'  C1'    38.92  30.0  1
 DIX  Var_03  C5'  C4'  C3'  C2'   -40.79  30.0  1
 DIX  Var_04  C1'  C1   C2   C3   -179.87  30.0  3
 DIX  Var_05  C1   C2   C3   N     178.32  30.0  3
 DIX  Var_06  C2   C3   N    CM    179.26  30.0  3
 DIX  Var_07  HM1  CM   N    C3   -176.84  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
 DIX  chir_01  C1'  C1  C2'  C5'  negativ

