# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 06:07:20 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: (3S)-3-aminoazacyclotridecan-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CCCCCCCCCCNC1=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
 RIN  RIN  (3S)-3-aminoazacyclotridecan-2-one  ligand  39  15  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RIN
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
 RIN  N    N  NH2   0  -0.795   0.8964  -1.3539   3.1082
 RIN  CA   C  CH1   0  -0.192   0.9965  -0.1663   2.2808
 RIN  CB   C  CH2   0  -0.455   1.7544  -0.5203   0.9929
 RIN  CG   C  CH2   0  -0.445   2.1840   0.6730   0.1441
 RIN  CD   C  CH2   0  -0.432   2.9095   0.3065  -1.1657
 RIN  CE   C  CH2   0  -0.437   2.0292   0.4524  -2.4081
 RIN  CZ   C  CH2   0  -0.450   0.8969  -0.5735  -2.4911
 RIN  C5   C  CH2   0  -0.424  -0.3447  -0.1171  -3.2754
 RIN  C4   C  CH2   0  -0.436  -1.6412  -0.5063  -2.5616
 RIN  C3   C  CH2   0  -0.433  -1.8343   0.2776  -1.2645
 RIN  C2   C  CH2   0  -0.433  -2.8326  -0.3427  -0.2925
 RIN  C1   C  CH2   0  -0.296  -2.6433   0.1339   1.1464
 RIN  N1   N  NH1   0  -0.614  -1.3638  -0.2806   1.6838
 RIN  C    C  C     0   0.513  -0.3241   0.5328   1.9306
 RIN  O    O  O     0  -0.503  -0.3894   1.7541   1.8548
 RIN  H    H  HNH2  0   0.349   0.5563  -2.1539   2.5896
 RIN  HN2  H  HNH2  0   0.355   0.2739  -1.2127   3.8927
 RIN  HA   H  HCH1  0   0.245   1.5814   0.5785   2.8299
 RIN  HB1  H  HCH2  0   0.243   2.6442  -1.0824   1.2916
 RIN  HB2  H  HCH2  0   0.225   1.1433  -1.2141   0.4055
 RIN  HG1  H  HCH2  0   0.229   1.3228   1.3017  -0.0971
 RIN  HG2  H  HCH2  0   0.229   2.8354   1.2998   0.7593
 RIN  HD1  H  HCH2  0   0.228   3.7772   0.9597  -1.2843
 RIN  HD2  H  HCH2  0   0.216   3.3126  -0.7106  -1.1060
 RIN  HE1  H  HCH2  0   0.211   1.6019   1.4610  -2.3989
 RIN  HE2  H  HCH2  0   0.221   2.6474   0.4004  -3.3090
 RIN  HZ1  H  HCH2  0   0.228   1.2803  -1.5089  -2.9078
 RIN  HZ2  H  HCH2  0   0.224   0.5846  -0.8290  -1.4772
 RIN  H51  H  HCH2  0   0.211  -0.3274   0.9708  -3.3998
 RIN  H52  H  HCH2  0   0.226  -0.3352  -0.5317  -4.2861
 RIN  H41  H  HCH2  0   0.222  -2.5000  -0.3583  -3.2224
 RIN  H42  H  HCH2  0   0.209  -1.6123  -1.5787  -2.3386
 RIN  H31  H  HCH2  0   0.223  -0.8671   0.3603  -0.7615
 RIN  H32  H  HCH2  0   0.221  -2.1311   1.3050  -1.4959
 RIN  H21  H  HCH2  0   0.230  -3.8590  -0.1257  -0.6009
 RIN  H22  H  HCH2  0   0.217  -2.7370  -1.4336  -0.3111
 RIN  H11  H  HCH2  0   0.242  -2.7020   1.2198   1.2062
 RIN  H12  H  HCH2  0   0.247  -3.4389  -0.2677   1.7777
 RIN  HN1  H  HNH1  0   0.382  -1.2187  -1.2730   1.7808

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
 RIN  N   CA   single  1.451  0.020  1.451
 RIN  N   H    single  0.860  0.020  1.020
 RIN  N   HN2  single  0.890  0.020  1.040
 RIN  CA  CB   single  1.536  0.020  1.536
 RIN  CA  C    single  1.535  0.020  1.535
 RIN  CA  HA   single  0.970  0.020  1.090
 RIN  CB  CG   single  1.526  0.020  1.526
 RIN  CB  HB1  single  0.970  0.020  1.090
 RIN  CB  HB2  single  0.970  0.020  1.090
 RIN  CG  CD   single  1.542  0.020  1.542
 RIN  CG  HG1  single  0.970  0.020  1.090
 RIN  CG  HG2  single  0.970  0.020  1.090
 RIN  CD  CE   single  1.530  0.020  1.530
 RIN  CD  HD1  single  0.970  0.020  1.090
 RIN  CD  HD2  single  0.970  0.020  1.090
 RIN  CE  CZ   single  1.530  0.020  1.530
 RIN  CE  HE1  single  0.970  0.020  1.090
 RIN  CE  HE2  single  0.970  0.020  1.090
 RIN  CZ  C5   single  1.538  0.020  1.538
 RIN  CZ  HZ1  single  0.970  0.020  1.090
 RIN  CZ  HZ2  single  0.970  0.020  1.090
 RIN  C5  C4   single  1.530  0.020  1.530
 RIN  C5  H51  single  0.970  0.020  1.090
 RIN  C5  H52  single  0.970  0.020  1.090
 RIN  C4  C3   single  1.528  0.020  1.528
 RIN  C4  H41  single  0.970  0.020  1.090
 RIN  C4  H42  single  0.970  0.020  1.090
 RIN  C3  C2   single  1.525  0.020  1.525
 RIN  C3  H31  single  0.970  0.020  1.090
 RIN  C3  H32  single  0.970  0.020  1.090
 RIN  C2  C1   single  1.528  0.020  1.528
 RIN  C2  H21  single  0.970  0.020  1.090
 RIN  C2  H22  single  0.970  0.020  1.090
 RIN  C1  N1   single  1.448  0.020  1.448
 RIN  C1  H11  single  0.970  0.020  1.090
 RIN  C1  H12  single  0.970  0.020  1.090
 RIN  N1  C    single  1.343  0.020  1.343
 RIN  N1  HN1  single  0.860  0.020  1.020
 RIN  C   O    double  1.225  0.020  1.225

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
 RIN  HN2  N   H    107.51  3.000
 RIN  HN2  N   CA   111.75  3.000
 RIN  H    N   CA   112.20  3.000
 RIN  HA   CA  C    105.32  3.000
 RIN  HA   CA  CB   108.29  3.000
 RIN  C    CA  CB   109.77  3.000
 RIN  HA   CA  N    107.92  3.000
 RIN  C    CA  N    116.34  3.000
 RIN  CB   CA  N    108.88  3.000
 RIN  HB2  CB  HB1  105.95  3.000
 RIN  HB2  CB  CG   110.74  3.000
 RIN  HB1  CB  CG   108.94  3.000
 RIN  HB2  CB  CA   108.69  3.000
 RIN  HB1  CB  CA   106.91  3.000
 RIN  CG   CB  CA   115.16  3.000
 RIN  HG2  CG  HG1  105.30  3.000
 RIN  HG2  CG  CD   109.51  3.000
 RIN  HG1  CG  CD   108.66  3.000
 RIN  HG2  CG  CB   107.64  3.000
 RIN  HG1  CG  CB   110.53  3.000
 RIN  CD   CG  CB   114.78  3.000
 RIN  HD2  CD  HD1  105.59  3.000
 RIN  HD2  CD  CE   110.16  3.000
 RIN  HD1  CD  CE   108.18  3.000
 RIN  HD2  CD  CG   110.34  3.000
 RIN  HD1  CD  CG   108.89  3.000
 RIN  CE   CD  CG   113.36  3.000
 RIN  HE2  CE  HE1  105.73  3.000
 RIN  HE2  CE  CZ   109.98  3.000
 RIN  HE1  CE  CZ   109.21  3.000
 RIN  HE2  CE  CD   109.82  3.000
 RIN  HE1  CE  CD   107.79  3.000
 RIN  CZ   CE  CD   113.95  3.000
 RIN  HZ2  CZ  HZ1  104.72  3.000
 RIN  HZ2  CZ  C5   108.20  3.000
 RIN  HZ1  CZ  C5   110.04  3.000
 RIN  HZ2  CZ  CE   108.56  3.000
 RIN  HZ1  CZ  CE   109.56  3.000
 RIN  C5   CZ  CE   115.22  3.000
 RIN  H52  C5  H51  105.78  3.000
 RIN  H52  C5  C4   110.02  3.000
 RIN  H51  C5  C4   108.60  3.000
 RIN  H52  C5  CZ   110.62  3.000
 RIN  H51  C5  CZ   109.88  3.000
 RIN  C4   C5  CZ   111.75  3.000
 RIN  H42  C4  H41  106.03  3.000
 RIN  H42  C4  C3   109.43  3.000
 RIN  H41  C4  C3   110.15  3.000
 RIN  H42  C4  C5   108.75  3.000
 RIN  H41  C4  C5   110.43  3.000
 RIN  C3   C4  C5   111.87  3.000
 RIN  H32  C3  H31  105.45  3.000
 RIN  H32  C3  C2   109.82  3.000
 RIN  H31  C3  C2   108.46  3.000
 RIN  H32  C3  C4   109.67  3.000
 RIN  H31  C3  C4   108.52  3.000
 RIN  C2   C3  C4   114.52  3.000
 RIN  H22  C2  H21  105.96  3.000
 RIN  H22  C2  C1   108.42  3.000
 RIN  H21  C2  C1   108.67  3.000
 RIN  H22  C2  C3   109.70  3.000
 RIN  H21  C2  C3   110.72  3.000
 RIN  C1   C2  C3   113.09  3.000
 RIN  H12  C1  H11  107.20  3.000
 RIN  H12  C1  N1   108.90  3.000
 RIN  H11  C1  N1   108.22  3.000
 RIN  H12  C1  C2   109.84  3.000
 RIN  H11  C1  C2   110.87  3.000
 RIN  N1   C1  C2   111.69  3.000
 RIN  HN1  N1  C    117.86  3.000
 RIN  HN1  N1  C1   116.42  3.000
 RIN  C    N1  C1   125.36  3.000
 RIN  O    C   N1   123.44  3.000
 RIN  O    C   CA   120.93  3.000
 RIN  N1   C   CA   115.60  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
 RIN  CONST_01  C1   N1  C   CA   180.00   0.0  0
 RIN  CONST_02  O    C   N1  C1     0.00   0.0  0
 RIN  CONST_03  HN1  N1  C   CA     0.00   0.0  0
 RIN  Var_01    CD   CG  CB  CA  -178.39  30.0  1
 RIN  Var_02    CE   CD  CG  CB   103.75  30.0  1
 RIN  Var_03    CZ   CE  CD  CG   -68.77  30.0  1
 RIN  Var_04    C5   CZ  CE  CD   152.63  30.0  1
 RIN  Var_05    C4   C5  CZ  CE  -136.97  30.0  1
 RIN  Var_06    C3   C4  C5  CZ    68.44  30.0  1
 RIN  Var_07    C2   C3  C4  C5  -161.49  30.0  1
 RIN  Var_08    C1   C2  C3  C4   159.01  30.0  1
 RIN  Var_09    N1   C1  C2  C3   -64.32  30.0  1
 RIN  Var_10    C    N1  C1  C2   108.80  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
 RIN  chir_01  CA  N  CB  C  negativ

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
 RIN  plan-1  CA   0.020
 RIN  plan-1  C1   0.020
 RIN  plan-1  N1   0.020
 RIN  plan-1  C    0.020
 RIN  plan-1  O    0.020
 RIN  plan-1  HN1  0.020

