# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 22:51:53 2022
#   Inital geometry file: a 75 line input string
#   Ligand name: (1R)-1-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]ethanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](N)C12CC3CC(CC(C3)C1)C2
#
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
 RIM  RIM  (1R)-1-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]ethanamine  ligand  34  13  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_RIM
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
 RIM  CA    C  CH3   0  -0.683  -2.9076   1.2560  -0.0874
 RIM  CB    C  CH1   0  -0.065  -2.1885   0.0022   0.4166
 RIM  NC    N  NH2   0  -0.791  -2.7926  -1.2203  -0.1109
 RIM  CD    C  C     0  -0.067  -0.6626   0.0039   0.1734
 RIM  CE1   C  C     0  -0.413  -0.0222   1.2553   0.7962
 RIM  CE2   C  C     0  -0.391  -0.0293  -1.2319   0.8342
 RIM  CE3   C  C     0  -0.429  -0.3088  -0.0209  -1.3222
 RIM  CF1   C  C     0  -0.242   1.4975   1.2457   0.6121
 RIM  CF2   C  C     0  -0.246   1.4888  -1.2447   0.6424
 RIM  CF3   C  C     0  -0.239   1.2118  -0.0250  -1.5178
 RIM  CG1   C  C     0  -0.415   2.0970   0.0064   1.2756
 RIM  CG2   C  C     0  -0.417   1.8067  -1.2672  -0.8539
 RIM  CG3   C  C     0  -0.418   1.8136   1.2301  -0.8848
 RIM  HA1   H  HCH3  0   0.216  -2.8081   1.3712  -1.1692
 RIM  HA2   H  HCH3  0   0.227  -3.9743   1.1781   0.1325
 RIM  HA3   H  HCH3  0   0.223  -2.5503   2.1738   0.3797
 RIM  HB    H  HCH1  0   0.210  -2.3198  -0.0349   1.5054
 RIM  HNC1  H  HNH2  0   0.342  -3.7741  -1.2308   0.1407
 RIM  HNC2  H  HNH2  0   0.334  -2.7851  -1.1864  -1.1241
 RIM  HE11  H  H     0   0.223  -0.4229   2.1603   0.3306
 RIM  HE12  H  H     0   0.215  -0.2749   1.3119   1.8617
 RIM  HE21  H  H     0   0.208  -0.2702  -1.2398   1.9042
 RIM  HE22  H  H     0   0.222  -0.4657  -2.1392   0.4096
 RIM  HE31  H  H     0   0.217  -0.7292  -0.9130  -1.7999
 RIM  HE32  H  H     0   0.222  -0.7370   0.8493  -1.8310
 RIM  HF1   H  H     0   0.218   1.9188   2.1478   1.0667
 RIM  HF2   H  H     0   0.216   1.9042  -2.1384   1.1189
 RIM  HF3   H  H     0   0.218   1.4336  -0.0386  -2.5895
 RIM  HG11  H  H     0   0.217   3.1855   0.0030   1.1559
 RIM  HG12  H  H     0   0.217   1.8972   0.0205   2.3521
 RIM  HG21  H  H     0   0.218   2.8899  -1.3024  -1.0122
 RIM  HG22  H  H     0   0.217   1.3914  -2.1719  -1.3117
 RIM  HG31  H  H     0   0.218   1.4019   2.1260  -1.3627
 RIM  HG32  H  H     0   0.219   2.8966   1.2563  -1.0455

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
 RIM  CA   CB    single  1.531  0.020  1.531
 RIM  CA   HA1   single  0.970  0.020  1.090
 RIM  CA   HA2   single  0.970  0.020  1.090
 RIM  CA   HA3   single  0.970  0.020  1.090
 RIM  CB   CD    single  1.545  0.020  1.545
 RIM  CB   NC    single  1.462  0.020  1.462
 RIM  CB   HB    single  0.970  0.020  1.090
 RIM  NC   HNC1  single  0.890  0.020  1.040
 RIM  NC   HNC2  single  0.890  0.020  1.040
 RIM  CD   CE2   single  1.538  0.020  1.538
 RIM  CD   CE1   single  1.537  0.020  1.537
 RIM  CD   CE3   single  1.537  0.020  1.537
 RIM  CE1  CF1   single  1.531  0.020  1.531
 RIM  CE1  HE11  single  0.970  0.020  1.090
 RIM  CE1  HE12  single  0.970  0.020  1.090
 RIM  CE2  CF2   single  1.530  0.020  1.530
 RIM  CE2  HE21  single  0.970  0.020  1.090
 RIM  CE2  HE22  single  0.970  0.020  1.090
 RIM  CE3  CF3   single  1.533  0.020  1.533
 RIM  CE3  HE31  single  0.970  0.020  1.090
 RIM  CE3  HE32  single  0.970  0.020  1.090
 RIM  CF1  CG1   single  1.528  0.020  1.528
 RIM  CF1  CG3   single  1.530  0.020  1.530
 RIM  CF1  HF1   single  0.970  0.020  1.090
 RIM  CF2  CG1   single  1.529  0.020  1.529
 RIM  CF2  CG2   single  1.530  0.020  1.530
 RIM  CF2  HF2   single  0.970  0.020  1.090
 RIM  CF3  CG2   single  1.529  0.020  1.529
 RIM  CF3  CG3   single  1.529  0.020  1.529
 RIM  CF3  HF3   single  0.970  0.020  1.090
 RIM  CG1  HG11  single  0.970  0.020  1.090
 RIM  CG1  HG12  single  0.970  0.020  1.090
 RIM  CG2  HG21  single  0.970  0.020  1.090
 RIM  CG2  HG22  single  0.970  0.020  1.090
 RIM  CG3  HG31  single  0.970  0.020  1.090
 RIM  CG3  HG32  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
 RIM  HA3   CA   HA2   107.10  3.000
 RIM  HA3   CA   HA1   107.80  3.000
 RIM  HA2   CA   HA1   107.21  3.000
 RIM  HA3   CA   CB    113.24  3.000
 RIM  HA2   CA   CB    109.52  3.000
 RIM  HA1   CA   CB    111.69  3.000
 RIM  HB    CB   CD    105.92  3.000
 RIM  HB    CB   NC    106.28  3.000
 RIM  CD    CB   NC    110.62  3.000
 RIM  HB    CB   CA    107.35  3.000
 RIM  NC    CB   CA    111.84  3.000
 RIM  CD    CB   CA    114.28  3.000
 RIM  HNC2  NC   HNC1  104.81  3.000
 RIM  HNC2  NC   CB    109.25  3.000
 RIM  HNC1  NC   CB    108.62  3.000
 RIM  CE3   CD   CE2   108.08  3.000
 RIM  CE3   CD   CE1   108.14  3.000
 RIM  CE2   CD   CE1   107.97  3.000
 RIM  CE3   CD   CB    112.36  3.000
 RIM  CE1   CD   CB    110.40  3.000
 RIM  CE2   CD   CB    109.76  3.000
 RIM  HE12  CE1  HE11  106.65  3.000
 RIM  HE12  CE1  CF1   110.24  3.000
 RIM  HE11  CE1  CF1   108.52  3.000
 RIM  HE12  CE1  CD    109.86  3.000
 RIM  HE11  CE1  CD    110.39  3.000
 RIM  CF1   CE1  CD    111.08  3.000
 RIM  HE22  CE2  HE21  106.58  3.000
 RIM  HE22  CE2  CF2   109.91  3.000
 RIM  HE21  CE2  CF2   109.88  3.000
 RIM  HE22  CE2  CD    109.62  3.000
 RIM  HE21  CE2  CD    109.54  3.000
 RIM  CF2   CE2  CD    111.19  3.000
 RIM  HE32  CE3  HE31  107.12  3.000
 RIM  HE32  CE3  CF3   109.30  3.000
 RIM  HE31  CE3  CF3   108.83  3.000
 RIM  HE32  CE3  CD    110.44  3.000
 RIM  HE31  CE3  CD    110.43  3.000
 RIM  CF3   CE3  CD    110.64  3.000
 RIM  HF1   CF1  CG3   109.59  3.000
 RIM  HF1   CF1  CG1   109.70  3.000
 RIM  CG3   CF1  CG1   109.61  3.000
 RIM  HF1   CF1  CE1   109.09  3.000
 RIM  CG3   CF1  CE1   108.83  3.000
 RIM  CG1   CF1  CE1   110.02  3.000
 RIM  HF2   CF2  CG2   109.57  3.000
 RIM  HF2   CF2  CG1   109.69  3.000
 RIM  CG2   CF2  CG1   109.55  3.000
 RIM  HF2   CF2  CE2   109.19  3.000
 RIM  CG2   CF2  CE2   109.20  3.000
 RIM  CG1   CF2  CE2   109.63  3.000
 RIM  HF3   CF3  CG3   109.62  3.000
 RIM  HF3   CF3  CG2   109.64  3.000
 RIM  CG3   CF3  CG2   109.51  3.000
 RIM  HF3   CF3  CE3   109.02  3.000
 RIM  CG3   CF3  CE3   109.60  3.000
 RIM  CG2   CF3  CE3   109.43  3.000
 RIM  HG12  CG1  HG11  106.79  3.000
 RIM  HG12  CG1  CF2   110.20  3.000
 RIM  HG11  CG1  CF2   110.34  3.000
 RIM  HG12  CG1  CF1   110.18  3.000
 RIM  HG11  CG1  CF1   110.18  3.000
 RIM  CF2   CG1  CF1   109.14  3.000
 RIM  HG22  CG2  HG21  106.74  3.000
 RIM  HG22  CG2  CF3   109.99  3.000
 RIM  HG21  CG2  CF3   110.37  3.000
 RIM  HG22  CG2  CF2   110.00  3.000
 RIM  HG21  CG2  CF2   110.32  3.000
 RIM  CF3   CG2  CF2   109.38  3.000
 RIM  HG32  CG3  HG31  106.74  3.000
 RIM  HG32  CG3  CF3   110.37  3.000
 RIM  HG31  CG3  CF3   110.04  3.000
 RIM  HG32  CG3  CF1   110.34  3.000
 RIM  HG31  CG3  CF1   109.92  3.000
 RIM  CF3   CG3  CF1   109.39  3.000

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
 RIM  chir_01  CB   CA   CD   NC   positiv
 RIM  chir_02  CD   CE2  CE1  CE3  negativ
 RIM  chir_03  CF1  CE1  CG1  CG3  negativ
 RIM  chir_04  CF2  CG2  CG1  CE2  negativ
 RIM  chir_05  CF3  CE3  CG2  CG3  positiv

