# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Nov  9 16:17:59 2022
#   Inital geometry file: a 51 line input string
#   Ligand name: (2R)-3,3-dimethylbutan-2-amine
#   Quantum optimisation: True
#   Basis set: def2-TZVP
#   Method: D3BJ
#   Random seed: 3628800
#   SMILES string: C[C@@H](N)C(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
 00D  00D  "(2R)-3,3-dimethylbutan-2-amine"  ligand  22  7  .  2022-11-14  2022-11-14
;
Directly from eLBOW using geometry from QM method B3-LYP-D3BJ, basis set def2-TZVP with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_00D
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
 00D  N     N  NH2   0  -0.579  15.7404  37.5414  25.0734
 00D  CA    C  CH1   0   0.092  16.2021  38.3675  26.2056
 00D  CB1   C  CT    0   0.211  17.4261  39.2336  25.7914
 00D  CB2   C  CH3   0  -0.407  15.0519  39.1614  26.8356
 00D  CD1   C  CH3   0  -0.379  18.5865  38.3102  25.3938
 00D  CD2   C  CH3   0  -0.445  17.0882  40.1540  24.6096
 00D  CD3   C  CH3   0  -0.412  17.8843  40.0922  26.9797
 00D  HN    H  HNH2  0   0.229  15.0447  36.8835  25.4105
 00D  HNA   H  HNH2  0   0.227  15.2538  38.1292  24.4026
 00D  HA    H  HCH1  0   0.077  16.5706  37.6652  26.9610
 00D  HB2   H  HCH3  0   0.118  15.3524  39.6738  27.7502
 00D  HB2A  H  HCH3  0   0.114  14.6578  39.9065  26.1400
 00D  HB2B  H  HCH3  0   0.114  14.2375  38.4789  27.0884
 00D  HD1   H  HCH3  0   0.114  19.4618  38.9012  25.1137
 00D  HD1A  H  HCH3  0   0.108  18.8696  37.6631  26.2286
 00D  HD1B  H  HCH3  0   0.103  18.3166  37.6755  24.5505
 00D  HD2   H  HCH3  0   0.118  17.9571  40.7643  24.3527
 00D  HD2A  H  HCH3  0   0.119  16.8135  39.5825  23.7210
 00D  HD2B  H  HCH3  0   0.121  16.2665  40.8313  24.8496
 00D  HD3   H  HCH3  0   0.117  18.8275  40.5880  26.7393
 00D  HD3A  H  HCH3  0   0.124  17.1572  40.8657  27.2281
 00D  HD3B  H  HCH3  0   0.117  18.0444  39.4774  27.8694

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
 00D  N    CA    single  1.476  0.020  1.476
 00D  N    HN    single  0.890  0.020  1.040
 00D  N    HNA   single  0.890  0.020  1.040
 00D  CB1  CA    single  1.556  0.020  1.556
 00D  CA   CB2   single  1.533  0.020  1.533
 00D  CA   HA    single  0.970  0.020  1.090
 00D  CD2  CB1   single  1.536  0.020  1.536
 00D  CD1  CB1   single  1.535  0.020  1.535
 00D  CB1  CD3   single  1.536  0.020  1.536
 00D  CB2  HB2   single  0.970  0.020  1.090
 00D  CB2  HB2A  single  0.970  0.020  1.090
 00D  CB2  HB2B  single  0.970  0.020  1.090
 00D  CD1  HD1   single  0.970  0.020  1.090
 00D  CD1  HD1A  single  0.970  0.020  1.090
 00D  CD1  HD1B  single  0.970  0.020  1.090
 00D  CD2  HD2   single  0.970  0.020  1.090
 00D  CD2  HD2A  single  0.970  0.020  1.090
 00D  CD2  HD2B  single  0.970  0.020  1.090
 00D  CD3  HD3   single  0.970  0.020  1.090
 00D  CD3  HD3A  single  0.970  0.020  1.090
 00D  CD3  HD3B  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
 00D  HNA   N    HN    105.42  3.000
 00D  HNA   N    CA    109.42  3.000
 00D  HN    N    CA    108.81  3.000
 00D  HA    CA   CB2   107.52  3.000
 00D  HA    CA   CB1   106.01  3.000
 00D  CB2   CA   CB1   114.30  3.000
 00D  HA    CA   N     105.99  3.000
 00D  CB2   CA   N     111.75  3.000
 00D  CB1   CA   N     110.71  3.000
 00D  CD3   CB1  CD2   109.02  3.000
 00D  CD3   CB1  CD1   108.13  3.000
 00D  CD2   CB1  CD1   109.12  3.000
 00D  CD3   CB1  CA    109.87  3.000
 00D  CD1   CB1  CA    109.20  3.000
 00D  CD2   CB1  CA    111.43  3.000
 00D  HB2B  CB2  HB2A  107.73  3.000
 00D  HB2B  CB2  HB2   107.76  3.000
 00D  HB2A  CB2  HB2   108.23  3.000
 00D  HB2B  CB2  CA    109.32  3.000
 00D  HB2A  CB2  CA    111.22  3.000
 00D  HB2   CB2  CA    112.41  3.000
 00D  HD1B  CD1  HD1A  108.08  3.000
 00D  HD1B  CD1  HD1   108.38  3.000
 00D  HD1A  CD1  HD1   107.96  3.000
 00D  HD1B  CD1  CB1   111.32  3.000
 00D  HD1A  CD1  CB1   110.72  3.000
 00D  HD1   CD1  CB1   110.27  3.000
 00D  HD2B  CD2  HD2A  108.32  3.000
 00D  HD2B  CD2  HD2   107.69  3.000
 00D  HD2A  CD2  HD2   107.53  3.000
 00D  HD2B  CD2  CB1   111.62  3.000
 00D  HD2A  CD2  CB1   111.59  3.000
 00D  HD2   CD2  CB1   109.93  3.000
 00D  HD3B  CD3  HD3A  108.14  3.000
 00D  HD3B  CD3  HD3   107.93  3.000
 00D  HD3A  CD3  HD3   107.70  3.000
 00D  HD3B  CD3  CB1   111.03  3.000
 00D  HD3A  CD3  CB1   111.96  3.000
 00D  HD3   CD3  CB1   109.93  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
 00D  Var_01  HD2   CD2  CB1  CA    178.86  30.0  3
 00D  Var_02  HD2A  CD2  CB1  CA    -61.93  30.0  3
 00D  Var_03  HD2B  CD2  CB1  CA     59.44  30.0  3
 00D  Var_04  HD1   CD1  CB1  CA   -179.14  30.0  3
 00D  Var_05  HD1A  CD1  CB1  CA    -59.72  30.0  3
 00D  Var_06  HD1B  CD1  CB1  CA     60.53  30.0  3
 00D  Var_07  HD3   CD3  CB1  CA    171.68  30.0  3
 00D  Var_08  HD3A  CD3  CB1  CA    -68.65  30.0  3
 00D  Var_09  HD3B  CD3  CB1  CA     52.32  30.0  3
 00D  Var_10  HD2   CD2  CB1  CD1   -60.48  30.0  3
 00D  Var_11  HD2A  CD2  CB1  CD1    58.73  30.0  3
 00D  Var_12  HD2B  CD2  CB1  CD1  -179.90  30.0  3
 00D  Var_13  HD3   CD3  CB1  CD1    52.59  30.0  3
 00D  Var_14  HD3A  CD3  CB1  CD1   172.26  30.0  3
 00D  Var_15  HD3B  CD3  CB1  CD1   -66.77  30.0  3
 00D  Var_16  HD1   CD1  CB1  CD2    58.84  30.0  3
 00D  Var_17  HD1A  CD1  CB1  CD2   178.26  30.0  3
 00D  Var_18  HD1B  CD1  CB1  CD2   -61.49  30.0  3
 00D  Var_19  HD3   CD3  CB1  CD2   -65.93  30.0  3
 00D  Var_20  HD3A  CD3  CB1  CD2    53.74  30.0  3
 00D  Var_21  HD3B  CD3  CB1  CD2   174.71  30.0  3
 00D  Var_22  HD2   CD2  CB1  CD3    57.42  30.0  3
 00D  Var_23  HD2A  CD2  CB1  CD3   176.62  30.0  3
 00D  Var_24  HD2B  CD2  CB1  CD3   -62.01  30.0  3
 00D  Var_25  HD1   CD1  CB1  CD3   -59.62  30.0  3
 00D  Var_26  HD1A  CD1  CB1  CD3    59.80  30.0  3
 00D  Var_27  HD1B  CD1  CB1  CD3  -179.95  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
 00D  chir_01  CA  N  CB1  CB2  negativ

