# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 06:49:48 2022
#   Inital geometry file: a 84 line input string
#   Ligand name: ~{N}-[(2~{S})-2-azanyl-3-naphthalen-1-yl-propyl]methanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CNC=O)Cc1cccc2ccccc12
#
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
 QQB  QQB  ~{N}-[(2~{S})-2-azanyl-3-naphthalen-1-yl-propyl]methanamide  L-peptide  33  17  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QQB
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
 QQB  CB   C  CH2   0  -0.562  -0.9809  -19.4958  -12.4791
 QQB  OCA  O  O     0  -0.487   1.3268  -18.1545   -8.7157
 QQB  CAO  C  C1    0   0.246   2.1391  -17.7820   -9.5450
 QQB  CM   C  CH2   0  -0.292   1.2353  -19.1068  -11.4038
 QQB  CAA  C  CH1   0  -0.098  -0.0689  -18.4335  -11.8536
 QQB  NA   N  NH2   0  -0.777   0.1172  -17.3295  -12.7755
 QQB  CG1  C  CR6   0   0.163  -2.3682  -19.0059  -12.7795
 QQB  CD2  C  CR66  0   0.084  -3.3398  -18.8501  -11.7461
 QQB  CG2  C  CR16  0  -0.341  -3.0751  -19.1741  -10.3917
 QQB  CD3  C  CR16  0  -0.250  -4.0283  -19.0104   -9.4227
 QQB  CE3  C  CR16  0  -0.260  -5.3051  -18.5141   -9.7524
 QQB  CZ2  C  CR16  0  -0.310  -5.5971  -18.1965  -11.0498
 QQB  CE2  C  CR66  0   0.116  -4.6325  -18.3546  -12.0732
 QQB  CZ1  C  CR16  0  -0.337  -4.9377  -18.0312  -13.4155
 QQB  CE1  C  CR16  0  -0.241  -3.9977  -18.1969  -14.3926
 QQB  CD1  C  CR16  0  -0.345  -2.7160  -18.6818  -14.0669
 QQB  H1   H  HCH2  0   0.251  -1.0140  -20.3688  -11.8213
 QQB  H2   H  HCH2  0   0.257  -0.5160  -19.8405  -13.4078
 QQB  H3   H  H     0   0.200   2.9409  -17.0652   -9.3089
 QQB  H4   H  HNH1  0   0.405   2.8915  -17.7819  -11.4126
 QQB  H5   H  HCH2  0   0.243   1.0198  -19.8993  -10.6843
 QQB  H6   H  HCH2  0   0.249   1.7186  -19.5766  -12.2633
 QQB  H7   H  HCH1  0   0.240  -0.5581  -18.0292  -10.9621
 QQB  H8   H  HNH2  0   0.345   0.6795  -16.6087  -12.3403
 QQB  H9   H  HNH2  0   0.334   0.6371  -17.6419  -13.5887
 QQB  H11  H  HCR6  0   0.251  -2.1052  -19.5614  -10.1089
 QQB  H12  H  HCR6  0   0.255  -3.8012  -19.2653   -8.3956
 QQB  H13  H  HCR6  0   0.254  -6.0510  -18.3882   -8.9784
 QQB  H14  H  HCR6  0   0.252  -6.5777  -17.8182  -11.3139
 QQB  H15  H  HCR6  0   0.250  -5.9254  -17.6558  -13.6552
 QQB  H16  H  HCR6  0   0.252  -4.2305  -17.9545  -15.4215
 QQB  H17  H  HCR6  0   0.245  -1.9853  -18.8048  -14.8572
 QQB  NM   N  NH1   0  -0.590   2.1824  -18.1831  -10.8208

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
 QQB  CE1  CD1  aromatic  1.409  0.020  1.409
 QQB  CE1  CZ1  aromatic  1.366  0.020  1.366
 QQB  CD1  CG1  aromatic  1.372  0.020  1.372
 QQB  CZ1  CE2  aromatic  1.414  0.020  1.414
 QQB  NA   CAA  single    1.450  0.020  1.450
 QQB  CG1  CB   single    1.502  0.020  1.502
 QQB  CG1  CD2  aromatic  1.427  0.020  1.427
 QQB  CB   CAA  single    1.533  0.020  1.533
 QQB  CE2  CD2  aromatic  1.423  0.020  1.423
 QQB  CE2  CZ2  aromatic  1.415  0.020  1.415
 QQB  CAA  CM   single    1.535  0.020  1.535
 QQB  CD2  CG2  aromatic  1.418  0.020  1.418
 QQB  CM   NM   single    1.446  0.020  1.446
 QQB  CZ2  CE3  aromatic  1.367  0.020  1.367
 QQB  NM   CAO  single    1.338  0.020  1.338
 QQB  CG2  CD3  aromatic  1.369  0.020  1.369
 QQB  CE3  CD3  aromatic  1.409  0.020  1.409
 QQB  CAO  OCA  double    1.219  0.020  1.219
 QQB  CB   H1   single    0.970  0.020  1.090
 QQB  CB   H2   single    0.970  0.020  1.090
 QQB  CAO  H3   single    0.930  0.020  1.080
 QQB  NM   H4   single    0.860  0.020  1.020
 QQB  CM   H5   single    0.970  0.020  1.090
 QQB  CM   H6   single    0.970  0.020  1.090
 QQB  CAA  H7   single    0.970  0.020  1.090
 QQB  NA   H8   single    0.890  0.020  1.040
 QQB  NA   H9   single    0.890  0.020  1.040
 QQB  CG2  H11  single    0.930  0.020  1.080
 QQB  CD3  H12  single    0.930  0.020  1.080
 QQB  CE3  H13  single    0.930  0.020  1.080
 QQB  CZ2  H14  single    0.930  0.020  1.080
 QQB  CZ1  H15  single    0.930  0.020  1.080
 QQB  CE1  H16  single    0.930  0.020  1.080
 QQB  CD1  H17  single    0.930  0.020  1.080

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
 QQB  H2   CB   H1   105.78  3.000
 QQB  H2   CB   CG1  108.99  3.000
 QQB  H1   CB   CG1  110.66  3.000
 QQB  H2   CB   CAA  108.16  3.000
 QQB  H1   CB   CAA  109.01  3.000
 QQB  CG1  CB   CAA  113.89  3.000
 QQB  H3   CAO  NM   112.09  3.000
 QQB  H3   CAO  OCA  122.56  3.000
 QQB  NM   CAO  OCA  125.34  3.000
 QQB  H6   CM   H5   107.09  3.000
 QQB  H6   CM   CAA  109.51  3.000
 QQB  H5   CM   CAA  110.10  3.000
 QQB  H6   CM   NM   107.60  3.000
 QQB  H5   CM   NM   109.11  3.000
 QQB  CAA  CM   NM   113.23  3.000
 QQB  H7   CAA  NA   107.10  3.000
 QQB  H7   CAA  CM   107.64  3.000
 QQB  NA   CAA  CM   114.27  3.000
 QQB  H7   CAA  CB   108.81  3.000
 QQB  CM   CAA  CB   108.72  3.000
 QQB  NA   CAA  CB   110.14  3.000
 QQB  H9   NA   H8   106.21  3.000
 QQB  H9   NA   CAA  109.93  3.000
 QQB  H8   NA   CAA  109.87  3.000
 QQB  CD1  CG1  CD2  118.75  3.000
 QQB  CD2  CG1  CB   121.32  3.000
 QQB  CD1  CG1  CB   119.93  3.000
 QQB  CE2  CD2  CG2  117.97  3.000
 QQB  CG2  CD2  CG1  122.67  3.000
 QQB  CE2  CD2  CG1  119.36  3.000
 QQB  H11  CG2  CD3  118.81  3.000
 QQB  H11  CG2  CD2  119.93  3.000
 QQB  CD3  CG2  CD2  121.26  3.000
 QQB  H12  CD3  CE3  119.68  3.000
 QQB  H12  CD3  CG2  119.83  3.000
 QQB  CE3  CD3  CG2  120.49  3.000
 QQB  H13  CE3  CZ2  120.29  3.000
 QQB  H13  CE3  CD3  119.88  3.000
 QQB  CZ2  CE3  CD3  119.83  3.000
 QQB  H14  CZ2  CE2  118.65  3.000
 QQB  H14  CZ2  CE3  120.37  3.000
 QQB  CE2  CZ2  CE3  120.98  3.000
 QQB  CZ1  CE2  CZ2  120.92  3.000
 QQB  CZ2  CE2  CD2  119.47  3.000
 QQB  CZ1  CE2  CD2  119.61  3.000
 QQB  H15  CZ1  CE1  120.74  3.000
 QQB  H15  CZ1  CE2  119.08  3.000
 QQB  CE1  CZ1  CE2  120.19  3.000
 QQB  H16  CE1  CD1  119.51  3.000
 QQB  H16  CE1  CZ1  120.32  3.000
 QQB  CD1  CE1  CZ1  120.17  3.000
 QQB  H17  CD1  CE1  118.95  3.000
 QQB  H17  CD1  CG1  119.11  3.000
 QQB  CE1  CD1  CG1  121.93  3.000
 QQB  H4   NM   CM   118.61  3.000
 QQB  H4   NM   CAO  117.63  3.000
 QQB  CM   NM   CAO  123.70  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
 QQB  CONST_01  CZ1  CE1  CD1  CG1    0.00   0.0  0
 QQB  CONST_02  CZ1  CE2  CD2  CG1    0.00   0.0  0
 QQB  CONST_03  CZ2  CE2  CD2  CG1  180.00   0.0  0
 QQB  CONST_04  CD3  CG2  CD2  CG1  180.00   0.0  0
 QQB  CONST_05  CE1  CD1  CG1  CD2    0.00   0.0  0
 QQB  CONST_06  CE1  CZ1  CE2  CD2    0.00   0.0  0
 QQB  CONST_07  CE3  CZ2  CE2  CD2    0.00   0.0  0
 QQB  CONST_08  CE3  CD3  CG2  CD2    0.00   0.0  0
 QQB  CONST_09  CD1  CG1  CD2  CG2  180.00   0.0  0
 QQB  CONST_10  CZ1  CE2  CD2  CG2  180.00   0.0  0
 QQB  CONST_11  CZ2  CE2  CD2  CG2    0.00   0.0  0
 QQB  CONST_12  CZ2  CE3  CD3  CG2    0.00   0.0  0
 QQB  CONST_13  CE2  CD2  CG2  CD3    0.00   0.0  0
 QQB  CONST_14  CE2  CZ2  CE3  CD3    0.00   0.0  0
 QQB  CONST_15  CZ1  CE2  CZ2  CE3  180.00   0.0  0
 QQB  CONST_16  CE1  CZ1  CE2  CZ2  180.00   0.0  0
 QQB  CONST_17  CD1  CE1  CZ1  CE2    0.00   0.0  0
 QQB  CONST_18  CD1  CG1  CD2  CE2    0.00   0.0  0
 QQB  CONST_19  CE1  CD1  CG1  CB   180.00   0.0  0
 QQB  CONST_20  CE2  CD2  CG1  CB   180.00   0.0  0
 QQB  CONST_21  CG2  CD2  CG1  CB     0.00   0.0  0
 QQB  CONST_22  H16  CE1  CD1  CG1  180.00   0.0  0
 QQB  CONST_23  H11  CG2  CD2  CG1    0.00   0.0  0
 QQB  CONST_24  H17  CD1  CG1  CD2  180.00   0.0  0
 QQB  CONST_25  H15  CZ1  CE2  CD2  180.00   0.0  0
 QQB  CONST_26  H14  CZ2  CE2  CD2  180.00   0.0  0
 QQB  CONST_27  H12  CD3  CG2  CD2  180.00   0.0  0
 QQB  CONST_28  H13  CE3  CD3  CG2  180.00   0.0  0
 QQB  CONST_29  CM   NM   CAO  OCA    0.00   0.0  0
 QQB  CONST_30  H4   NM   CAO  OCA  180.00   0.0  0
 QQB  Var_01    CD1  CG1  CB   CAA  102.22  30.0  2
 QQB  Var_02    CAA  CM   NM   CAO   82.60  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
 QQB  chir_01  CAA  NA  CB  CM  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
 QQB  plan-1  CB   0.020
 QQB  plan-1  CG1  0.020
 QQB  plan-1  CD2  0.020
 QQB  plan-1  CG2  0.020
 QQB  plan-1  CD3  0.020
 QQB  plan-1  CE3  0.020
 QQB  plan-1  CZ2  0.020
 QQB  plan-1  CE2  0.020
 QQB  plan-1  CZ1  0.020
 QQB  plan-1  CE1  0.020
 QQB  plan-1  CD1  0.020
 QQB  plan-1  H11  0.020
 QQB  plan-1  H12  0.020
 QQB  plan-1  H13  0.020
 QQB  plan-1  H14  0.020
 QQB  plan-1  H15  0.020
 QQB  plan-1  H16  0.020
 QQB  plan-1  H17  0.020
 QQB  plan-2  OCA  0.020
 QQB  plan-2  CAO  0.020
 QQB  plan-2  CM   0.020
 QQB  plan-2  H3   0.020
 QQB  plan-2  H4   0.020
 QQB  plan-2  NM   0.020

