# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 10:39:23 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: (4R)-3,4-dihydro-2H-chromen-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1CCOc2ccccc12
#
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
 1XY  1XY  (4R)-3,4-dihydro-2H-chromen-4-amine  ligand  22  11  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1XY
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
 1XY  N34  N  NH2   0  -0.797  -1.5889   2.1828   0.3963
 1XY  C35  C  CH1   0  -0.121  -1.3413   0.9303  -0.3037
 1XY  C37  C  CH2   0  -0.504  -2.2462  -0.1569   0.2565
 1XY  C38  C  CH2   0  -0.190  -1.8450  -1.4976  -0.3113
 1XY  O39  O  O2    0  -0.481  -0.5117  -1.8427   0.0423
 1XY  C40  C  CR6   0   0.366   0.4175  -0.8629   0.0052
 1XY  C41  C  CR16  0  -0.355   1.7433  -1.2699   0.1557
 1XY  C42  C  CR16  0  -0.258   2.7651  -0.3372   0.1401
 1XY  C43  C  CR16  0  -0.269   2.4725   1.0106  -0.0278
 1XY  C44  C  CR16  0  -0.310   1.1514   1.4062  -0.1676
 1XY  C45  C  CR6   0   0.012   0.1012   0.4906  -0.1540
 1XY  H36  H  HNH2  0   0.352  -1.1247   2.9456  -0.0805
 1XY  H37  H  HCH1  0   0.227  -1.5528   1.0124  -1.3815
 1XY  H38  H  HCH2  0   0.242  -2.1731  -0.1695   1.3479
 1XY  H39  H  HCH2  0   0.255  -3.2891   0.0423   0.0002
 1XY  H40  H  HCH2  0   0.250  -2.4750  -2.2981   0.0743
 1XY  H41  H  HCH2  0   0.224  -1.9411  -1.4919  -1.4032
 1XY  H42  H  HCR6  0   0.258   1.9602  -2.3230   0.2872
 1XY  H43  H  HCR6  0   0.254   3.7903  -0.6651   0.2566
 1XY  H44  H  HCR6  0   0.250   3.2640   1.7476  -0.0446
 1XY  H45  H  HCR6  0   0.244   0.9402   2.4608  -0.2945
 1XY  H2   H  HNH2  0   0.351  -2.5769   2.3964   0.3229

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
 1XY  C38  C37  single    1.510  0.020  1.510
 1XY  C38  O39  single    1.422  0.020  1.422
 1XY  C37  C35  single    1.521  0.020  1.521
 1XY  O39  C40  single    1.351  0.020  1.351
 1XY  N34  C35  single    1.456  0.020  1.456
 1XY  C35  C45  single    1.515  0.020  1.515
 1XY  C40  C45  aromatic  1.399  0.020  1.399
 1XY  C40  C41  aromatic  1.395  0.020  1.395
 1XY  C45  C44  aromatic  1.393  0.020  1.393
 1XY  C41  C42  aromatic  1.384  0.020  1.384
 1XY  C44  C43  aromatic  1.386  0.020  1.386
 1XY  C42  C43  aromatic  1.389  0.020  1.389
 1XY  N34  H36  single    0.890  0.020  1.040
 1XY  C35  H37  single    0.970  0.020  1.090
 1XY  C37  H38  single    0.970  0.020  1.090
 1XY  C37  H39  single    0.970  0.020  1.090
 1XY  C38  H40  single    0.970  0.020  1.090
 1XY  C38  H41  single    0.970  0.020  1.090
 1XY  C41  H42  single    0.930  0.020  1.080
 1XY  C42  H43  single    0.930  0.020  1.080
 1XY  C43  H44  single    0.930  0.020  1.080
 1XY  C44  H45  single    0.930  0.020  1.080
 1XY  N34  H2   single    0.890  0.020  1.040

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
 1XY  H2   N34  H36  104.72  3.000
 1XY  H2   N34  C35  108.19  3.000
 1XY  H36  N34  C35  110.11  3.000
 1XY  H37  C35  C45  107.53  3.000
 1XY  H37  C35  C37  107.42  3.000
 1XY  C45  C35  C37  108.81  3.000
 1XY  H37  C35  N34  111.94  3.000
 1XY  C45  C35  N34  111.34  3.000
 1XY  C37  C35  N34  109.67  3.000
 1XY  H39  C37  H38  107.46  3.000
 1XY  H39  C37  C38  109.12  3.000
 1XY  H38  C37  C38  110.31  3.000
 1XY  H39  C37  C35  110.56  3.000
 1XY  H38  C37  C35  109.62  3.000
 1XY  C38  C37  C35  109.75  3.000
 1XY  H41  C38  H40  107.80  3.000
 1XY  H41  C38  O39  109.34  3.000
 1XY  H40  C38  O39  106.02  3.000
 1XY  H41  C38  C37  110.28  3.000
 1XY  H40  C38  C37  111.45  3.000
 1XY  O39  C38  C37  111.78  3.000
 1XY  C40  O39  C38  117.53  3.000
 1XY  C45  C40  C41  120.62  3.000
 1XY  C41  C40  O39  116.05  3.000
 1XY  C45  C40  O39  123.32  3.000
 1XY  H42  C41  C42  120.59  3.000
 1XY  H42  C41  C40  119.14  3.000
 1XY  C42  C41  C40  120.26  3.000
 1XY  H43  C42  C43  120.41  3.000
 1XY  H43  C42  C41  119.60  3.000
 1XY  C43  C42  C41  119.98  3.000
 1XY  H44  C43  C44  120.09  3.000
 1XY  H44  C43  C42  120.58  3.000
 1XY  C44  C43  C42  119.33  3.000
 1XY  H45  C44  C45  119.61  3.000
 1XY  H45  C44  C43  118.40  3.000
 1XY  C45  C44  C43  121.99  3.000
 1XY  C44  C45  C40  117.80  3.000
 1XY  C44  C45  C35  121.72  3.000
 1XY  C40  C45  C35  120.47  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
 1XY  CONST_01  C43  C44  C45  C40    0.00   0.0  0
 1XY  CONST_02  C43  C42  C41  C40    0.00   0.0  0
 1XY  CONST_03  C44  C45  C40  C41    0.00   0.0  0
 1XY  CONST_04  C44  C43  C42  C41    0.00   0.0  0
 1XY  CONST_05  C45  C40  C41  C42    0.00   0.0  0
 1XY  CONST_06  C45  C44  C43  C42    0.00   0.0  0
 1XY  CONST_07  H45  C44  C45  C35    0.00   0.0  0
 1XY  CONST_08  H42  C41  C40  O39    0.00   0.0  0
 1XY  CONST_09  H43  C42  C41  C40  180.00   0.0  0
 1XY  CONST_10  H44  C43  C42  C41  180.00   0.0  0
 1XY  Var_01    O39  C38  C37  C35   61.41  30.0  1
 1XY  Var_02    C45  C40  O39  C38   10.36  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
 1XY  chir_01  C35  C37  N34  C45  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
 1XY  plan-1  C35  0.020
 1XY  plan-1  O39  0.020
 1XY  plan-1  C40  0.020
 1XY  plan-1  C41  0.020
 1XY  plan-1  C42  0.020
 1XY  plan-1  C43  0.020
 1XY  plan-1  C44  0.020
 1XY  plan-1  C45  0.020
 1XY  plan-1  H42  0.020
 1XY  plan-1  H43  0.020
 1XY  plan-1  H44  0.020
 1XY  plan-1  H45  0.020

