# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 01:59:16 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: (6S)-6-phenyl-5,6-dihydrobenzo[h]quinazolin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncc2C[C@@H](c3ccccc3)c4ccccc4c2n1
#
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
 3RH  3RH  (6S)-6-phenyl-5,6-dihydrobenzo[h]quinazolin-2-amine  ligand  36  21  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_3RH
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
 3RH  C1    C  CR66  0   0.239  -1.3888   0.3209   0.2460
 3RH  C2    C  CR66  0  -0.025  -0.9642  -0.5614   1.2398
 3RH  N3    N  N     0  -0.481  -2.5043   0.1273  -0.4443
 3RH  C4    C  CR6   0   0.530  -3.2193  -0.9606  -0.1558
 3RH  N5    N  NH2   0  -0.827  -4.3409  -1.1759  -0.8808
 3RH  N6    N  N     0  -0.454  -2.8981  -1.8765   0.7632
 3RH  C7    C  CR16  0  -0.064  -1.7819  -1.6594   1.4405
 3RH  C8    C  C     0  -0.483   0.2756  -0.2711   2.0233
 3RH  C9    C  CR16  0  -0.441   1.3451   0.3661   1.1279
 3RH  C10   C  CR6   0   0.172   1.9648  -0.6635   0.2015
 3RH  C11   C  CR66  0   0.126   0.7553   1.5447   0.3930
 3RH  C12   C  CR66  0   0.030  -0.5738   1.5098  -0.0472
 3RH  C13   C  CR16  0  -0.300   2.9101  -1.5438   0.7285
 3RH  C14   C  CR16  0  -0.243   3.4846  -2.5332  -0.0549
 3RH  C15   C  CR16  0  -0.273   3.1220  -2.6610  -1.3905
 3RH  C16   C  CR16  0  -0.238   2.1872  -1.7885  -1.9275
 3RH  C17   C  CR16  0  -0.309   1.6152  -0.7964  -1.1387
 3RH  C18   C  CR16  0  -0.307   1.5333   2.6588   0.1034
 3RH  C19   C  CR16  0  -0.244   1.0061   3.7298  -0.6032
 3RH  C20   C  CR16  0  -0.255  -0.3136   3.6931  -1.0381
 3RH  C21   C  CR16  0  -0.288  -1.0973   2.5851  -0.7644
 3RH  HN5   H  HNH2  0   0.391  -4.7129  -0.4078  -1.4123
 3RH  HN5A  H  HNH2  0   0.392  -5.0110  -1.8370  -0.5275
 3RH  H7    H  HCR6  0   0.264  -1.5207  -2.4032   2.1883
 3RH  H8    H  H     0   0.263   0.0452   0.4243   2.8375
 3RH  H8A   H  H     0   0.259   0.6599  -1.1802   2.4901
 3RH  H9    H  HCR6  0   0.276   2.1425   0.7409   1.7750
 3RH  H13   H  HCR6  0   0.251   3.2040  -1.4504   1.7681
 3RH  H14   H  HCR6  0   0.254   4.2193  -3.2014   0.3762
 3RH  H15   H  HCR6  0   0.254   3.5700  -3.4293  -2.0072
 3RH  H16   H  HCR6  0   0.254   1.9000  -1.8744  -2.9677
 3RH  H17   H  HCR6  0   0.250   0.8987  -0.1208  -1.5885
 3RH  H18   H  HCR6  0   0.255   2.5639   2.6879   0.4369
 3RH  H19   H  HCR6  0   0.261   1.6245   4.5928  -0.8140
 3RH  H20   H  HCR6  0   0.259  -0.7294   4.5277  -1.5870
 3RH  H21   H  HCR6  0   0.253  -2.1249   2.5477  -1.1009

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
 3RH  C12  C1    aromatic  1.471  0.020  1.471
 3RH  C2   C1    aromatic  1.395  0.020  1.395
 3RH  C1   N3    aromatic  1.326  0.020  1.326
 3RH  C8   C2    single    1.495  0.020  1.495
 3RH  C2   C7    aromatic  1.384  0.020  1.384
 3RH  N3   C4    aromatic  1.333  0.020  1.333
 3RH  N6   C4    aromatic  1.337  0.020  1.337
 3RH  C4   N5    single    1.353  0.020  1.353
 3RH  N5   HN5   single    0.890  0.020  1.040
 3RH  N5   HN5A  single    0.890  0.020  1.040
 3RH  C7   N6    aromatic  1.324  0.020  1.324
 3RH  C7   H7    single    0.930  0.020  1.080
 3RH  C9   C8    single    1.533  0.020  1.533
 3RH  C8   H8    single    0.970  0.020  1.090
 3RH  C8   H8A   single    0.970  0.020  1.090
 3RH  C10  C9    single    1.517  0.020  1.517
 3RH  C9   C11   single    1.509  0.020  1.509
 3RH  C9   H9    single    0.970  0.020  1.090
 3RH  C17  C10   aromatic  1.391  0.020  1.391
 3RH  C13  C10   aromatic  1.395  0.020  1.395
 3RH  C18  C11   aromatic  1.389  0.020  1.389
 3RH  C11  C12   aromatic  1.401  0.020  1.401
 3RH  C12  C21   aromatic  1.395  0.020  1.395
 3RH  C14  C13   aromatic  1.387  0.020  1.387
 3RH  C13  H13   single    0.930  0.020  1.080
 3RH  C15  C14   aromatic  1.390  0.020  1.390
 3RH  C14  H14   single    0.930  0.020  1.080
 3RH  C15  C16   aromatic  1.387  0.020  1.387
 3RH  C15  H15   single    0.930  0.020  1.080
 3RH  C16  C17   aromatic  1.390  0.020  1.390
 3RH  C16  H16   single    0.930  0.020  1.080
 3RH  C17  H17   single    0.930  0.020  1.080
 3RH  C18  C19   aromatic  1.387  0.020  1.387
 3RH  C18  H18   single    0.930  0.020  1.080
 3RH  C19  C20   aromatic  1.390  0.020  1.390
 3RH  C19  H19   single    0.930  0.020  1.080
 3RH  C20  C21   aromatic  1.384  0.020  1.384
 3RH  C20  H20   single    0.930  0.020  1.080
 3RH  C21  H21   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
 3RH  C12   C1   N3   118.71  3.000
 3RH  N3    C1   C2   122.31  3.000
 3RH  C12   C1   C2   118.98  3.000
 3RH  C8    C2   C7   124.62  3.000
 3RH  C7    C2   C1   115.17  3.000
 3RH  C8    C2   C1   120.19  3.000
 3RH  C4    N3   C1   117.23  3.000
 3RH  N6    C4   N5   117.31  3.000
 3RH  N5    C4   N3   117.29  3.000
 3RH  N6    C4   N3   125.37  3.000
 3RH  HN5A  N5   HN5  116.20  3.000
 3RH  HN5A  N5   C4   117.96  3.000
 3RH  HN5   N5   C4   117.94  3.000
 3RH  C7    N6   C4   116.24  3.000
 3RH  H7    C7   N6   116.27  3.000
 3RH  H7    C7   C2   120.06  3.000
 3RH  N6    C7   C2   123.67  3.000
 3RH  H8A   C8   H8   106.55  3.000
 3RH  H8A   C8   C9   110.50  3.000
 3RH  H8    C8   C9   108.48  3.000
 3RH  H8A   C8   C2   110.75  3.000
 3RH  H8    C8   C2   109.78  3.000
 3RH  C9    C8   C2   110.67  3.000
 3RH  H9    C9   C11  107.79  3.000
 3RH  H9    C9   C10  107.23  3.000
 3RH  C11   C9   C10  113.09  3.000
 3RH  H9    C9   C8   107.79  3.000
 3RH  C11   C9   C8   109.66  3.000
 3RH  C10   C9   C8   111.06  3.000
 3RH  C17   C10  C13  118.28  3.000
 3RH  C13   C10  C9   118.31  3.000
 3RH  C17   C10  C9   123.39  3.000
 3RH  C18   C11  C12  119.07  3.000
 3RH  C12   C11  C9   120.29  3.000
 3RH  C18   C11  C9   120.59  3.000
 3RH  C21   C12  C11  119.91  3.000
 3RH  C21   C12  C1   121.18  3.000
 3RH  C11   C12  C1   118.91  3.000
 3RH  H13   C13  C14  119.39  3.000
 3RH  H13   C13  C10  119.44  3.000
 3RH  C14   C13  C10  121.17  3.000
 3RH  H14   C14  C15  120.20  3.000
 3RH  H14   C14  C13  119.77  3.000
 3RH  C15   C14  C13  120.03  3.000
 3RH  H15   C15  C16  120.33  3.000
 3RH  H15   C15  C14  120.32  3.000
 3RH  C16   C15  C14  119.35  3.000
 3RH  H16   C16  C17  119.51  3.000
 3RH  H16   C16  C15  120.06  3.000
 3RH  C17   C16  C15  120.43  3.000
 3RH  H17   C17  C16  118.80  3.000
 3RH  H17   C17  C10  120.45  3.000
 3RH  C16   C17  C10  120.74  3.000
 3RH  H18   C18  C19  119.83  3.000
 3RH  H18   C18  C11  119.34  3.000
 3RH  C19   C18  C11  120.83  3.000
 3RH  H19   C19  C20  120.17  3.000
 3RH  H19   C19  C18  119.85  3.000
 3RH  C20   C19  C18  119.99  3.000
 3RH  H20   C20  C21  120.01  3.000
 3RH  H20   C20  C19  120.21  3.000
 3RH  C21   C20  C19  119.78  3.000
 3RH  H21   C21  C20  120.25  3.000
 3RH  H21   C21  C12  119.33  3.000
 3RH  C20   C21  C12  120.42  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
 3RH  CONST_01  C18  C11  C12  C1   180.00   0.0  0
 3RH  CONST_02  C20  C21  C12  C1   180.00   0.0  0
 3RH  CONST_03  N6   C7   C2   C1     0.00   0.0  0
 3RH  CONST_04  N6   C4   N3   C1     0.00   0.0  0
 3RH  CONST_07  C4   N3   C1   C2     0.00   0.0  0
 3RH  CONST_08  C4   N6   C7   C2     0.00   0.0  0
 3RH  CONST_11  C7   C2   C1   N3     0.00   0.0  0
 3RH  CONST_12  C7   N6   C4   N3     0.00   0.0  0
 3RH  CONST_13  C12  C1   N3   C4   180.00   0.0  0
 3RH  CONST_14  C12  C1   C2   C7   180.00   0.0  0
 3RH  CONST_15  C15  C16  C17  C10    0.00   0.0  0
 3RH  CONST_16  C15  C14  C13  C10    0.00   0.0  0
 3RH  CONST_17  C20  C19  C18  C11    0.00   0.0  0
 3RH  CONST_18  C20  C21  C12  C11    0.00   0.0  0
 3RH  CONST_19  C19  C18  C11  C12    0.00   0.0  0
 3RH  CONST_20  C19  C20  C21  C12    0.00   0.0  0
 3RH  CONST_21  C16  C17  C10  C13    0.00   0.0  0
 3RH  CONST_22  C16  C15  C14  C13    0.00   0.0  0
 3RH  CONST_23  C17  C10  C13  C14    0.00   0.0  0
 3RH  CONST_24  C17  C16  C15  C14    0.00   0.0  0
 3RH  CONST_25  C21  C12  C11  C18    0.00   0.0  0
 3RH  CONST_26  C21  C20  C19  C18    0.00   0.0  0
 3RH  CONST_27  C16  C17  C10  C9   180.00   0.0  0
 3RH  CONST_28  C14  C13  C10  C9   180.00   0.0  0
 3RH  CONST_29  N5   C4   N3   C1   180.00   0.0  0
 3RH  CONST_30  C7   N6   C4   N5   180.00   0.0  0
 3RH  CONST_31  H21  C21  C12  C1     0.00   0.0  0
 3RH  CONST_32  H7   C7   C2   C1   180.00   0.0  0
 3RH  CONST_33  H17  C17  C10  C9     0.00   0.0  0
 3RH  CONST_34  H13  C13  C10  C9     0.00   0.0  0
 3RH  CONST_35  H18  C18  C11  C9     0.00   0.0  0
 3RH  CONST_36  H16  C16  C17  C10  180.00   0.0  0
 3RH  CONST_37  H14  C14  C13  C10  180.00   0.0  0
 3RH  CONST_38  H19  C19  C18  C11  180.00   0.0  0
 3RH  CONST_39  H20  C20  C21  C12  180.00   0.0  0
 3RH  CONST_40  H15  C15  C14  C13  180.00   0.0  0
 3RH  Var_01    C9   C8   C2   C1   -37.22  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
 3RH  chir_01  C9  C8  C10  C11  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
 3RH  plan-1  C9    0.020
 3RH  plan-1  C10   0.020
 3RH  plan-1  C13   0.020
 3RH  plan-1  C14   0.020
 3RH  plan-1  C15   0.020
 3RH  plan-1  C16   0.020
 3RH  plan-1  C17   0.020
 3RH  plan-1  H13   0.020
 3RH  plan-1  H14   0.020
 3RH  plan-1  H15   0.020
 3RH  plan-1  H16   0.020
 3RH  plan-1  H17   0.020
 3RH  plan-2  C1    0.020
 3RH  plan-2  C9    0.020
 3RH  plan-2  C11   0.020
 3RH  plan-2  C12   0.020
 3RH  plan-2  C18   0.020
 3RH  plan-2  C19   0.020
 3RH  plan-2  C20   0.020
 3RH  plan-2  C21   0.020
 3RH  plan-2  H18   0.020
 3RH  plan-2  H19   0.020
 3RH  plan-2  H20   0.020
 3RH  plan-2  H21   0.020
 3RH  plan-3  C4    0.020
 3RH  plan-3  N5    0.020
 3RH  plan-3  HN5   0.020
 3RH  plan-3  HN5A  0.020
 3RH  plan-4  C1    0.020
 3RH  plan-4  C2    0.020
 3RH  plan-4  N3    0.020
 3RH  plan-4  C4    0.020
 3RH  plan-4  N5    0.020
 3RH  plan-4  N6    0.020
 3RH  plan-4  C7    0.020
 3RH  plan-4  C8    0.020
 3RH  plan-4  C12   0.020
 3RH  plan-4  H7    0.020

