# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 22:40:41 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 3-(2,7-dimethoxyacridin-9-yl)sulfanylpropan-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2nc3ccc(OC)cc3c(SCCCN)c2c1
#
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
 CQO  CQO  3-(2,7-dimethoxyacridin-9-yl)sulfanylpropan-1-amine  ligand  43  23  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CQO
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
 CQO  C10  C  CR16  0  -0.453  -2.6277  -0.3441  -0.4658
 CQO  C13  C  CR16  0  -0.380   3.4981  -2.0529   0.4807
 CQO  C17  C  CH2   0  -0.434   0.1223   3.9442  -0.1124
 CQO  C22  C  CH3   0  -0.442   5.8991  -0.7117  -0.1103
 CQO  C01  C  CR6   0  -0.151  -0.1465  -0.1595  -0.4878
 CQO  C02  C  CR66  0   0.181   1.0908  -0.7556  -0.1982
 CQO  C03  C  CR66  0   0.149   1.0739  -2.0577   0.4003
 CQO  C05  C  CR66  0   0.148  -1.2103  -2.1627   0.3697
 CQO  C06  C  CR66  0   0.158  -1.3323  -0.8569  -0.2112
 CQO  C07  C  CR16  0  -0.272  -2.3968  -2.8933   0.6560
 CQO  C08  C  CR16  0  -0.379  -3.6264  -2.3784   0.3944
 CQO  C09  C  CR6   0   0.423  -3.7477  -1.0771  -0.1756
 CQO  C11  C  CR16  0  -0.457   2.3401  -0.1412  -0.4565
 CQO  C12  C  CR6   0   0.422   3.5154  -0.7635  -0.1275
 CQO  C14  C  CR16  0  -0.273   2.3142  -2.6715   0.7287
 CQO  C16  C  CH2   0  -0.543   0.0730   2.4776   0.2824
 CQO  C18  C  CH2   0  -0.269   0.3628   4.8345   1.1000
 CQO  C23  C  CH3   0  -0.441  -6.1259  -1.2403  -0.2105
 CQO  N04  N  N     0  -0.461  -0.0440  -2.7232   0.6640
 CQO  N19  N  NH2   0  -0.799   0.4101   6.2337   0.7040
 CQO  O20  O  O2    0  -0.469  -4.9351  -0.5117  -0.4487
 CQO  O21  O  O2    0  -0.469   4.6531  -0.1065  -0.4047
 CQO  S15  S  S2    0  -0.015  -0.2093   1.4583  -1.2069
 CQO  H1   H  HCR6  0   0.263  -2.7323   0.6419  -0.8995
 CQO  H2   H  HCR6  0   0.291   4.4191  -2.5523   0.7471
 CQO  H3   H  HCH2  0   0.235   0.9152   4.1108  -0.8458
 CQO  H4   H  HCH2  0   0.233  -0.8211   4.2281  -0.5892
 CQO  H5   H  HCH3  0   0.264   6.6620  -0.0085  -0.4344
 CQO  H6   H  HCH3  0   0.233   6.0241  -0.8941   0.9597
 CQO  H7   H  HCH3  0   0.233   6.0374  -1.6513  -0.6503
 CQO  H8   H  HCR6  0   0.271  -2.2954  -3.8782   1.0931
 CQO  H9   H  HCR6  0   0.290  -4.5040  -2.9658   0.6268
 CQO  H10  H  HCR6  0   0.267   2.3671   0.8317  -0.9309
 CQO  H11  H  HCR6  0   0.271   2.2922  -3.6522   1.1863
 CQO  H12  H  HCH2  0   0.269   1.0132   2.1690   0.7419
 CQO  H13  H  HCH2  0   0.273  -0.7358   2.2910   0.9900
 CQO  H14  H  HCH2  0   0.195  -0.4019   4.6163   1.8592
 CQO  H15  H  HCH2  0   0.219   1.3250   4.5741   1.5484
 CQO  H16  H  HCH3  0   0.233  -6.1660  -2.1615  -0.7966
 CQO  H17  H  HCH3  0   0.233  -6.2537  -1.4846   0.8467
 CQO  H18  H  HCH3  0   0.264  -6.9439  -0.5944  -0.5193
 CQO  H19  H  HNH2  0   0.339  -0.5121   6.5284   0.4068
 CQO  H20  H  HNH2  0   0.349   0.6303   6.8033   1.5108

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
 CQO  C22  O21  single    1.416  0.020  1.416
 CQO  O21  C12  single    1.343  0.020  1.343
 CQO  C13  C12  aromatic  1.426  0.020  1.426
 CQO  C13  C14  aromatic  1.359  0.020  1.359
 CQO  N19  C18  single    1.455  0.020  1.455
 CQO  C12  C11  aromatic  1.370  0.020  1.370
 CQO  C14  C03  aromatic  1.422  0.020  1.422
 CQO  C18  C17  single    1.523  0.020  1.523
 CQO  C11  C02  aromatic  1.416  0.020  1.416
 CQO  C03  C02  aromatic  1.433  0.020  1.433
 CQO  C03  N04  aromatic  1.327  0.020  1.327
 CQO  C02  C01  aromatic  1.404  0.020  1.404
 CQO  N04  C05  aromatic  1.327  0.020  1.327
 CQO  C17  C16  single    1.520  0.020  1.520
 CQO  C01  C06  aromatic  1.403  0.020  1.403
 CQO  C01  S15  single    1.771  0.020  1.771
 CQO  C05  C06  aromatic  1.434  0.020  1.434
 CQO  C05  C07  aromatic  1.423  0.020  1.423
 CQO  C16  S15  single    1.827  0.020  1.827
 CQO  C06  C10  aromatic  1.416  0.020  1.416
 CQO  C07  C08  aromatic  1.358  0.020  1.358
 CQO  C10  C09  aromatic  1.370  0.020  1.370
 CQO  C08  C09  aromatic  1.426  0.020  1.426
 CQO  C09  O20  single    1.343  0.020  1.343
 CQO  O20  C23  single    1.416  0.020  1.416
 CQO  C10  H1   single    0.930  0.020  1.080
 CQO  C13  H2   single    0.930  0.020  1.080
 CQO  C17  H3   single    0.970  0.020  1.090
 CQO  C17  H4   single    0.970  0.020  1.090
 CQO  C22  H5   single    0.970  0.020  1.090
 CQO  C22  H6   single    0.970  0.020  1.090
 CQO  C22  H7   single    0.970  0.020  1.090
 CQO  C07  H8   single    0.930  0.020  1.080
 CQO  C08  H9   single    0.930  0.020  1.080
 CQO  C11  H10  single    0.930  0.020  1.080
 CQO  C14  H11  single    0.930  0.020  1.080
 CQO  C16  H12  single    0.970  0.020  1.090
 CQO  C16  H13  single    0.970  0.020  1.090
 CQO  C18  H14  single    0.970  0.020  1.090
 CQO  C18  H15  single    0.970  0.020  1.090
 CQO  C23  H16  single    0.970  0.020  1.090
 CQO  C23  H17  single    0.970  0.020  1.090
 CQO  C23  H18  single    0.970  0.020  1.090
 CQO  N19  H19  single    0.890  0.020  1.040
 CQO  N19  H20  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
 CQO  H1   C10  C09  119.56  3.000
 CQO  H1   C10  C06  119.37  3.000
 CQO  C09  C10  C06  121.07  3.000
 CQO  H2   C13  C14  119.15  3.000
 CQO  H2   C13  C12  120.84  3.000
 CQO  C14  C13  C12  120.01  3.000
 CQO  H4   C17  H3   107.07  3.000
 CQO  H4   C17  C18  109.34  3.000
 CQO  H3   C17  C18  109.29  3.000
 CQO  H4   C17  C16  109.61  3.000
 CQO  H3   C17  C16  110.18  3.000
 CQO  C18  C17  C16  111.25  3.000
 CQO  H7   C22  H6   109.03  3.000
 CQO  H7   C22  H5   108.67  3.000
 CQO  H6   C22  H5   108.65  3.000
 CQO  H7   C22  O21  112.09  3.000
 CQO  H6   C22  O21  112.06  3.000
 CQO  H5   C22  O21  106.20  3.000
 CQO  S15  C01  C06  120.26  3.000
 CQO  S15  C01  C02  120.19  3.000
 CQO  C06  C01  C02  119.55  3.000
 CQO  C11  C02  C03  118.74  3.000
 CQO  C03  C02  C01  117.49  3.000
 CQO  C11  C02  C01  123.76  3.000
 CQO  N04  C03  C14  118.17  3.000
 CQO  N04  C03  C02  123.26  3.000
 CQO  C14  C03  C02  118.57  3.000
 CQO  N04  C05  C07  118.13  3.000
 CQO  C07  C05  C06  118.56  3.000
 CQO  N04  C05  C06  123.30  3.000
 CQO  C05  C06  C01  117.42  3.000
 CQO  C05  C06  C10  118.70  3.000
 CQO  C01  C06  C10  123.88  3.000
 CQO  H8   C07  C08  120.50  3.000
 CQO  H8   C07  C05  118.06  3.000
 CQO  C08  C07  C05  121.44  3.000
 CQO  H9   C08  C09  120.84  3.000
 CQO  H9   C08  C07  119.16  3.000
 CQO  C09  C08  C07  119.99  3.000
 CQO  O20  C09  C08  122.72  3.000
 CQO  O20  C09  C10  117.04  3.000
 CQO  C08  C09  C10  120.24  3.000
 CQO  H10  C11  C12  119.47  3.000
 CQO  H10  C11  C02  119.47  3.000
 CQO  C12  C11  C02  121.06  3.000
 CQO  O21  C12  C11  117.07  3.000
 CQO  C11  C12  C13  120.19  3.000
 CQO  O21  C12  C13  122.74  3.000
 CQO  H11  C14  C03  118.09  3.000
 CQO  H11  C14  C13  120.49  3.000
 CQO  C03  C14  C13  121.42  3.000
 CQO  H13  C16  H12  108.50  3.000
 CQO  H13  C16  S15  108.59  3.000
 CQO  H12  C16  S15  108.58  3.000
 CQO  H13  C16  C17  110.97  3.000
 CQO  H12  C16  C17  110.76  3.000
 CQO  S15  C16  C17  109.37  3.000
 CQO  H15  C18  H14  106.36  3.000
 CQO  H15  C18  N19  108.19  3.000
 CQO  H14  C18  N19  113.67  3.000
 CQO  H15  C18  C17  109.04  3.000
 CQO  H14  C18  C17  108.89  3.000
 CQO  N19  C18  C17  110.52  3.000
 CQO  H18  C23  H17  108.65  3.000
 CQO  H18  C23  H16  108.72  3.000
 CQO  H17  C23  H16  109.04  3.000
 CQO  H18  C23  O20  106.22  3.000
 CQO  H17  C23  O20  112.10  3.000
 CQO  H16  C23  O20  111.99  3.000
 CQO  C05  N04  C03  118.97  3.000
 CQO  H20  N19  H19  105.56  3.000
 CQO  H20  N19  C18  109.35  3.000
 CQO  H19  N19  C18  109.28  3.000
 CQO  C23  O20  C09  119.51  3.000
 CQO  C12  O21  C22  119.57  3.000
 CQO  C16  S15  C01   99.97  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
 CQO  CONST_01  C02  C01  C06  C10   180.00   0.0  0
 CQO  CONST_02  N04  C05  C06  C10   180.00   0.0  0
 CQO  CONST_03  C07  C05  C06  C10     0.00   0.0  0
 CQO  CONST_04  C07  C08  C09  C10     0.00   0.0  0
 CQO  CONST_05  C02  C11  C12  C13     0.00   0.0  0
 CQO  CONST_06  C02  C03  C14  C13     0.00   0.0  0
 CQO  CONST_07  N04  C03  C14  C13   180.00   0.0  0
 CQO  CONST_08  C12  C11  C02  C01   180.00   0.0  0
 CQO  CONST_09  C14  C03  C02  C01   180.00   0.0  0
 CQO  CONST_10  N04  C03  C02  C01     0.00   0.0  0
 CQO  CONST_11  N04  C05  C06  C01     0.00   0.0  0
 CQO  CONST_12  C07  C05  C06  C01   180.00   0.0  0
 CQO  CONST_13  C09  C10  C06  C01   180.00   0.0  0
 CQO  CONST_14  C05  N04  C03  C02     0.00   0.0  0
 CQO  CONST_15  C05  C06  C01  C02     0.00   0.0  0
 CQO  CONST_16  C12  C13  C14  C03     0.00   0.0  0
 CQO  CONST_17  C12  C11  C02  C03     0.00   0.0  0
 CQO  CONST_18  C06  C01  C02  C03     0.00   0.0  0
 CQO  CONST_19  C06  C05  N04  C03     0.00   0.0  0
 CQO  CONST_20  C07  C05  N04  C03   180.00   0.0  0
 CQO  CONST_21  C14  C03  N04  C05   180.00   0.0  0
 CQO  CONST_22  C09  C10  C06  C05     0.00   0.0  0
 CQO  CONST_23  C09  C08  C07  C05     0.00   0.0  0
 CQO  CONST_24  C11  C02  C01  C06   180.00   0.0  0
 CQO  CONST_25  C08  C07  C05  C06     0.00   0.0  0
 CQO  CONST_26  C08  C09  C10  C06     0.00   0.0  0
 CQO  CONST_27  N04  C05  C07  C08   180.00   0.0  0
 CQO  CONST_28  C14  C13  C12  C11     0.00   0.0  0
 CQO  CONST_29  C14  C03  C02  C11     0.00   0.0  0
 CQO  CONST_30  N04  C03  C02  C11   180.00   0.0  0
 CQO  CONST_31  S15  C01  C06  C10     0.00   0.0  0
 CQO  CONST_32  O21  C12  C11  C02   180.00   0.0  0
 CQO  CONST_33  S15  C01  C02  C03   180.00   0.0  0
 CQO  CONST_34  S15  C01  C06  C05   180.00   0.0  0
 CQO  CONST_35  O20  C09  C10  C06   180.00   0.0  0
 CQO  CONST_36  O20  C09  C08  C07   180.00   0.0  0
 CQO  CONST_37  S15  C01  C02  C11     0.00   0.0  0
 CQO  CONST_38  O21  C12  C13  C14   180.00   0.0  0
 CQO  CONST_39  H9   C08  C09  C10   180.00   0.0  0
 CQO  CONST_40  H10  C11  C12  C13   180.00   0.0  0
 CQO  CONST_41  H1   C10  C06  C01     0.00   0.0  0
 CQO  CONST_42  H11  C14  C03  C02   180.00   0.0  0
 CQO  CONST_43  H2   C13  C14  C03   180.00   0.0  0
 CQO  CONST_44  H8   C07  C05  C06   180.00   0.0  0
 CQO  Var_01    C11  C12  O21  C22  -178.80  30.0  2
 CQO  Var_02    H12  C16  S15  C01    56.52  30.0  1
 CQO  Var_03    H16  C23  O20  C09   -60.46  30.0  3
 CQO  Var_04    H5   C22  O21  C12   179.01  30.0  3
 CQO  Var_05    N19  C18  C17  C16   179.87  30.0  1
 CQO  Var_06    S15  C16  C17  C18  -179.74  30.0  3
 CQO  Var_07    H19  N19  C18  C17    68.57  30.0  3

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
 CQO  plan-1  C10  0.020
 CQO  plan-1  C13  0.020
 CQO  plan-1  C01  0.020
 CQO  plan-1  C02  0.020
 CQO  plan-1  C03  0.020
 CQO  plan-1  C05  0.020
 CQO  plan-1  C06  0.020
 CQO  plan-1  C07  0.020
 CQO  plan-1  C08  0.020
 CQO  plan-1  C09  0.020
 CQO  plan-1  C11  0.020
 CQO  plan-1  C12  0.020
 CQO  plan-1  C14  0.020
 CQO  plan-1  N04  0.020
 CQO  plan-1  O20  0.020
 CQO  plan-1  O21  0.020
 CQO  plan-1  S15  0.020
 CQO  plan-1  H1   0.020
 CQO  plan-1  H2   0.020
 CQO  plan-1  H8   0.020
 CQO  plan-1  H9   0.020
 CQO  plan-1  H10  0.020
 CQO  plan-1  H11  0.020

