# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:24:52 2022
#   Inital geometry file: a 93 line input string
#   Ligand name: 6-methyl-5,6,6~{a},7-tetrahydro-4~{H}-dibenzo[de,g]quinoline-10,11-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCc2cccc3c2[C@@H]1Cc4ccc(O)c(O)c34
#
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
 5RL  5RL  6-methyl-5,6,6~{a},7-tetrahydro-4~{H}-dibenzo[de,g]quinoline-10,11-diol  ligand  37  20  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5RL
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
 5RL  C10  C  CR6   0   0.093   0.0337  -0.9978   0.1055
 5RL  C11  C  CR6   0   0.064   0.9708   1.2495   0.4620
 5RL  C12  C  CR6   0  -0.020   1.1814  -0.0717   0.0317
 5RL  C14  C  CR16  0  -0.318  -2.1956  -2.6632   0.2838
 5RL  C15  C  CR16  0  -0.384   0.1813  -2.3574   0.3813
 5RL  C16  C  CR16  0  -0.349   2.0288   2.1369   0.5008
 5RL  C19  C  CR6   0   0.275   3.5088   0.4630  -0.3883
 5RL  C20  C  CR16  0  -0.379   3.2996   1.7404   0.0994
 5RL  O02  O  OH1   0  -0.631   4.7033   0.0218  -0.8390
 5RL  N03  N  NT    0  -0.436  -2.7618   1.4892  -0.0050
 5RL  C04  C  CH1   0  -0.078  -1.3961   1.0322  -0.1914
 5RL  C05  C  CR6   0   0.019  -1.2627  -0.4664  -0.0267
 5RL  C06  C  CH2   0  -0.532  -0.4285   1.6644   0.8115
 5RL  C07  C  CR6   0   0.065  -2.3720  -1.3000   0.0518
 5RL  C08  C  CH2   0  -0.298  -3.6992   0.6493  -0.7292
 5RL  C09  C  CH2   0  -0.497  -3.7497  -0.7272  -0.1021
 5RL  C17  C  CR6   0   0.211   2.4405  -0.4436  -0.4453
 5RL  C18  C  CR16  0  -0.236  -0.9293  -3.1864   0.4640
 5RL  H1   H  HCH3  0   0.197  -2.6681   3.0608  -1.4457
 5RL  H2   H  HCH3  0   0.240  -3.9560   3.1819  -0.2357
 5RL  H3   H  HCH3  0   0.241  -2.3009   3.5325   0.2198
 5RL  H4   H  HCR6  0   0.249  -3.0630  -3.3103   0.3383
 5RL  H5   H  HCR6  0   0.268   1.1566  -2.7802   0.5850
 5RL  H6   H  HCR6  0   0.250   1.8693   3.1545   0.8349
 5RL  H7   H  HCR6  0   0.271   4.1242   2.4430   0.1366
 5RL  H8   H  HOH1  0   0.474   1.9160  -2.1034  -1.2447
 5RL  H9   H  HOH1  0   0.474   5.3634   0.7179  -0.7495
 5RL  H11  H  HCH2  0   0.242  -4.6883   1.1077  -0.6835
 5RL  H12  H  HCH2  0   0.201  -3.4365   0.5695  -1.7980
 5RL  H13  H  HCH2  0   0.248  -4.3670  -1.3935  -0.7087
 5RL  H14  H  HCH2  0   0.249  -4.2323  -0.6609   0.8776
 5RL  H15  H  HCR6  0   0.257  -0.7978  -4.2398   0.6737
 5RL  H10  H  HCH2  0   0.247  -0.7054   1.3380   1.8204
 5RL  H16  H  HCH2  0   0.262  -0.4889   2.7525   0.7958
 5RL  H17  H  HCH1  0   0.216  -1.0384   1.2950  -1.2079
 5RL  C13  C  CH3   0  -0.535  -2.9206   2.8774  -0.3903
 5RL  O01  O  OH1   0  -0.620   2.7269  -1.6469  -0.9916

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
 5RL  C13  N03  single    1.449  0.020  1.449
 5RL  C06  C04  single    1.530  0.020  1.530
 5RL  C06  C11  single    1.501  0.020  1.501
 5RL  N03  C04  single    1.452  0.020  1.452
 5RL  N03  C08  single    1.452  0.020  1.452
 5RL  C04  C05  single    1.514  0.020  1.514
 5RL  C08  C09  single    1.513  0.020  1.513
 5RL  C09  C07  single    1.500  0.020  1.500
 5RL  C16  C11  aromatic  1.381  0.020  1.381
 5RL  C16  C20  aromatic  1.390  0.020  1.390
 5RL  C11  C12  aromatic  1.405  0.020  1.405
 5RL  C05  C07  aromatic  1.390  0.020  1.390
 5RL  C05  C10  aromatic  1.407  0.020  1.407
 5RL  C07  C14  aromatic  1.394  0.020  1.394
 5RL  C20  C19  aromatic  1.383  0.020  1.383
 5RL  C12  C10  aromatic  1.477  0.020  1.477
 5RL  C12  C17  aromatic  1.397  0.020  1.397
 5RL  C10  C15  aromatic  1.395  0.020  1.395
 5RL  C14  C18  aromatic  1.382  0.020  1.382
 5RL  C19  C17  aromatic  1.402  0.020  1.402
 5RL  C19  O02  single    1.351  0.020  1.351
 5RL  C17  O01  single    1.352  0.020  1.352
 5RL  C15  C18  aromatic  1.388  0.020  1.388
 5RL  C13  H1   single    0.970  0.020  1.090
 5RL  C13  H2   single    0.970  0.020  1.090
 5RL  C13  H3   single    0.970  0.020  1.090
 5RL  C14  H4   single    0.930  0.020  1.080
 5RL  C15  H5   single    0.930  0.020  1.080
 5RL  C16  H6   single    0.930  0.020  1.080
 5RL  C20  H7   single    0.930  0.020  1.080
 5RL  O01  H8   single    0.850  0.020  0.980
 5RL  O02  H9   single    0.850  0.020  0.980
 5RL  C08  H11  single    0.970  0.020  1.090
 5RL  C08  H12  single    0.970  0.020  1.090
 5RL  C09  H13  single    0.970  0.020  1.090
 5RL  C09  H14  single    0.970  0.020  1.090
 5RL  C18  H15  single    0.930  0.020  1.080
 5RL  C06  H10  single    0.970  0.020  1.090
 5RL  C06  H16  single    0.970  0.020  1.090
 5RL  C04  H17  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
 5RL  C05  C10  C15  118.95  3.000
 5RL  C15  C10  C12  122.61  3.000
 5RL  C05  C10  C12  118.33  3.000
 5RL  C06  C11  C16  122.00  3.000
 5RL  C16  C11  C12  119.85  3.000
 5RL  C06  C11  C12  118.09  3.000
 5RL  C17  C12  C11  119.33  3.000
 5RL  C17  C12  C10  123.42  3.000
 5RL  C11  C12  C10  117.25  3.000
 5RL  H4   C14  C18  120.06  3.000
 5RL  H4   C14  C07  119.41  3.000
 5RL  C18  C14  C07  120.52  3.000
 5RL  H5   C15  C18  118.45  3.000
 5RL  H5   C15  C10  120.88  3.000
 5RL  C18  C15  C10  120.60  3.000
 5RL  H6   C16  C20  119.45  3.000
 5RL  H6   C16  C11  119.97  3.000
 5RL  C20  C16  C11  120.58  3.000
 5RL  C17  C19  O02  116.67  3.000
 5RL  O02  C19  C20  123.57  3.000
 5RL  C17  C19  C20  119.75  3.000
 5RL  H7   C20  C19  119.71  3.000
 5RL  H7   C20  C16  120.04  3.000
 5RL  C19  C20  C16  120.22  3.000
 5RL  H9   O02  C19  109.80  3.000
 5RL  C08  N03  C04  111.17  3.000
 5RL  C08  N03  C13  110.53  3.000
 5RL  C04  N03  C13  111.74  3.000
 5RL  H17  C04  C06  107.38  3.000
 5RL  H17  C04  C05  107.81  3.000
 5RL  C06  C04  C05  106.38  3.000
 5RL  H17  C04  N03  110.27  3.000
 5RL  C05  C04  N03  112.37  3.000
 5RL  C06  C04  N03  112.37  3.000
 5RL  C07  C05  C04  121.98  3.000
 5RL  C07  C05  C10  120.23  3.000
 5RL  C04  C05  C10  117.73  3.000
 5RL  H16  C06  H10  107.25  3.000
 5RL  H16  C06  C04  111.59  3.000
 5RL  H10  C06  C04  108.69  3.000
 5RL  H16  C06  C11  108.93  3.000
 5RL  H10  C06  C11  111.57  3.000
 5RL  C04  C06  C11  108.83  3.000
 5RL  C09  C07  C05  119.89  3.000
 5RL  C05  C07  C14  119.67  3.000
 5RL  C09  C07  C14  120.44  3.000
 5RL  H12  C08  H11  106.66  3.000
 5RL  H12  C08  C09  110.09  3.000
 5RL  H11  C08  C09  109.54  3.000
 5RL  H12  C08  N03  111.79  3.000
 5RL  H11  C08  N03  108.74  3.000
 5RL  C09  C08  N03  109.94  3.000
 5RL  H14  C09  H13  106.56  3.000
 5RL  H14  C09  C08  109.31  3.000
 5RL  H13  C09  C08  110.10  3.000
 5RL  H14  C09  C07  109.66  3.000
 5RL  H13  C09  C07  110.07  3.000
 5RL  C08  C09  C07  111.04  3.000
 5RL  O01  C17  C19  115.49  3.000
 5RL  O01  C17  C12  124.46  3.000
 5RL  C19  C17  C12  120.04  3.000
 5RL  H15  C18  C15  119.71  3.000
 5RL  H15  C18  C14  120.34  3.000
 5RL  C15  C18  C14  119.95  3.000
 5RL  H3   C13  H2   107.04  3.000
 5RL  H3   C13  H1   107.85  3.000
 5RL  H2   C13  H1   107.90  3.000
 5RL  H3   C13  N03  111.40  3.000
 5RL  H2   C13  N03  109.51  3.000
 5RL  H1   C13  N03  112.92  3.000
 5RL  H8   O01  C17  110.43  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
 5RL  CONST_01  C14  C07  C05  C10     0.00   0.0  0
 5RL  CONST_02  C16  C11  C12  C10   180.00   0.0  0
 5RL  CONST_03  C19  C17  C12  C10   180.00   0.0  0
 5RL  CONST_04  C14  C18  C15  C10     0.00   0.0  0
 5RL  CONST_05  C19  C20  C16  C11     0.00   0.0  0
 5RL  CONST_08  C19  C17  C12  C11     0.00   0.0  0
 5RL  CONST_09  C20  C16  C11  C12     0.00   0.0  0
 5RL  CONST_10  C07  C05  C10  C12   180.00   0.0  0
 5RL  CONST_11  C18  C15  C10  C12   180.00   0.0  0
 5RL  CONST_12  C20  C19  C17  C12     0.00   0.0  0
 5RL  CONST_13  C07  C05  C10  C15     0.00   0.0  0
 5RL  CONST_15  C07  C14  C18  C15     0.00   0.0  0
 5RL  CONST_16  C17  C12  C11  C16     0.00   0.0  0
 5RL  CONST_17  C17  C19  C20  C16     0.00   0.0  0
 5RL  CONST_18  C18  C14  C07  C05     0.00   0.0  0
 5RL  CONST_20  C18  C15  C10  C05     0.00   0.0  0
 5RL  CONST_21  O01  C17  C12  C10     0.00   0.0  0
 5RL  CONST_22  O01  C17  C12  C11   180.00   0.0  0
 5RL  CONST_23  O02  C19  C17  C12   180.00   0.0  0
 5RL  CONST_24  O02  C19  C20  C16   180.00   0.0  0
 5RL  CONST_25  O01  C17  C19  C20   180.00   0.0  0
 5RL  CONST_26  H15  C18  C15  C10   180.00   0.0  0
 5RL  CONST_27  H7   C20  C16  C11   180.00   0.0  0
 5RL  CONST_28  H6   C16  C11  C12   180.00   0.0  0
 5RL  CONST_29  H5   C15  C10  C12     0.00   0.0  0
 5RL  CONST_30  H4   C14  C18  C15   180.00   0.0  0
 5RL  Var_01    C04  C06  C11  C12   -39.29  30.0  1
 5RL  Var_02    C08  C09  C07  C14  -163.68  30.0  1
 5RL  Var_03    C07  C09  C08  N03   -51.54  30.0  1
 5RL  Var_04    C09  C08  N03  C04    68.26  30.0  1
 5RL  Var_05    H1   C13  N03  C04    59.78  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
 5RL  chir_01  C04  C06  N03  C05  positiv

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
 5RL  plan-1  C10  0.020
 5RL  plan-1  C11  0.020
 5RL  plan-1  C12  0.020
 5RL  plan-1  C16  0.020
 5RL  plan-1  C19  0.020
 5RL  plan-1  C20  0.020
 5RL  plan-1  O02  0.020
 5RL  plan-1  C06  0.020
 5RL  plan-1  C17  0.020
 5RL  plan-1  H6   0.020
 5RL  plan-1  H7   0.020
 5RL  plan-1  O01  0.020
 5RL  plan-2  C10  0.020
 5RL  plan-2  C12  0.020
 5RL  plan-2  C14  0.020
 5RL  plan-2  C15  0.020
 5RL  plan-2  C04  0.020
 5RL  plan-2  C05  0.020
 5RL  plan-2  C07  0.020
 5RL  plan-2  C09  0.020
 5RL  plan-2  C18  0.020
 5RL  plan-2  H4   0.020
 5RL  plan-2  H5   0.020
 5RL  plan-2  H15  0.020

