# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 20:05:10 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 1-ethyl-3-[8-methyl-5-(2-methylpyridin-4-yl)isoquinolin-3-yl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC(=O)Nc1cc2c(cn1)c(C)ccc2c3ccnc(C)c3
#
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
 O54  O54  1-ethyl-3-[8-methyl-5-(2-methylpyridin-4-yl)isoquinolin-3-yl]urea  ligand  44  24  .  2021-08-17  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_O54
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
 O54  O1   O  O     0  -0.496   3.9994  -0.3804  -1.2186
 O54  C2   C  C     0   0.725   3.7742   0.4106  -0.3231
 O54  N4   N  NH1   0  -0.663   4.6316   1.3892   0.0512
 O54  C6   C  CH2   0  -0.249   5.9332   1.5467  -0.5643
 O54  C9   C  CH3   0  -0.665   6.5069   2.9123  -0.2381
 O54  N3   N  NH1   0  -0.762   2.5916   0.4261   0.4003
 O54  C5   C  CR6   0   0.528   1.5823  -0.5227   0.2674
 O54  C8   C  CR16  0  -0.497   0.2679  -0.1258   0.2311
 O54  C11  C  CR66  0   0.250  -0.7532  -1.0939   0.1884
 O54  C13  C  CR6   0   0.049  -2.1408  -0.7694   0.1590
 O54  C16  C  CR16  0  -0.268  -3.0463  -1.7917   0.0391
 O54  C17  C  CR16  0  -0.297  -2.6470  -3.1389  -0.0270
 O54  C14  C  CR6   0   0.071  -1.3254  -3.4947   0.0212
 O54  C18  C  CH3   0  -0.725  -0.9111  -4.9334  -0.0349
 O54  C12  C  CR66  0  -0.030  -0.3604  -2.4548   0.1229
 O54  C10  C  CR16  0  -0.094   1.0268  -2.7211   0.1545
 O54  N7   N  N     0  -0.406   1.9585  -1.8122   0.2420
 O54  C15  C  CR6   0   0.134  -2.6189   0.6238   0.2512
 O54  C20  C  CR16  0  -0.363  -2.2688   1.4565   1.3110
 O54  C22  C  CR16  0  -0.044  -2.7837   2.7408   1.3425
 O54  N23  N  N     0  -0.423  -3.5979   3.2340   0.4192
 O54  C21  C  CR6   0   0.262  -3.9464   2.4483  -0.5962
 O54  C24  C  CH3   0  -0.700  -4.8494   3.0407  -1.6343
 O54  C19  C  CR16  0  -0.369  -3.4782   1.1433  -0.7107
 O54  H1   H  HNH1  0   0.366   4.5064   1.8155   0.9546
 O54  H2   H  HCH2  0   0.226   6.6223   0.7635  -0.2338
 O54  H3   H  HCH2  0   0.235   5.8232   1.4391  -1.6428
 O54  H4   H  HCH3  0   0.237   7.4823   3.0311  -0.7068
 O54  H5   H  HCH3  0   0.227   5.8581   3.7098  -0.5994
 O54  H6   H  HCH3  0   0.214   6.6447   3.0452   0.8363
 O54  H7   H  HNH1  0   0.376   2.3107   1.3060   0.8009
 O54  H8   H  HCR6  0   0.253   0.0253   0.9280   0.2180
 O54  H9   H  HCR6  0   0.240  -4.1053  -1.5669   0.0192
 O54  H10  H  HCR6  0   0.234  -3.4104  -3.9015  -0.1072
 O54  H11  H  HCH3  0   0.244  -0.3861  -5.2378   0.8719
 O54  H12  H  HCH3  0   0.247  -1.7773  -5.5821  -0.1449
 O54  H13  H  HCH3  0   0.241  -0.2434  -5.1303  -0.8746
 O54  H14  H  HCR6  0   0.246   1.3742  -3.7482   0.1180
 O54  H15  H  HCR6  0   0.252  -1.6299   1.1111   2.1124
 O54  H16  H  HCR6  0   0.243  -2.5271   3.4029   2.1618
 O54  H17  H  HCH3  0   0.244  -4.2818   3.6757  -2.3172
 O54  H18  H  HCH3  0   0.227  -5.3417   2.2743  -2.2307
 O54  H19  H  HCH3  0   0.244  -5.6133   3.6626  -1.1707
 O54  H20  H  HCR6  0   0.236  -3.7767   0.5368  -1.5568

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
 O54  C18  C14  single    1.498  0.020  1.498
 O54  C10  N7   aromatic  1.305  0.020  1.305
 O54  C10  C12  aromatic  1.413  0.020  1.413
 O54  N7   C5   aromatic  1.344  0.020  1.344
 O54  N3   C5   single    1.392  0.020  1.392
 O54  N3   C2   single    1.386  0.020  1.386
 O54  C14  C12  aromatic  1.422  0.020  1.422
 O54  C14  C17  aromatic  1.370  0.020  1.370
 O54  C12  C11  aromatic  1.418  0.020  1.418
 O54  C5   C8   aromatic  1.373  0.020  1.373
 O54  C9   C6   single    1.517  0.020  1.517
 O54  N4   C2   single    1.354  0.020  1.354
 O54  N4   C6   single    1.448  0.020  1.448
 O54  C2   O1   double    1.216  0.020  1.216
 O54  C17  C16  aromatic  1.407  0.020  1.407
 O54  C8   C11  aromatic  1.408  0.020  1.408
 O54  C11  C13  aromatic  1.425  0.020  1.425
 O54  C16  C13  aromatic  1.371  0.020  1.371
 O54  C13  C15  single    1.476  0.020  1.476
 O54  C15  C20  aromatic  1.392  0.020  1.392
 O54  C15  C19  aromatic  1.391  0.020  1.391
 O54  C20  C22  aromatic  1.384  0.020  1.384
 O54  C19  C21  aromatic  1.391  0.020  1.391
 O54  C22  N23  aromatic  1.326  0.020  1.326
 O54  C21  N23  aromatic  1.330  0.020  1.330
 O54  C21  C24  single    1.498  0.020  1.498
 O54  N4   H1   single    0.890  0.020  1.040
 O54  C6   H2   single    0.970  0.020  1.090
 O54  C6   H3   single    0.970  0.020  1.090
 O54  C9   H4   single    0.970  0.020  1.090
 O54  C9   H5   single    0.970  0.020  1.090
 O54  C9   H6   single    0.970  0.020  1.090
 O54  N3   H7   single    0.890  0.020  1.040
 O54  C8   H8   single    0.930  0.020  1.080
 O54  C16  H9   single    0.930  0.020  1.080
 O54  C17  H10  single    0.930  0.020  1.080
 O54  C18  H11  single    0.970  0.020  1.090
 O54  C18  H12  single    0.970  0.020  1.090
 O54  C18  H13  single    0.970  0.020  1.090
 O54  C10  H14  single    0.930  0.020  1.080
 O54  C20  H15  single    0.930  0.020  1.080
 O54  C22  H16  single    0.930  0.020  1.080
 O54  C24  H17  single    0.970  0.020  1.090
 O54  C24  H18  single    0.970  0.020  1.090
 O54  C24  H19  single    0.970  0.020  1.090
 O54  C19  H20  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
 O54  N3   C2   N4   112.82  3.000
 O54  N4   C2   O1   123.82  3.000
 O54  N3   C2   O1   123.34  3.000
 O54  H1   N4   C6   116.56  3.000
 O54  H1   N4   C2   118.39  3.000
 O54  C6   N4   C2   122.02  3.000
 O54  H3   C6   H2   106.97  3.000
 O54  H3   C6   C9   109.88  3.000
 O54  H2   C6   C9   109.95  3.000
 O54  H3   C6   N4   108.62  3.000
 O54  H2   C6   N4   111.08  3.000
 O54  C9   C6   N4   110.27  3.000
 O54  H6   C9   H5   108.21  3.000
 O54  H6   C9   H4   107.30  3.000
 O54  H5   C9   H4   108.11  3.000
 O54  H6   C9   C6   111.66  3.000
 O54  H5   C9   C6   111.25  3.000
 O54  H4   C9   C6   110.16  3.000
 O54  H7   N3   C5   115.57  3.000
 O54  H7   N3   C2   117.09  3.000
 O54  C5   N3   C2   124.14  3.000
 O54  N7   C5   C8   123.01  3.000
 O54  C8   C5   N3   119.98  3.000
 O54  N7   C5   N3   116.94  3.000
 O54  H8   C8   C11  120.47  3.000
 O54  H8   C8   C5   119.77  3.000
 O54  C11  C8   C5   119.75  3.000
 O54  C12  C11  C13  119.16  3.000
 O54  C13  C11  C8   123.38  3.000
 O54  C12  C11  C8   117.42  3.000
 O54  C15  C13  C16  119.70  3.000
 O54  C15  C13  C11  121.94  3.000
 O54  C16  C13  C11  118.37  3.000
 O54  H9   C16  C17  118.40  3.000
 O54  H9   C16  C13  119.53  3.000
 O54  C17  C16  C13  122.06  3.000
 O54  H10  C17  C14  120.02  3.000
 O54  H10  C17  C16  118.57  3.000
 O54  C14  C17  C16  121.41  3.000
 O54  C12  C14  C18  121.14  3.000
 O54  C12  C14  C17  117.86  3.000
 O54  C18  C14  C17  121.00  3.000
 O54  H13  C18  H12  107.58  3.000
 O54  H13  C18  H11  107.15  3.000
 O54  H12  C18  H11  107.51  3.000
 O54  H13  C18  C14  111.81  3.000
 O54  H12  C18  C14  110.87  3.000
 O54  H11  C18  C14  111.70  3.000
 O54  C10  C12  C14  122.00  3.000
 O54  C14  C12  C11  121.14  3.000
 O54  C10  C12  C11  116.86  3.000
 O54  H14  C10  N7   115.67  3.000
 O54  H14  C10  C12  119.48  3.000
 O54  N7   C10  C12  124.85  3.000
 O54  C10  N7   C5   118.03  3.000
 O54  C19  C15  C20  117.29  3.000
 O54  C19  C15  C13  120.64  3.000
 O54  C20  C15  C13  122.05  3.000
 O54  H15  C20  C22  119.95  3.000
 O54  H15  C20  C15  121.43  3.000
 O54  C22  C20  C15  118.60  3.000
 O54  H16  C22  N23  116.38  3.000
 O54  H16  C22  C20  119.72  3.000
 O54  N23  C22  C20  123.89  3.000
 O54  C21  N23  C22  118.20  3.000
 O54  C19  C21  C24  121.12  3.000
 O54  C24  C21  N23  116.95  3.000
 O54  C19  C21  N23  121.92  3.000
 O54  H19  C24  H18  108.55  3.000
 O54  H19  C24  H17  107.39  3.000
 O54  H18  C24  H17  107.57  3.000
 O54  H19  C24  C21  110.72  3.000
 O54  H18  C24  C21  111.95  3.000
 O54  H17  C24  C21  110.49  3.000
 O54  H20  C19  C21  119.79  3.000
 O54  H20  C19  C15  120.11  3.000
 O54  C21  C19  C15  120.10  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
 O54  CONST_01  C12  C10  N7   C5      0.00   0.0  0
 O54  CONST_02  C12  C11  C8   C5      0.00   0.0  0
 O54  CONST_03  C13  C11  C8   C5    180.00   0.0  0
 O54  CONST_04  C10  N7   C5   C8      0.00   0.0  0
 O54  CONST_05  C10  C12  C11  C8      0.00   0.0  0
 O54  CONST_06  C14  C12  C11  C8    180.00   0.0  0
 O54  CONST_07  C16  C13  C11  C8    180.00   0.0  0
 O54  CONST_08  C15  C13  C11  C8      0.00   0.0  0
 O54  CONST_09  N7   C10  C12  C11     0.00   0.0  0
 O54  CONST_10  C17  C14  C12  C11     0.00   0.0  0
 O54  CONST_11  N7   C5   C8   C11     0.00   0.0  0
 O54  CONST_12  C17  C16  C13  C11     0.00   0.0  0
 O54  CONST_15  C10  C12  C11  C13   180.00   0.0  0
 O54  CONST_16  C14  C12  C11  C13     0.00   0.0  0
 O54  CONST_17  C14  C17  C16  C13     0.00   0.0  0
 O54  CONST_18  C22  C20  C15  C13   180.00   0.0  0
 O54  CONST_19  C21  C19  C15  C13   180.00   0.0  0
 O54  CONST_20  C12  C14  C17  C16     0.00   0.0  0
 O54  CONST_21  C12  C11  C13  C16     0.00   0.0  0
 O54  CONST_24  C10  C12  C14  C17   180.00   0.0  0
 O54  CONST_25  C15  C13  C16  C17   180.00   0.0  0
 O54  CONST_26  N7   C10  C12  C14   180.00   0.0  0
 O54  CONST_27  C15  C13  C11  C12   180.00   0.0  0
 O54  CONST_28  N23  C22  C20  C15     0.00   0.0  0
 O54  CONST_29  N23  C21  C19  C15     0.00   0.0  0
 O54  CONST_30  C21  C19  C15  C20     0.00   0.0  0
 O54  CONST_31  C21  N23  C22  C20     0.00   0.0  0
 O54  CONST_32  C19  C15  C20  C22     0.00   0.0  0
 O54  CONST_33  C19  C21  N23  C22     0.00   0.0  0
 O54  CONST_34  C10  N7   C5   N3    180.00   0.0  0
 O54  CONST_35  C11  C8   C5   N3    180.00   0.0  0
 O54  CONST_36  C18  C14  C12  C11   180.00   0.0  0
 O54  CONST_37  C18  C14  C17  C16   180.00   0.0  0
 O54  CONST_38  C10  C12  C14  C18     0.00   0.0  0
 O54  CONST_39  C24  C21  C19  C15   180.00   0.0  0
 O54  CONST_40  C24  C21  N23  C22   180.00   0.0  0
 O54  CONST_41  H14  C10  N7   C5    180.00   0.0  0
 O54  CONST_42  H9   C16  C13  C11   180.00   0.0  0
 O54  CONST_43  H8   C8   C11  C13     0.00   0.0  0
 O54  CONST_44  H10  C17  C16  C13   180.00   0.0  0
 O54  CONST_45  H15  C20  C15  C13     0.00   0.0  0
 O54  CONST_46  H20  C19  C15  C13     0.00   0.0  0
 O54  CONST_47  H16  C22  C20  C15   180.00   0.0  0
 O54  CONST_51  C5   N3   C2   O1      0.00   0.0  0
 O54  CONST_52  C5   N3   C2   N4    180.00   0.0  0
 O54  CONST_53  C6   N4   C2   O1      0.00   0.0  0
 O54  CONST_54  N3   C2   N4   C6    180.00   0.0  0
 O54  Var_01    H11  C18  C14  C17  -118.14  30.0  2
 O54  Var_02    H17  C24  C21  N23    78.88  30.0  2
 O54  Var_03    C9   C6   N4   C2    164.42  30.0  3
 O54  Var_04    H4   C9   C6   N4   -179.65  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
 O54  plan-1  C13  0.020
 O54  plan-1  C15  0.020
 O54  plan-1  C20  0.020
 O54  plan-1  C22  0.020
 O54  plan-1  N23  0.020
 O54  plan-1  C21  0.020
 O54  plan-1  C24  0.020
 O54  plan-1  C19  0.020
 O54  plan-1  H15  0.020
 O54  plan-1  H16  0.020
 O54  plan-1  H20  0.020
 O54  plan-2  N3   0.020
 O54  plan-2  C5   0.020
 O54  plan-2  C8   0.020
 O54  plan-2  C11  0.020
 O54  plan-2  C13  0.020
 O54  plan-2  C16  0.020
 O54  plan-2  C17  0.020
 O54  plan-2  C14  0.020
 O54  plan-2  C18  0.020
 O54  plan-2  C12  0.020
 O54  plan-2  C10  0.020
 O54  plan-2  N7   0.020
 O54  plan-2  C15  0.020
 O54  plan-2  H8   0.020
 O54  plan-2  H9   0.020
 O54  plan-2  H10  0.020
 O54  plan-2  H14  0.020
 O54  plan-3  O1   0.020
 O54  plan-3  C2   0.020
 O54  plan-3  N4   0.020
 O54  plan-3  C6   0.020
 O54  plan-3  N3   0.020
 O54  plan-3  C5   0.020
 O54  plan-3  H1   0.020
 O54  plan-3  H7   0.020

