# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 20:09:08 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 5-methyl-3-[4-(piperazin-1-ylmethyl)phenyl]isoquinolin-1(2H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc2C(=O)NC(=Cc12)c3ccc(CN4CCNCC4)cc3
#
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
 T40  T40  5-methyl-3-[4-(piperazin-1-ylmethyl)phenyl]isoquinolin-1(2H)-one  ligand  48  25  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T40
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
 T40  O     O  O     0  -0.478   4.3914  -2.0880  -2.1793
 T40  C6    C  CR6   0   0.513   3.8125  -1.2931  -1.4498
 T40  C5    C  CR66  0  -0.154   4.4851  -0.3529  -0.5538
 T40  C     C  CR16  0  -0.301   5.8827  -0.3510  -0.5020
 T40  N     N  NR16  0  -0.739   2.4454  -1.2250  -1.4381
 T40  C7    C  CR6   0   0.392   1.6910  -0.3720  -0.6728
 T40  C8    C  CR16  0  -0.500   2.3072   0.5006   0.1578
 T40  C4    C  CR66  0   0.234   3.7359   0.5396   0.2362
 T40  C3    C  CR6   0   0.061   4.4122   1.4433   1.0908
 T40  C20   C  CH3   0  -0.752   3.6488   2.4105   1.9465
 T40  C2    C  CR16  0  -0.295   5.7925   1.4180   1.1183
 T40  C1    C  CR16  0  -0.249   6.5322   0.5298   0.3305
 T40  C9    C  CR6   0   0.047   0.2298  -0.4831  -0.7943
 T40  C14   C  CR16  0  -0.290  -0.3899  -1.7198  -0.9693
 T40  C13   C  CR16  0  -0.298  -1.7714  -1.8084  -1.0608
 T40  C12   C  CR6   0   0.079  -2.5687  -0.6722  -0.9910
 T40  C11   C  CR16  0  -0.265  -1.9471   0.5632  -0.8172
 T40  C10   C  CR16  0  -0.287  -0.5707   0.6587  -0.7213
 T40  C15   C  CH2   0  -0.314  -4.0651  -0.7635  -1.1421
 T40  N1    N  NT    0  -0.421  -4.7658   0.1389  -0.2582
 T40  C19   C  CH2   0  -0.276  -6.1502   0.3322  -0.6454
 T40  C18   C  CH2   0  -0.299  -6.8019   1.3748   0.2444
 T40  N2    N  NH1   0  -0.600  -6.7110   0.9548   1.6300
 T40  C17   C  CH2   0  -0.297  -5.3259   0.7816   2.0243
 T40  C16   C  CH2   0  -0.274  -4.6689  -0.2571   1.1344
 T40  H     H  HNR6  0   0.418   1.9718  -1.8319  -2.0945
 T40  HA    H  HCR6  0   0.261   6.4440  -1.0423  -1.1157
 T40  H1    H  HCR6  0   0.260   7.6130   0.5394   0.3803
 T40  H8    H  HCR6  0   0.269   1.7042   1.1411   0.7829
 T40  H201  H  HCH3  0   0.249   2.9842   1.8976   2.6445
 T40  H202  H  HCH3  0   0.258   4.3269   3.0280   2.5327
 T40  H203  H  HCH3  0   0.249   3.0288   3.0797   1.3471
 T40  H2    H  HCR6  0   0.257   6.3193   2.1066   1.7681
 T40  H14   H  HCR6  0   0.262   0.1960  -2.6305  -1.0008
 T40  H10   H  HCR6  0   0.258  -0.1121   1.6331  -0.6087
 T40  H13   H  HCR6  0   0.255  -2.2315  -2.7822  -1.1797
 T40  H11   H  HCR6  0   0.252  -2.5542   1.4573  -0.7555
 T40  H151  H  HCH2  0   0.256  -4.3234  -0.4927  -2.1713
 T40  H152  H  HCH2  0   0.214  -4.3826  -1.8123  -1.0156
 T40  H191  H  HCH2  0   0.234  -6.1851   0.6700  -1.6838
 T40  H192  H  HCH2  0   0.189  -6.7306  -0.6047  -0.5889
 T40  H161  H  HCH2  0   0.192  -5.1413  -1.2394   1.3094
 T40  H162  H  HCH2  0   0.237  -3.6174  -0.3519   1.4134
 T40  H181  H  HCH2  0   0.191  -6.3154   2.3456   0.0588
 T40  H182  H  HCH2  0   0.232  -7.8524   1.4797  -0.0338
 T40  HB    H  HNH1  0   0.353  -7.1513   1.6445   2.2245
 T40  H171  H  HCH2  0   0.191  -4.7425   1.7140   1.9611
 T40  H172  H  HCH2  0   0.231  -5.2848   0.4438   3.0618

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
 T40  O    C6    double    1.224  0.020  1.224
 T40  C6   C5    single    1.463  0.020  1.463
 T40  C6   N     single    1.369  0.020  1.369
 T40  C5   C     aromatic  1.398  0.020  1.398
 T40  C5   C4    aromatic  1.408  0.020  1.408
 T40  C    C1    aromatic  1.375  0.020  1.375
 T40  N    C7    single    1.372  0.020  1.372
 T40  C7   C8    double    1.353  0.020  1.353
 T40  C7   C9    single    1.470  0.020  1.470
 T40  C8   C4    single    1.431  0.020  1.431
 T40  C4   C3    aromatic  1.416  0.020  1.416
 T40  C3   C20   single    1.500  0.020  1.500
 T40  C3   C2    aromatic  1.381  0.020  1.381
 T40  C2   C1    aromatic  1.399  0.020  1.399
 T40  C9   C14   aromatic  1.394  0.020  1.394
 T40  C9   C10   aromatic  1.396  0.020  1.396
 T40  C14  C13   aromatic  1.387  0.020  1.387
 T40  C13  C12   aromatic  1.390  0.020  1.390
 T40  C12  C11   aromatic  1.394  0.020  1.394
 T40  C12  C15   single    1.507  0.020  1.507
 T40  C11  C10   aromatic  1.383  0.020  1.383
 T40  C15  N1    single    1.445  0.020  1.445
 T40  N1   C19   single    1.450  0.020  1.450
 T40  N1   C16   single    1.451  0.020  1.451
 T40  C19  C18   single    1.518  0.020  1.518
 T40  C18  N2    single    1.451  0.020  1.451
 T40  N2   C17   single    1.451  0.020  1.451
 T40  C17  C16   single    1.517  0.020  1.517
 T40  N    H     single    0.860  0.020  1.020
 T40  C    HA    single    0.930  0.020  1.080
 T40  C1   H1    single    0.930  0.020  1.080
 T40  C8   H8    single    0.930  0.020  1.080
 T40  C20  H201  single    0.970  0.020  1.090
 T40  C20  H202  single    0.970  0.020  1.090
 T40  C20  H203  single    0.970  0.020  1.090
 T40  C2   H2    single    0.930  0.020  1.080
 T40  C14  H14   single    0.930  0.020  1.080
 T40  C10  H10   single    0.930  0.020  1.080
 T40  C13  H13   single    0.930  0.020  1.080
 T40  C11  H11   single    0.930  0.020  1.080
 T40  C15  H151  single    0.970  0.020  1.090
 T40  C15  H152  single    0.970  0.020  1.090
 T40  C19  H191  single    0.970  0.020  1.090
 T40  C19  H192  single    0.970  0.020  1.090
 T40  C16  H161  single    0.970  0.020  1.090
 T40  C16  H162  single    0.970  0.020  1.090
 T40  C18  H181  single    0.970  0.020  1.090
 T40  C18  H182  single    0.970  0.020  1.090
 T40  N2   HB    single    0.890  0.020  1.040
 T40  C17  H171  single    0.970  0.020  1.090
 T40  C17  H172  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
 T40  N     C6   C5    114.96  3.000
 T40  N     C6   O     120.64  3.000
 T40  C5    C6   O     124.40  3.000
 T40  C4    C5   C     120.67  3.000
 T40  C4    C5   C6    120.43  3.000
 T40  C     C5   C6    118.89  3.000
 T40  HA    C    C1    120.52  3.000
 T40  HA    C    C5    119.79  3.000
 T40  C1    C    C5    119.69  3.000
 T40  H     N    C7    118.53  3.000
 T40  H     N    C6    115.59  3.000
 T40  C7    N    C6    125.80  3.000
 T40  C9    C7   C8    123.50  3.000
 T40  C9    C7   N     116.96  3.000
 T40  C8    C7   N     119.53  3.000
 T40  H8    C8   C4    120.65  3.000
 T40  H8    C8   C7    118.94  3.000
 T40  C4    C8   C7    120.38  3.000
 T40  C3    C4   C8    121.82  3.000
 T40  C3    C4   C5    119.28  3.000
 T40  C8    C4   C5    118.89  3.000
 T40  C2    C3   C20   120.60  3.000
 T40  C2    C3   C4    118.55  3.000
 T40  C20   C3   C4    120.85  3.000
 T40  H203  C20  H202  107.56  3.000
 T40  H203  C20  H201  107.05  3.000
 T40  H202  C20  H201  107.55  3.000
 T40  H203  C20  C3    111.78  3.000
 T40  H202  C20  C3    110.85  3.000
 T40  H201  C20  C3    111.81  3.000
 T40  H2    C2   C1    118.97  3.000
 T40  H2    C2   C3    119.10  3.000
 T40  C1    C2   C3    121.93  3.000
 T40  H1    C1   C2    119.77  3.000
 T40  H1    C1   C     120.36  3.000
 T40  C2    C1   C     119.87  3.000
 T40  C10   C9   C14   118.49  3.000
 T40  C10   C9   C7    120.24  3.000
 T40  C14   C9   C7    121.27  3.000
 T40  H14   C14  C13   118.88  3.000
 T40  H14   C14  C9    120.59  3.000
 T40  C13   C14  C9    120.50  3.000
 T40  H13   C13  C12   119.77  3.000
 T40  H13   C13  C14   119.17  3.000
 T40  C12   C13  C14   121.05  3.000
 T40  C15   C12  C11   120.61  3.000
 T40  C15   C12  C13   121.01  3.000
 T40  C11   C12  C13   118.36  3.000
 T40  H11   C11  C10   119.81  3.000
 T40  H11   C11  C12   119.28  3.000
 T40  C10   C11  C12   120.91  3.000
 T40  H10   C10  C11   119.40  3.000
 T40  H10   C10  C9    119.90  3.000
 T40  C11   C10  C9    120.69  3.000
 T40  H152  C15  H151  105.96  3.000
 T40  H152  C15  N1    112.60  3.000
 T40  H151  C15  N1    107.82  3.000
 T40  H152  C15  C12   109.39  3.000
 T40  H151  C15  C12   108.27  3.000
 T40  N1    C15  C12   112.49  3.000
 T40  C16   N1   C19   110.87  3.000
 T40  C16   N1   C15   112.60  3.000
 T40  C19   N1   C15   112.51  3.000
 T40  H192  C19  H191  107.12  3.000
 T40  H192  C19  C18   109.11  3.000
 T40  H191  C19  C18   109.34  3.000
 T40  H192  C19  N1    112.03  3.000
 T40  H191  C19  N1    108.99  3.000
 T40  C18   C19  N1    110.17  3.000
 T40  H182  C18  H181  107.29  3.000
 T40  H182  C18  N2    109.36  3.000
 T40  H181  C18  N2    112.86  3.000
 T40  H182  C18  C19   109.25  3.000
 T40  H181  C18  C19   108.48  3.000
 T40  N2    C18  C19   109.53  3.000
 T40  HB    N2   C17   109.72  3.000
 T40  HB    N2   C18   109.68  3.000
 T40  C17   N2   C18   110.73  3.000
 T40  H172  C17  H171  107.24  3.000
 T40  H172  C17  C16   109.22  3.000
 T40  H171  C17  C16   108.45  3.000
 T40  H172  C17  N2    109.34  3.000
 T40  H171  C17  N2    112.89  3.000
 T40  C16   C17  N2    109.62  3.000
 T40  H162  C16  H161  107.12  3.000
 T40  H162  C16  C17   109.05  3.000
 T40  H161  C16  C17   109.32  3.000
 T40  H162  C16  N1    109.46  3.000
 T40  H161  C16  N1    111.50  3.000
 T40  C17   C16  N1    110.31  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
 T40  CONST_01  C2    C1   C    C5     0.00   0.0  0
 T40  CONST_02  C2    C3   C4   C5     0.00   0.0  0
 T40  CONST_03  C3    C4   C5   C      0.00   0.0  0
 T40  CONST_04  C3    C2   C1   C      0.00   0.0  0
 T40  CONST_05  C1    C    C5   C4     0.00   0.0  0
 T40  CONST_06  C1    C2   C3   C4     0.00   0.0  0
 T40  CONST_07  C12   C13  C14  C9     0.00   0.0  0
 T40  CONST_08  C12   C11  C10  C9     0.00   0.0  0
 T40  CONST_09  C11   C10  C9   C14    0.00   0.0  0
 T40  CONST_10  C11   C12  C13  C14    0.00   0.0  0
 T40  CONST_11  C10   C9   C14  C13    0.00   0.0  0
 T40  CONST_12  C10   C11  C12  C13    0.00   0.0  0
 T40  CONST_13  C13   C14  C9   C7   180.00   0.0  0
 T40  CONST_14  C11   C10  C9   C7   180.00   0.0  0
 T40  CONST_15  C7    N    C6   C5     0.00   0.0  0
 T40  CONST_16  C20   C3   C4   C5   180.00   0.0  0
 T40  CONST_17  C20   C3   C4   C8     0.00   0.0  0
 T40  CONST_18  C1    C2   C3   C20  180.00   0.0  0
 T40  CONST_19  C15   C12  C13  C14  180.00   0.0  0
 T40  CONST_20  C15   C12  C11  C10  180.00   0.0  0
 T40  CONST_21  C7    N    C6   O    180.00   0.0  0
 T40  CONST_22  HA    C    C5   C6     0.00   0.0  0
 T40  CONST_23  H1    C1   C    C5   180.00   0.0  0
 T40  CONST_24  H2    C2   C1   C    180.00   0.0  0
 T40  CONST_25  H14   C14  C9   C7     0.00   0.0  0
 T40  CONST_26  H10   C10  C9   C7     0.00   0.0  0
 T40  CONST_27  H13   C13  C14  C9   180.00   0.0  0
 T40  CONST_28  H11   C11  C10  C9   180.00   0.0  0
 T40  CONST_29  H     N    C6   C5   180.00   0.0  0
 T40  Var_01    C14   C9   C7   N     36.50  30.0  2
 T40  Var_02    N2    C18  C19  N1   -58.02  30.0  1
 T40  Var_03    N2    C17  C16  N1    57.57  30.0  1
 T40  Var_04    C17   C16  N1   C19  -57.44  30.0  1
 T40  Var_05    C17   N2   C18  C19   59.23  30.0  1
 T40  Var_06    C16   N1   C19  C18   57.64  30.0  1
 T40  Var_07    C16   C17  N2   C18  -59.00  30.0  1
 T40  Var_08    N1    C15  C12  C13  141.85  30.0  2
 T40  Var_09    C19   N1   C15  C12  163.91  30.0  3
 T40  Var_10    H201  C20  C3   C4    60.27  30.0  2

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
 T40  plan-1  C7   0.020
 T40  plan-1  C9   0.020
 T40  plan-1  C14  0.020
 T40  plan-1  C13  0.020
 T40  plan-1  C12  0.020
 T40  plan-1  C11  0.020
 T40  plan-1  C10  0.020
 T40  plan-1  C15  0.020
 T40  plan-1  H14  0.020
 T40  plan-1  H10  0.020
 T40  plan-1  H13  0.020
 T40  plan-1  H11  0.020
 T40  plan-2  O    0.020
 T40  plan-2  C6   0.020
 T40  plan-2  C5   0.020
 T40  plan-2  C    0.020
 T40  plan-2  N    0.020
 T40  plan-2  C7   0.020
 T40  plan-2  C8   0.020
 T40  plan-2  C4   0.020
 T40  plan-2  C3   0.020
 T40  plan-2  C20  0.020
 T40  plan-2  C2   0.020
 T40  plan-2  C1   0.020
 T40  plan-2  C9   0.020
 T40  plan-2  H    0.020
 T40  plan-2  HA   0.020
 T40  plan-2  H1   0.020
 T40  plan-2  H8   0.020
 T40  plan-2  H2   0.020

