# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 06:00:57 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: 3-[4-(1H-indol-5-yl)-2-{[(2-piperazin-1-ylethyl)amino]methyl}phenoxy]propan-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCOc1ccc(cc1CNCCN2CCNCC2)c3ccc4[nH]ccc4c3
#
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
 P13  P13  3-[4-(1H-indol-5-yl)-2-{[(2-piperazin-1-ylethyl)amino]methyl}phenoxy]propan-1-amine  ligand  63  30  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_P13
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
 P13  C1    C  CR16  0  -0.326  -0.7498   5.1343  16.5549
 P13  C2    C  CR6   0   0.103  -0.6256   3.8744  15.9696
 P13  C3    C  CR16  0  -0.381   0.5945   3.2120  16.1147
 P13  C4    C  CR6   0   0.048   1.6631   3.7579  16.8156
 P13  C5    C  CR6   0   0.311   1.5084   5.0228  17.3877
 P13  C6    C  CR16  0  -0.314   0.3026   5.7002  17.2567
 P13  N     N  NH2   0  -0.801   6.1914   5.9008  20.3385
 P13  CB    C  CH2   0  -0.277   5.0211   5.3113  19.7007
 P13  CA    C  CH2   0  -0.471   3.7749   6.1214  20.0277
 P13  C     C  CH2   0  -0.162   2.4987   5.5434  19.4582
 P13  O     O  O2    0  -0.497   2.5531   5.6081  18.0324
 P13  CA1   C  CH2   0  -0.343   2.9426   2.9834  16.9664
 P13  NB    N  NH1   0  -0.562   3.0325   2.3932  18.2920
 P13  CG    C  CH2   0  -0.335   4.2949   1.7234  18.5427
 P13  CD    C  CH2   0  -0.288   4.5730   0.5120  17.6518
 P13  NE    N  NT    0  -0.413   3.4755  -0.4330  17.6689
 P13  CH1   C  CH2   0  -0.282   3.4008  -1.1876  18.9060
 P13  CI1   C  CH2   0  -0.296   2.1738  -2.0810  18.9125
 P13  NJ    N  NH1   0  -0.600   2.2180  -2.9737  17.7698
 P13  CI2   C  CH2   0  -0.299   2.2555  -2.2118  16.5354
 P13  CH2   C  CH2   0  -0.269   3.4885  -1.3270  16.5275
 P13  N1    N  NR15  0  -0.679  -4.9899   1.6856  13.2333
 P13  C21   C  CR15  0  -0.025  -6.0190   2.1505  14.0020
 P13  C31   C  CR15  0  -0.426  -5.5257   2.8944  15.0348
 P13  C41   C  CR16  0  -0.415  -3.0547   3.4638  15.6240
 P13  C51   C  CR6   0   0.075  -1.7429   3.2684  15.2164
 P13  C61   C  CR16  0  -0.338  -1.4832   2.4890  14.0669
 P13  C71   C  CR16  0  -0.289  -2.4948   1.9120  13.3280
 P13  C81   C  CR56  0   0.337  -3.8060   2.1204  13.7513
 P13  C91   C  CR56  0   0.085  -4.1025   2.8935  14.8957
 P13  H1    H  HCR6  0   0.252  -1.6679   5.6978  16.4436
 P13  H3    H  HCR6  0   0.241   0.7201   2.2239  15.6846
 P13  H6    H  HCR6  0   0.260   0.1936   6.6910  17.6814
 P13  HN1A  H  HNH2  0   0.345   7.0025   5.3280  20.1420
 P13  HN2   H  HNH2  0   0.337   6.3873   6.7962  19.9066
 P13  HB1   H  HCH2  0   0.218   4.8924   4.2969  20.0878
 P13  HB2   H  HCH2  0   0.196   5.1225   5.2130  18.6119
 P13  HA1   H  HCH2  0   0.229   3.6587   6.1686  21.1139
 P13  HA2   H  HCH2  0   0.223   3.8964   7.1548  19.6853
 P13  HC1   H  HCH2  0   0.219   1.6352   6.1106  19.8249
 P13  HC2   H  HCH2  0   0.216   2.3798   4.5006  19.7682
 P13  HA11  H  HCH2  0   0.235   3.7994   3.6490  16.8359
 P13  HA12  H  HCH2  0   0.213   2.9939   2.2420  16.1567
 P13  HB11  H  HNH1  0   0.338   2.2934   1.7032  18.3800
 P13  HG1   H  HCH2  0   0.230   4.3179   1.4300  19.5955
 P13  HG2   H  HCH2  0   0.233   5.1068   2.4451  18.4172
 P13  HD1   H  HCH2  0   0.199   5.5296   0.0529  17.9552
 P13  HD2   H  HCH2  0   0.228   4.7116   0.8489  16.6209
 P13  HH11  H  HCH2  0   0.187   4.3028  -1.8086  19.0522
 P13  HH12  H  HCH2  0   0.235   3.3418  -0.5021  19.7537
 P13  HI11  H  HCH2  0   0.190   1.2762  -1.4422  18.9173
 P13  HI12  H  HCH2  0   0.230   2.1605  -2.6686  19.8328
 P13  HJ1   H  HNH1  0   0.352   1.4076  -3.5788  17.7755
 P13  HI21  H  HCH2  0   0.230   2.2944  -2.8967  15.6861
 P13  HI22  H  HCH2  0   0.189   1.3679  -1.5721  16.4056
 P13  HH21  H  HCH2  0   0.229   3.5015  -0.7328  15.6107
 P13  HH22  H  HCH2  0   0.183   4.3896  -1.9650  16.5158
 P13  HN1   H  HNR5  0   0.410  -5.0964   1.1161  12.4106
 P13  H2    H  HCR5  0   0.282  -7.0396   1.9131  13.7489
 P13  H31   H  HCR5  0   0.248  -6.1062   3.3866  15.7985
 P13  H4    H  HCR6  0   0.244  -3.2703   4.0420  16.5148
 P13  H61   H  HCR6  0   0.248  -0.4604   2.3557  13.7377
 P13  H7    H  HCR6  0   0.260  -2.2724   1.3282  12.4438

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
 P13  C1   C2    aromatic  1.395  0.020  1.395
 P13  C1   C6    aromatic  1.386  0.020  1.386
 P13  C1   H1    single    0.930  0.020  1.080
 P13  C2   C3    aromatic  1.396  0.020  1.396
 P13  C2   C51   single    1.477  0.020  1.477
 P13  C3   C4    aromatic  1.390  0.020  1.390
 P13  C3   H3    single    0.930  0.020  1.080
 P13  C4   C5    aromatic  1.397  0.020  1.397
 P13  C4   CA1   single    1.503  0.020  1.503
 P13  C5   C6    aromatic  1.389  0.020  1.389
 P13  C5   O     single    1.360  0.020  1.360
 P13  C6   H6    single    0.930  0.020  1.080
 P13  N    CB    single    1.457  0.020  1.457
 P13  N    HN1A  single    0.890  0.020  1.040
 P13  N    HN2   single    0.890  0.020  1.040
 P13  CB   CA    single    1.522  0.020  1.522
 P13  CB   HB1   single    0.970  0.020  1.090
 P13  CB   HB2   single    0.970  0.020  1.090
 P13  CA   C     single    1.512  0.020  1.512
 P13  CA   HA1   single    0.970  0.020  1.090
 P13  CA   HA2   single    0.970  0.020  1.090
 P13  C    O     single    1.428  0.020  1.428
 P13  C    HC1   single    0.970  0.020  1.090
 P13  C    HC2   single    0.970  0.020  1.090
 P13  CA1  NB    single    1.454  0.020  1.454
 P13  CA1  HA11  single    0.970  0.020  1.090
 P13  CA1  HA12  single    0.970  0.020  1.090
 P13  NB   CG    single    1.451  0.020  1.451
 P13  NB   HB11  single    0.890  0.020  1.040
 P13  CG   CD    single    1.529  0.020  1.529
 P13  CG   HG1   single    0.970  0.020  1.090
 P13  CG   HG2   single    0.970  0.020  1.090
 P13  CD   NE    single    1.448  0.020  1.448
 P13  CD   HD1   single    0.970  0.020  1.090
 P13  CD   HD2   single    0.970  0.020  1.090
 P13  NE   CH1   single    1.451  0.020  1.451
 P13  NE   CH2   single    1.450  0.020  1.450
 P13  CH1  CI1   single    1.518  0.020  1.518
 P13  CH1  HH11  single    0.970  0.020  1.090
 P13  CH1  HH12  single    0.970  0.020  1.090
 P13  CI1  NJ    single    1.451  0.020  1.451
 P13  CI1  HI11  single    0.970  0.020  1.090
 P13  CI1  HI12  single    0.970  0.020  1.090
 P13  NJ   CI2   single    1.451  0.020  1.451
 P13  NJ   HJ1   single    0.890  0.020  1.040
 P13  CI2  CH2   single    1.518  0.020  1.518
 P13  CI2  HI21  single    0.970  0.020  1.090
 P13  CI2  HI22  single    0.970  0.020  1.090
 P13  CH2  HH21  single    0.970  0.020  1.090
 P13  CH2  HH22  single    0.970  0.020  1.090
 P13  N1   C21   aromatic  1.366  0.020  1.366
 P13  N1   C81   aromatic  1.363  0.020  1.363
 P13  N1   HN1   single    0.860  0.020  1.020
 P13  C21  C31   aromatic  1.365  0.020  1.365
 P13  C21  H2    single    0.930  0.020  1.080
 P13  C31  C91   aromatic  1.430  0.020  1.430
 P13  C31  H31   single    0.930  0.020  1.080
 P13  C41  C51   aromatic  1.387  0.020  1.387
 P13  C41  C91   aromatic  1.398  0.020  1.398
 P13  C41  H4    single    0.930  0.020  1.080
 P13  C51  C61   aromatic  1.413  0.020  1.413
 P13  C61  C71   aromatic  1.379  0.020  1.379
 P13  C61  H61   single    0.930  0.020  1.080
 P13  C71  C81   aromatic  1.394  0.020  1.394
 P13  C71  H7    single    0.930  0.020  1.080
 P13  C81  C91   aromatic  1.413  0.020  1.413

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
 P13  H1    C1   C6    118.91  3.000
 P13  H1    C1   C2    120.16  3.000
 P13  C6    C1   C2    120.92  3.000
 P13  C51   C2   C3    121.29  3.000
 P13  C51   C2   C1    121.14  3.000
 P13  C3    C2   C1    117.58  3.000
 P13  H3    C3   C4    117.95  3.000
 P13  H3    C3   C2    119.48  3.000
 P13  C4    C3   C2    122.56  3.000
 P13  CA1   C4   C5    121.32  3.000
 P13  CA1   C4   C3    120.18  3.000
 P13  C5    C4   C3    118.50  3.000
 P13  O     C5   C6    120.10  3.000
 P13  O     C5   C4    119.92  3.000
 P13  C6    C5   C4    119.94  3.000
 P13  H6    C6   C5    119.75  3.000
 P13  H6    C6   C1    119.71  3.000
 P13  C5    C6   C1    120.52  3.000
 P13  HN2   N    HN1A  105.21  3.000
 P13  HN2   N    CB    109.04  3.000
 P13  HN1A  N    CB    109.24  3.000
 P13  HB2   CB   HB1   106.19  3.000
 P13  HB2   CB   CA    109.66  3.000
 P13  HB1   CB   CA    108.75  3.000
 P13  HB2   CB   N     113.33  3.000
 P13  HB1   CB   N     108.36  3.000
 P13  CA    CB   N     110.38  3.000
 P13  HA2   CA   HA1   106.35  3.000
 P13  HA2   CA   C     109.66  3.000
 P13  HA1   CA   C     107.51  3.000
 P13  HA2   CA   CB    110.13  3.000
 P13  HA1   CA   CB    108.87  3.000
 P13  C     CA   CB    113.99  3.000
 P13  HC2   C    HC1   108.22  3.000
 P13  HC2   C    O     109.28  3.000
 P13  HC1   C    O     109.90  3.000
 P13  HC2   C    CA    110.44  3.000
 P13  HC1   C    CA    109.94  3.000
 P13  O     C    CA    109.06  3.000
 P13  C     O    C5    115.12  3.000
 P13  HA12  CA1  HA11  106.64  3.000
 P13  HA12  CA1  NB    113.27  3.000
 P13  HA11  CA1  NB    107.92  3.000
 P13  HA12  CA1  C4    108.27  3.000
 P13  HA11  CA1  C4    109.97  3.000
 P13  NB    CA1  C4    110.69  3.000
 P13  HB11  NB   CG    107.75  3.000
 P13  HB11  NB   CA1   108.06  3.000
 P13  CG    NB   CA1   113.50  3.000
 P13  HG2   CG   HG1   105.79  3.000
 P13  HG2   CG   CD    108.72  3.000
 P13  HG1   CG   CD    110.16  3.000
 P13  HG2   CG   NB    108.75  3.000
 P13  HG1   CG   NB    107.98  3.000
 P13  CD    CG   NB    115.04  3.000
 P13  HD2   CD   HD1   106.11  3.000
 P13  HD2   CD   NE    107.95  3.000
 P13  HD1   CD   NE    112.46  3.000
 P13  HD2   CD   CG    109.17  3.000
 P13  HD1   CD   CG    109.09  3.000
 P13  NE    CD   CG    111.85  3.000
 P13  CH2   NE   CH1   110.55  3.000
 P13  CH2   NE   CD    112.72  3.000
 P13  CH1   NE   CD    112.85  3.000
 P13  HH12  CH1  HH11  107.12  3.000
 P13  HH12  CH1  CI1   108.82  3.000
 P13  HH11  CH1  CI1   109.19  3.000
 P13  HH12  CH1  NE    109.77  3.000
 P13  HH11  CH1  NE    111.29  3.000
 P13  CI1   CH1  NE    110.57  3.000
 P13  HI12  CI1  HI11  107.37  3.000
 P13  HI12  CI1  NJ    109.45  3.000
 P13  HI11  CI1  NJ    112.65  3.000
 P13  HI12  CI1  CH1   109.28  3.000
 P13  HI11  CI1  CH1   108.50  3.000
 P13  NJ    CI1  CH1   109.52  3.000
 P13  HJ1   NJ   CI2   109.85  3.000
 P13  HJ1   NJ   CI1   109.84  3.000
 P13  CI2   NJ   CI1   110.35  3.000
 P13  HI22  CI2  HI21  107.54  3.000
 P13  HI22  CI2  CH2   108.39  3.000
 P13  HI21  CI2  CH2   109.43  3.000
 P13  HI22  CI2  NJ    112.60  3.000
 P13  HI21  CI2  NJ    109.47  3.000
 P13  CH2   CI2  NJ    109.36  3.000
 P13  HH22  CH2  HH21  107.20  3.000
 P13  HH22  CH2  CI2   109.04  3.000
 P13  HH21  CH2  CI2   109.34  3.000
 P13  HH22  CH2  NE    111.83  3.000
 P13  HH21  CH2  NE    108.99  3.000
 P13  CI2   CH2  NE    110.37  3.000
 P13  HN1   N1   C81   125.66  3.000
 P13  HN1   N1   C21   124.96  3.000
 P13  C81   N1   C21   109.38  3.000
 P13  H2    C21  C31   129.78  3.000
 P13  H2    C21  N1    120.41  3.000
 P13  C31   C21  N1    109.81  3.000
 P13  H31   C31  C91   127.23  3.000
 P13  H31   C31  C21   126.16  3.000
 P13  C91   C31  C21   106.61  3.000
 P13  H4    C41  C91   119.79  3.000
 P13  H4    C41  C51   120.31  3.000
 P13  C91   C41  C51   119.89  3.000
 P13  C61   C51  C41   119.37  3.000
 P13  C61   C51  C2    120.14  3.000
 P13  C41   C51  C2    120.49  3.000
 P13  H61   C61  C71   118.59  3.000
 P13  H61   C61  C51   119.27  3.000
 P13  C71   C61  C51   122.13  3.000
 P13  H7    C71  C81   121.47  3.000
 P13  H7    C71  C61   120.82  3.000
 P13  C81   C71  C61   117.70  3.000
 P13  C91   C81  C71   121.70  3.000
 P13  C91   C81  N1    107.46  3.000
 P13  C71   C81  N1    130.84  3.000
 P13  C81   C91  C41   119.22  3.000
 P13  C81   C91  C31   106.74  3.000
 P13  C41   C91  C31   134.05  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
 P13  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 P13  CONST_04  C4    C5   C6   C1      0.00   0.0  0
 P13  CONST_05  C5    C6   C1   C2      0.00   0.0  0
 P13  CONST_06  C5    C4   C3   C2      0.00   0.0  0
 P13  CONST_07  C91   C41  C51  C2    180.00   0.0  0
 P13  CONST_08  C71   C61  C51  C2    180.00   0.0  0
 P13  CONST_09  C6    C1   C2   C3      0.00   0.0  0
 P13  CONST_12  C6    C5   C4   C3      0.00   0.0  0
 P13  CONST_13  C51   C2   C3   C4    180.00   0.0  0
 P13  CONST_14  C51   C2   C1   C6    180.00   0.0  0
 P13  CONST_15  C91   C31  C21  N1      0.00   0.0  0
 P13  CONST_16  C61   C71  C81  N1    180.00   0.0  0
 P13  CONST_17  C31   C91  C81  N1      0.00   0.0  0
 P13  CONST_18  C41   C91  C81  N1    180.00   0.0  0
 P13  CONST_19  C71   C81  N1   C21   180.00   0.0  0
 P13  CONST_20  C91   C81  N1   C21     0.00   0.0  0
 P13  CONST_21  C41   C91  C31  C21   180.00   0.0  0
 P13  CONST_22  C81   C91  C31  C21     0.00   0.0  0
 P13  CONST_23  C81   N1   C21  C31     0.00   0.0  0
 P13  CONST_24  C51   C41  C91  C31   180.00   0.0  0
 P13  CONST_25  C71   C81  C91  C31   180.00   0.0  0
 P13  CONST_26  C71   C61  C51  C41     0.00   0.0  0
 P13  CONST_27  C71   C81  C91  C41     0.00   0.0  0
 P13  CONST_28  C81   C91  C41  C51     0.00   0.0  0
 P13  CONST_29  C81   C71  C61  C51     0.00   0.0  0
 P13  CONST_30  C91   C41  C51  C61     0.00   0.0  0
 P13  CONST_31  C91   C81  C71  C61     0.00   0.0  0
 P13  CONST_32  O     C5   C6   C1    180.00   0.0  0
 P13  CONST_33  CA1   C4   C3   C2    180.00   0.0  0
 P13  CONST_34  O     C5   C4   C3    180.00   0.0  0
 P13  CONST_35  CA1   C4   C5   C6    180.00   0.0  0
 P13  CONST_36  H3    C3   C2   C1    180.00   0.0  0
 P13  CONST_37  H6    C6   C1   C2    180.00   0.0  0
 P13  CONST_38  H4    C41  C51  C2      0.00   0.0  0
 P13  CONST_39  H61   C61  C51  C2      0.00   0.0  0
 P13  CONST_40  H1    C1   C2   C3    180.00   0.0  0
 P13  CONST_41  H31   C31  C21  N1    180.00   0.0  0
 P13  CONST_42  H7    C71  C81  N1      0.00   0.0  0
 P13  CONST_43  HN1   N1   C21  C31   180.00   0.0  0
 P13  CONST_44  H2    C21  N1   C81   180.00   0.0  0
 P13  Var_01    NJ    CI1  CH1  NE     57.78  30.0  1
 P13  Var_02    NJ    CI2  CH2  NE    -58.54  30.0  1
 P13  Var_03    CI2   CH2  NE   CH1    57.50  30.0  1
 P13  Var_04    CI2   NJ   CI1  CH1   -59.40  30.0  1
 P13  Var_05    CH2   NE   CH1  CI1   -57.14  30.0  1
 P13  Var_06    CH2   CI2  NJ   CI1    59.78  30.0  1
 P13  Var_07    NB    CA1  C4   C3   -102.16  30.0  2
 P13  Var_08    CH1   NE   CD   CG    -73.80  30.0  3
 P13  Var_09    CG    NB   CA1  C4   -175.18  30.0  3
 P13  Var_10    CA    C    O    C5    175.06  30.0  1
 P13  Var_11    NE    CD   CG   NB    -52.36  30.0  3
 P13  Var_12    C     CA   CB   N    -177.30  30.0  3
 P13  Var_13    O     C    CA   CB    -65.78  30.0  3
 P13  Var_14    CD    CG   NB   CA1   -63.77  30.0  3
 P13  Var_15    HN1A  N    CB   CA    177.66  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
 P13  plan-1  C1   0.020
 P13  plan-1  C2   0.020
 P13  plan-1  C3   0.020
 P13  plan-1  C4   0.020
 P13  plan-1  C5   0.020
 P13  plan-1  C6   0.020
 P13  plan-1  O    0.020
 P13  plan-1  CA1  0.020
 P13  plan-1  C51  0.020
 P13  plan-1  H1   0.020
 P13  plan-1  H3   0.020
 P13  plan-1  H6   0.020
 P13  plan-2  C2   0.020
 P13  plan-2  N1   0.020
 P13  plan-2  C21  0.020
 P13  plan-2  C31  0.020
 P13  plan-2  C41  0.020
 P13  plan-2  C51  0.020
 P13  plan-2  C61  0.020
 P13  plan-2  C71  0.020
 P13  plan-2  C81  0.020
 P13  plan-2  C91  0.020
 P13  plan-2  HN1  0.020
 P13  plan-2  H2   0.020
 P13  plan-2  H31  0.020
 P13  plan-2  H4   0.020
 P13  plan-2  H61  0.020
 P13  plan-2  H7   0.020

