# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 03:37:13 2021
#   Inital geometry file: a 113 line input string
#   Ligand name: 3-[(3~{S})-3-[(7-chloranyl-9~{H}-pyrimido[4,5-b]indol-4-yl)-methyl-amino]piperidin-1-yl]propanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN([C@H]1CCCN(CCC#N)C1)c2ncnc3[nH]c4cc(Cl)ccc4c23
#
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
 SZW  SZW  3-[(3~{S})-3-[(7-chloranyl-9~{H}-pyrimido[4,5-b]indol-4-yl)-methyl-amino]piperidin-1-yl]propanenitrile  ligand  47  26  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SZW
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
 SZW  N    N   NT    0  -0.474   -9.0012   2.2366  31.7774
 SZW  C    C   CR6   0  -0.067   -6.2382   7.5616  32.5610
 SZW  C1   C   CR16  0  -0.220   -5.7863   6.2485  32.4603
 SZW  C10  C   CH2   0  -0.446   -6.4618   1.1084  34.3603
 SZW  C11  C   CH2   0  -0.286   -5.3256   0.8600  33.3811
 SZW  C13  C   CH2   0  -0.576   -2.8697   2.0149  32.0327
 SZW  C14  C   CSP   0   0.153   -2.8535   3.3488  32.6105
 SZW  C15  C   CH2   0  -0.311   -6.5890   1.8211  31.5857
 SZW  C16  C   CH3   0  -0.538   -9.6031   0.9986  31.3105
 SZW  C17  C   CR16  0   0.051  -11.8599   4.1952  31.3496
 SZW  C18  C   CR56  0   0.461  -10.3130   5.6679  31.8742
 SZW  C2   C   CR16  0  -0.439   -6.6822   5.2132  32.2578
 SZW  C3   C   CR16  0  -0.264   -7.5764   7.8782  32.4569
 SZW  C4   C   CR56  0   0.351   -8.4546   6.8233  32.2525
 SZW  C5   C   CR56  0   0.083   -8.0555   5.4676  32.1585
 SZW  C6   C   CR56  0  -0.086   -9.2800   4.7061  31.9354
 SZW  C7   C   CR6   0   0.460   -9.7316   3.3710  31.7149
 SZW  C8   C   CH1   0  -0.133   -7.7587   2.1316  32.5188
 SZW  C9   C   CH2   0  -0.426   -7.8122   1.1123  33.6537
 SZW  N1   N   NT    0  -0.417   -5.3304   1.8421  32.3079
 SZW  N2   N   NS    0  -0.291   -2.8236   4.4078  33.0599
 SZW  N3   N   N     0  -0.489  -11.0208   3.1799  31.3885
 SZW  N4   N   N     0  -0.455  -11.5976   5.4613  31.6054
 SZW  N5   N   NR15  0  -0.750   -9.8079   6.9037  32.0919
 SZW  H1   H   HCR6  0   0.284   -4.7312   6.0281  32.5450
 SZW  H2   H   HCH2  0   0.244   -6.4423   0.3386  35.1334
 SZW  H3   H   HCH2  0   0.227   -6.3014   2.0682  34.8593
 SZW  H4   H   HCH2  0   0.196   -5.4031  -0.1645  32.9770
 SZW  H5   H   HCH2  0   0.246   -4.3787   0.9148  33.9210
 SZW  H6   H   HCH2  0   0.258   -4.3712   2.3508  30.5488
 SZW  H7   H   HCH2  0   0.233   -4.1479   0.6609  30.9903
 SZW  H8   H   HCH2  0   0.309   -2.5919   1.3017  32.8099
 SZW  H9   H   HCH2  0   0.323   -2.0900   1.9627  31.2713
 SZW  H10  H   HCH2  0   0.253   -6.5518   2.5668  30.7867
 SZW  H11  H   HCH2  0   0.229   -6.7602   0.8467  31.0950
 SZW  H12  H   HCH3  0   0.246   -8.8259   0.2465  31.2059
 SZW  H13  H   HCH3  0   0.241  -10.3615   0.6140  31.9943
 SZW  H14  H   HCH3  0   0.255  -10.0643   1.1358  30.3358
 SZW  H15  H   HCR6  0   0.250  -12.8848   3.9551  31.0842
 SZW  H16  H   HCR6  0   0.277   -6.2612   4.2217  32.1934
 SZW  H17  H   HCR6  0   0.287   -7.9302   8.8984  32.5235
 SZW  H18  H   HCH1  0   0.262   -7.5874   3.0918  32.9986
 SZW  H19  H   HCH2  0   0.249   -8.6154   1.3633  34.3502
 SZW  H20  H   HCH2  0   0.228   -8.0197   0.1102  33.2682
 SZW  H22  H   HNR5  0   0.416  -10.3522   7.7515  32.0705
 SZW  CL   CL  CL    0  -0.132   -5.0873   8.8324  32.8186
 SZW  C12  C   CH2   0  -0.273   -4.2183   1.6814  31.3970

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
 SZW  C16  N    single    1.454  0.020  1.454
 SZW  C12  C13  single    1.528  0.020  1.528
 SZW  C12  N1   single    1.446  0.020  1.446
 SZW  C15  N1   single    1.451  0.020  1.451
 SZW  C15  C8   single    1.528  0.020  1.528
 SZW  C17  N4   aromatic  1.318  0.020  1.318
 SZW  C17  N3   aromatic  1.318  0.020  1.318
 SZW  N4   C18  aromatic  1.329  0.020  1.329
 SZW  N3   C7   aromatic  1.344  0.020  1.344
 SZW  N    C7   single    1.351  0.020  1.351
 SZW  N    C8   single    1.451  0.020  1.451
 SZW  C18  N5   aromatic  1.353  0.020  1.353
 SZW  C18  C6   aromatic  1.413  0.020  1.413
 SZW  C7   C6   aromatic  1.427  0.020  1.427
 SZW  N5   C4   aromatic  1.365  0.020  1.365
 SZW  C6   C5   aromatic  1.459  0.020  1.459
 SZW  C4   C3   aromatic  1.388  0.020  1.388
 SZW  C4   C5   aromatic  1.416  0.020  1.416
 SZW  C3   C    aromatic  1.379  0.020  1.379
 SZW  C5   C2   aromatic  1.400  0.020  1.400
 SZW  C13  C14  single    1.454  0.020  1.454
 SZW  N1   C11  single    1.455  0.020  1.455
 SZW  CL   C    single    1.734  0.020  1.734
 SZW  C    C1   aromatic  1.392  0.020  1.392
 SZW  C2   C1   aromatic  1.384  0.020  1.384
 SZW  C8   C9   single    1.526  0.020  1.526
 SZW  C14  N2   triple    1.151  0.020  1.151
 SZW  C11  C10  single    1.520  0.020  1.520
 SZW  C9   C10  single    1.524  0.020  1.524
 SZW  C1   H1   single    0.930  0.020  1.080
 SZW  C10  H2   single    0.970  0.020  1.090
 SZW  C10  H3   single    0.970  0.020  1.090
 SZW  C11  H4   single    0.970  0.020  1.090
 SZW  C11  H5   single    0.970  0.020  1.090
 SZW  C12  H6   single    0.970  0.020  1.090
 SZW  C12  H7   single    0.970  0.020  1.090
 SZW  C13  H8   single    0.970  0.020  1.090
 SZW  C13  H9   single    0.970  0.020  1.090
 SZW  C15  H10  single    0.970  0.020  1.090
 SZW  C15  H11  single    0.970  0.020  1.090
 SZW  C16  H12  single    0.970  0.020  1.090
 SZW  C16  H13  single    0.970  0.020  1.090
 SZW  C16  H14  single    0.970  0.020  1.090
 SZW  C17  H15  single    0.930  0.020  1.080
 SZW  C2   H16  single    0.930  0.020  1.080
 SZW  C3   H17  single    0.930  0.020  1.080
 SZW  C8   H18  single    0.970  0.020  1.090
 SZW  C9   H19  single    0.970  0.020  1.090
 SZW  C9   H20  single    0.970  0.020  1.090
 SZW  N5   H22  single    0.860  0.020  1.020

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
 SZW  C8   N    C7   123.20  3.000
 SZW  C8   N    C16  117.21  3.000
 SZW  C7   N    C16  118.46  3.000
 SZW  CL   C    C3   119.15  3.000
 SZW  CL   C    C1   119.11  3.000
 SZW  C3   C    C1   121.74  3.000
 SZW  H1   C1   C2   119.38  3.000
 SZW  H1   C1   C    120.22  3.000
 SZW  C2   C1   C    120.40  3.000
 SZW  H3   C10  H2   107.06  3.000
 SZW  H3   C10  C9   109.83  3.000
 SZW  H2   C10  C9   110.25  3.000
 SZW  H3   C10  C11  109.13  3.000
 SZW  H2   C10  C11  109.13  3.000
 SZW  C9   C10  C11  111.34  3.000
 SZW  H5   C11  H4   106.77  3.000
 SZW  H5   C11  N1   109.50  3.000
 SZW  H4   C11  N1   110.87  3.000
 SZW  H5   C11  C10  108.76  3.000
 SZW  H4   C11  C10  109.57  3.000
 SZW  N1   C11  C10  111.24  3.000
 SZW  H9   C13  H8   106.50  3.000
 SZW  H9   C13  C14  108.26  3.000
 SZW  H8   C13  C14  108.29  3.000
 SZW  H9   C13  C12  109.27  3.000
 SZW  H8   C13  C12  112.24  3.000
 SZW  C14  C13  C12  112.06  3.000
 SZW  N2   C14  C13  180.00  3.000
 SZW  H11  C15  H10  106.40  3.000
 SZW  H11  C15  N1   111.61  3.000
 SZW  H10  C15  N1   108.92  3.000
 SZW  H11  C15  C8   109.39  3.000
 SZW  H10  C15  C8   109.49  3.000
 SZW  N1   C15  C8   110.92  3.000
 SZW  H14  C16  H13  108.15  3.000
 SZW  H14  C16  H12  107.73  3.000
 SZW  H13  C16  H12  108.26  3.000
 SZW  H14  C16  N    110.87  3.000
 SZW  H13  C16  N    112.75  3.000
 SZW  H12  C16  N    108.92  3.000
 SZW  H15  C17  N4   116.60  3.000
 SZW  H15  C17  N3   115.98  3.000
 SZW  N4   C17  N3   127.42  3.000
 SZW  N5   C18  N4   122.39  3.000
 SZW  N5   C18  C6   109.99  3.000
 SZW  N4   C18  C6   127.58  3.000
 SZW  H16  C2   C5   123.05  3.000
 SZW  H16  C2   C1   116.33  3.000
 SZW  C5   C2   C1   120.62  3.000
 SZW  H17  C3   C4   121.26  3.000
 SZW  H17  C3   C    121.95  3.000
 SZW  C4   C3   C    116.79  3.000
 SZW  N5   C4   C5   109.14  3.000
 SZW  C5   C4   C3   123.99  3.000
 SZW  N5   C4   C3   126.87  3.000
 SZW  C6   C5   C4   105.86  3.000
 SZW  C4   C5   C2   116.47  3.000
 SZW  C6   C5   C2   137.65  3.000
 SZW  C7   C6   C5   141.05  3.000
 SZW  C5   C6   C18  105.36  3.000
 SZW  C7   C6   C18  113.51  3.000
 SZW  N3   C7   C6   118.32  3.000
 SZW  C6   C7   N    127.42  3.000
 SZW  N3   C7   N    114.25  3.000
 SZW  H18  C8   C9   105.50  3.000
 SZW  H18  C8   C15  109.17  3.000
 SZW  C9   C8   C15  110.19  3.000
 SZW  H18  C8   N    107.26  3.000
 SZW  C9   C8   N    113.47  3.000
 SZW  C15  C8   N    110.99  3.000
 SZW  H20  C9   H19  107.20  3.000
 SZW  H20  C9   C8   110.88  3.000
 SZW  H19  C9   C8   110.27  3.000
 SZW  H20  C9   C10  109.22  3.000
 SZW  H19  C9   C10  110.88  3.000
 SZW  C8   C9   C10  108.38  3.000
 SZW  C15  N1   C12  110.59  3.000
 SZW  C15  N1   C11  111.11  3.000
 SZW  C12  N1   C11  112.77  3.000
 SZW  C7   N3   C17  120.57  3.000
 SZW  C18  N4   C17  112.40  3.000
 SZW  H22  N5   C4   125.98  3.000
 SZW  H22  N5   C18  124.30  3.000
 SZW  C4   N5   C18  109.59  3.000
 SZW  H7   C12  H6   106.88  3.000
 SZW  H7   C12  N1   112.64  3.000
 SZW  H6   C12  N1   108.28  3.000
 SZW  H7   C12  C13  107.43  3.000
 SZW  H6   C12  C13  108.25  3.000
 SZW  N1   C12  C13  113.10  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
 SZW  CONST_01  N5   C4   C3   C    180.00   0.0  0
 SZW  CONST_02  C5   C4   C3   C      0.00   0.0  0
 SZW  CONST_03  C5   C2   C1   C      0.00   0.0  0
 SZW  CONST_04  C4   C3   C    C1     0.00   0.0  0
 SZW  CONST_05  C6   C5   C2   C1   180.00   0.0  0
 SZW  CONST_06  C4   C5   C2   C1     0.00   0.0  0
 SZW  CONST_07  N5   C18  N4   C17  180.00   0.0  0
 SZW  CONST_08  C6   C18  N4   C17    0.00   0.0  0
 SZW  CONST_09  C6   C7   N3   C17    0.00   0.0  0
 SZW  CONST_10  N3   C17  N4   C18    0.00   0.0  0
 SZW  CONST_11  C3   C4   N5   C18  180.00   0.0  0
 SZW  CONST_12  C5   C4   N5   C18    0.00   0.0  0
 SZW  CONST_13  N3   C7   C6   C18    0.00   0.0  0
 SZW  CONST_14  C4   C5   C6   C18    0.00   0.0  0
 SZW  CONST_15  C2   C5   C6   C18  180.00   0.0  0
 SZW  CONST_16  C7   C6   C5   C2     0.00   0.0  0
 SZW  CONST_17  N5   C4   C5   C2   180.00   0.0  0
 SZW  CONST_18  C3   C4   C5   C2     0.00   0.0  0
 SZW  CONST_19  C3   C    C1   C2     0.00   0.0  0
 SZW  CONST_20  C6   C5   C4   C3   180.00   0.0  0
 SZW  CONST_21  N4   C18  N5   C4   180.00   0.0  0
 SZW  CONST_22  C6   C18  N5   C4     0.00   0.0  0
 SZW  CONST_23  C7   C6   C5   C4   180.00   0.0  0
 SZW  CONST_24  N4   C18  C6   C5   180.00   0.0  0
 SZW  CONST_25  N5   C18  C6   C5     0.00   0.0  0
 SZW  CONST_26  N3   C7   C6   C5   180.00   0.0  0
 SZW  CONST_27  N5   C4   C5   C6     0.00   0.0  0
 SZW  CONST_28  N4   C17  N3   C7     0.00   0.0  0
 SZW  CONST_29  N4   C18  C6   C7     0.00   0.0  0
 SZW  CONST_30  N5   C18  C6   C7   180.00   0.0  0
 SZW  CONST_31  C17  N3   C7   N    180.00   0.0  0
 SZW  CONST_32  C18  C6   C7   N    180.00   0.0  0
 SZW  CONST_33  C5   C6   C7   N      0.00   0.0  0
 SZW  CONST_34  CL   C    C1   C2   180.00   0.0  0
 SZW  CONST_35  CL   C    C3   C4   180.00   0.0  0
 SZW  CONST_38  H16  C2   C1   C    180.00   0.0  0
 SZW  CONST_39  H17  C3   C    C1   180.00   0.0  0
 SZW  CONST_40  H15  C17  N4   C18  180.00   0.0  0
 SZW  CONST_41  H22  N5   C4   C3     0.00   0.0  0
 SZW  CONST_42  H1   C1   C    C3   180.00   0.0  0
 SZW  CONST_43  N3   C7   N    C16    0.00   0.0  0
 SZW  CONST_44  C6   C7   N    C16  180.00   0.0  0
 SZW  Var_01    C15  N1   C11  C10  -58.39  30.0  1
 SZW  Var_02    C8   C15  N1   C11   59.72  30.0  1
 SZW  Var_03    C8   C9   C10  C11  -54.70  30.0  1
 SZW  Var_04    N1   C11  C10  C9    56.55  30.0  1
 SZW  Var_05    C13  C12  N1   C11  -68.25  30.0  2
 SZW  Var_06    N1   C12  C13  C14  -54.83  30.0  1
 SZW  Var_07    H12  C16  N    C7   166.66  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
 SZW  chir_01  C8  C15  N  C9  negativ

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
 SZW  plan-1  N    0.020
 SZW  plan-1  C    0.020
 SZW  plan-1  C1   0.020
 SZW  plan-1  C17  0.020
 SZW  plan-1  C18  0.020
 SZW  plan-1  C2   0.020
 SZW  plan-1  C3   0.020
 SZW  plan-1  C4   0.020
 SZW  plan-1  C5   0.020
 SZW  plan-1  C6   0.020
 SZW  plan-1  C7   0.020
 SZW  plan-1  N3   0.020
 SZW  plan-1  N4   0.020
 SZW  plan-1  N5   0.020
 SZW  plan-1  H1   0.020
 SZW  plan-1  H15  0.020
 SZW  plan-1  H16  0.020
 SZW  plan-1  H17  0.020
 SZW  plan-1  H22  0.020
 SZW  plan-1  CL   0.020
 SZW  plan-2  N    0.020
 SZW  plan-2  C16  0.020
 SZW  plan-2  C7   0.020
 SZW  plan-2  C8   0.020

