# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 21:40:59 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: (2S)-N~1~-[5-(1H-indazol-5-yl)-1,3,4-thiadiazol-2-yl]-3-(4-methylphenyl)propane-1,2-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(C[C@H](N)CNc2sc(nn2)c3ccc4[nH]ncc4c3)cc1
#
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
 L9N  L9N  (2S)-N~1~-[5-(1H-indazol-5-yl)-1,3,4-thiadiazol-2-yl]-3-(4-methylphenyl)propane-1,2-diamine  ligand  46  26  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L9N
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
 L9N  C1    C  CR16  0  -0.298   -6.3356  -0.4618  -1.2164
 L9N  N1    N  N     0  -0.221    8.4987  -0.3989  -1.0598
 L9N  S1    S  S2    0   0.147    1.5790   0.8315   1.1206
 L9N  C2    C  CR16  0  -0.283   -7.5846   0.1217  -1.3624
 L9N  N2    N  N     0  -0.321    0.7494  -1.2061  -0.1763
 L9N  C3    C  CR6   0   0.080   -8.3388   0.4984  -0.2512
 L9N  N3    N  NH2   0  -0.775   -3.2499   0.5907  -0.7552
 L9N  C4    C  CR16  0  -0.291   -7.7945   0.2696   1.0087
 L9N  N4    N  NR15  0  -0.544    8.1253   0.6938  -0.3881
 L9N  C5    C  CR16  0  -0.299   -6.5439  -0.3189   1.1538
 L9N  N5    N  N     0  -0.263    2.0689  -1.1142  -0.4303
 L9N  C6    C  CR6   0   0.155   -5.7938  -0.6962   0.0453
 L9N  C7    C  CH2   0  -0.269   -2.0049  -1.0325   0.6821
 L9N  C8    C  CH2   0  -0.532   -4.4390  -1.3218   0.2116
 L9N  C9    C  CR15  0  -0.126    7.4206  -1.1121  -1.2575
 L9N  C10   C  CH1   0  -0.112   -3.3163  -0.2973   0.3884
 L9N  C11   C  CR16  0  -0.330    4.6408   1.3327   0.6009
 L9N  C12   C  CR5   0   0.341    0.3218  -0.2603   0.6117
 L9N  C13   C  CR16  0  -0.267    5.9784   1.6340   0.5234
 L9N  C14   C  CR56  0   0.417    6.7988   0.7133  -0.1361
 L9N  C15   C  CR56  0  -0.058    6.2826  -0.4694  -0.6960
 L9N  C16   C  CR16  0  -0.360    4.9207  -0.7556  -0.6033
 L9N  C17   C  CR6   0   0.090    4.0967   0.1474   0.0467
 L9N  C18   C  CR5   0   0.027    2.6675  -0.1343   0.1524
 L9N  CL1   C  CH3   0  -0.723   -9.6978   1.1149  -0.4185
 L9N  H1    H  HCR6  0   0.237   -5.7773  -0.7482  -2.0998
 L9N  H2    H  HCR6  0   0.242   -7.9807   0.2863  -2.3582
 L9N  HN3   H  HNH2  0   0.347   -2.4551   1.2110  -0.6575
 L9N  HN3A  H  HNH2  0   0.335   -3.0816   0.0519  -1.5974
 L9N  H4    H  HCR6  0   0.242   -8.3566   0.5462   1.8932
 L9N  H5    H  HCR6  0   0.241   -6.1515  -0.4929   2.1496
 L9N  H7    H  HCH2  0   0.253   -1.7026  -1.6091  -0.1920
 L9N  H7A   H  HCH2  0   0.238   -2.1376  -1.7381   1.5094
 L9N  H8    H  HCH2  0   0.251   -4.4445  -1.9818   1.0829
 L9N  H8A   H  HCH2  0   0.244   -4.2139  -1.9550  -0.6532
 L9N  H9    H  HCR5  0   0.272    7.4688  -2.0518  -1.7862
 L9N  H10   H  HCH1  0   0.234   -3.5593   0.3145   1.2666
 L9N  H11   H  HCR6  0   0.259    3.9912   2.0392   1.1037
 L9N  H13   H  HCR6  0   0.280    6.3708   2.5452   0.9533
 L9N  H16   H  HCR6  0   0.262    4.5166  -1.6659  -1.0259
 L9N  HL1   H  HCH3  0   0.244  -10.3898   0.4217  -0.9002
 L9N  HL1A  H  HCH3  0   0.241  -10.1299   1.3979   0.5406
 L9N  HL1B  H  HCH3  0   0.243   -9.6566   2.0086  -1.0432
 L9N  N6    N  NH1   0  -0.676   -0.9522  -0.0858   0.9919
 L9N  HN4   H  HNR5  0   0.420    8.8153   1.3808  -0.1313
 L9N  HN6   H  HNH1  0   0.408   -1.1282   0.5495   1.7540

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
 L9N  C1   C2    aromatic  1.386  0.020  1.386
 L9N  C1   C6    aromatic  1.393  0.020  1.393
 L9N  N1   N4    aromatic  1.336  0.020  1.336
 L9N  N1   C9    aromatic  1.308  0.020  1.308
 L9N  S1   C12   aromatic  1.741  0.020  1.741
 L9N  S1   C18   aromatic  1.748  0.020  1.748
 L9N  C2   C3    aromatic  1.395  0.020  1.395
 L9N  N2   N5    aromatic  1.347  0.020  1.347
 L9N  N2   C12   aromatic  1.303  0.020  1.303
 L9N  C3   C4    aromatic  1.391  0.020  1.391
 L9N  C3   CL1   single    1.502  0.020  1.502
 L9N  N3   C10   single    1.449  0.020  1.449
 L9N  C4   C5    aromatic  1.390  0.020  1.390
 L9N  N4   C14   aromatic  1.350  0.020  1.350
 L9N  C5   C6    aromatic  1.391  0.020  1.391
 L9N  N5   C18   aromatic  1.288  0.020  1.288
 L9N  C6   C8    single    1.501  0.020  1.501
 L9N  N6   C7    single    1.449  0.020  1.449
 L9N  N6   C12   single    1.341  0.020  1.341
 L9N  C7   C10   single    1.532  0.020  1.532
 L9N  C8   C10   single    1.530  0.020  1.530
 L9N  C9   C15   aromatic  1.422  0.020  1.422
 L9N  C11  C13   aromatic  1.373  0.020  1.373
 L9N  C11  C17   aromatic  1.417  0.020  1.417
 L9N  C13  C14   aromatic  1.398  0.020  1.398
 L9N  C14  C15   aromatic  1.407  0.020  1.407
 L9N  C15  C16   aromatic  1.395  0.020  1.395
 L9N  C16  C17   aromatic  1.385  0.020  1.385
 L9N  C17  C18   single    1.460  0.020  1.460
 L9N  C1   H1    single    0.930  0.020  1.080
 L9N  C2   H2    single    0.930  0.020  1.080
 L9N  N3   HN3   single    0.890  0.020  1.040
 L9N  N3   HN3A  single    0.890  0.020  1.040
 L9N  C4   H4    single    0.930  0.020  1.080
 L9N  N4   HN4   single    0.860  0.020  1.020
 L9N  C5   H5    single    0.930  0.020  1.080
 L9N  N6   HN6   single    0.890  0.020  1.040
 L9N  C7   H7    single    0.970  0.020  1.090
 L9N  C7   H7A   single    0.970  0.020  1.090
 L9N  C8   H8    single    0.970  0.020  1.090
 L9N  C8   H8A   single    0.970  0.020  1.090
 L9N  C9   H9    single    0.930  0.020  1.080
 L9N  C10  H10   single    0.970  0.020  1.090
 L9N  C11  H11   single    0.930  0.020  1.080
 L9N  C13  H13   single    0.930  0.020  1.080
 L9N  C16  H16   single    0.930  0.020  1.080
 L9N  CL1  HL1   single    0.970  0.020  1.090
 L9N  CL1  HL1A  single    0.970  0.020  1.090
 L9N  CL1  HL1B  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
 L9N  H1    C1   C6    119.57  3.000
 L9N  H1    C1   C2    119.32  3.000
 L9N  C6    C1   C2    121.11  3.000
 L9N  C9    N1   N4    106.96  3.000
 L9N  C18   S1   C12    86.64  3.000
 L9N  H2    C2   C3    119.54  3.000
 L9N  H2    C2   C1    119.33  3.000
 L9N  C3    C2   C1    121.13  3.000
 L9N  C12   N2   N5    112.70  3.000
 L9N  CL1   C3   C4    121.50  3.000
 L9N  CL1   C3   C2    120.76  3.000
 L9N  C4    C3   C2    117.74  3.000
 L9N  HN3A  N3   HN3   105.98  3.000
 L9N  HN3A  N3   C10   109.73  3.000
 L9N  HN3   N3   C10   109.58  3.000
 L9N  H4    C4   C5    119.31  3.000
 L9N  H4    C4   C3    119.61  3.000
 L9N  C5    C4   C3    121.08  3.000
 L9N  HN4   N4   C14   128.00  3.000
 L9N  HN4   N4   N1    119.66  3.000
 L9N  C14   N4   N1    112.35  3.000
 L9N  H5    C5   C6    119.56  3.000
 L9N  H5    C5   C4    119.31  3.000
 L9N  C6    C5   C4    121.13  3.000
 L9N  C18   N5   N2    114.96  3.000
 L9N  C8    C6   C5    120.76  3.000
 L9N  C8    C6   C1    121.43  3.000
 L9N  C5    C6   C1    117.81  3.000
 L9N  H7A   C7   H7    107.37  3.000
 L9N  H7A   C7   C10   110.50  3.000
 L9N  H7    C7   C10   109.73  3.000
 L9N  H7A   C7   N6    110.33  3.000
 L9N  H7    C7   N6    108.40  3.000
 L9N  C10   C7   N6    110.44  3.000
 L9N  H8A   C8   H8    106.34  3.000
 L9N  H8A   C8   C10   109.12  3.000
 L9N  H8    C8   C10   108.41  3.000
 L9N  H8A   C8   C6    109.80  3.000
 L9N  H8    C8   C6    109.60  3.000
 L9N  C10   C8   C6    113.32  3.000
 L9N  H9    C9   C15   128.50  3.000
 L9N  H9    C9   N1    120.80  3.000
 L9N  C15   C9   N1    110.70  3.000
 L9N  H10   C10  C8    107.65  3.000
 L9N  H10   C10  C7    107.68  3.000
 L9N  C8    C10  C7    109.20  3.000
 L9N  H10   C10  N3    107.46  3.000
 L9N  C8    C10  N3    110.65  3.000
 L9N  C7    C10  N3    113.96  3.000
 L9N  H11   C11  C17   119.78  3.000
 L9N  H11   C11  C13   117.85  3.000
 L9N  C17   C11  C13   122.37  3.000
 L9N  N6    C12  N2    125.28  3.000
 L9N  N6    C12  S1    121.44  3.000
 L9N  N2    C12  S1    113.26  3.000
 L9N  H13   C13  C14   121.97  3.000
 L9N  H13   C13  C11   121.06  3.000
 L9N  C14   C13  C11   116.97  3.000
 L9N  C15   C14  C13   121.74  3.000
 L9N  C15   C14  N4    105.90  3.000
 L9N  C13   C14  N4    132.36  3.000
 L9N  C16   C15  C14   120.29  3.000
 L9N  C16   C15  C9    135.62  3.000
 L9N  C14   C15  C9    104.09  3.000
 L9N  H16   C16  C17   120.65  3.000
 L9N  H16   C16  C15   120.76  3.000
 L9N  C17   C16  C15   118.59  3.000
 L9N  C18   C17  C16   119.38  3.000
 L9N  C18   C17  C11   120.58  3.000
 L9N  C16   C17  C11   120.04  3.000
 L9N  C17   C18  N5    124.67  3.000
 L9N  C17   C18  S1    122.89  3.000
 L9N  N5    C18  S1    112.43  3.000
 L9N  HL1B  CL1  HL1A  107.83  3.000
 L9N  HL1B  CL1  HL1   106.95  3.000
 L9N  HL1A  CL1  HL1   107.58  3.000
 L9N  HL1B  CL1  C3    111.46  3.000
 L9N  HL1A  CL1  C3    111.56  3.000
 L9N  HL1   CL1  C3    111.23  3.000
 L9N  HN6   N6   C12   117.54  3.000
 L9N  HN6   N6   C7    116.53  3.000
 L9N  C12   N6   C7    122.99  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
 L9N  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 L9N  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 L9N  CONST_03  C13  C14  N4   N1    180.00   0.0  0
 L9N  CONST_04  C15  C14  N4   N1      0.00   0.0  0
 L9N  CONST_05  C14  C15  C9   N1      0.00   0.0  0
 L9N  CONST_06  C16  C15  C9   N1    180.00   0.0  0
 L9N  CONST_07  N5   N2   C12  S1      0.00   0.0  0
 L9N  CONST_08  N2   N5   C18  S1      0.00   0.0  0
 L9N  CONST_09  C11  C17  C18  S1      0.00   0.0  0
 L9N  CONST_10  C16  C17  C18  S1    180.00   0.0  0
 L9N  CONST_11  C5   C6   C1   C2      0.00   0.0  0
 L9N  CONST_12  C5   C4   C3   C2      0.00   0.0  0
 L9N  CONST_13  C17  C18  N5   N2    180.00   0.0  0
 L9N  CONST_14  C18  S1   C12  N2      0.00   0.0  0
 L9N  CONST_15  C6   C1   C2   C3      0.00   0.0  0
 L9N  CONST_16  C6   C5   C4   C3      0.00   0.0  0
 L9N  CONST_17  C15  C9   N1   N4      0.00   0.0  0
 L9N  CONST_18  C11  C13  C14  N4    180.00   0.0  0
 L9N  CONST_19  C9   C15  C14  N4      0.00   0.0  0
 L9N  CONST_20  C16  C15  C14  N4    180.00   0.0  0
 L9N  CONST_21  C12  S1   C18  N5      0.00   0.0  0
 L9N  CONST_22  C11  C17  C18  N5    180.00   0.0  0
 L9N  CONST_23  C16  C17  C18  N5      0.00   0.0  0
 L9N  CONST_24  C14  N4   N1   C9      0.00   0.0  0
 L9N  CONST_25  C13  C14  C15  C9    180.00   0.0  0
 L9N  CONST_26  C17  C16  C15  C9    180.00   0.0  0
 L9N  CONST_27  C15  C14  C13  C11     0.00   0.0  0
 L9N  CONST_28  C15  C16  C17  C11     0.00   0.0  0
 L9N  CONST_29  C17  C18  S1   C12   180.00   0.0  0
 L9N  CONST_30  C18  N5   N2   C12     0.00   0.0  0
 L9N  CONST_31  C16  C17  C11  C13     0.00   0.0  0
 L9N  CONST_32  C18  C17  C11  C13   180.00   0.0  0
 L9N  CONST_33  C16  C15  C14  C13     0.00   0.0  0
 L9N  CONST_34  C17  C11  C13  C14     0.00   0.0  0
 L9N  CONST_35  C17  C16  C15  C14     0.00   0.0  0
 L9N  CONST_36  C18  C17  C16  C15   180.00   0.0  0
 L9N  CONST_37  CL1  C3   C2   C1    180.00   0.0  0
 L9N  CONST_38  C8   C6   C1   C2    180.00   0.0  0
 L9N  CONST_39  C8   C6   C5   C4    180.00   0.0  0
 L9N  CONST_40  CL1  C3   C4   C5    180.00   0.0  0
 L9N  CONST_41  N6   C12  N2   N5    180.00   0.0  0
 L9N  CONST_42  C18  S1   C12  N6    180.00   0.0  0
 L9N  CONST_43  H5   C5   C6   C1    180.00   0.0  0
 L9N  CONST_44  H4   C4   C3   C2    180.00   0.0  0
 L9N  CONST_45  H1   C1   C2   C3    180.00   0.0  0
 L9N  CONST_46  H2   C2   C3   C4    180.00   0.0  0
 L9N  CONST_47  H9   C9   N1   N4    180.00   0.0  0
 L9N  CONST_48  H13  C13  C14  N4      0.00   0.0  0
 L9N  CONST_49  HN4  N4   N1   C9    180.00   0.0  0
 L9N  CONST_50  H16  C16  C15  C9      0.00   0.0  0
 L9N  CONST_51  H11  C11  C13  C14   180.00   0.0  0
 L9N  CONST_52  C7   N6   C12  S1    180.00   0.0  0
 L9N  CONST_53  C7   N6   C12  N2      0.00   0.0  0
 L9N  CONST_54  HN6  N6   C12  S1      0.00   0.0  0
 L9N  Var_01    C10  C8   C6   C1     95.20  30.0  2
 L9N  Var_02    HL1  CL1  C3   C2     62.85  30.0  2
 L9N  Var_03    C12  N6   C7   C10  -143.44  30.0  1

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
 L9N  chir_01  C10  N3  C7  C8  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
 L9N  plan-1  S1   0.020
 L9N  plan-1  N2   0.020
 L9N  plan-1  N5   0.020
 L9N  plan-1  C12  0.020
 L9N  plan-1  C17  0.020
 L9N  plan-1  C18  0.020
 L9N  plan-1  N6   0.020
 L9N  plan-2  C1   0.020
 L9N  plan-2  C2   0.020
 L9N  plan-2  C3   0.020
 L9N  plan-2  C4   0.020
 L9N  plan-2  C5   0.020
 L9N  plan-2  C6   0.020
 L9N  plan-2  C8   0.020
 L9N  plan-2  CL1  0.020
 L9N  plan-2  H1   0.020
 L9N  plan-2  H2   0.020
 L9N  plan-2  H4   0.020
 L9N  plan-2  H5   0.020
 L9N  plan-3  N1   0.020
 L9N  plan-3  N4   0.020
 L9N  plan-3  C9   0.020
 L9N  plan-3  C11  0.020
 L9N  plan-3  C13  0.020
 L9N  plan-3  C14  0.020
 L9N  plan-3  C15  0.020
 L9N  plan-3  C16  0.020
 L9N  plan-3  C17  0.020
 L9N  plan-3  C18  0.020
 L9N  plan-3  H9   0.020
 L9N  plan-3  H11  0.020
 L9N  plan-3  H13  0.020
 L9N  plan-3  H16  0.020
 L9N  plan-3  HN4  0.020
 L9N  plan-4  C7   0.020
 L9N  plan-4  C12  0.020
 L9N  plan-4  N6   0.020
 L9N  plan-4  HN6  0.020

