# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:36:47 2022
#   Inital geometry file: a 117 line input string
#   Ligand name: (2S)-N1-[5-(3-methyl-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]nc(C)c4c3)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
 L9M  L9M  (2S)-N1-[5-(3-methyl-1H-indazol-5-yl)-1,3,4-thiadiazol-2-yl]-3-(4-methylphenyl)propane-1,2-diamine  ligand  49  27  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L9M
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
 L9M  C1    C  CR16  0  -0.309   -6.8480  -0.4400  -1.1554
 L9M  N1    N  N     0  -0.248    8.3755  -0.4406   0.0114
 L9M  S1    S  S2    0   0.148    1.2399   1.2674  -0.1695
 L9M  C2    C  CR16  0  -0.282   -8.1215   0.0926  -1.0106
 L9M  N2    N  N     0  -0.324    0.5700  -1.1814   0.1163
 L9M  C3    C  CR6   0   0.081   -8.6798   0.2897   0.2503
 L9M  N3    N  NH2   0  -0.794   -3.7494   0.8161  -1.1454
 L9M  C4    C  CR16  0  -0.286   -7.9153  -0.0625   1.3606
 L9M  N4    N  NR15  0  -0.552    7.9244   0.8033   0.2234
 L9M  C5    C  CR16  0  -0.293   -6.6417  -0.5944   1.2157
 L9M  N5    N  N     0  -0.261    1.9135  -1.1487   0.2157
 L9M  C6    C  CR6   0   0.122   -6.0854  -0.7952  -0.0450
 L9M  C7    C  CH2   0  -0.249   -2.2350  -0.8156  -0.1871
 L9M  C8    C  CH2   0  -0.522   -4.6879  -1.3235  -0.1937
 L9M  C9    C  CR5   0   0.212    7.3319  -1.2196  -0.1202
 L9M  C10   C  CH1   0  -0.129   -3.6331  -0.2084  -0.1216
 L9M  C11   C  CR16  0  -0.325    4.3406   1.6170   0.3532
 L9M  C12   C  CR5   0   0.330    0.0509  -0.0004  -0.0758
 L9M  C13   C  CR16  0  -0.274    5.6794   1.9209   0.4072
 L9M  C14   C  CR56  0   0.422    6.5771   0.8626   0.2336
 L9M  C15   C  CR56  0  -0.076    6.1346  -0.4528   0.0115
 L9M  C16   C  CR16  0  -0.372    4.7715  -0.7382  -0.0425
 L9M  C17   C  CR6   0   0.090    3.8703   0.2998   0.1292
 L9M  C19   C  CR5   0   0.020    2.4377   0.0211   0.0897
 L9M  CL1   C  CH3   0  -0.722  -10.0706   0.8336   0.4057
 L9M  H1    H  HCR6  0   0.245   -6.4447  -0.5892  -2.1504
 L9M  H2    H  HCR6  0   0.244   -8.6886   0.3569  -1.8959
 L9M  HN3   H  HNH2  0   0.346   -3.8165   0.3878  -2.0626
 L9M  HN3A  H  HNH2  0   0.362   -4.6001   1.3491  -1.0176
 L9M  H4    H  HCR6  0   0.244   -8.3205   0.0812   2.3556
 L9M  HN4   H  HNR5  0   0.417    8.5802   1.5556   0.3533
 L9M  H5    H  HCR6  0   0.243   -6.0738  -0.8585   2.1006
 L9M  H7    H  HCH2  0   0.230   -2.1290  -1.4229  -1.0959
 L9M  H7A   H  HCH2  0   0.250   -2.0826  -1.4833   0.6623
 L9M  H8    H  HCH2  0   0.247   -4.4838  -2.0564   0.5918
 L9M  H8A   H  HCH2  0   0.244   -4.5846  -1.8480  -1.1489
 L9M  H10   H  HCH1  0   0.249   -3.7305   0.2937   0.8467
 L9M  H11   H  HCR6  0   0.259    3.6299   2.4213   0.5005
 L9M  H13   H  HCR6  0   0.277    6.0147   2.9339   0.5829
 L9M  H16   H  HCR6  0   0.259    4.4208  -1.7459  -0.2259
 L9M  H18   H  HCH3  0   0.251    7.0581  -3.2543   0.4791
 L9M  H18A  H  HCH3  0   0.249    6.8859  -2.9804  -1.2468
 L9M  H18B  H  HCH3  0   0.254    8.4905  -2.9670  -0.5106
 L9M  HL1   H  HCH3  0   0.246  -10.8163   0.0453   0.2826
 L9M  HL1A  H  HCH3  0   0.242  -10.2205   1.2699   1.3928
 L9M  HL1B  H  HCH3  0   0.242  -10.2880   1.6003  -0.3380
 L9M  N6    N  NH1   0  -0.665   -1.2609   0.2517  -0.1513
 L9M  C18   C  CH3   0  -0.742    7.4507  -2.6814  -0.3628
 L9M  HN6   H  HNH1  0   0.402   -1.5797   1.1117  -0.5774

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
 L9M  C1   C2    aromatic  1.388  0.020  1.388
 L9M  C1   C6    aromatic  1.393  0.020  1.393
 L9M  N1   N4    aromatic  1.340  0.020  1.340
 L9M  N1   C9    aromatic  1.309  0.020  1.309
 L9M  S1   C12   aromatic  1.741  0.020  1.741
 L9M  S1   C19   aromatic  1.748  0.020  1.748
 L9M  C2   C3    aromatic  1.393  0.020  1.393
 L9M  N2   N5    aromatic  1.348  0.020  1.348
 L9M  N2   C12   aromatic  1.304  0.020  1.304
 L9M  C3   C4    aromatic  1.393  0.020  1.393
 L9M  C3   CL1   single    1.502  0.020  1.502
 L9M  N3   C10   single    1.453  0.020  1.453
 L9M  C4   C5    aromatic  1.388  0.020  1.388
 L9M  N4   C14   aromatic  1.349  0.020  1.349
 L9M  C5   C6    aromatic  1.393  0.020  1.393
 L9M  N5   C19   aromatic  1.288  0.020  1.288
 L9M  C6   C8    single    1.501  0.020  1.501
 L9M  N6   C7    single    1.445  0.020  1.445
 L9M  N6   C12   single    1.338  0.020  1.338
 L9M  C7   C10   single    1.526  0.020  1.526
 L9M  C8   C10   single    1.537  0.020  1.537
 L9M  C9   C15   aromatic  1.428  0.020  1.428
 L9M  C9   C18   single    1.487  0.020  1.487
 L9M  C11  C13   aromatic  1.374  0.020  1.374
 L9M  C11  C17   aromatic  1.417  0.020  1.417
 L9M  C13  C14   aromatic  1.399  0.020  1.399
 L9M  C14  C15   aromatic  1.406  0.020  1.406
 L9M  C15  C16   aromatic  1.394  0.020  1.394
 L9M  C16  C17   aromatic  1.385  0.020  1.385
 L9M  C17  C19   single    1.460  0.020  1.460
 L9M  C1   H1    single    0.930  0.020  1.080
 L9M  C2   H2    single    0.930  0.020  1.080
 L9M  N3   HN3   single    0.890  0.020  1.040
 L9M  N3   HN3A  single    0.890  0.020  1.040
 L9M  C4   H4    single    0.930  0.020  1.080
 L9M  N4   HN4   single    0.860  0.020  1.020
 L9M  C5   H5    single    0.930  0.020  1.080
 L9M  N6   HN6   single    0.890  0.020  1.040
 L9M  C7   H7    single    0.970  0.020  1.090
 L9M  C7   H7A   single    0.970  0.020  1.090
 L9M  C8   H8    single    0.970  0.020  1.090
 L9M  C8   H8A   single    0.970  0.020  1.090
 L9M  C10  H10   single    0.970  0.020  1.090
 L9M  C11  H11   single    0.930  0.020  1.080
 L9M  C13  H13   single    0.930  0.020  1.080
 L9M  C16  H16   single    0.930  0.020  1.080
 L9M  C18  H18   single    0.970  0.020  1.090
 L9M  C18  H18A  single    0.970  0.020  1.090
 L9M  C18  H18B  single    0.970  0.020  1.090
 L9M  CL1  HL1   single    0.970  0.020  1.090
 L9M  CL1  HL1A  single    0.970  0.020  1.090
 L9M  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
 L9M  H1    C1   C6    119.53  3.000
 L9M  H1    C1   C2    119.34  3.000
 L9M  C6    C1   C2    121.13  3.000
 L9M  C9    N1   N4    107.46  3.000
 L9M  C19   S1   C12    86.61  3.000
 L9M  H2    C2   C3    119.67  3.000
 L9M  H2    C2   C1    119.23  3.000
 L9M  C3    C2   C1    121.09  3.000
 L9M  C12   N2   N5    112.68  3.000
 L9M  CL1   C3   C4    121.15  3.000
 L9M  CL1   C3   C2    121.07  3.000
 L9M  C4    C3   C2    117.76  3.000
 L9M  HN3A  N3   HN3   106.31  3.000
 L9M  HN3A  N3   C10   110.47  3.000
 L9M  HN3   N3   C10   110.16  3.000
 L9M  H4    C4   C5    119.32  3.000
 L9M  H4    C4   C3    119.54  3.000
 L9M  C5    C4   C3    121.14  3.000
 L9M  HN4   N4   C14   128.10  3.000
 L9M  HN4   N4   N1    119.67  3.000
 L9M  C14   N4   N1    112.23  3.000
 L9M  H5    C5   C6    119.64  3.000
 L9M  H5    C5   C4    119.27  3.000
 L9M  C6    C5   C4    121.09  3.000
 L9M  C19   N5   N2    114.87  3.000
 L9M  C8    C6   C5    120.81  3.000
 L9M  C8    C6   C1    121.36  3.000
 L9M  C5    C6   C1    117.78  3.000
 L9M  H7A   C7   H7    107.00  3.000
 L9M  H7A   C7   C10   109.76  3.000
 L9M  H7    C7   C10   110.13  3.000
 L9M  H7A   C7   N6    109.78  3.000
 L9M  H7    C7   N6    111.33  3.000
 L9M  C10   C7   N6    108.82  3.000
 L9M  H8A   C8   H8    106.75  3.000
 L9M  H8A   C8   C10   108.89  3.000
 L9M  H8    C8   C10   108.93  3.000
 L9M  H8A   C8   C6    110.05  3.000
 L9M  H8    C8   C6    109.78  3.000
 L9M  C10   C8   C6    112.27  3.000
 L9M  C18   C9   C15   127.60  3.000
 L9M  C18   C9   N1    122.55  3.000
 L9M  C15   C9   N1    109.86  3.000
 L9M  H10   C10  C8    108.25  3.000
 L9M  H10   C10  C7    107.58  3.000
 L9M  C8    C10  C7    109.77  3.000
 L9M  H10   C10  N3    107.01  3.000
 L9M  C8    C10  N3    115.07  3.000
 L9M  C7    C10  N3    108.89  3.000
 L9M  H11   C11  C17   119.61  3.000
 L9M  H11   C11  C13   118.02  3.000
 L9M  C17   C11  C13   122.37  3.000
 L9M  N6    C12  N2    124.68  3.000
 L9M  N6    C12  S1    121.98  3.000
 L9M  N2    C12  S1    113.30  3.000
 L9M  H13   C13  C14   122.00  3.000
 L9M  H13   C13  C11   121.05  3.000
 L9M  C14   C13  C11   116.95  3.000
 L9M  C15   C14  C13   121.72  3.000
 L9M  C15   C14  N4    105.79  3.000
 L9M  C13   C14  N4    132.49  3.000
 L9M  C16   C15  C14   120.38  3.000
 L9M  C16   C15  C9    134.96  3.000
 L9M  C14   C15  C9    104.67  3.000
 L9M  H16   C16  C17   120.51  3.000
 L9M  H16   C16  C15   120.93  3.000
 L9M  C17   C16  C15   118.56  3.000
 L9M  C19   C17  C16   119.47  3.000
 L9M  C19   C17  C11   120.50  3.000
 L9M  C16   C17  C11   120.03  3.000
 L9M  C17   C19  N5    124.75  3.000
 L9M  C17   C19  S1    122.71  3.000
 L9M  N5    C19  S1    112.53  3.000
 L9M  HL1B  CL1  HL1A  108.00  3.000
 L9M  HL1B  CL1  HL1   107.14  3.000
 L9M  HL1A  CL1  HL1   107.29  3.000
 L9M  HL1B  CL1  C3    111.65  3.000
 L9M  HL1A  CL1  C3    111.48  3.000
 L9M  HL1   CL1  C3    111.06  3.000
 L9M  HN6   N6   C12   119.54  3.000
 L9M  HN6   N6   C7    113.89  3.000
 L9M  C12   N6   C7    121.54  3.000
 L9M  H18B  C18  H18A  108.22  3.000
 L9M  H18B  C18  H18   108.10  3.000
 L9M  H18A  C18  H18   107.16  3.000
 L9M  H18B  C18  C9    110.89  3.000
 L9M  H18A  C18  C9    111.13  3.000
 L9M  H18   C18  C9    111.20  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
 L9M  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 L9M  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 L9M  CONST_03  C13  C14  N4   N1   180.00   0.0  0
 L9M  CONST_04  C15  C14  N4   N1     0.00   0.0  0
 L9M  CONST_05  C14  C15  C9   N1     0.00   0.0  0
 L9M  CONST_06  C16  C15  C9   N1   180.00   0.0  0
 L9M  CONST_07  N5   N2   C12  S1     0.00   0.0  0
 L9M  CONST_08  N2   N5   C19  S1     0.00   0.0  0
 L9M  CONST_11  C5   C6   C1   C2     0.00   0.0  0
 L9M  CONST_12  C5   C4   C3   C2     0.00   0.0  0
 L9M  CONST_13  C17  C19  N5   N2   180.00   0.0  0
 L9M  CONST_14  C19  S1   C12  N2     0.00   0.0  0
 L9M  CONST_15  C6   C1   C2   C3     0.00   0.0  0
 L9M  CONST_16  C6   C5   C4   C3     0.00   0.0  0
 L9M  CONST_17  C15  C9   N1   N4     0.00   0.0  0
 L9M  CONST_18  C11  C13  C14  N4   180.00   0.0  0
 L9M  CONST_19  C9   C15  C14  N4     0.00   0.0  0
 L9M  CONST_20  C16  C15  C14  N4   180.00   0.0  0
 L9M  CONST_21  C12  S1   C19  N5     0.00   0.0  0
 L9M  CONST_24  C14  N4   N1   C9     0.00   0.0  0
 L9M  CONST_25  C13  C14  C15  C9   180.00   0.0  0
 L9M  CONST_26  C17  C16  C15  C9   180.00   0.0  0
 L9M  CONST_27  C15  C14  C13  C11    0.00   0.0  0
 L9M  CONST_28  C15  C16  C17  C11    0.00   0.0  0
 L9M  CONST_29  C17  C19  S1   C12  180.00   0.0  0
 L9M  CONST_30  C19  N5   N2   C12    0.00   0.0  0
 L9M  CONST_31  C16  C17  C11  C13    0.00   0.0  0
 L9M  CONST_32  C19  C17  C11  C13  180.00   0.0  0
 L9M  CONST_33  C16  C15  C14  C13    0.00   0.0  0
 L9M  CONST_34  C17  C11  C13  C14    0.00   0.0  0
 L9M  CONST_35  C17  C16  C15  C14    0.00   0.0  0
 L9M  CONST_36  C19  C17  C16  C15  180.00   0.0  0
 L9M  CONST_37  CL1  C3   C2   C1   180.00   0.0  0
 L9M  CONST_38  C8   C6   C1   C2   180.00   0.0  0
 L9M  CONST_39  C8   C6   C5   C4   180.00   0.0  0
 L9M  CONST_40  C18  C9   N1   N4   180.00   0.0  0
 L9M  CONST_41  CL1  C3   C4   C5   180.00   0.0  0
 L9M  CONST_42  N6   C12  N2   N5   180.00   0.0  0
 L9M  CONST_43  C19  S1   C12  N6   180.00   0.0  0
 L9M  CONST_44  C18  C9   C15  C14  180.00   0.0  0
 L9M  CONST_45  C18  C9   C15  C16    0.00   0.0  0
 L9M  CONST_46  H5   C5   C6   C1   180.00   0.0  0
 L9M  CONST_47  H4   C4   C3   C2   180.00   0.0  0
 L9M  CONST_48  H1   C1   C2   C3   180.00   0.0  0
 L9M  CONST_49  H2   C2   C3   C4   180.00   0.0  0
 L9M  CONST_50  H13  C13  C14  N4     0.00   0.0  0
 L9M  CONST_51  HN4  N4   N1   C9   180.00   0.0  0
 L9M  CONST_52  H16  C16  C15  C9     0.00   0.0  0
 L9M  CONST_53  H11  C11  C13  C14  180.00   0.0  0
 L9M  CONST_54  C7   N6   C12  S1   180.00   0.0  0
 L9M  CONST_55  C7   N6   C12  N2     0.00   0.0  0
 L9M  Var_01    C10  C8   C6   C1    92.24  30.0  2
 L9M  Var_02    H18  C18  C9   N1   114.60  30.0  2
 L9M  Var_03    HL1  CL1  C3   C2    81.66  30.0  2
 L9M  Var_04    C12  N6   C7   C10  173.99  30.0  2

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
 L9M  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
 L9M  plan-1  S1   0.020
 L9M  plan-1  N2   0.020
 L9M  plan-1  N5   0.020
 L9M  plan-1  C12  0.020
 L9M  plan-1  C17  0.020
 L9M  plan-1  C19  0.020
 L9M  plan-1  N6   0.020
 L9M  plan-2  C1   0.020
 L9M  plan-2  C2   0.020
 L9M  plan-2  C3   0.020
 L9M  plan-2  C4   0.020
 L9M  plan-2  C5   0.020
 L9M  plan-2  C6   0.020
 L9M  plan-2  C8   0.020
 L9M  plan-2  CL1  0.020
 L9M  plan-2  H1   0.020
 L9M  plan-2  H2   0.020
 L9M  plan-2  H4   0.020
 L9M  plan-2  H5   0.020
 L9M  plan-3  N1   0.020
 L9M  plan-3  N4   0.020
 L9M  plan-3  C9   0.020
 L9M  plan-3  C11  0.020
 L9M  plan-3  C13  0.020
 L9M  plan-3  C14  0.020
 L9M  plan-3  C15  0.020
 L9M  plan-3  C16  0.020
 L9M  plan-3  C17  0.020
 L9M  plan-3  C19  0.020
 L9M  plan-3  HN4  0.020
 L9M  plan-3  H11  0.020
 L9M  plan-3  H13  0.020
 L9M  plan-3  H16  0.020
 L9M  plan-3  C18  0.020
 L9M  plan-4  C7   0.020
 L9M  plan-4  C12  0.020
 L9M  plan-4  N6   0.020
 L9M  plan-4  HN6  0.020

