FMO DATABASE

FMODB ID: G5VK1

Calculation Name: 3KFQ-C-Xray372

Preferred Name: Cathepsin L2

Target Type: SINGLE PROTEIN

Ligand Name: s-methyl-thio-cysteine

ligand 3-letter code: SCH

PDB ID: 3KFQ

Chain ID: C

ChEMBL ID: CHEMBL3272

UniProt ID: O60911

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	98
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-721702.027211
FMO2-HF: Nuclear repulsion	683355.384051
FMO2-HF: Total energy	-38346.643161
FMO2-MP2: Total energy	-38459.424903

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(C:1:MET)

Summations of interaction energy for fragment #1(C:1:MET)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-4.627	1.644	5.047	-3.597	-7.719	-0.025

Interaction energy analysis for fragmet #1(C:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : 0.024

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	C	3	PRO	0	0.054	0.012	3.238	0.982	4.570	1.775	-2.094	-3.268	-0.007
4	C	4	GLY	0	0.038	0.033	5.164	-0.247	-0.139	-0.001	-0.023	-0.084	0.000
5	C	5	GLY	0	-0.019	-0.005	3.816	-1.589	-1.002	0.180	-0.257	-0.509	0.001
6	C	6	LEU	0	-0.064	-0.036	2.953	-3.334	-1.301	0.370	-1.019	-1.384	-0.013
7	C	7	SER	0	-0.009	-0.006	2.416	-1.721	-0.854	2.680	-1.408	-2.139	-0.006
8	C	8	GLU	-1	-0.853	-0.917	3.122	2.465	1.453	0.044	1.215	-0.247	0.000
9	C	9	ALA	0	-0.021	-0.019	6.010	-0.287	-0.287	0.000	0.000	0.000	0.000
10	C	10	LYS	1	0.890	0.948	7.994	-0.250	-0.250	0.000	0.000	0.000	0.000
11	C	11	PRO	0	0.015	-0.004	11.936	-0.022	-0.022	0.000	0.000	0.000	0.000
12	C	12	ALA	0	-0.009	0.001	15.277	-0.010	-0.010	0.000	0.000	0.000	0.000
13	C	13	THR	0	0.036	0.014	15.841	-0.004	-0.004	0.000	0.000	0.000	0.000
14	C	14	PRO	0	0.055	0.004	18.575	-0.001	-0.001	0.000	0.000	0.000	0.000
15	C	15	GLU	-1	-0.846	-0.909	15.920	0.071	0.071	0.000	0.000	0.000	0.000
16	C	16	ILE	0	-0.023	-0.021	13.821	-0.001	-0.001	0.000	0.000	0.000	0.000
17	C	17	GLN	0	-0.022	-0.025	17.337	0.006	0.006	0.000	0.000	0.000	0.000
18	C	18	GLU	-1	-0.808	-0.883	20.733	0.057	0.057	0.000	0.000	0.000	0.000
19	C	19	ILE	0	-0.065	-0.021	15.637	-0.003	-0.003	0.000	0.000	0.000	0.000
20	C	20	VAL	0	-0.015	-0.008	18.692	0.000	0.000	0.000	0.000	0.000	0.000
21	C	21	ASP	-1	-0.863	-0.926	20.869	0.066	0.066	0.000	0.000	0.000	0.000
22	C	22	LYS	1	0.810	0.876	21.791	-0.065	-0.065	0.000	0.000	0.000	0.000
23	C	23	VAL	0	-0.037	-0.011	19.941	-0.002	-0.002	0.000	0.000	0.000	0.000
24	C	24	LYS	1	0.833	0.921	23.074	-0.056	-0.056	0.000	0.000	0.000	0.000
25	C	25	PRO	0	0.020	0.009	25.356	-0.001	-0.001	0.000	0.000	0.000	0.000
26	C	26	GLN	0	0.055	0.016	22.983	0.002	0.002	0.000	0.000	0.000	0.000
27	C	27	LEU	0	-0.031	-0.025	22.472	0.001	0.001	0.000	0.000	0.000	0.000
28	C	28	GLU	-1	-0.793	-0.880	25.202	0.054	0.054	0.000	0.000	0.000	0.000
29	C	29	GLU	-1	-0.952	-0.965	28.541	0.045	0.045	0.000	0.000	0.000	0.000
30	C	30	LYS	1	0.846	0.925	22.794	-0.072	-0.072	0.000	0.000	0.000	0.000
31	C	31	THR	0	-0.023	-0.014	26.173	0.000	0.000	0.000	0.000	0.000	0.000
32	C	32	ASN	0	-0.061	-0.024	28.840	-0.004	-0.004	0.000	0.000	0.000	0.000
33	C	33	GLU	-1	-0.943	-0.942	29.891	0.050	0.050	0.000	0.000	0.000	0.000
34	C	34	THR	0	-0.031	-0.010	31.355	-0.001	-0.001	0.000	0.000	0.000	0.000
35	C	35	TYR	0	-0.001	-0.035	27.007	0.003	0.003	0.000	0.000	0.000	0.000
36	C	36	GLY	0	-0.018	-0.011	30.364	-0.001	-0.001	0.000	0.000	0.000	0.000
37	C	37	LYS	1	0.817	0.884	27.368	-0.078	-0.078	0.000	0.000	0.000	0.000
38	C	38	LEU	0	0.019	0.004	23.743	0.002	0.002	0.000	0.000	0.000	0.000
39	C	39	GLU	-1	-0.841	-0.897	23.364	0.086	0.086	0.000	0.000	0.000	0.000
40	C	40	ALA	0	0.026	0.008	18.009	0.007	0.007	0.000	0.000	0.000	0.000
41	C	41	VAL	0	-0.019	-0.005	18.358	0.001	0.001	0.000	0.000	0.000	0.000
42	C	42	GLN	0	-0.002	-0.011	13.593	0.034	0.034	0.000	0.000	0.000	0.000
43	C	43	TYR	0	-0.008	0.002	10.690	-0.013	-0.013	0.000	0.000	0.000	0.000
44	C	44	LYS	1	0.840	0.926	6.440	-0.515	-0.515	0.000	0.000	0.000	0.000
45	C	45	THR	0	0.006	0.001	6.098	0.032	0.032	0.000	0.000	0.000	0.000
46	C	46	GLN	0	0.014	-0.005	4.796	-0.681	-0.581	-0.001	-0.011	-0.088	0.000
47	C	47	VAL	0	-0.006	0.009	5.373	-0.032	-0.032	0.000	0.000	0.000	0.000
48	C	48	VAL	0	0.002	-0.009	7.409	0.176	0.176	0.000	0.000	0.000	0.000
49	C	49	ALA	0	0.011	0.024	10.566	-0.021	-0.021	0.000	0.000	0.000	0.000
50	C	50	GLY	0	0.052	0.013	12.748	-0.035	-0.035	0.000	0.000	0.000	0.000
51	C	51	THR	0	-0.094	-0.050	9.094	0.040	0.040	0.000	0.000	0.000	0.000
52	C	52	ASN	0	-0.017	0.001	9.495	-0.044	-0.044	0.000	0.000	0.000	0.000
53	C	53	TYR	0	0.007	0.000	9.134	-0.036	-0.036	0.000	0.000	0.000	0.000
54	C	54	TYR	0	-0.035	-0.027	8.616	0.012	0.012	0.000	0.000	0.000	0.000
55	C	55	ILE	0	0.027	-0.002	11.560	0.006	0.006	0.000	0.000	0.000	0.000
56	C	56	LYS	1	0.766	0.888	14.344	-0.186	-0.186	0.000	0.000	0.000	0.000
57	C	57	VAL	0	0.004	-0.009	16.494	-0.001	-0.001	0.000	0.000	0.000	0.000
58	C	58	ARG	1	0.869	0.937	20.073	-0.091	-0.091	0.000	0.000	0.000	0.000
59	C	59	ALA	0	0.065	0.032	23.336	-0.004	-0.004	0.000	0.000	0.000	0.000
60	C	60	GLY	0	-0.018	-0.015	26.315	0.001	0.001	0.000	0.000	0.000	0.000
61	C	61	ASP	-1	-0.853	-0.933	28.976	0.068	0.068	0.000	0.000	0.000	0.000
62	C	62	ASN	0	-0.065	-0.031	27.548	0.004	0.004	0.000	0.000	0.000	0.000
63	C	63	LYS	1	0.908	0.967	26.249	-0.061	-0.061	0.000	0.000	0.000	0.000
64	C	64	TYR	0	-0.011	-0.024	20.774	0.005	0.005	0.000	0.000	0.000	0.000
65	C	65	MET	0	-0.020	0.012	20.702	-0.004	-0.004	0.000	0.000	0.000	0.000
66	C	66	HIS	0	-0.015	0.004	15.323	0.011	0.011	0.000	0.000	0.000	0.000
67	C	67	LEU	0	0.041	0.017	16.425	-0.006	-0.006	0.000	0.000	0.000	0.000
68	C	68	LYS	1	0.914	0.966	13.043	-0.142	-0.142	0.000	0.000	0.000	0.000
69	C	69	VAL	0	0.009	-0.004	14.113	-0.006	-0.006	0.000	0.000	0.000	0.000
70	C	70	PHE	0	-0.021	-0.008	13.937	0.006	0.006	0.000	0.000	0.000	0.000
71	C	71	LYS	1	0.961	0.971	14.127	-0.086	-0.086	0.000	0.000	0.000	0.000
72	C	72	SER	0	0.007	0.004	14.983	0.015	0.015	0.000	0.000	0.000	0.000
73	C	73	LEU	0	0.009	-0.001	14.359	0.000	0.000	0.000	0.000	0.000	0.000
74	C	74	PRO	0	0.009	-0.015	16.949	-0.006	-0.006	0.000	0.000	0.000	0.000
75	C	75	GLY	0	-0.009	-0.005	20.160	-0.001	-0.001	0.000	0.000	0.000	0.000
76	C	76	GLN	0	-0.049	-0.021	20.273	-0.006	-0.006	0.000	0.000	0.000	0.000
77	C	77	ASN	0	-0.094	-0.039	23.073	-0.001	-0.001	0.000	0.000	0.000	0.000
78	C	78	GLU	-1	-0.834	-0.896	21.236	0.065	0.065	0.000	0.000	0.000	0.000
79	C	79	ASP	-1	-0.894	-0.942	22.281	0.052	0.052	0.000	0.000	0.000	0.000
80	C	80	LEU	0	-0.065	-0.039	17.462	0.005	0.005	0.000	0.000	0.000	0.000
81	C	81	VAL	0	0.040	0.025	19.015	-0.003	-0.003	0.000	0.000	0.000	0.000
82	C	82	LEU	0	0.001	0.016	18.421	0.009	0.009	0.000	0.000	0.000	0.000
83	C	83	THR	0	-0.015	-0.027	16.263	-0.001	-0.001	0.000	0.000	0.000	0.000
84	C	84	GLY	0	-0.019	-0.009	17.928	0.000	0.000	0.000	0.000	0.000	0.000
85	C	85	TYR	0	0.017	-0.007	18.257	0.003	0.003	0.000	0.000	0.000	0.000
86	C	86	GLN	0	-0.007	0.007	16.004	0.002	0.002	0.000	0.000	0.000	0.000
87	C	87	VAL	0	0.064	0.021	20.077	0.005	0.005	0.000	0.000	0.000	0.000
88	C	88	ASP	-1	-0.840	-0.905	22.955	0.075	0.075	0.000	0.000	0.000	0.000
89	C	89	LYS	1	0.836	0.919	18.131	-0.127	-0.127	0.000	0.000	0.000	0.000
90	C	90	ASN	0	-0.006	-0.026	21.085	-0.013	-0.013	0.000	0.000	0.000	0.000
91	C	91	LYS	1	0.875	0.911	20.056	-0.141	-0.141	0.000	0.000	0.000	0.000
92	C	92	ASP	-1	-0.847	-0.925	18.678	0.180	0.180	0.000	0.000	0.000	0.000
93	C	93	ASP	-1	-0.809	-0.847	17.192	0.161	0.161	0.000	0.000	0.000	0.000
94	C	94	GLU	-1	-0.835	-0.907	9.720	0.577	0.577	0.000	0.000	0.000	0.000
95	C	95	LEU	0	-0.012	0.003	10.532	-0.029	-0.029	0.000	0.000	0.000	0.000
96	C	96	THR	0	0.017	0.002	9.794	0.040	0.040	0.000	0.000	0.000	0.000
97	C	97	GLY	0	0.022	0.003	9.723	-0.034	-0.034	0.000	0.000	0.000	0.000
98	C	98	PHE	0	-0.025	0.007	10.575	-0.034	-0.034	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:1:MET)