FMO DATABASE

FMODB ID: 89QZY

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	OptAll
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	-722441.289524
FMO2-HF: Nuclear repulsion	684094.508161
FMO2-HF: Total energy	-38346.781363
FMO2-MP2: Total energy	-38459.610517

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.
-4.057	1.712	5.113	-3.294	-7.587	-0.021

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 : 0.031 / q_NPA : 0.035

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	0.038	0.002	3.341	1.219	4.874	1.302	-2.002	-2.955	-0.006
4	C	4	GLY	0	0.045	0.038	5.449	-0.262	-0.176	-0.001	-0.014	-0.070	0.000
5	C	5	GLY	0	-0.017	0.000	3.662	-1.666	-1.060	0.289	-0.317	-0.578	0.002
6	C	6	LEU	0	-0.046	-0.026	3.205	-2.546	-1.216	0.162	-0.460	-1.033	-0.007
7	C	7	SER	0	-0.044	-0.036	2.517	-1.542	-0.734	3.330	-1.574	-2.563	-0.010
8	C	8	GLU	-1	-0.826	-0.905	3.249	2.317	1.472	0.032	1.092	-0.279	0.000
9	C	9	ALA	0	-0.009	0.000	5.913	-0.385	-0.385	0.000	0.000	0.000	0.000
10	C	10	LYS	1	0.874	0.936	7.853	-0.280	-0.280	0.000	0.000	0.000	0.000
11	C	11	PRO	0	0.035	0.012	11.976	-0.018	-0.018	0.000	0.000	0.000	0.000
12	C	12	ALA	0	-0.008	0.002	15.134	-0.007	-0.007	0.000	0.000	0.000	0.000
13	C	13	THR	0	0.023	0.006	15.609	-0.005	-0.005	0.000	0.000	0.000	0.000
14	C	14	PRO	0	0.059	0.006	18.448	0.000	0.000	0.000	0.000	0.000	0.000
15	C	15	GLU	-1	-0.830	-0.875	15.260	0.100	0.100	0.000	0.000	0.000	0.000
16	C	16	ILE	0	-0.015	-0.010	13.564	0.001	0.001	0.000	0.000	0.000	0.000
17	C	17	GLN	0	-0.025	-0.023	17.130	0.007	0.007	0.000	0.000	0.000	0.000
18	C	18	GLU	-1	-0.815	-0.889	20.732	0.072	0.072	0.000	0.000	0.000	0.000
19	C	19	ILE	0	-0.042	-0.013	15.412	-0.002	-0.002	0.000	0.000	0.000	0.000
20	C	20	VAL	0	-0.017	-0.016	18.373	0.000	0.000	0.000	0.000	0.000	0.000
21	C	21	ASP	-1	-0.856	-0.928	20.632	0.076	0.076	0.000	0.000	0.000	0.000
22	C	22	LYS	1	0.806	0.877	21.752	-0.082	-0.082	0.000	0.000	0.000	0.000
23	C	23	VAL	0	-0.043	-0.015	19.425	-0.001	-0.001	0.000	0.000	0.000	0.000
24	C	24	LYS	1	0.820	0.914	22.575	-0.066	-0.066	0.000	0.000	0.000	0.000
25	C	25	PRO	0	0.032	0.014	25.066	-0.001	-0.001	0.000	0.000	0.000	0.000
26	C	26	GLN	0	0.043	0.015	22.444	0.003	0.003	0.000	0.000	0.000	0.000
27	C	27	LEU	0	-0.031	-0.024	22.074	0.000	0.000	0.000	0.000	0.000	0.000
28	C	28	GLU	-1	-0.784	-0.878	24.925	0.063	0.063	0.000	0.000	0.000	0.000
29	C	29	GLU	-1	-0.951	-0.959	28.321	0.061	0.061	0.000	0.000	0.000	0.000
30	C	30	LYS	1	0.837	0.909	22.259	-0.093	-0.093	0.000	0.000	0.000	0.000
31	C	31	THR	0	-0.038	-0.022	26.169	-0.001	-0.001	0.000	0.000	0.000	0.000
32	C	32	ASN	0	-0.056	-0.026	28.878	-0.006	-0.006	0.000	0.000	0.000	0.000
33	C	33	GLU	-1	-0.937	-0.943	29.614	0.055	0.055	0.000	0.000	0.000	0.000
34	C	34	THR	0	-0.045	-0.029	31.362	-0.001	-0.001	0.000	0.000	0.000	0.000
35	C	35	TYR	0	0.006	-0.011	26.691	0.000	0.000	0.000	0.000	0.000	0.000
36	C	36	GLY	0	-0.009	-0.012	30.095	0.000	0.000	0.000	0.000	0.000	0.000
37	C	37	LYS	1	0.803	0.882	27.314	-0.079	-0.079	0.000	0.000	0.000	0.000
38	C	38	LEU	0	0.023	0.009	23.541	0.001	0.001	0.000	0.000	0.000	0.000
39	C	39	GLU	-1	-0.838	-0.895	23.378	0.085	0.085	0.000	0.000	0.000	0.000
40	C	40	ALA	0	0.031	0.012	17.899	0.006	0.006	0.000	0.000	0.000	0.000
41	C	41	VAL	0	-0.038	-0.017	18.183	-0.002	-0.002	0.000	0.000	0.000	0.000
42	C	42	GLN	0	-0.008	-0.015	13.693	0.037	0.037	0.000	0.000	0.000	0.000
43	C	43	TYR	0	-0.024	-0.008	10.435	-0.011	-0.011	0.000	0.000	0.000	0.000
44	C	44	LYS	1	0.829	0.916	6.478	-0.656	-0.656	0.000	0.000	0.000	0.000
45	C	45	THR	0	0.002	-0.004	5.907	0.017	0.017	0.000	0.000	0.000	0.000
46	C	46	GLN	0	0.033	0.019	4.473	-0.851	-0.722	-0.001	-0.019	-0.109	0.000
47	C	47	VAL	0	0.010	0.015	5.087	-0.035	-0.035	0.000	0.000	0.000	0.000
48	C	48	VAL	0	-0.005	-0.005	7.132	0.166	0.166	0.000	0.000	0.000	0.000
49	C	49	ALA	0	0.016	0.019	10.474	-0.021	-0.021	0.000	0.000	0.000	0.000
50	C	50	GLY	0	0.036	0.005	12.558	-0.050	-0.050	0.000	0.000	0.000	0.000
51	C	51	THR	0	-0.105	-0.058	8.447	0.054	0.054	0.000	0.000	0.000	0.000
52	C	52	ASN	0	-0.007	0.005	9.286	-0.061	-0.061	0.000	0.000	0.000	0.000
53	C	53	TYR	0	-0.003	-0.032	8.815	-0.030	-0.030	0.000	0.000	0.000	0.000
54	C	54	TYR	0	-0.031	-0.034	8.255	0.008	0.008	0.000	0.000	0.000	0.000
55	C	55	ILE	0	0.033	0.004	11.300	0.009	0.009	0.000	0.000	0.000	0.000
56	C	56	LYS	1	0.748	0.891	14.136	-0.188	-0.188	0.000	0.000	0.000	0.000
57	C	57	VAL	0	0.016	0.000	16.495	-0.001	-0.001	0.000	0.000	0.000	0.000
58	C	58	ARG	1	0.873	0.932	19.910	-0.087	-0.087	0.000	0.000	0.000	0.000
59	C	59	ALA	0	0.054	0.025	23.316	-0.003	-0.003	0.000	0.000	0.000	0.000
60	C	60	GLY	0	-0.023	-0.016	26.363	0.000	0.000	0.000	0.000	0.000	0.000
61	C	61	ASP	-1	-0.817	-0.910	28.871	0.071	0.071	0.000	0.000	0.000	0.000
62	C	62	ASN	0	-0.078	-0.037	27.770	0.001	0.001	0.000	0.000	0.000	0.000
63	C	63	LYS	1	0.874	0.939	25.749	-0.066	-0.066	0.000	0.000	0.000	0.000
64	C	64	TYR	0	0.004	-0.007	20.676	0.005	0.005	0.000	0.000	0.000	0.000
65	C	65	MET	0	-0.009	0.011	20.552	-0.005	-0.005	0.000	0.000	0.000	0.000
66	C	66	HIS	0	-0.013	0.008	15.180	0.007	0.007	0.000	0.000	0.000	0.000
67	C	67	LEU	0	0.053	0.015	16.661	-0.004	-0.004	0.000	0.000	0.000	0.000
68	C	68	LYS	1	0.840	0.926	12.938	-0.170	-0.170	0.000	0.000	0.000	0.000
69	C	69	VAL	0	-0.004	-0.004	13.753	-0.007	-0.007	0.000	0.000	0.000	0.000
70	C	70	PHE	0	-0.015	0.004	13.631	0.010	0.010	0.000	0.000	0.000	0.000
71	C	71	LYS	1	0.947	0.963	13.666	-0.141	-0.141	0.000	0.000	0.000	0.000
72	C	72	SER	0	0.007	-0.018	14.404	0.024	0.024	0.000	0.000	0.000	0.000
73	C	73	LEU	0	-0.008	-0.011	14.174	-0.001	-0.001	0.000	0.000	0.000	0.000
74	C	74	PRO	0	-0.012	-0.021	16.902	-0.011	-0.011	0.000	0.000	0.000	0.000
75	C	75	GLY	0	0.007	0.009	20.075	0.000	0.000	0.000	0.000	0.000	0.000
76	C	76	GLN	0	-0.056	-0.036	20.103	-0.007	-0.007	0.000	0.000	0.000	0.000
77	C	77	ASN	0	-0.086	-0.039	22.824	-0.003	-0.003	0.000	0.000	0.000	0.000
78	C	78	GLU	-1	-0.796	-0.852	20.624	0.105	0.105	0.000	0.000	0.000	0.000
79	C	79	ASP	-1	-0.893	-0.947	21.891	0.075	0.075	0.000	0.000	0.000	0.000
80	C	80	LEU	0	-0.055	-0.028	17.133	0.007	0.007	0.000	0.000	0.000	0.000
81	C	81	VAL	0	0.046	0.035	18.706	-0.006	-0.006	0.000	0.000	0.000	0.000
82	C	82	LEU	0	0.009	0.010	17.975	0.013	0.013	0.000	0.000	0.000	0.000
83	C	83	THR	0	-0.016	-0.015	15.517	-0.005	-0.005	0.000	0.000	0.000	0.000
84	C	84	GLY	0	-0.005	-0.011	17.730	0.006	0.006	0.000	0.000	0.000	0.000
85	C	85	TYR	0	0.019	0.000	18.074	0.003	0.003	0.000	0.000	0.000	0.000
86	C	86	GLN	0	-0.015	0.003	15.745	-0.004	-0.004	0.000	0.000	0.000	0.000
87	C	87	VAL	0	0.065	0.023	20.045	0.003	0.003	0.000	0.000	0.000	0.000
88	C	88	ASP	-1	-0.844	-0.911	22.648	0.080	0.080	0.000	0.000	0.000	0.000
89	C	89	LYS	1	0.843	0.927	18.351	-0.128	-0.128	0.000	0.000	0.000	0.000
90	C	90	ASN	0	-0.009	-0.030	21.285	-0.014	-0.014	0.000	0.000	0.000	0.000
91	C	91	LYS	1	0.868	0.902	20.412	-0.132	-0.132	0.000	0.000	0.000	0.000
92	C	92	ASP	-1	-0.835	-0.914	18.465	0.169	0.169	0.000	0.000	0.000	0.000
93	C	93	ASP	-1	-0.807	-0.845	17.460	0.154	0.154	0.000	0.000	0.000	0.000
94	C	94	GLU	-1	-0.819	-0.902	9.712	0.628	0.628	0.000	0.000	0.000	0.000
95	C	95	LEU	0	-0.019	-0.007	10.227	-0.023	-0.023	0.000	0.000	0.000	0.000
96	C	96	THR	0	0.019	0.008	9.825	0.061	0.061	0.000	0.000	0.000	0.000
97	C	97	GLY	0	0.025	0.009	9.679	-0.028	-0.028	0.000	0.000	0.000	0.000
98	C	98	PHE	0	-0.015	0.010	10.307	-0.042	-0.042	0.000	0.000	0.000	0.000

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