FMO DATABASE

FMODB ID: 1N9GZ

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	OptH
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	-720992.543586
FMO2-HF: Nuclear repulsion	682646.765276
FMO2-HF: Total energy	-38345.77831
FMO2-MP2: Total energy	-38458.561168

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.
-3.55	1.957	3.857	-2.733	-6.63	-0.022

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 : -0.009 / q_NPA : -0.005

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	0.044	0.009	3.307	0.151	3.423	0.731	-1.505	-2.497	-0.011
4	C	4	GLY	0	0.045	0.035	5.124	0.029	0.137	-0.001	-0.018	-0.089	0.000
5	C	5	GLY	0	-0.018	0.001	3.827	-1.266	-0.770	0.160	-0.201	-0.455	0.001
6	C	6	LEU	0	-0.067	-0.038	3.411	-2.486	-0.824	0.323	-0.793	-1.192	-0.010
7	C	7	SER	0	-0.017	-0.013	2.197	-1.358	-0.095	2.570	-1.802	-2.031	-0.002
8	C	8	GLU	-1	-0.894	-0.945	2.973	2.074	0.676	0.075	1.598	-0.275	0.000
9	C	9	ALA	0	-0.011	-0.012	5.984	-0.194	-0.194	0.000	0.000	0.000	0.000
10	C	10	LYS	1	0.937	0.980	8.518	0.418	0.418	0.000	0.000	0.000	0.000
11	C	11	PRO	0	-0.004	-0.016	11.644	0.040	0.040	0.000	0.000	0.000	0.000
12	C	12	ALA	0	0.005	0.007	14.960	-0.031	-0.031	0.000	0.000	0.000	0.000
13	C	13	THR	0	0.033	0.014	15.785	-0.002	-0.002	0.000	0.000	0.000	0.000
14	C	14	PRO	0	0.041	-0.005	18.232	0.011	0.011	0.000	0.000	0.000	0.000
15	C	15	GLU	-1	-0.888	-0.927	16.051	-0.092	-0.092	0.000	0.000	0.000	0.000
16	C	16	ILE	0	-0.028	-0.020	13.464	0.014	0.014	0.000	0.000	0.000	0.000
17	C	17	GLN	0	0.005	-0.005	17.087	0.022	0.022	0.000	0.000	0.000	0.000
18	C	18	GLU	-1	-0.903	-0.944	20.520	-0.010	-0.010	0.000	0.000	0.000	0.000
19	C	19	ILE	0	-0.043	-0.016	15.434	0.009	0.009	0.000	0.000	0.000	0.000
20	C	20	VAL	0	-0.014	-0.008	18.654	0.013	0.013	0.000	0.000	0.000	0.000
21	C	21	ASP	-1	-0.864	-0.934	20.779	0.048	0.048	0.000	0.000	0.000	0.000
22	C	22	LYS	1	0.875	0.935	21.912	-0.011	-0.011	0.000	0.000	0.000	0.000
23	C	23	VAL	0	-0.040	-0.014	19.835	0.003	0.003	0.000	0.000	0.000	0.000
24	C	24	LYS	1	0.912	0.969	23.056	-0.059	-0.059	0.000	0.000	0.000	0.000
25	C	25	PRO	0	0.025	0.011	25.355	0.005	0.005	0.000	0.000	0.000	0.000
26	C	26	GLN	0	0.075	0.032	23.054	0.015	0.015	0.000	0.000	0.000	0.000
27	C	27	LEU	0	-0.019	-0.016	22.800	0.008	0.008	0.000	0.000	0.000	0.000
28	C	28	GLU	-1	-0.859	-0.931	25.318	0.079	0.079	0.000	0.000	0.000	0.000
29	C	29	GLU	-1	-0.953	-0.963	28.717	0.078	0.078	0.000	0.000	0.000	0.000
30	C	30	LYS	1	0.868	0.935	23.612	-0.133	-0.133	0.000	0.000	0.000	0.000
31	C	31	THR	0	-0.053	-0.027	26.403	0.001	0.001	0.000	0.000	0.000	0.000
32	C	32	ASN	0	-0.038	-0.016	29.053	-0.006	-0.006	0.000	0.000	0.000	0.000
33	C	33	GLU	-1	-0.927	-0.936	30.080	0.097	0.097	0.000	0.000	0.000	0.000
34	C	34	THR	0	-0.033	-0.011	31.467	-0.004	-0.004	0.000	0.000	0.000	0.000
35	C	35	TYR	0	-0.007	-0.027	27.420	0.005	0.005	0.000	0.000	0.000	0.000
36	C	36	GLY	0	-0.026	-0.018	30.403	-0.005	-0.005	0.000	0.000	0.000	0.000
37	C	37	LYS	1	0.941	0.953	27.470	-0.065	-0.065	0.000	0.000	0.000	0.000
38	C	38	LEU	0	0.030	0.001	23.511	0.008	0.008	0.000	0.000	0.000	0.000
39	C	39	GLU	-1	-0.979	-0.972	22.757	0.067	0.067	0.000	0.000	0.000	0.000
40	C	40	ALA	0	0.015	-0.001	17.830	0.018	0.018	0.000	0.000	0.000	0.000
41	C	41	VAL	0	-0.007	0.003	17.938	-0.010	-0.010	0.000	0.000	0.000	0.000
42	C	42	GLN	0	-0.015	-0.013	13.545	0.028	0.028	0.000	0.000	0.000	0.000
43	C	43	TYR	0	-0.006	0.001	10.115	0.002	0.002	0.000	0.000	0.000	0.000
44	C	44	LYS	1	0.844	0.937	6.526	-1.154	-1.154	0.000	0.000	0.000	0.000
45	C	45	THR	0	0.012	0.005	5.929	-0.024	-0.024	0.000	0.000	0.000	0.000
46	C	46	GLN	0	-0.002	-0.020	4.787	-0.626	-0.522	-0.001	-0.012	-0.091	0.000
47	C	47	VAL	0	-0.009	0.006	5.383	-0.127	-0.127	0.000	0.000	0.000	0.000
48	C	48	VAL	0	0.008	-0.007	7.398	0.247	0.247	0.000	0.000	0.000	0.000
49	C	49	ALA	0	0.012	0.025	10.685	-0.072	-0.072	0.000	0.000	0.000	0.000
50	C	50	GLY	0	0.041	0.003	12.697	-0.021	-0.021	0.000	0.000	0.000	0.000
51	C	51	THR	0	-0.091	-0.047	8.927	0.007	0.007	0.000	0.000	0.000	0.000
52	C	52	ASN	0	0.002	0.013	9.578	-0.078	-0.078	0.000	0.000	0.000	0.000
53	C	53	TYR	0	0.017	0.000	9.140	-0.032	-0.032	0.000	0.000	0.000	0.000
54	C	54	TYR	0	-0.029	-0.022	8.753	0.058	0.058	0.000	0.000	0.000	0.000
55	C	55	ILE	0	0.029	-0.004	11.579	-0.017	-0.017	0.000	0.000	0.000	0.000
56	C	56	LYS	1	0.777	0.885	14.355	-0.298	-0.298	0.000	0.000	0.000	0.000
57	C	57	VAL	0	0.003	-0.005	16.537	-0.029	-0.029	0.000	0.000	0.000	0.000
58	C	58	ARG	1	0.898	0.953	20.086	-0.087	-0.087	0.000	0.000	0.000	0.000
59	C	59	ALA	0	0.061	0.032	23.348	-0.013	-0.013	0.000	0.000	0.000	0.000
60	C	60	GLY	0	-0.037	-0.025	26.350	-0.001	-0.001	0.000	0.000	0.000	0.000
61	C	61	ASP	-1	-0.860	-0.935	29.163	0.110	0.110	0.000	0.000	0.000	0.000
62	C	62	ASN	0	-0.086	-0.052	27.567	0.002	0.002	0.000	0.000	0.000	0.000
63	C	63	LYS	1	0.978	1.020	26.512	-0.124	-0.124	0.000	0.000	0.000	0.000
64	C	64	TYR	0	-0.003	-0.011	20.775	-0.010	-0.010	0.000	0.000	0.000	0.000
65	C	65	MET	0	0.002	0.017	20.867	0.003	0.003	0.000	0.000	0.000	0.000
66	C	66	HIS	0	-0.024	0.006	15.363	-0.027	-0.027	0.000	0.000	0.000	0.000
67	C	67	LEU	0	0.042	0.016	16.547	0.004	0.004	0.000	0.000	0.000	0.000
68	C	68	LYS	1	0.914	0.963	13.040	-0.354	-0.354	0.000	0.000	0.000	0.000
69	C	69	VAL	0	0.006	-0.004	14.198	-0.015	-0.015	0.000	0.000	0.000	0.000
70	C	70	PHE	0	-0.019	-0.006	13.846	0.002	0.002	0.000	0.000	0.000	0.000
71	C	71	LYS	1	0.999	0.998	13.934	0.040	0.040	0.000	0.000	0.000	0.000
72	C	72	SER	0	0.031	0.016	14.905	0.003	0.003	0.000	0.000	0.000	0.000
73	C	73	LEU	0	0.003	-0.010	14.303	-0.019	-0.019	0.000	0.000	0.000	0.000
74	C	74	PRO	0	0.005	-0.014	16.709	0.003	0.003	0.000	0.000	0.000	0.000
75	C	75	GLY	0	-0.002	-0.002	19.936	0.002	0.002	0.000	0.000	0.000	0.000
76	C	76	GLN	0	-0.003	-0.001	20.356	-0.007	-0.007	0.000	0.000	0.000	0.000
77	C	77	ASN	0	-0.086	-0.030	22.969	0.002	0.002	0.000	0.000	0.000	0.000
78	C	78	GLU	-1	-0.923	-0.941	21.304	0.064	0.064	0.000	0.000	0.000	0.000
79	C	79	ASP	-1	-0.891	-0.939	22.173	0.024	0.024	0.000	0.000	0.000	0.000
80	C	80	LEU	0	-0.065	-0.043	17.363	0.009	0.009	0.000	0.000	0.000	0.000
81	C	81	VAL	0	0.037	0.019	19.032	0.003	0.003	0.000	0.000	0.000	0.000
82	C	82	LEU	0	-0.030	0.001	18.501	0.018	0.018	0.000	0.000	0.000	0.000
83	C	83	THR	0	-0.027	-0.031	16.429	0.013	0.013	0.000	0.000	0.000	0.000
84	C	84	GLY	0	-0.024	-0.014	18.218	0.015	0.015	0.000	0.000	0.000	0.000
85	C	85	TYR	0	0.002	-0.009	18.473	-0.005	-0.005	0.000	0.000	0.000	0.000
86	C	86	GLN	0	-0.021	-0.001	16.668	0.011	0.011	0.000	0.000	0.000	0.000
87	C	87	VAL	0	0.070	0.025	20.374	-0.003	-0.003	0.000	0.000	0.000	0.000
88	C	88	ASP	-1	-0.909	-0.960	23.247	0.184	0.184	0.000	0.000	0.000	0.000
89	C	89	LYS	1	0.892	0.959	17.935	-0.354	-0.354	0.000	0.000	0.000	0.000
90	C	90	ASN	0	0.002	-0.021	21.317	-0.043	-0.043	0.000	0.000	0.000	0.000
91	C	91	LYS	1	0.982	0.974	20.221	-0.130	-0.130	0.000	0.000	0.000	0.000
92	C	92	ASP	-1	-0.933	-0.976	18.911	0.241	0.241	0.000	0.000	0.000	0.000
93	C	93	ASP	-1	-0.857	-0.894	17.510	0.380	0.380	0.000	0.000	0.000	0.000
94	C	94	GLU	-1	-0.857	-0.928	10.049	1.278	1.278	0.000	0.000	0.000	0.000
95	C	95	LEU	0	-0.041	-0.010	10.599	-0.020	-0.020	0.000	0.000	0.000	0.000
96	C	96	THR	0	0.021	0.011	10.126	0.133	0.133	0.000	0.000	0.000	0.000
97	C	97	GLY	0	0.038	0.009	10.186	-0.126	-0.126	0.000	0.000	0.000	0.000
98	C	98	PHE	0	-0.027	0.008	11.022	-0.101	-0.101	0.000	0.000	0.000	0.000

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