FMO DATABASE

FMODB ID: 14M6Z

Calculation Name: 3F62-A-Xray372

Preferred Name: Interleukin-18

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3F62

Chain ID: A

ChEMBL ID: CHEMBL1741305

UniProt ID: Q14116

Base Structure: X-ray

Registration Date: 2023-06-19

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	107
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-822232.681691
FMO2-HF: Nuclear repulsion	777906.536635
FMO2-HF: Total energy	-44326.145056
FMO2-MP2: Total energy	-44450.496359

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(A:18:GLY)

Summations of interaction energy for fragment #1(A:18:GLY)

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.
1.969	2.863	-0.002	-0.325	-0.567	0.001

Interaction energy analysis for fragmet #1(A:18:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : 0.001

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	A	20	MET	0	-0.015	-0.001	3.844	0.474	1.368	-0.002	-0.325	-0.567	0.001
4	A	21	VAL	0	-0.024	-0.016	5.978	0.327	0.327	0.000	0.000	0.000	0.000
5	A	22	GLU	-1	-0.911	-0.949	8.146	0.204	0.204	0.000	0.000	0.000	0.000
6	A	23	THR	0	-0.022	-0.016	8.913	0.177	0.177	0.000	0.000	0.000	0.000
7	A	24	LYS	1	0.908	0.946	10.993	-0.313	-0.313	0.000	0.000	0.000	0.000
8	A	25	CYS	0	0.013	0.024	14.471	0.052	0.052	0.000	0.000	0.000	0.000
9	A	26	PRO	0	0.009	0.002	16.515	-0.037	-0.037	0.000	0.000	0.000	0.000
10	A	27	ASN	0	-0.031	-0.035	15.562	0.005	0.005	0.000	0.000	0.000	0.000
11	A	28	LEU	0	0.040	0.025	17.539	0.025	0.025	0.000	0.000	0.000	0.000
12	A	29	ASP	-1	-0.853	-0.918	18.784	0.202	0.202	0.000	0.000	0.000	0.000
13	A	30	ILE	0	-0.021	-0.015	20.565	0.007	0.007	0.000	0.000	0.000	0.000
14	A	31	VAL	0	0.031	0.039	19.450	-0.012	-0.012	0.000	0.000	0.000	0.000
15	A	32	THR	0	-0.001	-0.002	22.708	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	33	SER	0	-0.020	-0.041	25.419	0.005	0.005	0.000	0.000	0.000	0.000
17	A	34	SER	0	-0.038	-0.027	27.423	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	35	GLY	0	0.044	0.032	30.994	0.001	0.001	0.000	0.000	0.000	0.000
19	A	36	GLU	-1	-0.829	-0.881	27.858	0.122	0.122	0.000	0.000	0.000	0.000
20	A	37	PHE	0	0.024	0.011	27.175	0.001	0.001	0.000	0.000	0.000	0.000
21	A	38	HIS	0	-0.019	-0.029	22.482	0.015	0.015	0.000	0.000	0.000	0.000
22	A	39	CYS	0	-0.038	0.026	22.536	0.019	0.019	0.000	0.000	0.000	0.000
23	A	40	SER	0	-0.013	-0.012	17.883	0.025	0.025	0.000	0.000	0.000	0.000
24	A	41	GLY	0	0.033	0.014	17.870	-0.018	-0.018	0.000	0.000	0.000	0.000
25	A	42	CYS	0	-0.065	-0.011	15.132	0.013	0.013	0.000	0.000	0.000	0.000
26	A	43	VAL	0	0.024	0.004	16.876	-0.042	-0.042	0.000	0.000	0.000	0.000
27	A	44	GLU	-1	-0.921	-0.970	14.121	0.296	0.296	0.000	0.000	0.000	0.000
28	A	45	HIS	0	0.064	0.039	16.751	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	46	MET	0	-0.063	-0.028	19.976	0.000	0.000	0.000	0.000	0.000	0.000
30	A	47	PRO	0	0.062	0.053	18.932	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	48	GLU	-1	-0.827	-0.911	21.175	0.168	0.168	0.000	0.000	0.000	0.000
32	A	49	PHE	0	-0.039	-0.013	24.316	-0.010	-0.010	0.000	0.000	0.000	0.000
33	A	50	SER	0	-0.028	-0.038	22.765	0.005	0.005	0.000	0.000	0.000	0.000
34	A	51	TYR	0	-0.029	-0.018	25.175	0.000	0.000	0.000	0.000	0.000	0.000
35	A	52	MET	0	-0.022	-0.006	21.372	0.001	0.001	0.000	0.000	0.000	0.000
36	A	53	TYR	0	-0.007	-0.009	26.215	-0.007	-0.007	0.000	0.000	0.000	0.000
37	A	54	TRP	0	-0.008	-0.011	26.824	0.003	0.003	0.000	0.000	0.000	0.000
38	A	55	LEU	0	-0.022	-0.002	31.113	-0.006	-0.006	0.000	0.000	0.000	0.000
39	A	56	ALA	0	0.006	-0.002	33.792	0.004	0.004	0.000	0.000	0.000	0.000
40	A	57	LYS	1	0.801	0.872	36.513	-0.054	-0.054	0.000	0.000	0.000	0.000
41	A	58	ASP	-1	-0.774	-0.852	39.379	0.050	0.050	0.000	0.000	0.000	0.000
42	A	59	MET	0	-0.068	-0.027	39.098	0.000	0.000	0.000	0.000	0.000	0.000
43	A	60	LYS	1	0.865	0.947	42.304	-0.045	-0.045	0.000	0.000	0.000	0.000
44	A	61	SER	0	-0.042	-0.043	45.413	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	62	ASP	-1	-0.890	-0.950	45.802	0.041	0.041	0.000	0.000	0.000	0.000
46	A	63	GLU	-1	-0.849	-0.905	45.051	0.049	0.049	0.000	0.000	0.000	0.000
47	A	64	ASP	-1	-0.843	-0.909	43.084	0.057	0.057	0.000	0.000	0.000	0.000
48	A	65	THR	0	-0.087	-0.052	37.129	0.002	0.002	0.000	0.000	0.000	0.000
49	A	66	LYS	1	0.792	0.896	39.242	-0.055	-0.055	0.000	0.000	0.000	0.000
50	A	67	PHE	0	0.039	0.015	34.932	0.004	0.004	0.000	0.000	0.000	0.000
51	A	68	ILE	0	0.027	0.007	33.462	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	69	GLU	-1	-0.849	-0.930	36.772	0.075	0.075	0.000	0.000	0.000	0.000
53	A	70	HIS	0	-0.088	-0.045	39.182	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	71	LEU	0	-0.031	0.001	37.701	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	72	GLY	0	0.024	0.022	41.826	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	73	ASP	-1	-0.902	-0.956	41.681	0.055	0.055	0.000	0.000	0.000	0.000
57	A	74	GLY	0	0.010	0.005	40.846	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	75	ILE	0	-0.045	-0.017	35.278	0.002	0.002	0.000	0.000	0.000	0.000
59	A	76	ASN	0	-0.023	-0.016	32.743	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	77	GLU	-1	-0.792	-0.908	30.336	0.119	0.119	0.000	0.000	0.000	0.000
61	A	78	ASP	-1	-0.806	-0.869	28.157	0.113	0.113	0.000	0.000	0.000	0.000
62	A	79	GLU	-1	-0.833	-0.949	28.412	0.128	0.128	0.000	0.000	0.000	0.000
63	A	80	THR	0	-0.098	-0.032	23.742	0.006	0.006	0.000	0.000	0.000	0.000
64	A	81	VAL	0	-0.004	0.015	20.120	0.003	0.003	0.000	0.000	0.000	0.000
65	A	82	ARG	1	0.868	0.923	20.263	-0.190	-0.190	0.000	0.000	0.000	0.000
66	A	83	THR	0	-0.060	-0.037	15.365	0.009	0.009	0.000	0.000	0.000	0.000
67	A	84	THR	0	0.005	-0.023	14.568	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	85	ASP	-1	-0.890	-0.937	8.244	0.945	0.945	0.000	0.000	0.000	0.000
69	A	86	GLY	0	-0.010	-0.002	8.492	0.072	0.072	0.000	0.000	0.000	0.000
70	A	87	GLY	0	-0.038	-0.010	9.361	-0.053	-0.053	0.000	0.000	0.000	0.000
71	A	88	ILE	0	0.004	0.012	10.352	-0.084	-0.084	0.000	0.000	0.000	0.000
72	A	89	THR	0	0.016	0.010	13.031	0.005	0.005	0.000	0.000	0.000	0.000
73	A	90	THR	0	-0.057	-0.037	13.838	0.024	0.024	0.000	0.000	0.000	0.000
74	A	91	LEU	0	-0.004	0.010	16.386	-0.024	-0.024	0.000	0.000	0.000	0.000
75	A	92	ARG	1	0.953	0.949	14.086	-0.424	-0.424	0.000	0.000	0.000	0.000
76	A	93	LYS	1	0.823	0.913	21.382	-0.149	-0.149	0.000	0.000	0.000	0.000
77	A	94	VAL	0	0.012	0.026	24.977	0.000	0.000	0.000	0.000	0.000	0.000
78	A	95	LEU	0	0.006	0.006	26.854	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	96	HIS	1	0.820	0.899	29.582	-0.111	-0.111	0.000	0.000	0.000	0.000
80	A	97	VAL	0	-0.004	-0.015	32.437	-0.004	-0.004	0.000	0.000	0.000	0.000
81	A	98	THR	0	0.000	-0.005	35.308	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	99	ASP	-1	-0.851	-0.919	37.838	0.049	0.049	0.000	0.000	0.000	0.000
83	A	100	THR	0	-0.014	-0.031	36.509	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	101	ASN	0	-0.051	-0.015	39.167	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	102	LYS	1	0.842	0.914	42.717	-0.057	-0.057	0.000	0.000	0.000	0.000
86	A	103	PHE	0	0.023	-0.011	38.111	0.000	0.000	0.000	0.000	0.000	0.000
87	A	104	ALA	0	-0.030	-0.008	38.833	0.003	0.003	0.000	0.000	0.000	0.000
88	A	105	HIS	0	-0.019	-0.018	39.964	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	106	TYR	0	0.026	0.020	37.969	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	107	ARG	1	0.831	0.939	34.024	-0.074	-0.074	0.000	0.000	0.000	0.000
91	A	108	PHE	0	0.029	0.006	32.085	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	109	THR	0	-0.031	-0.048	30.502	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	111	VAL	0	-0.035	-0.028	27.729	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	112	LEU	0	0.017	0.010	20.909	0.007	0.007	0.000	0.000	0.000	0.000
95	A	113	THR	0	-0.021	-0.017	25.503	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	114	THR	0	0.009	-0.003	22.138	0.013	0.013	0.000	0.000	0.000	0.000
97	A	115	LEU	0	0.035	0.003	25.382	-0.011	-0.011	0.000	0.000	0.000	0.000
98	A	116	ASP	-1	-0.871	-0.914	22.621	0.130	0.130	0.000	0.000	0.000	0.000
99	A	117	GLY	0	-0.033	-0.011	25.925	-0.010	-0.010	0.000	0.000	0.000	0.000
100	A	118	VAL	0	-0.041	-0.018	26.713	0.010	0.010	0.000	0.000	0.000	0.000
101	A	119	SER	0	-0.035	-0.015	24.100	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	120	LYS	1	0.967	0.972	26.090	-0.093	-0.093	0.000	0.000	0.000	0.000
103	A	121	LYS	1	0.806	0.891	21.374	-0.188	-0.188	0.000	0.000	0.000	0.000
104	A	122	ASN	0	0.002	0.010	26.809	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	123	ILE	0	-0.005	0.007	27.068	0.004	0.004	0.000	0.000	0.000	0.000
106	A	124	TRP	0	0.058	0.019	30.470	-0.006	-0.006	0.000	0.000	0.000	0.000
107	A	125	LEU	0	0.008	0.027	32.438	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:18:GLY)