FMO DATABASE

FMODB ID: YY4N2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-822753.750589
FMO2-HF: Nuclear repulsion	778428.811764
FMO2-HF: Total energy	-44324.938825
FMO2-MP2: Total energy	-44449.110194

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.
1.817	2.645	0	-0.3	-0.529	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 : 0.027 / 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].	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	-0.025	-0.015	3.814	0.597	1.425	-0.300	-0.529	0.001
4	A	21	VAL	0	-0.028	-0.007	6.108	0.081	0.081	0.000	0.000	0.000
5	A	22	GLU	-1	-0.914	-0.953	8.206	0.434	0.434	0.000	0.000	0.000
6	A	23	THR	0	-0.004	-0.004	9.120	0.218	0.218	0.000	0.000	0.000
7	A	24	LYS	1	0.931	0.963	11.005	-0.402	-0.402	0.000	0.000	0.000
8	A	25	CYS	0	0.021	0.032	14.164	0.063	0.063	0.000	0.000	0.000
9	A	26	PRO	0	0.029	0.006	16.434	-0.031	-0.031	0.000	0.000	0.000
10	A	27	ASN	0	-0.065	-0.057	13.202	-0.034	-0.034	0.000	0.000	0.000
11	A	28	LEU	0	0.011	0.003	17.033	0.006	0.006	0.000	0.000	0.000
12	A	29	ASP	-1	-0.914	-0.942	17.772	0.192	0.192	0.000	0.000	0.000
13	A	30	ILE	0	-0.061	-0.050	19.850	-0.004	-0.004	0.000	0.000	0.000
14	A	31	VAL	0	0.022	0.031	18.996	-0.009	-0.009	0.000	0.000	0.000
15	A	32	THR	0	-0.008	-0.008	22.326	-0.005	-0.005	0.000	0.000	0.000
16	A	33	SER	0	0.019	0.007	24.836	0.001	0.001	0.000	0.000	0.000
17	A	34	SER	0	-0.025	-0.019	26.671	-0.002	-0.002	0.000	0.000	0.000
18	A	35	GLY	0	0.035	0.022	30.248	0.001	0.001	0.000	0.000	0.000
19	A	36	GLU	-1	-0.932	-0.960	27.181	0.075	0.075	0.000	0.000	0.000
20	A	37	PHE	0	0.005	-0.004	26.505	0.001	0.001	0.000	0.000	0.000
21	A	38	HIS	0	-0.003	-0.005	21.732	0.012	0.012	0.000	0.000	0.000
22	A	39	CYS	0	-0.042	0.019	22.207	0.012	0.012	0.000	0.000	0.000
23	A	40	SER	0	-0.010	-0.012	17.111	0.014	0.014	0.000	0.000	0.000
24	A	41	GLY	0	0.032	0.013	17.544	-0.007	-0.007	0.000	0.000	0.000
25	A	42	CYS	0	-0.095	-0.020	14.262	0.012	0.012	0.000	0.000	0.000
26	A	43	VAL	0	0.030	-0.017	16.260	-0.030	-0.030	0.000	0.000	0.000
27	A	44	GLU	-1	-0.929	-0.970	14.416	0.301	0.301	0.000	0.000	0.000
28	A	45	HIS	0	0.074	0.052	16.691	-0.010	-0.010	0.000	0.000	0.000
29	A	46	MET	0	-0.040	-0.022	20.110	-0.009	-0.009	0.000	0.000	0.000
30	A	47	PRO	0	0.035	0.022	18.569	-0.008	-0.008	0.000	0.000	0.000
31	A	48	GLU	-1	-0.890	-0.945	20.945	0.145	0.145	0.000	0.000	0.000
32	A	49	PHE	0	-0.035	0.004	23.951	-0.013	-0.013	0.000	0.000	0.000
33	A	50	SER	0	0.014	-0.016	22.443	0.008	0.008	0.000	0.000	0.000
34	A	51	TYR	0	-0.028	-0.018	24.726	-0.005	-0.005	0.000	0.000	0.000
35	A	52	MET	0	-0.021	-0.005	20.946	0.004	0.004	0.000	0.000	0.000
36	A	53	TYR	0	-0.009	-0.012	25.750	-0.008	-0.008	0.000	0.000	0.000
37	A	54	TRP	0	-0.005	-0.006	25.984	0.004	0.004	0.000	0.000	0.000
38	A	55	LEU	0	-0.032	-0.010	30.557	-0.005	-0.005	0.000	0.000	0.000
39	A	56	ALA	0	0.012	-0.006	33.297	0.002	0.002	0.000	0.000	0.000
40	A	57	LYS	1	0.902	0.962	36.023	-0.050	-0.050	0.000	0.000	0.000
41	A	58	ASP	-1	-0.795	-0.889	38.771	0.041	0.041	0.000	0.000	0.000
42	A	59	MET	0	-0.086	-0.038	38.189	0.000	0.000	0.000	0.000	0.000
43	A	60	LYS	1	0.903	0.954	41.593	-0.033	-0.033	0.000	0.000	0.000
44	A	61	SER	0	-0.039	-0.009	44.496	-0.002	-0.002	0.000	0.000	0.000
45	A	62	ASP	-1	-0.971	-1.012	45.339	0.035	0.035	0.000	0.000	0.000
46	A	63	GLU	-1	-0.822	-0.867	44.501	0.039	0.039	0.000	0.000	0.000
47	A	64	ASP	-1	-0.967	-0.989	42.670	0.045	0.045	0.000	0.000	0.000
48	A	65	THR	0	-0.129	-0.090	36.299	0.000	0.000	0.000	0.000	0.000
49	A	66	LYS	1	0.928	0.978	38.727	-0.045	-0.045	0.000	0.000	0.000
50	A	67	PHE	0	0.024	0.005	35.041	0.004	0.004	0.000	0.000	0.000
51	A	68	ILE	0	0.038	0.009	33.023	-0.004	-0.004	0.000	0.000	0.000
52	A	69	GLU	-1	-0.877	-0.936	36.330	0.061	0.061	0.000	0.000	0.000
53	A	70	HIS	0	-0.056	-0.030	38.726	-0.003	-0.003	0.000	0.000	0.000
54	A	71	LEU	0	-0.025	-0.005	37.247	-0.002	-0.002	0.000	0.000	0.000
55	A	72	GLY	0	-0.014	-0.005	41.365	-0.002	-0.002	0.000	0.000	0.000
56	A	73	ASP	-1	-0.889	-0.946	41.297	0.039	0.039	0.000	0.000	0.000
57	A	74	GLY	0	0.028	0.005	40.165	0.000	0.000	0.000	0.000	0.000
58	A	75	ILE	0	-0.055	-0.021	34.641	0.002	0.002	0.000	0.000	0.000
59	A	76	ASN	0	0.031	0.016	33.647	-0.004	-0.004	0.000	0.000	0.000
60	A	77	GLU	-1	-0.812	-0.915	30.109	0.090	0.090	0.000	0.000	0.000
61	A	78	ASP	-1	-0.835	-0.879	27.816	0.074	0.074	0.000	0.000	0.000
62	A	79	GLU	-1	-0.901	-0.963	28.253	0.087	0.087	0.000	0.000	0.000
63	A	80	THR	0	-0.071	-0.034	22.835	0.002	0.002	0.000	0.000	0.000
64	A	81	VAL	0	0.011	0.014	19.832	-0.004	-0.004	0.000	0.000	0.000
65	A	82	ARG	1	0.869	0.924	19.546	-0.148	-0.148	0.000	0.000	0.000
66	A	83	THR	0	-0.056	-0.024	14.956	0.001	0.001	0.000	0.000	0.000
67	A	84	THR	0	-0.006	-0.030	13.608	0.012	0.012	0.000	0.000	0.000
68	A	85	ASP	-1	-0.938	-0.965	7.517	0.562	0.562	0.000	0.000	0.000
69	A	86	GLY	0	0.028	0.032	7.952	0.085	0.085	0.000	0.000	0.000
70	A	87	GLY	0	-0.007	-0.004	8.913	0.046	0.046	0.000	0.000	0.000
71	A	88	ILE	0	0.026	0.026	10.299	-0.056	-0.056	0.000	0.000	0.000
72	A	89	THR	0	0.008	-0.002	12.806	-0.019	-0.019	0.000	0.000	0.000
73	A	90	THR	0	-0.061	-0.035	13.264	0.030	0.030	0.000	0.000	0.000
74	A	91	LEU	0	-0.026	-0.017	15.849	-0.036	-0.036	0.000	0.000	0.000
75	A	92	ARG	1	0.985	0.970	13.443	-0.292	-0.292	0.000	0.000	0.000
76	A	93	LYS	1	0.873	0.933	20.694	-0.117	-0.117	0.000	0.000	0.000
77	A	94	VAL	0	0.027	0.030	24.370	0.003	0.003	0.000	0.000	0.000
78	A	95	LEU	0	0.003	0.013	26.339	-0.005	-0.005	0.000	0.000	0.000
79	A	96	HIS	1	0.828	0.891	29.456	-0.072	-0.072	0.000	0.000	0.000
80	A	97	VAL	0	-0.009	-0.011	31.933	-0.002	-0.002	0.000	0.000	0.000
81	A	98	THR	0	-0.028	-0.021	34.576	-0.003	-0.003	0.000	0.000	0.000
82	A	99	ASP	-1	-0.873	-0.932	37.002	0.033	0.033	0.000	0.000	0.000
83	A	100	THR	0	-0.020	-0.035	36.007	0.000	0.000	0.000	0.000	0.000
84	A	101	ASN	0	-0.032	-0.024	38.635	-0.001	-0.001	0.000	0.000	0.000
85	A	102	LYS	1	0.869	0.961	41.808	-0.041	-0.041	0.000	0.000	0.000
86	A	103	PHE	0	0.007	-0.008	37.851	0.000	0.000	0.000	0.000	0.000
87	A	104	ALA	0	0.003	0.009	38.158	0.003	0.003	0.000	0.000	0.000
88	A	105	HIS	0	-0.044	-0.030	38.970	0.001	0.001	0.000	0.000	0.000
89	A	106	TYR	0	0.037	0.025	37.225	0.000	0.000	0.000	0.000	0.000
90	A	107	ARG	1	0.883	0.962	33.648	-0.061	-0.061	0.000	0.000	0.000
91	A	108	PHE	0	0.039	0.008	31.379	0.000	0.000	0.000	0.000	0.000
92	A	109	THR	0	-0.050	-0.057	29.792	0.001	0.001	0.000	0.000	0.000
93	A	111	VAL	0	-0.024	-0.014	26.910	0.005	0.005	0.000	0.000	0.000
94	A	112	LEU	0	0.020	0.004	20.387	0.002	0.002	0.000	0.000	0.000
95	A	113	THR	0	-0.042	-0.030	24.766	-0.005	-0.005	0.000	0.000	0.000
96	A	114	THR	0	0.029	0.006	21.898	0.007	0.007	0.000	0.000	0.000
97	A	115	LEU	0	0.018	-0.002	25.092	-0.011	-0.011	0.000	0.000	0.000
98	A	116	ASP	-1	-0.875	-0.916	22.951	0.147	0.147	0.000	0.000	0.000
99	A	117	GLY	0	-0.052	-0.021	25.809	-0.008	-0.008	0.000	0.000	0.000
100	A	118	VAL	0	-0.039	-0.016	26.427	0.007	0.007	0.000	0.000	0.000
101	A	119	SER	0	-0.041	-0.016	23.486	0.006	0.006	0.000	0.000	0.000
102	A	120	LYS	1	0.988	0.984	25.425	-0.089	-0.089	0.000	0.000	0.000
103	A	121	LYS	1	0.950	0.984	22.406	-0.138	-0.138	0.000	0.000	0.000
104	A	122	ASN	0	-0.014	0.007	26.469	-0.002	-0.002	0.000	0.000	0.000
105	A	123	ILE	0	0.002	0.003	26.557	0.004	0.004	0.000	0.000	0.000
106	A	124	TRP	0	0.053	0.016	29.764	-0.004	-0.004	0.000	0.000	0.000
107	A	125	LEU	0	0.006	0.021	31.780	0.001	0.001	0.000	0.000	0.000

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