FMO DATABASE

FMODB ID: VR9K1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-823289.318144
FMO2-HF: Nuclear repulsion	778963.519171
FMO2-HF: Total energy	-44325.798973
FMO2-MP2: Total energy	-44450.003654

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.
2.323	3.155	0	-0.299	-0.533	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 : 0.003

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	-0.018	-0.011	3.814	0.873	1.705	-0.299	-0.533	0.001
4	A	21	VAL	0	-0.025	-0.009	6.107	0.101	0.101	0.000	0.000	0.000
5	A	22	GLU	-1	-0.909	-0.947	8.205	0.458	0.458	0.000	0.000	0.000
6	A	23	THR	0	-0.017	-0.010	9.053	0.204	0.204	0.000	0.000	0.000
7	A	24	LYS	1	0.896	0.946	11.005	-0.386	-0.386	0.000	0.000	0.000
8	A	25	CYS	0	-0.020	0.002	14.164	0.054	0.054	0.000	0.000	0.000
9	A	26	PRO	0	0.042	0.014	16.434	-0.033	-0.033	0.000	0.000	0.000
10	A	27	ASN	0	-0.032	-0.034	14.844	0.004	0.004	0.000	0.000	0.000
11	A	28	LEU	0	0.042	0.022	17.002	0.007	0.007	0.000	0.000	0.000
12	A	29	ASP	-1	-0.847	-0.929	17.764	0.149	0.149	0.000	0.000	0.000
13	A	30	ILE	0	-0.049	-0.032	19.748	0.001	0.001	0.000	0.000	0.000
14	A	31	VAL	0	0.009	0.021	18.884	-0.009	-0.009	0.000	0.000	0.000
15	A	32	THR	0	0.009	0.012	22.252	-0.001	-0.001	0.000	0.000	0.000
16	A	33	SER	0	-0.008	-0.012	24.800	0.000	0.000	0.000	0.000	0.000
17	A	34	SER	0	-0.024	-0.022	26.627	-0.001	-0.001	0.000	0.000	0.000
18	A	35	GLY	0	0.031	0.018	30.210	0.002	0.002	0.000	0.000	0.000
19	A	36	GLU	-1	-0.861	-0.916	27.114	0.073	0.073	0.000	0.000	0.000
20	A	37	PHE	0	0.008	-0.005	26.449	-0.001	-0.001	0.000	0.000	0.000
21	A	38	HIS	0	-0.018	-0.016	21.658	0.014	0.014	0.000	0.000	0.000
22	A	39	CYS	0	-0.039	0.021	22.138	0.012	0.012	0.000	0.000	0.000
23	A	40	SER	0	-0.020	-0.015	17.173	0.018	0.018	0.000	0.000	0.000
24	A	41	GLY	0	0.032	0.013	17.527	-0.011	-0.011	0.000	0.000	0.000
25	A	42	CYS	0	-0.052	-0.003	14.401	0.015	0.015	0.000	0.000	0.000
26	A	43	VAL	0	0.023	-0.010	16.375	-0.035	-0.035	0.000	0.000	0.000
27	A	44	GLU	-1	-0.921	-0.972	14.666	0.355	0.355	0.000	0.000	0.000
28	A	45	HIS	0	0.068	0.055	16.843	-0.006	-0.006	0.000	0.000	0.000
29	A	46	MET	0	-0.049	-0.023	20.267	-0.012	-0.012	0.000	0.000	0.000
30	A	47	PRO	0	0.023	0.017	18.616	-0.010	-0.010	0.000	0.000	0.000
31	A	48	GLU	-1	-0.868	-0.922	21.082	0.168	0.168	0.000	0.000	0.000
32	A	49	PHE	0	-0.040	0.001	24.080	-0.016	-0.016	0.000	0.000	0.000
33	A	50	SER	0	0.013	-0.027	22.633	0.008	0.008	0.000	0.000	0.000
34	A	51	TYR	0	-0.040	-0.020	24.852	-0.004	-0.004	0.000	0.000	0.000
35	A	52	MET	0	-0.020	-0.012	21.034	0.003	0.003	0.000	0.000	0.000
36	A	53	TYR	0	-0.017	-0.011	25.845	-0.008	-0.008	0.000	0.000	0.000
37	A	54	TRP	0	0.003	-0.006	25.900	0.003	0.003	0.000	0.000	0.000
38	A	55	LEU	0	-0.021	-0.003	30.544	-0.004	-0.004	0.000	0.000	0.000
39	A	56	ALA	0	0.011	-0.001	33.213	0.002	0.002	0.000	0.000	0.000
40	A	57	LYS	1	0.819	0.893	35.937	-0.044	-0.044	0.000	0.000	0.000
41	A	58	ASP	-1	-0.766	-0.849	38.674	0.037	0.037	0.000	0.000	0.000
42	A	59	MET	0	-0.092	-0.037	38.241	0.000	0.000	0.000	0.000	0.000
43	A	60	LYS	1	0.885	0.951	41.487	-0.032	-0.032	0.000	0.000	0.000
44	A	61	SER	0	-0.028	-0.025	44.391	-0.002	-0.002	0.000	0.000	0.000
45	A	62	ASP	-1	-0.966	-1.001	45.235	0.033	0.033	0.000	0.000	0.000
46	A	63	GLU	-1	-0.810	-0.861	44.221	0.040	0.040	0.000	0.000	0.000
47	A	64	ASP	-1	-0.891	-0.937	42.587	0.045	0.045	0.000	0.000	0.000
48	A	65	THR	0	-0.123	-0.085	36.226	0.001	0.001	0.000	0.000	0.000
49	A	66	LYS	1	0.874	0.934	38.633	-0.045	-0.045	0.000	0.000	0.000
50	A	67	PHE	0	0.016	0.001	34.755	0.004	0.004	0.000	0.000	0.000
51	A	68	ILE	0	0.034	0.008	32.958	-0.004	-0.004	0.000	0.000	0.000
52	A	69	GLU	-1	-0.879	-0.940	36.346	0.062	0.062	0.000	0.000	0.000
53	A	70	HIS	0	-0.051	-0.026	38.790	-0.003	-0.003	0.000	0.000	0.000
54	A	71	LEU	0	-0.023	0.003	37.093	-0.002	-0.002	0.000	0.000	0.000
55	A	72	GLY	0	0.012	0.015	41.303	-0.003	-0.003	0.000	0.000	0.000
56	A	73	ASP	-1	-0.893	-0.946	41.250	0.039	0.039	0.000	0.000	0.000
57	A	74	GLY	0	0.017	0.006	40.121	0.000	0.000	0.000	0.000	0.000
58	A	75	ILE	0	-0.036	-0.014	34.623	0.001	0.001	0.000	0.000	0.000
59	A	76	ASN	0	0.012	0.014	33.019	-0.004	-0.004	0.000	0.000	0.000
60	A	77	GLU	-1	-0.793	-0.910	30.101	0.094	0.094	0.000	0.000	0.000
61	A	78	ASP	-1	-0.822	-0.878	27.784	0.077	0.077	0.000	0.000	0.000
62	A	79	GLU	-1	-0.873	-0.947	28.204	0.097	0.097	0.000	0.000	0.000
63	A	80	THR	0	-0.087	-0.038	22.855	0.001	0.001	0.000	0.000	0.000
64	A	81	VAL	0	0.007	0.014	19.837	-0.003	-0.003	0.000	0.000	0.000
65	A	82	ARG	1	0.870	0.916	19.631	-0.170	-0.170	0.000	0.000	0.000
66	A	83	THR	0	-0.048	-0.023	14.972	-0.001	-0.001	0.000	0.000	0.000
67	A	84	THR	0	-0.025	-0.032	13.838	0.000	0.000	0.000	0.000	0.000
68	A	85	ASP	-1	-0.891	-0.947	7.684	0.731	0.731	0.000	0.000	0.000
69	A	86	GLY	0	0.006	0.022	8.085	0.098	0.098	0.000	0.000	0.000
70	A	87	GLY	0	-0.012	-0.006	9.043	0.042	0.042	0.000	0.000	0.000
71	A	88	ILE	0	0.016	0.017	10.496	-0.077	-0.077	0.000	0.000	0.000
72	A	89	THR	0	0.007	0.004	12.944	-0.016	-0.016	0.000	0.000	0.000
73	A	90	THR	0	-0.064	-0.036	13.448	0.028	0.028	0.000	0.000	0.000
74	A	91	LEU	0	-0.014	-0.010	15.942	-0.036	-0.036	0.000	0.000	0.000
75	A	92	ARG	1	0.976	0.968	13.407	-0.314	-0.314	0.000	0.000	0.000
76	A	93	LYS	1	0.859	0.920	20.752	-0.120	-0.120	0.000	0.000	0.000
77	A	94	VAL	0	0.013	0.026	24.242	0.002	0.002	0.000	0.000	0.000
78	A	95	LEU	0	-0.001	0.012	26.300	-0.005	-0.005	0.000	0.000	0.000
79	A	96	HIS	1	0.814	0.886	29.265	-0.072	-0.072	0.000	0.000	0.000
80	A	97	VAL	0	-0.001	-0.005	31.892	-0.002	-0.002	0.000	0.000	0.000
81	A	98	THR	0	-0.011	-0.017	34.524	-0.002	-0.002	0.000	0.000	0.000
82	A	99	ASP	-1	-0.876	-0.927	36.960	0.031	0.031	0.000	0.000	0.000
83	A	100	THR	0	-0.011	-0.032	35.861	0.000	0.000	0.000	0.000	0.000
84	A	101	ASN	0	-0.049	-0.028	38.572	0.000	0.000	0.000	0.000	0.000
85	A	102	LYS	1	0.842	0.926	41.743	-0.040	-0.040	0.000	0.000	0.000
86	A	103	PHE	0	0.013	-0.008	37.682	0.000	0.000	0.000	0.000	0.000
87	A	104	ALA	0	-0.007	0.004	38.076	0.002	0.002	0.000	0.000	0.000
88	A	105	HIS	0	-0.030	-0.023	38.879	0.000	0.000	0.000	0.000	0.000
89	A	106	TYR	0	0.038	0.020	37.254	0.001	0.001	0.000	0.000	0.000
90	A	107	ARG	1	0.897	0.969	33.539	-0.059	-0.059	0.000	0.000	0.000
91	A	108	PHE	0	0.033	0.012	31.332	0.000	0.000	0.000	0.000	0.000
92	A	109	THR	0	-0.049	-0.049	29.719	0.000	0.000	0.000	0.000	0.000
93	A	111	VAL	0	-0.023	-0.017	26.847	0.004	0.004	0.000	0.000	0.000
94	A	112	LEU	0	0.015	0.007	20.258	0.003	0.003	0.000	0.000	0.000
95	A	113	THR	0	-0.042	-0.033	24.845	-0.006	-0.006	0.000	0.000	0.000
96	A	114	THR	0	0.025	0.003	21.978	0.010	0.010	0.000	0.000	0.000
97	A	115	LEU	0	0.022	0.002	25.247	-0.013	-0.013	0.000	0.000	0.000
98	A	116	ASP	-1	-0.862	-0.911	22.754	0.165	0.165	0.000	0.000	0.000
99	A	117	GLY	0	-0.039	-0.013	25.856	-0.010	-0.010	0.000	0.000	0.000
100	A	118	VAL	0	-0.048	-0.023	26.466	0.008	0.008	0.000	0.000	0.000
101	A	119	SER	0	-0.036	-0.011	23.489	0.004	0.004	0.000	0.000	0.000
102	A	120	LYS	1	0.983	0.980	25.425	-0.088	-0.088	0.000	0.000	0.000
103	A	121	LYS	1	0.840	0.925	20.820	-0.148	-0.148	0.000	0.000	0.000
104	A	122	ASN	0	-0.021	-0.006	26.357	-0.002	-0.002	0.000	0.000	0.000
105	A	123	ILE	0	-0.001	0.005	26.252	0.002	0.002	0.000	0.000	0.000
106	A	124	TRP	0	0.046	0.013	29.662	-0.003	-0.003	0.000	0.000	0.000
107	A	125	LEU	0	0.011	0.022	31.687	0.000	0.000	0.000	0.000	0.000

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