FMO DATABASE

FMODB ID: YV312

Calculation Name: 2IKB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2IKB

Chain ID: A

ChEMBL ID:

UniProt ID: Q7DDI9

Base Structure: X-ray

Registration Date: 2023-09-24

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	163
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1613330.078311
FMO2-HF: Nuclear repulsion	1549198.387816
FMO2-HF: Total energy	-64131.690495
FMO2-MP2: Total energy	-64318.454561

3D Structure Molmil

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:1:MET)

Summations of interaction energy for fragment #1(A: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.
-17.086	-9.971	10.934	-5.5	-12.549	-0.005

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.060 / q_NPA : 0.021

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	3	ASP	-1	-0.837	-0.911	2.379	-9.642	-5.630	3.560	-2.725	-4.847	-0.027
4	A	4	LYS	1	0.827	0.900	2.010	-8.992	-7.675	7.328	-2.288	-6.357	0.023
5	A	5	PHE	0	0.020	0.014	3.602	-1.160	-0.620	0.013	-0.093	-0.460	0.000
6	A	6	ASN	0	0.012	-0.006	5.700	0.228	0.228	0.000	0.000	0.000	0.000
7	A	7	GLN	0	-0.007	-0.004	6.459	0.170	0.170	0.000	0.000	0.000	0.000
8	A	8	PHE	0	-0.014	-0.008	7.715	-0.096	-0.096	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.016	0.003	9.610	-0.089	-0.089	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.034	-0.035	10.860	-0.037	-0.037	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.867	0.943	10.963	-0.961	-0.961	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.046	-0.003	13.307	-0.013	-0.013	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.044	-0.002	15.671	-0.031	-0.031	0.000	0.000	0.000	0.000
14	A	14	SER	0	0.014	0.019	17.228	-0.013	-0.013	0.000	0.000	0.000	0.000
15	A	15	HIS	0	0.045	0.002	16.669	-0.045	-0.045	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.907	-0.946	21.194	-0.047	-0.047	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.026	0.014	23.429	0.008	0.008	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.017	0.008	24.506	0.003	0.003	0.000	0.000	0.000	0.000
19	A	19	TYR	0	-0.112	-0.089	26.933	0.003	0.003	0.000	0.000	0.000	0.000
20	A	20	ALA	0	0.008	0.005	28.510	0.008	0.008	0.000	0.000	0.000	0.000
21	A	21	ASN	0	-0.023	-0.028	30.201	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	22	HIS	0	0.055	0.043	32.864	0.000	0.000	0.000	0.000	0.000	0.000
23	A	23	PRO	0	0.039	0.005	35.648	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.911	0.945	38.211	0.011	0.011	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.761	-0.850	31.747	-0.012	-0.012	0.000	0.000	0.000	0.000
26	A	26	PRO	0	0.055	0.032	32.637	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	27	GLY	0	-0.010	-0.004	29.863	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.016	-0.010	28.132	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.836	-0.877	28.828	-0.059	-0.059	0.000	0.000	0.000	0.000
30	A	30	THR	0	-0.033	-0.045	24.206	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	31	ASN	0	-0.006	-0.013	24.459	0.012	0.012	0.000	0.000	0.000	0.000
32	A	32	TRP	0	0.028	0.008	19.757	-0.010	-0.010	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.023	0.027	19.802	0.001	0.001	0.000	0.000	0.000	0.000
34	A	34	ILE	0	-0.031	0.001	17.495	0.007	0.007	0.000	0.000	0.000	0.000
35	A	35	THR	0	0.046	0.029	21.410	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.949	0.967	23.583	0.069	0.069	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.807	0.880	25.362	0.010	0.010	0.000	0.000	0.000	0.000
38	A	38	THR	0	-0.022	-0.012	19.262	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	39	ALA	0	0.026	0.015	20.926	-0.019	-0.019	0.000	0.000	0.000	0.000
40	A	40	GLN	0	0.037	0.012	21.921	-0.015	-0.015	0.000	0.000	0.000	0.000
41	A	41	ALA	0	-0.042	0.003	21.527	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	42	ASN	0	-0.107	-0.070	17.213	-0.029	-0.029	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.041	0.030	19.113	-0.026	-0.026	0.000	0.000	0.000	0.000
44	A	44	TYR	0	-0.027	-0.011	21.105	-0.010	-0.010	0.000	0.000	0.000	0.000
45	A	45	ASN	0	0.006	-0.024	22.882	0.024	0.024	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.022	0.029	26.025	0.009	0.009	0.000	0.000	0.000	0.000
47	A	47	SER	0	0.016	0.000	27.807	0.008	0.008	0.000	0.000	0.000	0.000
48	A	48	MET	0	0.025	0.039	23.579	-0.015	-0.015	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.951	0.978	26.342	0.056	0.056	0.000	0.000	0.000	0.000
50	A	50	ALA	0	-0.014	-0.007	27.877	0.000	0.000	0.000	0.000	0.000	0.000
51	A	51	MET	0	-0.033	0.019	21.453	-0.010	-0.010	0.000	0.000	0.000	0.000
52	A	52	THR	0	0.006	-0.013	20.655	0.010	0.010	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.888	0.934	15.384	0.106	0.106	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.806	-0.890	16.447	-0.264	-0.264	0.000	0.000	0.000	0.000
55	A	55	GLN	0	0.011	0.006	16.145	-0.028	-0.028	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.039	0.014	17.241	-0.010	-0.010	0.000	0.000	0.000	0.000
57	A	57	ILE	0	-0.013	-0.003	11.729	0.003	0.003	0.000	0.000	0.000	0.000
58	A	58	SER	0	-0.020	-0.019	12.387	-0.074	-0.074	0.000	0.000	0.000	0.000
59	A	59	ILE	0	-0.020	-0.003	13.220	-0.018	-0.018	0.000	0.000	0.000	0.000
60	A	60	TYR	0	-0.019	-0.044	12.407	0.020	0.020	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.854	0.933	4.512	1.873	1.974	-0.001	-0.011	-0.089	0.000
62	A	62	LYS	1	0.961	0.982	9.538	0.205	0.205	0.000	0.000	0.000	0.000
63	A	63	ALA	0	-0.041	-0.029	12.123	0.043	0.043	0.000	0.000	0.000	0.000
64	A	64	PHE	0	-0.022	-0.025	10.637	0.040	0.040	0.000	0.000	0.000	0.000
65	A	65	TRP	0	0.022	0.016	3.194	0.051	0.490	0.010	-0.131	-0.318	0.000
66	A	66	GLU	-1	-0.865	-0.942	7.332	-0.982	-0.982	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.886	0.964	8.910	0.133	0.133	0.000	0.000	0.000	0.000
68	A	68	TYR	0	-0.024	-0.030	11.471	0.018	0.018	0.000	0.000	0.000	0.000
69	A	69	ARG	1	0.979	0.994	7.974	0.288	0.288	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.021	0.011	8.406	0.155	0.155	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.891	-0.936	3.363	0.326	1.032	0.024	-0.252	-0.478	-0.001
72	A	72	GLN	0	-0.007	0.003	5.471	0.593	0.593	0.000	0.000	0.000	0.000
73	A	73	MET	0	-0.043	0.011	8.381	-0.137	-0.137	0.000	0.000	0.000	0.000
74	A	74	PRO	0	0.070	0.043	10.044	0.257	0.257	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.851	-0.921	9.765	1.440	1.440	0.000	0.000	0.000	0.000
76	A	76	ALA	0	0.013	0.007	12.123	-0.128	-0.128	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.012	0.008	14.216	-0.098	-0.098	0.000	0.000	0.000	0.000
78	A	78	ALA	0	0.038	0.015	10.582	-0.101	-0.101	0.000	0.000	0.000	0.000
79	A	79	PHE	0	-0.018	-0.015	12.534	-0.119	-0.119	0.000	0.000	0.000	0.000
80	A	80	GLN	0	0.049	0.025	14.729	-0.109	-0.109	0.000	0.000	0.000	0.000
81	A	81	PHE	0	0.023	0.004	13.478	-0.065	-0.065	0.000	0.000	0.000	0.000
82	A	82	PHE	0	0.042	0.012	13.305	-0.050	-0.050	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.734	-0.829	15.664	0.110	0.110	0.000	0.000	0.000	0.000
84	A	84	ALA	0	0.009	0.007	19.153	-0.032	-0.032	0.000	0.000	0.000	0.000
85	A	85	CYS	0	-0.072	-0.022	17.175	-0.028	-0.028	0.000	0.000	0.000	0.000
86	A	86	VAL	0	-0.042	-0.015	17.894	-0.024	-0.024	0.000	0.000	0.000	0.000
87	A	87	ASN	0	-0.075	-0.037	20.488	-0.025	-0.025	0.000	0.000	0.000	0.000
88	A	88	HIS	0	-0.004	0.007	23.130	0.004	0.004	0.000	0.000	0.000	0.000
89	A	89	GLY	0	0.049	0.048	22.837	-0.009	-0.009	0.000	0.000	0.000	0.000
90	A	90	TYR	0	0.029	0.003	15.559	0.012	0.012	0.000	0.000	0.000	0.000
91	A	91	GLY	0	-0.002	0.010	19.999	0.014	0.014	0.000	0.000	0.000	0.000
92	A	92	ASN	0	-0.031	-0.032	22.057	0.008	0.008	0.000	0.000	0.000	0.000
93	A	93	ALA	0	0.034	0.005	19.731	0.012	0.012	0.000	0.000	0.000	0.000
94	A	94	ALA	0	0.002	-0.011	18.316	0.022	0.022	0.000	0.000	0.000	0.000
95	A	95	ARG	1	0.859	0.923	19.482	-0.031	-0.031	0.000	0.000	0.000	0.000
96	A	96	MET	0	-0.048	-0.004	22.499	0.010	0.010	0.000	0.000	0.000	0.000
97	A	97	LEU	0	0.027	0.006	15.782	0.009	0.009	0.000	0.000	0.000	0.000
98	A	98	GLN	0	-0.029	-0.016	19.724	0.009	0.009	0.000	0.000	0.000	0.000
99	A	99	ARG	1	0.828	0.869	21.505	-0.098	-0.098	0.000	0.000	0.000	0.000
100	A	100	ALA	0	-0.067	-0.034	22.104	0.001	0.001	0.000	0.000	0.000	0.000
101	A	101	ALA	0	0.016	-0.004	20.033	0.011	0.011	0.000	0.000	0.000	0.000
102	A	102	GLY	0	-0.029	-0.002	22.096	0.003	0.003	0.000	0.000	0.000	0.000
103	A	103	VAL	0	-0.048	-0.019	20.483	-0.007	-0.007	0.000	0.000	0.000	0.000
104	A	104	PRO	0	0.030	-0.002	23.930	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	105	ASP	-1	-0.810	-0.887	23.667	0.087	0.087	0.000	0.000	0.000	0.000
106	A	106	ASP	-1	-0.804	-0.891	21.965	0.055	0.055	0.000	0.000	0.000	0.000
107	A	107	GLY	0	-0.057	-0.025	21.117	-0.016	-0.016	0.000	0.000	0.000	0.000
108	A	108	VAL	0	-0.061	-0.035	18.138	-0.014	-0.014	0.000	0.000	0.000	0.000
109	A	109	ILE	0	-0.018	-0.010	14.095	0.017	0.017	0.000	0.000	0.000	0.000
110	A	110	GLY	0	0.058	0.031	14.354	-0.022	-0.022	0.000	0.000	0.000	0.000
111	A	111	ALA	0	0.009	-0.002	15.173	0.037	0.037	0.000	0.000	0.000	0.000
112	A	112	VAL	0	0.044	0.010	16.195	0.038	0.038	0.000	0.000	0.000	0.000
113	A	113	SER	0	0.032	0.017	16.751	0.017	0.017	0.000	0.000	0.000	0.000
114	A	114	LEU	0	0.004	0.009	11.278	0.028	0.028	0.000	0.000	0.000	0.000
115	A	115	LYS	1	0.961	0.989	14.880	-0.293	-0.293	0.000	0.000	0.000	0.000
116	A	116	ALA	0	0.024	0.030	17.033	0.026	0.026	0.000	0.000	0.000	0.000
117	A	117	ILE	0	-0.032	-0.028	14.495	0.012	0.012	0.000	0.000	0.000	0.000
118	A	118	ASN	0	-0.066	-0.051	12.336	0.116	0.116	0.000	0.000	0.000	0.000
119	A	119	SER	0	-0.093	-0.048	16.174	0.004	0.004	0.000	0.000	0.000	0.000
120	A	120	LEU	0	-0.031	0.001	19.627	-0.019	-0.019	0.000	0.000	0.000	0.000
121	A	121	PRO	0	0.052	0.033	20.274	0.045	0.045	0.000	0.000	0.000	0.000
122	A	122	GLU	-1	-0.822	-0.936	16.602	0.635	0.635	0.000	0.000	0.000	0.000
123	A	123	ASN	0	-0.019	-0.020	20.056	0.001	0.001	0.000	0.000	0.000	0.000
124	A	124	ASP	-1	-0.806	-0.904	23.269	0.233	0.233	0.000	0.000	0.000	0.000
125	A	125	LEU	0	-0.030	-0.003	17.871	-0.025	-0.025	0.000	0.000	0.000	0.000
126	A	126	LEU	0	-0.015	-0.017	18.390	-0.030	-0.030	0.000	0.000	0.000	0.000
127	A	127	LEU	0	0.010	0.015	22.110	-0.027	-0.027	0.000	0.000	0.000	0.000
128	A	128	ARG	1	0.897	0.953	24.959	-0.197	-0.197	0.000	0.000	0.000	0.000
129	A	129	PHE	0	-0.012	0.003	19.701	-0.019	-0.019	0.000	0.000	0.000	0.000
130	A	130	ASN	0	-0.012	-0.037	22.483	-0.031	-0.031	0.000	0.000	0.000	0.000
131	A	131	ALA	0	0.031	0.023	25.409	-0.017	-0.017	0.000	0.000	0.000	0.000
132	A	132	GLU	-1	-0.805	-0.874	25.285	0.103	0.103	0.000	0.000	0.000	0.000
133	A	133	ARG	1	0.794	0.870	21.890	-0.182	-0.182	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.006	0.002	26.765	-0.013	-0.013	0.000	0.000	0.000	0.000
135	A	135	VAL	0	0.016	0.014	30.107	-0.012	-0.012	0.000	0.000	0.000	0.000
136	A	136	PHE	0	0.005	0.002	28.179	-0.010	-0.010	0.000	0.000	0.000	0.000
137	A	137	TYR	0	0.010	-0.022	30.265	-0.008	-0.008	0.000	0.000	0.000	0.000
138	A	138	THR	0	-0.071	-0.039	32.022	-0.007	-0.007	0.000	0.000	0.000	0.000
139	A	139	LYS	1	0.903	0.968	32.721	-0.076	-0.076	0.000	0.000	0.000	0.000
140	A	140	LEU	0	0.000	-0.005	31.178	-0.006	-0.006	0.000	0.000	0.000	0.000
141	A	141	GLY	0	-0.024	0.010	32.716	-0.002	-0.002	0.000	0.000	0.000	0.000
142	A	142	THR	0	0.020	0.013	33.588	-0.004	-0.004	0.000	0.000	0.000	0.000
143	A	143	PHE	0	0.044	0.019	35.227	0.005	0.005	0.000	0.000	0.000	0.000
144	A	144	THR	0	0.047	0.015	34.507	0.000	0.000	0.000	0.000	0.000	0.000
145	A	145	SER	0	0.030	0.005	34.188	0.005	0.005	0.000	0.000	0.000	0.000
146	A	146	PHE	0	0.022	0.010	26.753	0.008	0.008	0.000	0.000	0.000	0.000
147	A	147	GLY	0	0.018	0.019	30.330	0.008	0.008	0.000	0.000	0.000	0.000
148	A	148	LYS	1	0.927	0.948	31.726	-0.046	-0.046	0.000	0.000	0.000	0.000
149	A	149	GLY	0	-0.006	-0.001	30.282	0.008	0.008	0.000	0.000	0.000	0.000
150	A	150	TRP	0	-0.011	-0.001	26.317	0.015	0.015	0.000	0.000	0.000	0.000
151	A	151	VAL	0	0.038	0.028	27.707	0.014	0.014	0.000	0.000	0.000	0.000
152	A	152	ARG	1	0.945	0.977	30.205	-0.086	-0.086	0.000	0.000	0.000	0.000
153	A	153	ARG	1	0.849	0.908	22.850	-0.146	-0.146	0.000	0.000	0.000	0.000
154	A	154	VAL	0	0.001	0.006	25.157	0.016	0.016	0.000	0.000	0.000	0.000
155	A	155	ALA	0	0.022	0.010	26.903	0.010	0.010	0.000	0.000	0.000	0.000
156	A	156	GLN	0	-0.016	-0.011	27.315	0.012	0.012	0.000	0.000	0.000	0.000
157	A	157	ASN	0	-0.011	-0.028	22.884	0.018	0.018	0.000	0.000	0.000	0.000
158	A	158	LEU	0	-0.018	0.003	25.545	0.015	0.015	0.000	0.000	0.000	0.000
159	A	159	ILE	0	-0.021	0.009	28.037	0.003	0.003	0.000	0.000	0.000	0.000
160	A	160	HIS	0	-0.026	-0.019	24.578	0.022	0.022	0.000	0.000	0.000	0.000
161	A	161	ALA	0	-0.045	-0.007	24.485	0.012	0.012	0.000	0.000	0.000	0.000
162	A	162	SER	0	-0.061	-0.042	25.712	-0.001	-0.001	0.000	0.000	0.000	0.000
163	A	163	ALA	0	-0.027	-0.001	27.333	-0.008	-0.008	0.000	0.000	0.000	0.000

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