FMO DATABASE

FMODB ID: LJG99

Calculation Name: 2D4Z-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D4Z

Chain ID: B

ChEMBL ID:

UniProt ID: P21564

Base Structure: X-ray

Registration Date: 2023-03-13

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	171
LigandCharge	DGL=-1,DAR=1,DLY=1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1586428.877407
FMO2-HF: Nuclear repulsion	1519025.775673
FMO2-HF: Total energy	-67403.101733
FMO2-MP2: Total energy	-67601.34481

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(B:527:DLE)

Summations of interaction energy for fragment #1(B:527:DLE)

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.
0.527	2.527	-0.015	-1.027	-0.957	0.002

Interaction energy analysis for fragmet #1(B:527:DLE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.004

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	B	529	TRP	0	0.029	0.024	3.792	0.794	2.794	-0.015	-1.027	-0.957	0.002
4	B	530	DSN	0	0.006	-0.019	7.150	-0.324	-0.324	0.000	0.000	0.000	0.000
5	B	531	SER	0	-0.053	-0.018	9.964	0.035	0.035	0.000	0.000	0.000	0.000
6	B	532	ALA	0	0.041	0.029	13.704	-0.044	-0.044	0.000	0.000	0.000	0.000
7	B	533	ASN	0	-0.017	-0.016	16.760	0.012	0.012	0.000	0.000	0.000	0.000
8	B	534	DLY	1	0.909	0.953	20.563	0.031	0.031	0.000	0.000	0.000	0.000
9	B	535	TYR	0	0.031	0.014	23.775	0.005	0.005	0.000	0.000	0.000	0.000
10	B	536	ASN	0	-0.024	-0.020	26.725	0.006	0.006	0.000	0.000	0.000	0.000
11	B	537	ILE	0	0.106	0.073	28.548	0.004	0.004	0.000	0.000	0.000	0.000
12	B	538	GLN	0	-0.030	-0.031	31.185	-0.005	-0.005	0.000	0.000	0.000	0.000
13	B	539	VAL	0	0.001	0.028	34.586	0.001	0.001	0.000	0.000	0.000	0.000
14	B	540	GLY	0	0.032	-0.041	38.177	0.001	0.001	0.000	0.000	0.000	0.000
15	B	541	ASP	-1	-0.926	-0.962	34.825	0.010	0.010	0.000	0.000	0.000	0.000
16	B	542	ILE	0	-0.062	-0.051	37.129	-0.002	-0.002	0.000	0.000	0.000	0.000
17	B	543	MET	0	-0.097	0.026	40.782	0.000	0.000	0.000	0.000	0.000	0.000
18	B	544	VAL	0	0.031	0.028	43.074	0.002	0.002	0.000	0.000	0.000	0.000
19	B	545	ARG	1	0.934	0.939	40.591	-0.010	-0.010	0.000	0.000	0.000	0.000
20	B	546	ASP	-1	-0.955	-0.954	47.188	0.004	0.004	0.000	0.000	0.000	0.000
21	B	547	VAL	0	-0.033	0.001	49.306	-0.001	-0.001	0.000	0.000	0.000	0.000
22	B	548	THR	0	-0.002	0.003	52.030	0.000	0.000	0.000	0.000	0.000	0.000
23	B	549	SER	0	-0.036	-0.033	54.251	-0.001	-0.001	0.000	0.000	0.000	0.000
24	B	550	ILE	0	0.012	0.019	56.198	0.000	0.000	0.000	0.000	0.000	0.000
25	B	551	ALA	0	0.043	0.042	58.154	0.000	0.000	0.000	0.000	0.000	0.000
26	B	552	SER	0	-0.016	0.017	59.572	0.000	0.000	0.000	0.000	0.000	0.000
27	B	553	THR	0	0.027	0.008	61.686	0.000	0.000	0.000	0.000	0.000	0.000
28	B	554	SER	0	-0.057	-0.055	62.538	0.000	0.000	0.000	0.000	0.000	0.000
29	B	555	THR	0	0.015	0.002	64.359	0.000	0.000	0.000	0.000	0.000	0.000
30	B	556	TYR	0	0.016	-0.004	67.067	0.000	0.000	0.000	0.000	0.000	0.000
31	B	557	GLY	0	0.032	0.015	69.214	0.000	0.000	0.000	0.000	0.000	0.000
32	B	558	ASP	-1	-0.834	-0.901	63.629	0.002	0.002	0.000	0.000	0.000	0.000
33	B	559	LEU	0	-0.021	-0.009	64.152	0.000	0.000	0.000	0.000	0.000	0.000
34	B	560	LEU	0	0.007	-0.011	65.403	0.000	0.000	0.000	0.000	0.000	0.000
35	B	561	HIS	0	-0.024	0.008	61.605	-0.001	-0.001	0.000	0.000	0.000	0.000
36	B	562	VAL	0	0.088	0.050	60.566	0.000	0.000	0.000	0.000	0.000	0.000
37	B	563	LEU	0	-0.057	0.007	62.166	-0.001	-0.001	0.000	0.000	0.000	0.000
38	B	564	ARG	1	0.829	0.898	64.417	0.000	0.000	0.000	0.000	0.000	0.000
39	B	565	GLN	0	-0.040	-0.011	62.442	0.000	0.000	0.000	0.000	0.000	0.000
40	B	566	THR	0	-0.031	-0.036	58.398	0.000	0.000	0.000	0.000	0.000	0.000
41	B	567	LYS	1	0.957	0.961	58.295	0.004	0.004	0.000	0.000	0.000	0.000
42	B	568	LEU	0	0.004	0.015	54.192	-0.001	-0.001	0.000	0.000	0.000	0.000
43	B	569	LYS	1	1.000	0.992	56.126	0.011	0.011	0.000	0.000	0.000	0.000
44	B	570	PHE	0	0.022	0.021	51.212	0.000	0.000	0.000	0.000	0.000	0.000
45	B	571	PHE	0	-0.009	-0.005	55.294	0.000	0.000	0.000	0.000	0.000	0.000
46	B	572	PRO	0	0.004	0.021	51.907	-0.001	-0.001	0.000	0.000	0.000	0.000
47	B	573	PHE	0	0.010	-0.021	53.992	0.001	0.001	0.000	0.000	0.000	0.000
48	B	574	VAL	0	-0.028	0.002	53.288	0.000	0.000	0.000	0.000	0.000	0.000
49	B	575	ASP	-1	-0.875	-0.932	54.826	0.003	0.003	0.000	0.000	0.000	0.000
50	B	576	THR	0	-0.025	-0.003	56.223	0.000	0.000	0.000	0.000	0.000	0.000
51	B	577	PRO	0	-0.004	-0.004	55.975	0.000	0.000	0.000	0.000	0.000	0.000
52	B	578	ASP	-1	-0.872	-0.938	55.417	0.007	0.007	0.000	0.000	0.000	0.000
53	B	579	THR	0	-0.037	-0.028	52.859	0.001	0.001	0.000	0.000	0.000	0.000
54	B	580	ASN	0	-0.012	-0.048	50.816	-0.001	-0.001	0.000	0.000	0.000	0.000
55	B	581	THR	0	0.035	0.010	51.036	0.000	0.000	0.000	0.000	0.000	0.000
56	B	582	LEU	0	-0.032	-0.026	48.476	0.000	0.000	0.000	0.000	0.000	0.000
57	B	583	LEU	0	-0.018	-0.008	51.483	0.000	0.000	0.000	0.000	0.000	0.000
58	B	584	GLY	0	0.054	0.039	52.996	-0.001	-0.001	0.000	0.000	0.000	0.000
59	B	585	SER	0	-0.040	-0.015	53.215	0.000	0.000	0.000	0.000	0.000	0.000
60	B	586	ILE	0	-0.004	0.020	55.229	0.000	0.000	0.000	0.000	0.000	0.000
61	B	587	ASP	-1	-0.797	-0.901	58.387	-0.008	-0.008	0.000	0.000	0.000	0.000
62	B	588	ARG	1	0.843	0.909	59.849	0.005	0.005	0.000	0.000	0.000	0.000
63	B	589	THR	0	0.028	0.006	61.965	0.000	0.000	0.000	0.000	0.000	0.000
64	B	590	GLU	-1	-0.922	-0.960	62.695	-0.006	-0.006	0.000	0.000	0.000	0.000
65	B	591	VAL	0	-0.003	-0.006	62.046	0.001	0.001	0.000	0.000	0.000	0.000
66	B	592	GLU	-1	-0.923	-0.984	65.036	-0.005	-0.005	0.000	0.000	0.000	0.000
67	B	593	GLY	0	0.030	0.019	67.549	0.000	0.000	0.000	0.000	0.000	0.000
68	B	594	LEU	0	-0.049	-0.005	65.640	0.000	0.000	0.000	0.000	0.000	0.000
69	B	595	LEU	0	0.007	0.000	68.180	0.000	0.000	0.000	0.000	0.000	0.000
70	B	596	GLN	0	-0.024	0.002	71.115	0.000	0.000	0.000	0.000	0.000	0.000
71	B	597	ARG	1	0.917	0.948	67.835	0.004	0.004	0.000	0.000	0.000	0.000
72	B	598	ARG	1	0.851	0.924	73.179	0.001	0.001	0.000	0.000	0.000	0.000
73	B	599	ILE	0	0.000	0.015	74.441	0.000	0.000	0.000	0.000	0.000	0.000
74	B	600	SER	0	-0.065	-0.058	77.183	0.000	0.000	0.000	0.000	0.000	0.000
75	B	601	ALA	0	-0.074	-0.038	77.799	0.000	0.000	0.000	0.000	0.000	0.000
76	B	602	TYR	0	0.013	0.022	79.070	0.000	0.000	0.000	0.000	0.000	0.000
77	B	603	ARG	1	0.882	0.912	80.944	0.003	0.003	0.000	0.000	0.000	0.000
78	B	604	DAR	1	0.853	0.902	83.047	0.003	0.003	0.000	0.000	0.000	0.000
79	B	605	GLN	0	0.031	0.020	84.714	0.000	0.000	0.000	0.000	0.000	0.000
80	B	606	PRO	0	-0.058	-0.007	86.310	0.000	0.000	0.000	0.000	0.000	0.000
81	B	680	DLY	1	0.966	0.965	92.022	0.003	0.003	0.000	0.000	0.000	0.000
82	B	681	DGN	0	0.034	0.024	96.250	0.000	0.000	0.000	0.000	0.000	0.000
83	B	682	LYS	1	0.923	0.953	87.984	0.002	0.002	0.000	0.000	0.000	0.000
84	B	683	GLY	0	0.018	0.017	89.823	0.000	0.000	0.000	0.000	0.000	0.000
85	B	684	THR	0	-0.007	-0.011	85.501	0.000	0.000	0.000	0.000	0.000	0.000
86	B	685	GLY	0	0.043	0.041	82.621	0.000	0.000	0.000	0.000	0.000	0.000
87	B	686	DGN	0	0.076	0.001	77.337	0.000	0.000	0.000	0.000	0.000	0.000
88	B	687	DVA	0	-0.017	-0.001	80.313	0.000	0.000	0.000	0.000	0.000	0.000
89	B	688	DAL	0	0.041	0.023	80.866	0.000	0.000	0.000	0.000	0.000	0.000
90	B	689	SER	0	0.003	0.012	77.975	0.000	0.000	0.000	0.000	0.000	0.000
91	B	690	ARG	1	0.925	0.967	78.561	0.004	0.004	0.000	0.000	0.000	0.000
92	B	691	DPN	0	0.015	0.000	81.816	0.000	0.000	0.000	0.000	0.000	0.000
93	B	692	GLU	-1	-0.800	-0.852	84.746	-0.003	-0.003	0.000	0.000	0.000	0.000
94	B	693	DGL	-1	-0.837	-0.921	87.062	-0.003	-0.003	0.000	0.000	0.000	0.000
95	B	694	MED	0	-0.102	-0.043	84.738	0.000	0.000	0.000	0.000	0.000	0.000
96	B	695	LEU	0	-0.015	0.020	80.611	0.000	0.000	0.000	0.000	0.000	0.000
97	B	696	THR	0	-0.013	-0.037	82.632	0.000	0.000	0.000	0.000	0.000	0.000
98	B	697	LEU	0	0.058	0.004	78.131	0.000	0.000	0.000	0.000	0.000	0.000
99	B	698	GLU	-1	-0.860	-0.899	80.613	0.000	0.000	0.000	0.000	0.000	0.000
100	B	699	GLU	-1	-0.875	-0.958	82.486	-0.001	-0.001	0.000	0.000	0.000	0.000
101	B	700	ILE	0	0.027	0.016	76.378	0.000	0.000	0.000	0.000	0.000	0.000
102	B	701	TYR	0	-0.027	0.016	76.847	0.000	0.000	0.000	0.000	0.000	0.000
103	B	702	ARG	1	0.809	0.864	78.565	0.000	0.000	0.000	0.000	0.000	0.000
104	B	703	TRP	0	-0.006	-0.018	72.551	0.000	0.000	0.000	0.000	0.000	0.000
105	B	704	GLU	-1	-0.805	-0.906	73.169	0.000	0.000	0.000	0.000	0.000	0.000
106	B	705	GLN	0	-0.089	-0.050	75.457	0.000	0.000	0.000	0.000	0.000	0.000
107	B	706	ARG	1	0.856	0.928	77.824	0.000	0.000	0.000	0.000	0.000	0.000
108	B	707	GLU	-1	-0.762	-0.868	75.085	0.000	0.000	0.000	0.000	0.000	0.000
109	B	708	LYS	1	0.969	1.000	72.020	-0.002	-0.002	0.000	0.000	0.000	0.000
110	B	709	ASN	0	-0.040	-0.032	70.942	0.000	0.000	0.000	0.000	0.000	0.000
111	B	710	VAL	0	-0.019	0.011	71.540	0.000	0.000	0.000	0.000	0.000	0.000
112	B	711	VAL	0	0.015	-0.004	66.968	0.000	0.000	0.000	0.000	0.000	0.000
113	B	712	VAL	0	-0.044	-0.028	66.537	0.000	0.000	0.000	0.000	0.000	0.000
114	B	713	ASN	0	0.019	0.016	67.499	0.000	0.000	0.000	0.000	0.000	0.000
115	B	714	PHE	0	0.004	-0.026	63.613	-0.001	-0.001	0.000	0.000	0.000	0.000
116	B	715	GLU	-1	-0.887	-0.938	65.000	-0.002	-0.002	0.000	0.000	0.000	0.000
117	B	716	THR	0	-0.067	-0.034	67.097	0.000	0.000	0.000	0.000	0.000	0.000
118	B	717	CYS	0	-0.120	-0.040	63.638	0.000	0.000	0.000	0.000	0.000	0.000
119	B	718	ARG	1	0.852	0.929	59.487	0.008	0.008	0.000	0.000	0.000	0.000
120	B	719	ILE	0	0.010	0.004	57.022	0.000	0.000	0.000	0.000	0.000	0.000
121	B	720	ASP	-1	-0.851	-0.911	55.377	-0.008	-0.008	0.000	0.000	0.000	0.000
122	B	721	GLN	0	0.045	0.009	51.970	0.001	0.001	0.000	0.000	0.000	0.000
123	B	722	SER	0	-0.018	0.001	47.997	-0.001	-0.001	0.000	0.000	0.000	0.000
124	B	723	PRO	0	-0.015	-0.020	46.977	0.000	0.000	0.000	0.000	0.000	0.000
125	B	724	PHE	0	-0.008	-0.007	42.686	-0.001	-0.001	0.000	0.000	0.000	0.000
126	B	725	GLN	0	0.010	0.005	40.861	0.002	0.002	0.000	0.000	0.000	0.000
127	B	726	LEU	0	-0.009	0.006	39.008	-0.001	-0.001	0.000	0.000	0.000	0.000
128	B	727	VAL	0	0.026	0.009	37.372	0.002	0.002	0.000	0.000	0.000	0.000
129	B	728	GLU	-1	-0.787	-0.918	37.640	0.008	0.008	0.000	0.000	0.000	0.000
130	B	729	GLY	0	-0.022	-0.008	33.797	0.000	0.000	0.000	0.000	0.000	0.000
131	B	730	THR	0	-0.071	-0.024	32.786	-0.003	-0.003	0.000	0.000	0.000	0.000
132	B	731	SER	0	0.027	0.016	30.596	-0.001	-0.001	0.000	0.000	0.000	0.000
133	B	732	LEU	0	0.105	0.031	32.550	-0.002	-0.002	0.000	0.000	0.000	0.000
134	B	733	GLN	0	0.045	0.027	31.002	0.000	0.000	0.000	0.000	0.000	0.000
135	B	734	LYS	1	0.923	0.950	28.466	0.027	0.027	0.000	0.000	0.000	0.000
136	B	735	THR	0	0.033	0.018	34.420	0.001	0.001	0.000	0.000	0.000	0.000
137	B	736	HIS	0	0.053	0.036	36.588	0.002	0.002	0.000	0.000	0.000	0.000
138	B	737	THR	0	-0.032	-0.008	35.212	-0.002	-0.002	0.000	0.000	0.000	0.000
139	B	738	LEU	0	-0.019	0.004	37.783	0.000	0.000	0.000	0.000	0.000	0.000
140	B	739	PHE	0	0.001	-0.020	40.053	0.001	0.001	0.000	0.000	0.000	0.000
141	B	740	SER	0	-0.046	-0.034	40.400	0.000	0.000	0.000	0.000	0.000	0.000
142	B	741	LEU	0	-0.040	-0.022	38.598	0.000	0.000	0.000	0.000	0.000	0.000
143	B	742	LEU	0	-0.029	-0.009	42.790	0.000	0.000	0.000	0.000	0.000	0.000
144	B	743	GLY	0	-0.010	0.018	45.334	0.001	0.001	0.000	0.000	0.000	0.000
145	B	744	LEU	0	-0.066	-0.025	44.539	0.002	0.002	0.000	0.000	0.000	0.000
146	B	745	ASP	-1	-0.919	-0.955	46.917	-0.013	-0.013	0.000	0.000	0.000	0.000
147	B	746	ARG	1	0.969	0.966	47.599	0.007	0.007	0.000	0.000	0.000	0.000
148	B	747	ALA	0	0.004	0.019	44.235	-0.001	-0.001	0.000	0.000	0.000	0.000
149	B	748	TYR	0	0.019	0.000	46.073	0.001	0.001	0.000	0.000	0.000	0.000
150	B	749	VAL	0	0.009	0.010	40.892	-0.001	-0.001	0.000	0.000	0.000	0.000
151	B	750	THR	0	-0.027	-0.022	42.955	0.001	0.001	0.000	0.000	0.000	0.000
152	B	751	SER	0	0.023	-0.005	42.011	0.001	0.001	0.000	0.000	0.000	0.000
153	B	752	MET	0	-0.049	-0.026	41.894	0.002	0.002	0.000	0.000	0.000	0.000
154	B	753	GLY	0	0.047	0.029	44.084	0.000	0.000	0.000	0.000	0.000	0.000
155	B	754	LYS	1	0.919	0.974	46.652	-0.009	-0.009	0.000	0.000	0.000	0.000
156	B	755	LEU	0	-0.006	-0.005	46.546	0.000	0.000	0.000	0.000	0.000	0.000
157	B	756	VAL	0	-0.029	-0.012	42.897	0.001	0.001	0.000	0.000	0.000	0.000
158	B	757	GLY	0	0.068	0.003	45.575	0.001	0.001	0.000	0.000	0.000	0.000
159	B	758	VAL	0	-0.097	-0.038	46.424	-0.001	-0.001	0.000	0.000	0.000	0.000
160	B	759	VAL	0	0.015	0.024	41.475	0.001	0.001	0.000	0.000	0.000	0.000
161	B	760	ALA	0	0.009	0.000	44.706	-0.001	-0.001	0.000	0.000	0.000	0.000
162	B	761	LEU	0	0.011	0.000	42.856	0.000	0.000	0.000	0.000	0.000	0.000
163	B	762	ALA	0	0.010	0.014	43.698	-0.001	-0.001	0.000	0.000	0.000	0.000
164	B	763	GLU	-1	-0.878	-0.966	43.532	-0.006	-0.006	0.000	0.000	0.000	0.000
165	B	764	ILE	0	-0.023	-0.010	38.721	0.000	0.000	0.000	0.000	0.000	0.000
166	B	765	GLN	0	-0.020	-0.015	39.270	0.000	0.000	0.000	0.000	0.000	0.000
167	B	766	ALA	0	0.088	0.039	39.528	-0.001	-0.001	0.000	0.000	0.000	0.000
168	B	767	ALA	0	-0.033	-0.013	37.643	0.000	0.000	0.000	0.000	0.000	0.000
169	B	768	ILE	0	-0.105	-0.053	34.707	0.000	0.000	0.000	0.000	0.000	0.000
170	B	769	GLU	-1	-0.988	-0.987	35.197	-0.026	-0.026	0.000	0.000	0.000	0.000
171	B	770	GLY	0	-0.076	-0.019	34.203	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:527:DLE)