FMO DATABASE

FMODB ID: 9G7K2

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	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	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	-1585287.564241
FMO2-HF: Nuclear repulsion	1517883.271006
FMO2-HF: Total energy	-67404.293235
FMO2-MP2: Total energy	-67602.352813

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.
-1.185	1.442	-0.015	-1.46	-1.153	0.005

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 : 0.029 / q_NPA : 0.025

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	0.018	0.017	3.784	-1.667	0.960	-0.015	-1.460	-1.153	0.005
4	B	530	DSN	0	0.010	-0.016	6.694	0.092	0.092	0.000	0.000	0.000	0.000
5	B	531	SER	0	-0.054	-0.019	9.740	0.172	0.172	0.000	0.000	0.000	0.000
6	B	532	ALA	0	0.038	0.032	13.451	-0.006	-0.006	0.000	0.000	0.000	0.000
7	B	533	ASN	0	-0.011	-0.015	16.639	0.063	0.063	0.000	0.000	0.000	0.000
8	B	534	DLY	1	0.904	0.950	20.449	0.293	0.293	0.000	0.000	0.000	0.000
9	B	535	TYR	0	0.037	0.012	23.760	0.002	0.002	0.000	0.000	0.000	0.000
10	B	536	ASN	0	-0.047	-0.027	26.353	-0.008	-0.008	0.000	0.000	0.000	0.000
11	B	537	ILE	0	0.095	0.065	28.544	0.005	0.005	0.000	0.000	0.000	0.000
12	B	538	GLN	0	-0.031	-0.031	31.113	-0.010	-0.010	0.000	0.000	0.000	0.000
13	B	539	VAL	0	0.004	0.023	34.568	0.005	0.005	0.000	0.000	0.000	0.000
14	B	540	GLY	0	0.041	-0.021	38.150	0.003	0.003	0.000	0.000	0.000	0.000
15	B	541	ASP	-1	-0.915	-0.947	34.768	-0.109	-0.109	0.000	0.000	0.000	0.000
16	B	542	ILE	0	-0.049	-0.045	37.146	-0.003	-0.003	0.000	0.000	0.000	0.000
17	B	543	MET	0	-0.099	0.014	40.786	0.005	0.005	0.000	0.000	0.000	0.000
18	B	544	VAL	0	0.024	0.020	43.064	0.000	0.000	0.000	0.000	0.000	0.000
19	B	545	ARG	1	0.888	0.908	40.264	0.074	0.074	0.000	0.000	0.000	0.000
20	B	546	ASP	-1	-0.948	-0.948	47.205	-0.046	-0.046	0.000	0.000	0.000	0.000
21	B	547	VAL	0	-0.032	-0.006	49.400	0.000	0.000	0.000	0.000	0.000	0.000
22	B	548	THR	0	-0.002	0.000	52.024	0.002	0.002	0.000	0.000	0.000	0.000
23	B	549	SER	0	-0.019	-0.021	54.202	0.000	0.000	0.000	0.000	0.000	0.000
24	B	550	ILE	0	0.006	0.015	56.173	0.001	0.001	0.000	0.000	0.000	0.000
25	B	551	ALA	0	0.040	0.042	58.116	-0.001	-0.001	0.000	0.000	0.000	0.000
26	B	552	SER	0	-0.025	-0.003	59.543	0.001	0.001	0.000	0.000	0.000	0.000
27	B	553	THR	0	0.008	-0.003	61.393	0.001	0.001	0.000	0.000	0.000	0.000
28	B	554	SER	0	-0.066	-0.030	62.387	0.000	0.000	0.000	0.000	0.000	0.000
29	B	555	THR	0	0.024	-0.011	64.342	0.001	0.001	0.000	0.000	0.000	0.000
30	B	556	TYR	0	0.023	-0.001	67.043	-0.001	-0.001	0.000	0.000	0.000	0.000
31	B	557	GLY	0	0.040	0.019	69.201	0.000	0.000	0.000	0.000	0.000	0.000
32	B	558	ASP	-1	-0.827	-0.888	63.564	-0.031	-0.031	0.000	0.000	0.000	0.000
33	B	559	LEU	0	-0.016	0.001	64.082	-0.001	-0.001	0.000	0.000	0.000	0.000
34	B	560	LEU	0	-0.017	-0.016	65.370	-0.001	-0.001	0.000	0.000	0.000	0.000
35	B	561	HIS	0	-0.024	0.005	61.794	-0.001	-0.001	0.000	0.000	0.000	0.000
36	B	562	VAL	0	0.081	0.040	60.365	-0.001	-0.001	0.000	0.000	0.000	0.000
37	B	563	LEU	0	-0.053	-0.002	62.133	-0.001	-0.001	0.000	0.000	0.000	0.000
38	B	564	ARG	1	0.801	0.878	64.379	0.029	0.029	0.000	0.000	0.000	0.000
39	B	565	GLN	0	-0.056	-0.020	62.487	-0.001	-0.001	0.000	0.000	0.000	0.000
40	B	566	THR	0	-0.021	-0.013	58.437	-0.002	-0.002	0.000	0.000	0.000	0.000
41	B	567	LYS	1	0.955	0.961	58.342	0.045	0.045	0.000	0.000	0.000	0.000
42	B	568	LEU	0	-0.004	0.013	53.956	-0.001	-0.001	0.000	0.000	0.000	0.000
43	B	569	LYS	1	0.927	0.949	53.857	0.053	0.053	0.000	0.000	0.000	0.000
44	B	570	PHE	0	0.022	0.016	50.931	0.001	0.001	0.000	0.000	0.000	0.000
45	B	571	PHE	0	-0.003	0.002	55.255	-0.001	-0.001	0.000	0.000	0.000	0.000
46	B	572	PRO	0	-0.012	0.013	51.822	0.001	0.001	0.000	0.000	0.000	0.000
47	B	573	PHE	0	0.006	-0.031	53.939	0.001	0.001	0.000	0.000	0.000	0.000
48	B	574	VAL	0	-0.010	-0.007	53.121	0.000	0.000	0.000	0.000	0.000	0.000
49	B	575	ASP	-1	-0.840	-0.889	54.890	-0.031	-0.031	0.000	0.000	0.000	0.000
50	B	576	THR	0	-0.007	-0.006	56.209	0.002	0.002	0.000	0.000	0.000	0.000
51	B	577	PRO	0	0.029	0.010	55.971	-0.001	-0.001	0.000	0.000	0.000	0.000
52	B	578	ASP	-1	-0.873	-0.922	55.433	-0.033	-0.033	0.000	0.000	0.000	0.000
53	B	579	THR	0	-0.037	-0.034	52.732	-0.001	-0.001	0.000	0.000	0.000	0.000
54	B	580	ASN	0	-0.059	-0.058	51.114	-0.003	-0.003	0.000	0.000	0.000	0.000
55	B	581	THR	0	-0.002	-0.024	50.704	-0.003	-0.003	0.000	0.000	0.000	0.000
56	B	582	LEU	0	-0.047	-0.030	48.489	0.001	0.001	0.000	0.000	0.000	0.000
57	B	583	LEU	0	-0.011	-0.003	51.422	0.000	0.000	0.000	0.000	0.000	0.000
58	B	584	GLY	0	0.034	0.025	52.912	0.001	0.001	0.000	0.000	0.000	0.000
59	B	585	SER	0	-0.032	-0.007	53.245	-0.002	-0.002	0.000	0.000	0.000	0.000
60	B	586	ILE	0	-0.007	0.012	55.152	0.001	0.001	0.000	0.000	0.000	0.000
61	B	587	ASP	-1	-0.754	-0.861	58.365	-0.041	-0.041	0.000	0.000	0.000	0.000
62	B	588	ARG	1	0.826	0.908	59.761	0.040	0.040	0.000	0.000	0.000	0.000
63	B	589	THR	0	0.048	0.014	61.888	0.001	0.001	0.000	0.000	0.000	0.000
64	B	590	GLU	-1	-0.883	-0.931	62.511	-0.029	-0.029	0.000	0.000	0.000	0.000
65	B	591	VAL	0	0.017	0.006	62.132	0.001	0.001	0.000	0.000	0.000	0.000
66	B	592	GLU	-1	-0.911	-0.983	64.967	-0.033	-0.033	0.000	0.000	0.000	0.000
67	B	593	GLY	0	0.012	0.014	67.455	0.001	0.001	0.000	0.000	0.000	0.000
68	B	594	LEU	0	-0.007	0.008	65.671	0.001	0.001	0.000	0.000	0.000	0.000
69	B	595	LEU	0	0.007	-0.002	68.003	0.001	0.001	0.000	0.000	0.000	0.000
70	B	596	GLN	0	-0.026	0.000	70.873	0.001	0.001	0.000	0.000	0.000	0.000
71	B	597	ARG	1	0.818	0.880	67.521	0.028	0.028	0.000	0.000	0.000	0.000
72	B	598	ARG	1	0.849	0.925	73.054	0.023	0.023	0.000	0.000	0.000	0.000
73	B	599	ILE	0	0.000	0.016	74.257	0.001	0.001	0.000	0.000	0.000	0.000
74	B	600	SER	0	-0.052	-0.048	77.127	0.001	0.001	0.000	0.000	0.000	0.000
75	B	601	ALA	0	-0.073	-0.038	77.679	0.001	0.001	0.000	0.000	0.000	0.000
76	B	602	TYR	0	0.001	0.012	79.016	0.000	0.000	0.000	0.000	0.000	0.000
77	B	603	ARG	1	0.866	0.912	80.890	0.020	0.020	0.000	0.000	0.000	0.000
78	B	604	DAR	1	0.852	0.904	82.986	0.019	0.019	0.000	0.000	0.000	0.000
79	B	605	GLN	0	0.031	0.020	84.637	0.000	0.000	0.000	0.000	0.000	0.000
80	B	606	PRO	0	-0.052	-0.005	86.206	0.000	0.000	0.000	0.000	0.000	0.000
81	B	680	DLY	1	0.965	0.964	92.097	0.018	0.018	0.000	0.000	0.000	0.000
82	B	681	DGN	0	0.030	0.021	96.135	0.000	0.000	0.000	0.000	0.000	0.000
83	B	682	LYS	1	0.924	0.954	87.946	0.020	0.020	0.000	0.000	0.000	0.000
84	B	683	GLY	0	0.020	0.020	89.769	0.000	0.000	0.000	0.000	0.000	0.000
85	B	684	THR	0	-0.007	-0.011	85.440	0.000	0.000	0.000	0.000	0.000	0.000
86	B	685	GLY	0	0.043	0.041	82.572	0.000	0.000	0.000	0.000	0.000	0.000
87	B	686	DGN	0	0.059	-0.005	77.134	0.000	0.000	0.000	0.000	0.000	0.000
88	B	687	DVA	0	-0.018	-0.007	79.985	0.000	0.000	0.000	0.000	0.000	0.000
89	B	688	DAL	0	0.044	0.027	80.647	0.000	0.000	0.000	0.000	0.000	0.000
90	B	689	SER	0	0.009	0.013	77.920	0.000	0.000	0.000	0.000	0.000	0.000
91	B	690	ARG	1	0.921	0.965	78.371	0.022	0.022	0.000	0.000	0.000	0.000
92	B	691	DPN	0	0.012	-0.002	81.716	0.000	0.000	0.000	0.000	0.000	0.000
93	B	692	GLU	-1	-0.797	-0.853	84.654	-0.019	-0.019	0.000	0.000	0.000	0.000
94	B	693	DGL	-1	-0.844	-0.919	87.196	-0.018	-0.018	0.000	0.000	0.000	0.000
95	B	694	MED	0	-0.106	-0.043	84.569	0.000	0.000	0.000	0.000	0.000	0.000
96	B	695	LEU	0	-0.027	0.016	80.545	0.000	0.000	0.000	0.000	0.000	0.000
97	B	696	THR	0	-0.001	-0.026	82.571	-0.001	-0.001	0.000	0.000	0.000	0.000
98	B	697	LEU	0	0.060	0.007	77.469	0.000	0.000	0.000	0.000	0.000	0.000
99	B	698	GLU	-1	-0.847	-0.891	80.579	-0.021	-0.021	0.000	0.000	0.000	0.000
100	B	699	GLU	-1	-0.869	-0.955	82.460	-0.020	-0.020	0.000	0.000	0.000	0.000
101	B	700	ILE	0	0.027	0.011	76.411	0.000	0.000	0.000	0.000	0.000	0.000
102	B	701	TYR	0	-0.028	0.012	77.035	0.000	0.000	0.000	0.000	0.000	0.000
103	B	702	ARG	1	0.824	0.864	78.549	0.021	0.021	0.000	0.000	0.000	0.000
104	B	703	TRP	0	-0.020	-0.018	72.701	0.000	0.000	0.000	0.000	0.000	0.000
105	B	704	GLU	-1	-0.796	-0.892	73.274	-0.027	-0.027	0.000	0.000	0.000	0.000
106	B	705	GLN	0	-0.073	-0.043	75.447	0.000	0.000	0.000	0.000	0.000	0.000
107	B	706	ARG	1	0.881	0.948	77.819	0.020	0.020	0.000	0.000	0.000	0.000
108	B	707	GLU	-1	-0.776	-0.882	75.108	-0.021	-0.021	0.000	0.000	0.000	0.000
109	B	708	LYS	1	0.975	1.005	71.623	0.024	0.024	0.000	0.000	0.000	0.000
110	B	709	ASN	0	-0.042	-0.033	70.950	-0.001	-0.001	0.000	0.000	0.000	0.000
111	B	710	VAL	0	-0.020	0.002	71.536	0.000	0.000	0.000	0.000	0.000	0.000
112	B	711	VAL	0	0.020	0.000	66.806	-0.001	-0.001	0.000	0.000	0.000	0.000
113	B	712	VAL	0	-0.025	-0.025	66.436	0.001	0.001	0.000	0.000	0.000	0.000
114	B	713	ASN	0	0.005	0.007	67.456	-0.001	-0.001	0.000	0.000	0.000	0.000
115	B	714	PHE	0	-0.008	-0.026	63.380	0.000	0.000	0.000	0.000	0.000	0.000
116	B	715	GLU	-1	-0.898	-0.941	64.923	-0.023	-0.023	0.000	0.000	0.000	0.000
117	B	716	THR	0	-0.035	-0.017	67.004	0.000	0.000	0.000	0.000	0.000	0.000
118	B	717	CYS	0	-0.072	-0.006	62.846	0.000	0.000	0.000	0.000	0.000	0.000
119	B	718	ARG	1	0.783	0.854	58.837	0.036	0.036	0.000	0.000	0.000	0.000
120	B	719	ILE	0	0.000	-0.001	56.821	-0.001	-0.001	0.000	0.000	0.000	0.000
121	B	720	ASP	-1	-0.846	-0.892	55.231	-0.038	-0.038	0.000	0.000	0.000	0.000
122	B	721	GLN	0	0.046	0.008	51.931	-0.001	-0.001	0.000	0.000	0.000	0.000
123	B	722	SER	0	0.000	0.009	47.895	0.000	0.000	0.000	0.000	0.000	0.000
124	B	723	PRO	0	-0.027	-0.025	46.845	0.000	0.000	0.000	0.000	0.000	0.000
125	B	724	PHE	0	-0.012	-0.009	42.623	-0.002	-0.002	0.000	0.000	0.000	0.000
126	B	725	GLN	0	0.015	0.003	41.027	0.001	0.001	0.000	0.000	0.000	0.000
127	B	726	LEU	0	-0.014	0.007	38.802	-0.004	-0.004	0.000	0.000	0.000	0.000
128	B	727	VAL	0	0.037	0.018	37.427	0.003	0.003	0.000	0.000	0.000	0.000
129	B	728	GLU	-1	-0.743	-0.865	37.595	-0.079	-0.079	0.000	0.000	0.000	0.000
130	B	729	GLY	0	-0.004	0.007	33.772	-0.004	-0.004	0.000	0.000	0.000	0.000
131	B	730	THR	0	-0.085	-0.051	32.754	-0.009	-0.009	0.000	0.000	0.000	0.000
132	B	731	SER	0	0.032	0.017	30.458	-0.003	-0.003	0.000	0.000	0.000	0.000
133	B	732	LEU	0	0.081	0.032	32.492	0.005	0.005	0.000	0.000	0.000	0.000
134	B	733	GLN	0	0.055	0.030	30.901	0.002	0.002	0.000	0.000	0.000	0.000
135	B	734	LYS	1	0.922	0.960	28.351	0.146	0.146	0.000	0.000	0.000	0.000
136	B	735	THR	0	0.030	0.013	34.311	0.008	0.008	0.000	0.000	0.000	0.000
137	B	736	HIS	0	0.051	0.032	36.534	0.008	0.008	0.000	0.000	0.000	0.000
138	B	737	THR	0	-0.046	-0.030	35.068	0.003	0.003	0.000	0.000	0.000	0.000
139	B	738	LEU	0	-0.009	0.008	37.647	0.004	0.004	0.000	0.000	0.000	0.000
140	B	739	PHE	0	0.006	-0.018	39.925	0.005	0.005	0.000	0.000	0.000	0.000
141	B	740	SER	0	-0.040	-0.025	40.275	0.004	0.004	0.000	0.000	0.000	0.000
142	B	741	LEU	0	-0.048	-0.024	38.349	0.003	0.003	0.000	0.000	0.000	0.000
143	B	742	LEU	0	-0.031	-0.010	42.628	0.004	0.004	0.000	0.000	0.000	0.000
144	B	743	GLY	0	-0.007	0.020	45.192	0.003	0.003	0.000	0.000	0.000	0.000
145	B	744	LEU	0	-0.053	-0.018	44.301	0.003	0.003	0.000	0.000	0.000	0.000
146	B	745	ASP	-1	-0.869	-0.930	46.809	-0.061	-0.061	0.000	0.000	0.000	0.000
147	B	746	ARG	1	0.970	0.967	47.505	0.057	0.057	0.000	0.000	0.000	0.000
148	B	747	ALA	0	0.011	0.021	44.133	0.002	0.002	0.000	0.000	0.000	0.000
149	B	748	TYR	0	0.016	-0.005	46.017	-0.001	-0.001	0.000	0.000	0.000	0.000
150	B	749	VAL	0	0.005	0.007	40.890	-0.001	-0.001	0.000	0.000	0.000	0.000
151	B	750	THR	0	-0.037	-0.028	42.930	0.004	0.004	0.000	0.000	0.000	0.000
152	B	751	SER	0	0.028	-0.001	42.006	-0.005	-0.005	0.000	0.000	0.000	0.000
153	B	752	MET	0	-0.057	-0.030	41.791	0.002	0.002	0.000	0.000	0.000	0.000
154	B	753	GLY	0	0.055	0.031	44.053	0.003	0.003	0.000	0.000	0.000	0.000
155	B	754	LYS	1	0.931	0.980	46.619	0.044	0.044	0.000	0.000	0.000	0.000
156	B	755	LEU	0	-0.004	-0.008	46.527	-0.003	-0.003	0.000	0.000	0.000	0.000
157	B	756	VAL	0	-0.032	-0.011	43.022	0.001	0.001	0.000	0.000	0.000	0.000
158	B	757	GLY	0	0.079	0.002	45.609	-0.001	-0.001	0.000	0.000	0.000	0.000
159	B	758	VAL	0	-0.093	-0.039	46.412	0.001	0.001	0.000	0.000	0.000	0.000
160	B	759	VAL	0	0.014	0.028	41.472	-0.002	-0.002	0.000	0.000	0.000	0.000
161	B	760	ALA	0	-0.012	-0.023	44.662	0.003	0.003	0.000	0.000	0.000	0.000
162	B	761	LEU	0	0.005	-0.005	42.582	-0.003	-0.003	0.000	0.000	0.000	0.000
163	B	762	ALA	0	-0.004	0.005	43.625	-0.004	-0.004	0.000	0.000	0.000	0.000
164	B	763	GLU	-1	-0.829	-0.932	43.620	-0.074	-0.074	0.000	0.000	0.000	0.000
165	B	764	ILE	0	-0.017	-0.007	38.628	-0.005	-0.005	0.000	0.000	0.000	0.000
166	B	765	GLN	0	-0.022	-0.014	39.212	-0.003	-0.003	0.000	0.000	0.000	0.000
167	B	766	ALA	0	0.078	0.036	39.542	-0.005	-0.005	0.000	0.000	0.000	0.000
168	B	767	ALA	0	-0.017	-0.006	37.707	-0.004	-0.004	0.000	0.000	0.000	0.000
169	B	768	ILE	0	-0.098	-0.053	34.436	-0.009	-0.009	0.000	0.000	0.000	0.000
170	B	769	GLU	-1	-0.972	-0.977	35.211	-0.108	-0.108	0.000	0.000	0.000	0.000
171	B	770	GLY	0	-0.101	-0.030	34.905	-0.008	-0.008	0.000	0.000	0.000	0.000

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