FMO DATABASE

FMODB ID: M38JZ

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	OptAll
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	-1584645.73386
FMO2-HF: Nuclear repulsion	1517240.369636
FMO2-HF: Total energy	-67405.364224
FMO2-MP2: Total energy	-67603.352251

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.
-1.318	1.387	-0.015	-1.52	-1.171	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	0.013	0.008	3.794	-1.788	0.917	-0.015	-1.520	-1.171	0.005
4	B	530	DSN	0	0.010	-0.005	6.776	0.110	0.110	0.000	0.000	0.000	0.000
5	B	531	SER	0	-0.042	-0.009	9.764	0.159	0.159	0.000	0.000	0.000	0.000
6	B	532	ALA	0	0.036	0.014	13.429	-0.028	-0.028	0.000	0.000	0.000	0.000
7	B	533	ASN	0	-0.013	-0.010	16.772	0.054	0.054	0.000	0.000	0.000	0.000
8	B	534	DLY	1	0.909	0.957	20.610	0.293	0.293	0.000	0.000	0.000	0.000
9	B	535	TYR	0	0.067	0.021	23.851	-0.001	-0.001	0.000	0.000	0.000	0.000
10	B	536	ASN	0	-0.071	-0.035	25.945	-0.005	-0.005	0.000	0.000	0.000	0.000
11	B	537	ILE	0	0.112	0.077	28.304	0.006	0.006	0.000	0.000	0.000	0.000
12	B	538	GLN	0	-0.060	-0.037	31.699	-0.005	-0.005	0.000	0.000	0.000	0.000
13	B	539	VAL	0	0.033	0.019	34.295	0.003	0.003	0.000	0.000	0.000	0.000
14	B	540	GLY	0	0.031	0.014	37.127	0.005	0.005	0.000	0.000	0.000	0.000
15	B	541	ASP	-1	-0.865	-0.930	34.497	-0.109	-0.109	0.000	0.000	0.000	0.000
16	B	542	ILE	0	-0.057	-0.031	37.196	-0.001	-0.001	0.000	0.000	0.000	0.000
17	B	543	MET	0	-0.094	-0.010	40.592	0.005	0.005	0.000	0.000	0.000	0.000
18	B	544	VAL	0	0.013	0.009	43.213	0.001	0.001	0.000	0.000	0.000	0.000
19	B	545	ARG	1	0.810	0.853	39.798	0.075	0.075	0.000	0.000	0.000	0.000
20	B	546	ASP	-1	-0.933	-0.938	46.963	-0.045	-0.045	0.000	0.000	0.000	0.000
21	B	547	VAL	0	-0.023	-0.018	49.444	-0.002	-0.002	0.000	0.000	0.000	0.000
22	B	548	THR	0	-0.005	0.000	52.263	0.002	0.002	0.000	0.000	0.000	0.000
23	B	549	SER	0	-0.022	-0.015	54.317	-0.001	-0.001	0.000	0.000	0.000	0.000
24	B	550	ILE	0	-0.009	0.008	56.327	0.001	0.001	0.000	0.000	0.000	0.000
25	B	551	ALA	0	0.031	0.018	57.825	-0.001	-0.001	0.000	0.000	0.000	0.000
26	B	552	SER	0	-0.037	-0.016	59.552	0.001	0.001	0.000	0.000	0.000	0.000
27	B	553	THR	0	0.000	-0.010	61.312	0.001	0.001	0.000	0.000	0.000	0.000
28	B	554	SER	0	-0.056	-0.029	62.061	0.000	0.000	0.000	0.000	0.000	0.000
29	B	555	THR	0	0.005	-0.036	64.053	0.001	0.001	0.000	0.000	0.000	0.000
30	B	556	TYR	0	0.028	0.000	66.802	-0.001	-0.001	0.000	0.000	0.000	0.000
31	B	557	GLY	0	0.018	0.006	69.000	0.000	0.000	0.000	0.000	0.000	0.000
32	B	558	ASP	-1	-0.810	-0.867	63.286	-0.031	-0.031	0.000	0.000	0.000	0.000
33	B	559	LEU	0	-0.019	-0.009	63.989	-0.001	-0.001	0.000	0.000	0.000	0.000
34	B	560	LEU	0	-0.035	-0.024	65.481	-0.001	-0.001	0.000	0.000	0.000	0.000
35	B	561	HIS	0	-0.012	0.003	61.334	-0.001	-0.001	0.000	0.000	0.000	0.000
36	B	562	VAL	0	0.061	0.018	60.152	-0.001	-0.001	0.000	0.000	0.000	0.000
37	B	563	LEU	0	-0.040	0.008	61.663	-0.001	-0.001	0.000	0.000	0.000	0.000
38	B	564	ARG	1	0.786	0.856	64.176	0.028	0.028	0.000	0.000	0.000	0.000
39	B	565	GLN	0	-0.075	-0.030	62.211	0.000	0.000	0.000	0.000	0.000	0.000
40	B	566	THR	0	-0.006	-0.003	58.062	-0.002	-0.002	0.000	0.000	0.000	0.000
41	B	567	LYS	1	0.941	0.964	58.277	0.045	0.045	0.000	0.000	0.000	0.000
42	B	568	LEU	0	0.014	0.023	53.902	-0.001	-0.001	0.000	0.000	0.000	0.000
43	B	569	LYS	1	0.920	0.930	54.020	0.053	0.053	0.000	0.000	0.000	0.000
44	B	570	PHE	0	-0.010	0.004	50.788	0.001	0.001	0.000	0.000	0.000	0.000
45	B	571	PHE	0	0.015	0.014	55.361	-0.001	-0.001	0.000	0.000	0.000	0.000
46	B	572	PRO	0	0.004	0.018	51.724	0.001	0.001	0.000	0.000	0.000	0.000
47	B	573	PHE	0	-0.002	-0.014	53.807	0.001	0.001	0.000	0.000	0.000	0.000
48	B	574	VAL	0	-0.001	-0.004	53.189	-0.001	-0.001	0.000	0.000	0.000	0.000
49	B	575	ASP	-1	-0.782	-0.873	55.026	-0.030	-0.030	0.000	0.000	0.000	0.000
50	B	576	THR	0	0.017	0.026	56.326	0.002	0.002	0.000	0.000	0.000	0.000
51	B	577	PRO	0	0.021	0.009	55.969	-0.001	-0.001	0.000	0.000	0.000	0.000
52	B	578	ASP	-1	-0.865	-0.907	55.221	-0.032	-0.032	0.000	0.000	0.000	0.000
53	B	579	THR	0	-0.052	-0.052	53.161	-0.002	-0.002	0.000	0.000	0.000	0.000
54	B	580	ASN	0	-0.095	-0.073	50.744	-0.003	-0.003	0.000	0.000	0.000	0.000
55	B	581	THR	0	-0.009	-0.019	50.596	-0.003	-0.003	0.000	0.000	0.000	0.000
56	B	582	LEU	0	-0.026	-0.009	48.609	0.001	0.001	0.000	0.000	0.000	0.000
57	B	583	LEU	0	-0.014	-0.003	51.450	0.000	0.000	0.000	0.000	0.000	0.000
58	B	584	GLY	0	0.017	0.015	52.767	0.001	0.001	0.000	0.000	0.000	0.000
59	B	585	SER	0	-0.064	-0.031	53.065	-0.002	-0.002	0.000	0.000	0.000	0.000
60	B	586	ILE	0	0.033	0.016	55.019	0.001	0.001	0.000	0.000	0.000	0.000
61	B	587	ASP	-1	-0.754	-0.847	58.411	-0.039	-0.039	0.000	0.000	0.000	0.000
62	B	588	ARG	1	0.805	0.878	59.469	0.039	0.039	0.000	0.000	0.000	0.000
63	B	589	THR	0	-0.014	-0.027	61.576	0.002	0.002	0.000	0.000	0.000	0.000
64	B	590	GLU	-1	-0.825	-0.891	62.766	-0.029	-0.029	0.000	0.000	0.000	0.000
65	B	591	VAL	0	0.016	0.006	61.913	0.001	0.001	0.000	0.000	0.000	0.000
66	B	592	GLU	-1	-0.840	-0.928	64.946	-0.033	-0.033	0.000	0.000	0.000	0.000
67	B	593	GLY	0	-0.006	0.007	67.340	0.001	0.001	0.000	0.000	0.000	0.000
68	B	594	LEU	0	-0.031	-0.021	65.480	0.001	0.001	0.000	0.000	0.000	0.000
69	B	595	LEU	0	0.009	0.010	68.231	0.001	0.001	0.000	0.000	0.000	0.000
70	B	596	GLN	0	-0.042	-0.021	70.481	0.002	0.002	0.000	0.000	0.000	0.000
71	B	597	ARG	1	0.817	0.903	67.517	0.028	0.028	0.000	0.000	0.000	0.000
72	B	598	ARG	1	0.863	0.914	73.015	0.023	0.023	0.000	0.000	0.000	0.000
73	B	599	ILE	0	-0.010	0.003	74.250	0.001	0.001	0.000	0.000	0.000	0.000
74	B	600	SER	0	-0.063	-0.048	77.177	0.001	0.001	0.000	0.000	0.000	0.000
75	B	601	ALA	0	-0.021	-0.013	77.727	0.001	0.001	0.000	0.000	0.000	0.000
76	B	602	TYR	0	-0.032	-0.008	78.858	0.001	0.001	0.000	0.000	0.000	0.000
77	B	603	ARG	1	0.850	0.911	80.664	0.020	0.020	0.000	0.000	0.000	0.000
78	B	604	DAR	1	0.847	0.908	83.083	0.018	0.018	0.000	0.000	0.000	0.000
79	B	605	GLN	0	0.007	0.012	84.668	0.000	0.000	0.000	0.000	0.000	0.000
80	B	606	PRO	0	-0.017	-0.001	86.065	0.000	0.000	0.000	0.000	0.000	0.000
81	B	680	DLY	1	0.963	0.962	92.066	0.018	0.018	0.000	0.000	0.000	0.000
82	B	681	DGN	0	0.025	0.016	96.083	0.000	0.000	0.000	0.000	0.000	0.000
83	B	682	LYS	1	0.912	0.945	88.004	0.019	0.019	0.000	0.000	0.000	0.000
84	B	683	GLY	0	0.033	0.039	89.546	0.000	0.000	0.000	0.000	0.000	0.000
85	B	684	THR	0	0.000	-0.018	85.546	0.000	0.000	0.000	0.000	0.000	0.000
86	B	685	GLY	0	0.046	0.040	82.294	0.000	0.000	0.000	0.000	0.000	0.000
87	B	686	DGN	0	0.046	0.004	77.022	0.000	0.000	0.000	0.000	0.000	0.000
88	B	687	DVA	0	-0.012	-0.007	79.819	0.000	0.000	0.000	0.000	0.000	0.000
89	B	688	DAL	0	0.025	0.036	80.796	0.000	0.000	0.000	0.000	0.000	0.000
90	B	689	SER	0	0.035	0.009	77.538	0.000	0.000	0.000	0.000	0.000	0.000
91	B	690	ARG	1	0.896	0.942	78.140	0.022	0.022	0.000	0.000	0.000	0.000
92	B	691	DPN	0	0.009	0.009	81.756	0.000	0.000	0.000	0.000	0.000	0.000
93	B	692	GLU	-1	-0.797	-0.866	84.281	-0.019	-0.019	0.000	0.000	0.000	0.000
94	B	693	DGL	-1	-0.843	-0.910	86.584	-0.017	-0.017	0.000	0.000	0.000	0.000
95	B	694	MED	0	-0.105	-0.043	84.740	0.000	0.000	0.000	0.000	0.000	0.000
96	B	695	LEU	0	-0.033	-0.004	80.612	0.000	0.000	0.000	0.000	0.000	0.000
97	B	696	THR	0	0.013	-0.004	82.856	-0.001	-0.001	0.000	0.000	0.000	0.000
98	B	697	LEU	0	0.008	-0.021	77.117	0.000	0.000	0.000	0.000	0.000	0.000
99	B	698	GLU	-1	-0.824	-0.881	80.186	-0.021	-0.021	0.000	0.000	0.000	0.000
100	B	699	GLU	-1	-0.821	-0.926	82.101	-0.020	-0.020	0.000	0.000	0.000	0.000
101	B	700	ILE	0	0.009	0.008	76.286	0.000	0.000	0.000	0.000	0.000	0.000
102	B	701	TYR	0	-0.010	0.007	76.847	0.000	0.000	0.000	0.000	0.000	0.000
103	B	702	ARG	1	0.798	0.849	78.675	0.021	0.021	0.000	0.000	0.000	0.000
104	B	703	TRP	0	-0.012	-0.008	72.586	0.000	0.000	0.000	0.000	0.000	0.000
105	B	704	GLU	-1	-0.725	-0.827	73.282	-0.026	-0.026	0.000	0.000	0.000	0.000
106	B	705	GLN	0	-0.075	-0.035	75.745	0.000	0.000	0.000	0.000	0.000	0.000
107	B	706	ARG	1	0.858	0.928	77.931	0.020	0.020	0.000	0.000	0.000	0.000
108	B	707	GLU	-1	-0.759	-0.860	75.046	-0.021	-0.021	0.000	0.000	0.000	0.000
109	B	708	LYS	1	0.932	0.977	71.174	0.024	0.024	0.000	0.000	0.000	0.000
110	B	709	ASN	0	-0.009	-0.017	70.680	-0.001	-0.001	0.000	0.000	0.000	0.000
111	B	710	VAL	0	-0.030	-0.002	71.354	0.000	0.000	0.000	0.000	0.000	0.000
112	B	711	VAL	0	0.030	0.010	66.642	-0.001	-0.001	0.000	0.000	0.000	0.000
113	B	712	VAL	0	-0.013	-0.010	66.231	0.001	0.001	0.000	0.000	0.000	0.000
114	B	713	ASN	0	-0.020	-0.017	67.167	-0.001	-0.001	0.000	0.000	0.000	0.000
115	B	714	PHE	0	0.013	-0.022	63.275	0.000	0.000	0.000	0.000	0.000	0.000
116	B	715	GLU	-1	-0.884	-0.910	65.245	-0.022	-0.022	0.000	0.000	0.000	0.000
117	B	716	THR	0	-0.039	-0.024	67.183	0.000	0.000	0.000	0.000	0.000	0.000
118	B	717	CYS	0	-0.096	-0.037	62.581	0.000	0.000	0.000	0.000	0.000	0.000
119	B	718	ARG	1	0.772	0.858	58.950	0.036	0.036	0.000	0.000	0.000	0.000
120	B	719	ILE	0	0.026	0.009	56.796	-0.001	-0.001	0.000	0.000	0.000	0.000
121	B	720	ASP	-1	-0.840	-0.886	55.276	-0.038	-0.038	0.000	0.000	0.000	0.000
122	B	721	GLN	0	0.017	-0.011	51.817	-0.001	-0.001	0.000	0.000	0.000	0.000
123	B	722	SER	0	0.014	0.016	47.604	0.000	0.000	0.000	0.000	0.000	0.000
124	B	723	PRO	0	-0.031	-0.020	47.000	0.000	0.000	0.000	0.000	0.000	0.000
125	B	724	PHE	0	-0.026	-0.014	42.749	-0.002	-0.002	0.000	0.000	0.000	0.000
126	B	725	GLN	0	0.012	0.005	41.052	0.000	0.000	0.000	0.000	0.000	0.000
127	B	726	LEU	0	0.002	0.008	38.918	-0.004	-0.004	0.000	0.000	0.000	0.000
128	B	727	VAL	0	0.036	0.024	37.609	0.003	0.003	0.000	0.000	0.000	0.000
129	B	728	GLU	-1	-0.700	-0.831	37.390	-0.082	-0.082	0.000	0.000	0.000	0.000
130	B	729	GLY	0	0.026	0.022	33.615	-0.004	-0.004	0.000	0.000	0.000	0.000
131	B	730	THR	0	-0.074	-0.052	32.637	-0.008	-0.008	0.000	0.000	0.000	0.000
132	B	731	SER	0	-0.027	-0.020	30.235	-0.002	-0.002	0.000	0.000	0.000	0.000
133	B	732	LEU	0	0.071	0.024	32.278	0.003	0.003	0.000	0.000	0.000	0.000
134	B	733	GLN	0	0.064	0.031	31.276	0.003	0.003	0.000	0.000	0.000	0.000
135	B	734	LYS	1	0.911	0.969	28.543	0.143	0.143	0.000	0.000	0.000	0.000
136	B	735	THR	0	0.048	0.025	34.389	0.005	0.005	0.000	0.000	0.000	0.000
137	B	736	HIS	0	0.060	0.038	36.701	0.008	0.008	0.000	0.000	0.000	0.000
138	B	737	THR	0	-0.051	-0.030	35.232	0.003	0.003	0.000	0.000	0.000	0.000
139	B	738	LEU	0	-0.003	0.000	37.733	0.004	0.004	0.000	0.000	0.000	0.000
140	B	739	PHE	0	0.014	-0.013	39.996	0.004	0.004	0.000	0.000	0.000	0.000
141	B	740	SER	0	-0.037	-0.022	40.454	0.004	0.004	0.000	0.000	0.000	0.000
142	B	741	LEU	0	-0.060	-0.038	38.295	0.003	0.003	0.000	0.000	0.000	0.000
143	B	742	LEU	0	-0.035	-0.013	42.615	0.004	0.004	0.000	0.000	0.000	0.000
144	B	743	GLY	0	-0.005	0.018	45.586	0.003	0.003	0.000	0.000	0.000	0.000
145	B	744	LEU	0	-0.064	-0.021	44.354	0.003	0.003	0.000	0.000	0.000	0.000
146	B	745	ASP	-1	-0.852	-0.909	46.750	-0.060	-0.060	0.000	0.000	0.000	0.000
147	B	746	ARG	1	0.847	0.885	47.459	0.059	0.059	0.000	0.000	0.000	0.000
148	B	747	ALA	0	0.005	0.009	44.473	0.001	0.001	0.000	0.000	0.000	0.000
149	B	748	TYR	0	0.022	0.000	46.446	-0.001	-0.001	0.000	0.000	0.000	0.000
150	B	749	VAL	0	-0.017	0.000	40.888	-0.001	-0.001	0.000	0.000	0.000	0.000
151	B	750	THR	0	-0.029	-0.029	42.663	0.004	0.004	0.000	0.000	0.000	0.000
152	B	751	SER	0	0.020	-0.010	41.710	-0.004	-0.004	0.000	0.000	0.000	0.000
153	B	752	MET	0	-0.020	-0.018	41.607	0.003	0.003	0.000	0.000	0.000	0.000
154	B	753	GLY	0	0.050	0.037	43.699	0.003	0.003	0.000	0.000	0.000	0.000
155	B	754	LYS	1	0.916	0.977	46.400	0.043	0.043	0.000	0.000	0.000	0.000
156	B	755	LEU	0	0.021	-0.004	46.259	-0.003	-0.003	0.000	0.000	0.000	0.000
157	B	756	VAL	0	-0.078	-0.037	42.741	0.001	0.001	0.000	0.000	0.000	0.000
158	B	757	GLY	0	0.089	0.021	45.665	-0.001	-0.001	0.000	0.000	0.000	0.000
159	B	758	VAL	0	-0.070	-0.023	46.480	0.001	0.001	0.000	0.000	0.000	0.000
160	B	759	VAL	0	0.008	0.018	41.563	-0.002	-0.002	0.000	0.000	0.000	0.000
161	B	760	ALA	0	0.013	-0.004	44.830	0.003	0.003	0.000	0.000	0.000	0.000
162	B	761	LEU	0	0.031	0.019	42.625	-0.004	-0.004	0.000	0.000	0.000	0.000
163	B	762	ALA	0	0.026	0.008	43.515	-0.004	-0.004	0.000	0.000	0.000	0.000
164	B	763	GLU	-1	-0.802	-0.889	43.826	-0.071	-0.071	0.000	0.000	0.000	0.000
165	B	764	ILE	0	-0.005	-0.012	38.504	-0.005	-0.005	0.000	0.000	0.000	0.000
166	B	765	GLN	0	-0.071	-0.040	39.235	-0.002	-0.002	0.000	0.000	0.000	0.000
167	B	766	ALA	0	0.040	0.020	39.864	-0.005	-0.005	0.000	0.000	0.000	0.000
168	B	767	ALA	0	0.008	0.013	37.577	-0.004	-0.004	0.000	0.000	0.000	0.000
169	B	768	ILE	0	-0.092	-0.042	33.884	-0.008	-0.008	0.000	0.000	0.000	0.000
170	B	769	GLU	-1	-0.926	-0.952	35.101	-0.106	-0.106	0.000	0.000	0.000	0.000
171	B	770	GLY	0	-0.097	-0.046	35.236	-0.006	-0.006	0.000	0.000	0.000	0.000

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