FMO DATABASE

FMODB ID: 89LNY

Calculation Name: 2D4Z-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D4Z

Chain ID: A

ChEMBL ID:

UniProt ID: P21564

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:

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	169
LigandCharge	DLY=1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1575511.933539
FMO2-HF: Nuclear repulsion	1508964.421385
FMO2-HF: Total energy	-66547.512154
FMO2-MP2: Total energy	-66742.973112

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:527:LEU)

Summations of interaction energy for fragment #1(A:527:LEU)

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.
-6.092	-0.185	0.723	-3.235	-3.394	-0.004

Interaction energy analysis for fragmet #1(A:527:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : 0.012

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	529	DTR	0	-0.003	-0.005	2.673	-5.855	0.020	0.724	-3.233	-3.366	-0.004
4	A	530	SER	0	-0.025	-0.022	5.277	0.037	0.069	-0.001	-0.002	-0.028	0.000
5	A	531	SER	0	-0.010	0.011	9.122	0.071	0.071	0.000	0.000	0.000	0.000
6	A	532	ALA	0	0.023	0.008	12.429	0.028	0.028	0.000	0.000	0.000	0.000
7	A	533	ASN	0	0.017	0.012	15.338	0.011	0.011	0.000	0.000	0.000	0.000
8	A	534	DLY	1	0.849	0.937	18.852	0.193	0.193	0.000	0.000	0.000	0.000
9	A	535	TYR	0	0.027	-0.004	21.419	0.017	0.017	0.000	0.000	0.000	0.000
10	A	536	ASN	0	-0.038	-0.014	25.538	0.008	0.008	0.000	0.000	0.000	0.000
11	A	537	ILE	0	-0.013	-0.014	23.277	0.000	0.000	0.000	0.000	0.000	0.000
12	A	538	GLN	0	0.010	0.008	27.164	0.012	0.012	0.000	0.000	0.000	0.000
13	A	539	VAL	0	0.008	0.036	27.723	-0.013	-0.013	0.000	0.000	0.000	0.000
14	A	540	GLY	0	0.070	-0.009	27.399	0.008	0.008	0.000	0.000	0.000	0.000
15	A	541	ASP	-1	-0.891	-0.947	23.827	-0.201	-0.201	0.000	0.000	0.000	0.000
16	A	542	ILE	0	-0.036	-0.043	23.147	-0.010	-0.010	0.000	0.000	0.000	0.000
17	A	543	MET	0	-0.081	0.024	24.268	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	544	VAL	0	0.028	0.031	23.535	-0.013	-0.013	0.000	0.000	0.000	0.000
19	A	545	ARG	1	0.920	0.927	25.094	0.194	0.194	0.000	0.000	0.000	0.000
20	A	546	ASP	-1	-0.945	-0.945	25.010	-0.189	-0.189	0.000	0.000	0.000	0.000
21	A	547	VAL	0	-0.034	-0.011	26.935	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	548	THR	0	0.002	0.013	28.424	0.003	0.003	0.000	0.000	0.000	0.000
23	A	549	SER	0	-0.032	-0.039	30.597	0.004	0.004	0.000	0.000	0.000	0.000
24	A	550	ILE	0	0.023	0.026	34.333	0.000	0.000	0.000	0.000	0.000	0.000
25	A	551	ALA	0	0.030	0.020	37.538	0.000	0.000	0.000	0.000	0.000	0.000
26	A	552	SER	0	-0.032	0.011	40.330	0.003	0.003	0.000	0.000	0.000	0.000
27	A	553	THR	0	0.002	-0.001	42.166	0.002	0.002	0.000	0.000	0.000	0.000
28	A	554	SER	0	-0.036	-0.040	39.071	0.000	0.000	0.000	0.000	0.000	0.000
29	A	555	THR	0	0.005	-0.002	39.898	0.005	0.005	0.000	0.000	0.000	0.000
30	A	556	TYR	0	0.035	0.010	40.674	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	557	GLY	0	0.032	0.020	38.541	0.000	0.000	0.000	0.000	0.000	0.000
32	A	558	ASP	-1	-0.852	-0.912	35.910	-0.088	-0.088	0.000	0.000	0.000	0.000
33	A	559	LEU	0	-0.008	-0.002	35.539	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	560	LEU	0	0.032	0.001	36.202	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	561	HIS	0	-0.064	-0.014	28.972	0.001	0.001	0.000	0.000	0.000	0.000
36	A	562	VAL	0	0.059	0.028	31.665	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	563	LEU	0	-0.030	0.047	31.910	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	564	ARG	1	0.838	0.908	31.288	0.068	0.068	0.000	0.000	0.000	0.000
39	A	565	GLN	0	-0.029	-0.006	27.162	-0.008	-0.008	0.000	0.000	0.000	0.000
40	A	566	THR	0	-0.060	-0.070	26.676	-0.012	-0.012	0.000	0.000	0.000	0.000
41	A	567	LYS	1	0.957	0.961	23.258	0.142	0.142	0.000	0.000	0.000	0.000
42	A	568	LEU	0	-0.013	0.001	28.060	0.003	0.003	0.000	0.000	0.000	0.000
43	A	569	LYS	1	0.994	0.994	30.662	0.097	0.097	0.000	0.000	0.000	0.000
44	A	570	PHE	0	0.030	0.026	33.645	0.005	0.005	0.000	0.000	0.000	0.000
45	A	571	PHE	0	-0.016	-0.004	31.853	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	572	PRO	0	0.001	0.022	33.705	0.006	0.006	0.000	0.000	0.000	0.000
47	A	573	PHE	0	0.018	-0.014	36.806	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	574	VAL	0	-0.025	-0.012	37.323	0.002	0.002	0.000	0.000	0.000	0.000
49	A	575	ASP	-1	-0.912	-0.952	40.408	-0.068	-0.068	0.000	0.000	0.000	0.000
50	A	576	THR	0	-0.007	0.014	41.487	0.003	0.003	0.000	0.000	0.000	0.000
51	A	577	PRO	0	-0.001	0.005	36.974	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	578	ASP	-1	-0.865	-0.938	37.000	-0.095	-0.095	0.000	0.000	0.000	0.000
53	A	579	THR	0	-0.042	-0.042	38.947	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	580	ASN	0	-0.028	-0.026	35.958	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	581	THR	0	0.061	0.022	39.205	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	582	LEU	0	-0.023	-0.020	37.939	0.000	0.000	0.000	0.000	0.000	0.000
57	A	583	LEU	0	-0.023	-0.015	40.990	0.003	0.003	0.000	0.000	0.000	0.000
58	A	584	GLY	0	0.060	0.038	41.832	0.004	0.004	0.000	0.000	0.000	0.000
59	A	585	SER	0	-0.046	-0.025	38.262	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	586	ILE	0	0.010	0.024	39.013	0.004	0.004	0.000	0.000	0.000	0.000
61	A	587	ASP	-1	-0.819	-0.915	38.249	-0.072	-0.072	0.000	0.000	0.000	0.000
62	A	588	ARG	1	0.847	0.906	31.637	0.090	0.090	0.000	0.000	0.000	0.000
63	A	589	THR	0	0.049	0.023	37.607	0.001	0.001	0.000	0.000	0.000	0.000
64	A	590	GLU	-1	-0.924	-0.966	40.702	-0.048	-0.048	0.000	0.000	0.000	0.000
65	A	591	VAL	0	-0.023	-0.021	37.923	0.002	0.002	0.000	0.000	0.000	0.000
66	A	592	GLU	-1	-0.907	-0.975	37.715	-0.058	-0.058	0.000	0.000	0.000	0.000
67	A	593	GLY	0	0.046	0.033	41.045	0.003	0.003	0.000	0.000	0.000	0.000
68	A	594	LEU	0	-0.062	-0.017	43.266	0.003	0.003	0.000	0.000	0.000	0.000
69	A	595	LEU	0	-0.006	-0.005	39.135	0.002	0.002	0.000	0.000	0.000	0.000
70	A	596	GLN	0	0.031	0.022	42.695	0.004	0.004	0.000	0.000	0.000	0.000
71	A	597	ARG	1	0.906	0.941	45.745	0.048	0.048	0.000	0.000	0.000	0.000
72	A	598	ARG	1	0.803	0.901	46.428	0.046	0.046	0.000	0.000	0.000	0.000
73	A	599	ILE	0	0.020	0.020	43.067	0.002	0.002	0.000	0.000	0.000	0.000
74	A	600	SER	0	0.033	-0.014	47.645	0.002	0.002	0.000	0.000	0.000	0.000
75	A	601	ALA	0	-0.012	0.023	50.685	0.002	0.002	0.000	0.000	0.000	0.000
76	A	602	TYR	0	-0.014	-0.019	49.558	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	603	ARG	1	0.758	0.876	50.128	0.029	0.029	0.000	0.000	0.000	0.000
78	A	604	ARG	1	0.808	0.871	53.673	0.024	0.024	0.000	0.000	0.000	0.000
79	A	605	DGN	0	0.006	0.005	56.372	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	606	PRO	0	-0.070	-0.030	56.156	0.001	0.001	0.000	0.000	0.000	0.000
81	A	607	DAL	0	0.030	0.000	55.001	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	608	DAL	0	-0.030	-0.020	54.986	0.001	0.001	0.000	0.000	0.000	0.000
83	A	609	DAL	0	0.030	0.013	52.385	0.001	0.001	0.000	0.000	0.000	0.000
84	A	610	DAL	0	-0.052	-0.042	48.712	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	611	GLU	-1	-0.931	-0.950	42.348	-0.037	-0.037	0.000	0.000	0.000	0.000
86	A	612	DAL	0	0.008	-0.002	43.140	0.001	0.001	0.000	0.000	0.000	0.000
87	A	613	ASP	-1	-0.942	-0.970	41.171	-0.026	-0.026	0.000	0.000	0.000	0.000
88	A	614	GLU	-1	-0.840	-0.936	44.481	-0.022	-0.022	0.000	0.000	0.000	0.000
89	A	615	GLU	-1	-1.039	-1.013	46.885	-0.008	-0.008	0.000	0.000	0.000	0.000
90	A	691	PHE	0	-0.067	-0.063	53.424	0.000	0.000	0.000	0.000	0.000	0.000
91	A	692	GLU	-1	-0.885	-0.931	54.246	-0.014	-0.014	0.000	0.000	0.000	0.000
92	A	693	GLU	-1	-0.879	-0.912	55.565	-0.021	-0.021	0.000	0.000	0.000	0.000
93	A	694	MED	0	-0.043	-0.008	50.690	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	695	LEU	0	-0.041	-0.010	48.400	0.000	0.000	0.000	0.000	0.000	0.000
95	A	696	THR	0	0.032	0.009	47.574	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	697	LEU	0	0.075	0.022	40.199	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	698	GLU	-1	-0.853	-0.905	43.000	-0.032	-0.032	0.000	0.000	0.000	0.000
98	A	699	GLU	-1	-0.819	-0.887	44.815	-0.028	-0.028	0.000	0.000	0.000	0.000
99	A	700	ILE	0	0.046	0.026	41.835	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	701	TYR	0	-0.020	0.008	38.315	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	702	ARG	1	0.813	0.875	42.179	0.030	0.030	0.000	0.000	0.000	0.000
102	A	703	TRP	0	-0.043	-0.039	41.665	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	704	GLU	-1	-0.831	-0.918	38.016	-0.061	-0.061	0.000	0.000	0.000	0.000
104	A	705	GLN	0	-0.065	-0.033	39.742	-0.005	-0.005	0.000	0.000	0.000	0.000
105	A	706	ARG	1	0.889	0.956	42.931	0.035	0.035	0.000	0.000	0.000	0.000
106	A	707	GLU	-1	-0.805	-0.893	45.226	-0.043	-0.043	0.000	0.000	0.000	0.000
107	A	708	LYS	1	1.003	1.026	36.219	0.069	0.069	0.000	0.000	0.000	0.000
108	A	709	ASN	0	-0.070	-0.054	40.797	-0.007	-0.007	0.000	0.000	0.000	0.000
109	A	710	VAL	0	-0.025	0.000	42.999	0.000	0.000	0.000	0.000	0.000	0.000
110	A	711	VAL	0	0.002	-0.008	44.451	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	712	VAL	0	0.004	-0.009	42.504	0.003	0.003	0.000	0.000	0.000	0.000
112	A	713	ASN	0	0.010	0.019	45.606	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	714	PHE	0	0.000	-0.022	41.625	0.001	0.001	0.000	0.000	0.000	0.000
114	A	715	GLU	-1	-0.908	-0.962	47.221	-0.044	-0.044	0.000	0.000	0.000	0.000
115	A	716	THR	0	-0.067	-0.032	49.910	0.000	0.000	0.000	0.000	0.000	0.000
116	A	717	CYS	0	-0.093	-0.020	44.037	0.000	0.000	0.000	0.000	0.000	0.000
117	A	718	ARG	1	0.887	0.958	43.734	0.057	0.057	0.000	0.000	0.000	0.000
118	A	719	ILE	0	-0.009	-0.004	43.365	-0.003	-0.003	0.000	0.000	0.000	0.000
119	A	720	ASP	-1	-0.864	-0.923	42.546	-0.059	-0.059	0.000	0.000	0.000	0.000
120	A	721	GLN	0	0.007	-0.003	43.281	-0.005	-0.005	0.000	0.000	0.000	0.000
121	A	722	SER	0	0.010	0.005	40.864	0.000	0.000	0.000	0.000	0.000	0.000
122	A	723	PRO	0	-0.014	-0.012	42.203	0.001	0.001	0.000	0.000	0.000	0.000
123	A	724	PHE	0	-0.023	-0.015	37.537	0.001	0.001	0.000	0.000	0.000	0.000
124	A	725	GLN	0	0.028	0.017	40.661	0.000	0.000	0.000	0.000	0.000	0.000
125	A	726	LEU	0	-0.030	-0.008	33.050	0.001	0.001	0.000	0.000	0.000	0.000
126	A	727	VAL	0	0.019	0.006	36.343	-0.004	-0.004	0.000	0.000	0.000	0.000
127	A	728	GLU	-1	-0.785	-0.923	31.357	-0.141	-0.141	0.000	0.000	0.000	0.000
128	A	729	GLY	0	-0.009	0.007	32.555	-0.003	-0.003	0.000	0.000	0.000	0.000
129	A	730	THR	0	-0.082	-0.034	34.342	0.005	0.005	0.000	0.000	0.000	0.000
130	A	731	SER	0	-0.004	-0.008	32.282	-0.005	-0.005	0.000	0.000	0.000	0.000
131	A	732	LEU	0	0.098	0.024	26.571	0.005	0.005	0.000	0.000	0.000	0.000
132	A	733	GLN	0	0.059	0.040	30.708	-0.002	-0.002	0.000	0.000	0.000	0.000
133	A	734	LYS	1	0.908	0.943	33.372	0.086	0.086	0.000	0.000	0.000	0.000
134	A	735	THR	0	0.073	0.031	31.505	0.007	0.007	0.000	0.000	0.000	0.000
135	A	736	HIS	0	0.069	0.058	31.797	-0.002	-0.002	0.000	0.000	0.000	0.000
136	A	737	THR	0	-0.027	0.006	33.521	0.006	0.006	0.000	0.000	0.000	0.000
137	A	738	LEU	0	-0.034	-0.008	36.570	0.004	0.004	0.000	0.000	0.000	0.000
138	A	739	PHE	0	-0.004	-0.026	31.726	0.003	0.003	0.000	0.000	0.000	0.000
139	A	740	SER	0	-0.040	-0.038	35.362	0.004	0.004	0.000	0.000	0.000	0.000
140	A	741	LEU	0	-0.053	-0.025	37.116	0.004	0.004	0.000	0.000	0.000	0.000
141	A	742	LEU	0	-0.023	-0.011	39.596	0.003	0.003	0.000	0.000	0.000	0.000
142	A	743	GLY	0	-0.005	0.019	37.412	0.002	0.002	0.000	0.000	0.000	0.000
143	A	744	LEU	0	-0.072	-0.029	35.264	0.000	0.000	0.000	0.000	0.000	0.000
144	A	745	ASP	-1	-0.912	-0.952	30.126	-0.118	-0.118	0.000	0.000	0.000	0.000
145	A	746	ARG	1	0.974	0.967	27.231	0.135	0.135	0.000	0.000	0.000	0.000
146	A	747	ALA	0	-0.008	0.017	32.032	0.009	0.009	0.000	0.000	0.000	0.000
147	A	748	TYR	0	0.031	0.002	32.579	-0.011	-0.011	0.000	0.000	0.000	0.000
148	A	749	VAL	0	-0.005	-0.004	31.164	0.006	0.006	0.000	0.000	0.000	0.000
149	A	750	THR	0	-0.018	-0.013	34.256	0.000	0.000	0.000	0.000	0.000	0.000
150	A	751	SER	0	0.013	-0.006	36.396	-0.001	-0.001	0.000	0.000	0.000	0.000
151	A	752	MET	0	-0.061	-0.042	38.256	0.002	0.002	0.000	0.000	0.000	0.000
152	A	753	GLY	0	0.054	0.036	41.229	0.003	0.003	0.000	0.000	0.000	0.000
153	A	754	LYS	1	0.910	0.967	38.035	0.095	0.095	0.000	0.000	0.000	0.000
154	A	755	LEU	0	-0.008	0.001	33.894	-0.002	-0.002	0.000	0.000	0.000	0.000
155	A	756	VAL	0	-0.044	-0.021	31.361	-0.003	-0.003	0.000	0.000	0.000	0.000
156	A	757	GLY	0	0.068	0.003	29.738	-0.011	-0.011	0.000	0.000	0.000	0.000
157	A	758	VAL	0	-0.076	-0.017	28.498	0.013	0.013	0.000	0.000	0.000	0.000
158	A	759	VAL	0	0.001	0.012	27.914	-0.014	-0.014	0.000	0.000	0.000	0.000
159	A	760	ALA	0	0.015	0.010	26.191	0.014	0.014	0.000	0.000	0.000	0.000
160	A	761	LEU	0	0.027	0.006	27.571	-0.007	-0.007	0.000	0.000	0.000	0.000
161	A	762	ALA	0	0.011	0.012	23.741	-0.002	-0.002	0.000	0.000	0.000	0.000
162	A	763	GLU	-1	-0.873	-0.959	22.815	-0.211	-0.211	0.000	0.000	0.000	0.000
163	A	764	ILE	0	-0.022	-0.015	24.189	-0.006	-0.006	0.000	0.000	0.000	0.000
164	A	765	GLN	0	-0.021	-0.014	25.823	-0.004	-0.004	0.000	0.000	0.000	0.000
165	A	766	ALA	0	0.093	0.047	20.780	0.000	0.000	0.000	0.000	0.000	0.000
166	A	767	ALA	0	-0.052	-0.020	22.398	-0.006	-0.006	0.000	0.000	0.000	0.000
167	A	768	ILE	0	-0.101	-0.056	23.412	0.003	0.003	0.000	0.000	0.000	0.000
168	A	769	GLU	-1	-0.975	-0.975	23.122	-0.123	-0.123	0.000	0.000	0.000	0.000
169	A	770	GLY	0	-0.080	-0.032	20.090	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:527:LEU)