FMO DATABASE

FMODB ID: NN42Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1574182.925116
FMO2-HF: Nuclear repulsion	1507634.156768
FMO2-HF: Total energy	-66548.768348
FMO2-MP2: Total energy	-66744.06128

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.
-6.131	-0.189	0.733	-3.231	-3.442	-0.003

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 : 0.019 / q_NPA : 0.011

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	0.002	-0.002	2.676	-5.862	0.049	0.734	-3.229	-3.415	-0.003
4	A	530	SER	0	-0.026	-0.023	5.277	0.023	0.054	-0.001	-0.002	-0.027	0.000
5	A	531	SER	0	-0.008	0.013	9.116	0.074	0.074	0.000	0.000	0.000	0.000
6	A	532	ALA	0	0.020	0.005	12.416	0.029	0.029	0.000	0.000	0.000	0.000
7	A	533	ASN	0	0.046	0.025	15.331	0.010	0.010	0.000	0.000	0.000	0.000
8	A	534	DLY	1	0.867	0.946	18.848	0.193	0.193	0.000	0.000	0.000	0.000
9	A	535	TYR	0	-0.018	-0.026	21.128	0.020	0.020	0.000	0.000	0.000	0.000
10	A	536	ASN	0	-0.045	-0.011	25.538	0.005	0.005	0.000	0.000	0.000	0.000
11	A	537	ILE	0	-0.008	-0.013	23.589	0.000	0.000	0.000	0.000	0.000	0.000
12	A	538	GLN	0	-0.014	-0.020	27.171	0.010	0.010	0.000	0.000	0.000	0.000
13	A	539	VAL	0	0.021	0.032	27.738	-0.014	-0.014	0.000	0.000	0.000	0.000
14	A	540	GLY	0	0.073	0.004	27.423	0.009	0.009	0.000	0.000	0.000	0.000
15	A	541	ASP	-1	-0.925	-0.942	23.764	-0.204	-0.204	0.000	0.000	0.000	0.000
16	A	542	ILE	0	-0.013	-0.037	23.162	-0.011	-0.011	0.000	0.000	0.000	0.000
17	A	543	MET	0	-0.079	0.010	24.276	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	544	VAL	0	0.023	0.025	23.256	-0.013	-0.013	0.000	0.000	0.000	0.000
19	A	545	ARG	1	0.869	0.889	25.105	0.192	0.192	0.000	0.000	0.000	0.000
20	A	546	ASP	-1	-0.937	-0.941	25.017	-0.193	-0.193	0.000	0.000	0.000	0.000
21	A	547	VAL	0	-0.045	-0.014	26.980	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	548	THR	0	0.013	0.012	28.411	0.002	0.002	0.000	0.000	0.000	0.000
23	A	549	SER	0	-0.019	-0.022	30.636	0.004	0.004	0.000	0.000	0.000	0.000
24	A	550	ILE	0	0.020	0.025	34.373	0.000	0.000	0.000	0.000	0.000	0.000
25	A	551	ALA	0	0.026	0.034	37.576	0.001	0.001	0.000	0.000	0.000	0.000
26	A	552	SER	0	-0.026	-0.007	40.371	0.003	0.003	0.000	0.000	0.000	0.000
27	A	553	THR	0	0.007	-0.004	42.506	0.002	0.002	0.000	0.000	0.000	0.000
28	A	554	SER	0	-0.064	-0.032	39.118	0.000	0.000	0.000	0.000	0.000	0.000
29	A	555	THR	0	0.000	-0.025	39.760	0.005	0.005	0.000	0.000	0.000	0.000
30	A	556	TYR	0	0.062	0.015	40.705	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	557	GLY	0	0.032	0.023	38.565	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	558	ASP	-1	-0.843	-0.897	35.939	-0.092	-0.092	0.000	0.000	0.000	0.000
33	A	559	LEU	0	-0.003	0.008	35.568	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	560	LEU	0	0.023	0.002	36.225	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	561	HIS	0	-0.051	-0.011	29.013	0.000	0.000	0.000	0.000	0.000	0.000
36	A	562	VAL	0	0.042	0.011	31.689	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	563	LEU	0	-0.039	0.011	31.932	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	564	ARG	1	0.790	0.852	31.196	0.070	0.070	0.000	0.000	0.000	0.000
39	A	565	GLN	0	-0.043	-0.014	27.036	-0.011	-0.011	0.000	0.000	0.000	0.000
40	A	566	THR	0	-0.039	-0.021	26.697	-0.014	-0.014	0.000	0.000	0.000	0.000
41	A	567	LYS	1	0.958	0.963	23.387	0.150	0.150	0.000	0.000	0.000	0.000
42	A	568	LEU	0	-0.011	0.004	28.118	0.003	0.003	0.000	0.000	0.000	0.000
43	A	569	LYS	1	0.917	0.945	30.683	0.107	0.107	0.000	0.000	0.000	0.000
44	A	570	PHE	0	0.037	0.024	33.667	0.005	0.005	0.000	0.000	0.000	0.000
45	A	571	PHE	0	-0.014	0.000	31.724	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	572	PRO	0	-0.021	0.006	33.883	0.006	0.006	0.000	0.000	0.000	0.000
47	A	573	PHE	0	0.017	-0.012	36.845	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	574	VAL	0	-0.032	-0.036	37.368	0.002	0.002	0.000	0.000	0.000	0.000
49	A	575	ASP	-1	-0.852	-0.892	40.451	-0.070	-0.070	0.000	0.000	0.000	0.000
50	A	576	THR	0	-0.009	-0.013	41.654	0.003	0.003	0.000	0.000	0.000	0.000
51	A	577	PRO	0	0.006	0.006	37.002	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	578	ASP	-1	-0.879	-0.929	37.020	-0.096	-0.096	0.000	0.000	0.000	0.000
53	A	579	THR	0	-0.027	-0.027	38.965	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	580	ASN	0	-0.027	-0.018	35.961	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	581	THR	0	0.020	-0.006	39.223	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	582	LEU	0	-0.028	-0.023	37.977	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	583	LEU	0	-0.006	-0.001	41.005	0.003	0.003	0.000	0.000	0.000	0.000
58	A	584	GLY	0	0.052	0.031	41.871	0.004	0.004	0.000	0.000	0.000	0.000
59	A	585	SER	0	-0.031	-0.014	38.451	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	586	ILE	0	0.001	0.016	39.058	0.004	0.004	0.000	0.000	0.000	0.000
61	A	587	ASP	-1	-0.777	-0.873	38.277	-0.075	-0.075	0.000	0.000	0.000	0.000
62	A	588	ARG	1	0.818	0.898	31.612	0.093	0.093	0.000	0.000	0.000	0.000
63	A	589	THR	0	0.050	0.022	37.626	0.001	0.001	0.000	0.000	0.000	0.000
64	A	590	GLU	-1	-0.848	-0.914	40.717	-0.051	-0.051	0.000	0.000	0.000	0.000
65	A	591	VAL	0	-0.003	-0.013	37.928	0.002	0.002	0.000	0.000	0.000	0.000
66	A	592	GLU	-1	-0.874	-0.964	37.162	-0.066	-0.066	0.000	0.000	0.000	0.000
67	A	593	GLY	0	0.037	0.030	41.062	0.003	0.003	0.000	0.000	0.000	0.000
68	A	594	LEU	0	-0.032	-0.009	43.538	0.003	0.003	0.000	0.000	0.000	0.000
69	A	595	LEU	0	-0.005	-0.007	39.231	0.002	0.002	0.000	0.000	0.000	0.000
70	A	596	GLN	0	0.025	0.019	42.774	0.003	0.003	0.000	0.000	0.000	0.000
71	A	597	ARG	1	0.822	0.883	45.759	0.051	0.051	0.000	0.000	0.000	0.000
72	A	598	ARG	1	0.809	0.906	46.516	0.048	0.048	0.000	0.000	0.000	0.000
73	A	599	ILE	0	0.015	0.018	43.023	0.002	0.002	0.000	0.000	0.000	0.000
74	A	600	SER	0	0.030	-0.008	47.661	0.002	0.002	0.000	0.000	0.000	0.000
75	A	601	ALA	0	-0.005	0.026	50.698	0.002	0.002	0.000	0.000	0.000	0.000
76	A	602	TYR	0	0.003	-0.015	49.817	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	603	ARG	1	0.756	0.886	50.130	0.031	0.031	0.000	0.000	0.000	0.000
78	A	604	ARG	1	0.813	0.877	53.686	0.026	0.026	0.000	0.000	0.000	0.000
79	A	605	DGN	0	0.001	0.003	56.388	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	606	PRO	0	-0.068	-0.028	56.155	0.001	0.001	0.000	0.000	0.000	0.000
81	A	607	DAL	0	0.030	-0.003	54.977	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	608	DAL	0	-0.025	-0.016	54.951	0.001	0.001	0.000	0.000	0.000	0.000
83	A	609	DAL	0	0.021	0.008	52.302	0.001	0.001	0.000	0.000	0.000	0.000
84	A	610	DAL	0	-0.052	-0.042	48.673	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	611	GLU	-1	-0.934	-0.950	42.433	-0.042	-0.042	0.000	0.000	0.000	0.000
86	A	612	DAL	0	-0.005	-0.003	43.192	0.001	0.001	0.000	0.000	0.000	0.000
87	A	613	ASP	-1	-0.938	-0.968	41.185	-0.031	-0.031	0.000	0.000	0.000	0.000
88	A	614	GLU	-1	-0.829	-0.933	44.473	-0.026	-0.026	0.000	0.000	0.000	0.000
89	A	615	GLU	-1	-1.040	-1.014	46.874	-0.012	-0.012	0.000	0.000	0.000	0.000
90	A	691	PHE	0	-0.045	-0.026	53.426	0.000	0.000	0.000	0.000	0.000	0.000
91	A	692	GLU	-1	-0.912	-0.962	54.238	-0.017	-0.017	0.000	0.000	0.000	0.000
92	A	693	GLU	-1	-0.875	-0.915	55.590	-0.023	-0.023	0.000	0.000	0.000	0.000
93	A	694	MED	0	-0.048	-0.017	50.759	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	695	LEU	0	-0.040	-0.017	48.391	0.000	0.000	0.000	0.000	0.000	0.000
95	A	696	THR	0	0.030	-0.008	47.563	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	697	LEU	0	0.053	0.017	39.725	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	698	GLU	-1	-0.762	-0.853	43.003	-0.036	-0.036	0.000	0.000	0.000	0.000
98	A	699	GLU	-1	-0.830	-0.869	44.818	-0.031	-0.031	0.000	0.000	0.000	0.000
99	A	700	ILE	0	0.028	0.014	41.979	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	701	TYR	0	0.000	0.018	38.471	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	702	ARG	1	0.756	0.836	42.188	0.033	0.033	0.000	0.000	0.000	0.000
102	A	703	TRP	0	-0.049	-0.035	42.119	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	704	GLU	-1	-0.784	-0.853	37.856	-0.065	-0.065	0.000	0.000	0.000	0.000
104	A	705	GLN	0	-0.057	-0.034	39.926	-0.006	-0.006	0.000	0.000	0.000	0.000
105	A	706	ARG	1	0.882	0.950	42.950	0.037	0.037	0.000	0.000	0.000	0.000
106	A	707	GLU	-1	-0.815	-0.907	45.237	-0.044	-0.044	0.000	0.000	0.000	0.000
107	A	708	LYS	1	0.974	1.010	37.373	0.073	0.073	0.000	0.000	0.000	0.000
108	A	709	ASN	0	-0.058	-0.048	40.757	-0.007	-0.007	0.000	0.000	0.000	0.000
109	A	710	VAL	0	-0.017	0.001	43.031	0.000	0.000	0.000	0.000	0.000	0.000
110	A	711	VAL	0	0.001	-0.005	44.487	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	712	VAL	0	0.007	-0.007	42.369	0.003	0.003	0.000	0.000	0.000	0.000
112	A	713	ASN	0	-0.045	-0.031	45.638	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	714	PHE	0	-0.007	-0.019	41.675	0.001	0.001	0.000	0.000	0.000	0.000
114	A	715	GLU	-1	-0.853	-0.916	47.253	-0.044	-0.044	0.000	0.000	0.000	0.000
115	A	716	THR	0	-0.059	-0.023	50.027	0.000	0.000	0.000	0.000	0.000	0.000
116	A	717	CYS	0	-0.096	-0.015	44.631	0.000	0.000	0.000	0.000	0.000	0.000
117	A	718	ARG	1	0.793	0.859	43.108	0.061	0.061	0.000	0.000	0.000	0.000
118	A	719	ILE	0	-0.006	-0.006	43.641	-0.003	-0.003	0.000	0.000	0.000	0.000
119	A	720	ASP	-1	-0.822	-0.877	42.613	-0.061	-0.061	0.000	0.000	0.000	0.000
120	A	721	GLN	0	-0.028	-0.023	43.315	-0.006	-0.006	0.000	0.000	0.000	0.000
121	A	722	SER	0	0.020	0.017	41.008	0.000	0.000	0.000	0.000	0.000	0.000
122	A	723	PRO	0	-0.019	-0.021	42.400	0.001	0.001	0.000	0.000	0.000	0.000
123	A	724	PHE	0	-0.019	-0.014	37.374	0.001	0.001	0.000	0.000	0.000	0.000
124	A	725	GLN	0	0.027	0.012	40.624	0.001	0.001	0.000	0.000	0.000	0.000
125	A	726	LEU	0	-0.029	-0.002	33.193	0.001	0.001	0.000	0.000	0.000	0.000
126	A	727	VAL	0	0.035	0.018	36.350	-0.004	-0.004	0.000	0.000	0.000	0.000
127	A	728	GLU	-1	-0.721	-0.855	31.291	-0.144	-0.144	0.000	0.000	0.000	0.000
128	A	729	GLY	0	-0.016	0.005	32.571	-0.003	-0.003	0.000	0.000	0.000	0.000
129	A	730	THR	0	-0.077	-0.043	34.349	0.005	0.005	0.000	0.000	0.000	0.000
130	A	731	SER	0	0.025	0.010	32.285	-0.005	-0.005	0.000	0.000	0.000	0.000
131	A	732	LEU	0	0.067	0.018	26.478	0.006	0.006	0.000	0.000	0.000	0.000
132	A	733	GLN	0	0.068	0.042	30.716	-0.002	-0.002	0.000	0.000	0.000	0.000
133	A	734	LYS	1	0.920	0.959	33.376	0.084	0.084	0.000	0.000	0.000	0.000
134	A	735	THR	0	0.058	0.026	31.555	0.004	0.004	0.000	0.000	0.000	0.000
135	A	736	HIS	0	0.057	0.042	31.660	-0.002	-0.002	0.000	0.000	0.000	0.000
136	A	737	THR	0	-0.040	-0.020	33.528	0.006	0.006	0.000	0.000	0.000	0.000
137	A	738	LEU	0	-0.027	-0.003	36.639	0.004	0.004	0.000	0.000	0.000	0.000
138	A	739	PHE	0	-0.006	-0.028	31.488	0.003	0.003	0.000	0.000	0.000	0.000
139	A	740	SER	0	-0.032	-0.021	35.335	0.004	0.004	0.000	0.000	0.000	0.000
140	A	741	LEU	0	-0.059	-0.028	37.127	0.004	0.004	0.000	0.000	0.000	0.000
141	A	742	LEU	0	-0.025	-0.011	39.572	0.003	0.003	0.000	0.000	0.000	0.000
142	A	743	GLY	0	-0.002	0.021	37.420	0.002	0.002	0.000	0.000	0.000	0.000
143	A	744	LEU	0	-0.061	-0.022	35.334	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	745	ASP	-1	-0.863	-0.928	30.353	-0.120	-0.120	0.000	0.000	0.000	0.000
145	A	746	ARG	1	0.989	0.975	26.728	0.146	0.146	0.000	0.000	0.000	0.000
146	A	747	ALA	0	-0.007	0.015	32.068	0.009	0.009	0.000	0.000	0.000	0.000
147	A	748	TYR	0	0.027	-0.003	32.591	-0.011	-0.011	0.000	0.000	0.000	0.000
148	A	749	VAL	0	-0.009	-0.005	31.107	0.007	0.007	0.000	0.000	0.000	0.000
149	A	750	THR	0	-0.011	-0.017	34.266	0.000	0.000	0.000	0.000	0.000	0.000
150	A	751	SER	0	0.002	-0.010	36.405	0.000	0.000	0.000	0.000	0.000	0.000
151	A	752	MET	0	-0.062	-0.040	38.265	0.001	0.001	0.000	0.000	0.000	0.000
152	A	753	GLY	0	0.062	0.039	41.240	0.003	0.003	0.000	0.000	0.000	0.000
153	A	754	LYS	1	0.883	0.944	38.001	0.095	0.095	0.000	0.000	0.000	0.000
154	A	755	LEU	0	0.001	-0.003	33.878	-0.002	-0.002	0.000	0.000	0.000	0.000
155	A	756	VAL	0	-0.057	-0.025	31.275	-0.002	-0.002	0.000	0.000	0.000	0.000
156	A	757	GLY	0	0.075	0.005	29.746	-0.011	-0.011	0.000	0.000	0.000	0.000
157	A	758	VAL	0	-0.075	-0.017	28.647	0.013	0.013	0.000	0.000	0.000	0.000
158	A	759	VAL	0	0.003	0.013	27.880	-0.013	-0.013	0.000	0.000	0.000	0.000
159	A	760	ALA	0	-0.012	-0.011	26.246	0.014	0.014	0.000	0.000	0.000	0.000
160	A	761	LEU	0	0.014	-0.002	27.578	-0.007	-0.007	0.000	0.000	0.000	0.000
161	A	762	ALA	0	0.000	0.007	23.804	-0.002	-0.002	0.000	0.000	0.000	0.000
162	A	763	GLU	-1	-0.832	-0.930	22.969	-0.210	-0.210	0.000	0.000	0.000	0.000
163	A	764	ILE	0	-0.003	-0.006	24.197	-0.006	-0.006	0.000	0.000	0.000	0.000
164	A	765	GLN	0	-0.011	-0.007	25.865	0.000	0.000	0.000	0.000	0.000	0.000
165	A	766	ALA	0	0.076	0.038	20.781	0.001	0.001	0.000	0.000	0.000	0.000
166	A	767	ALA	0	-0.032	-0.011	22.396	-0.005	-0.005	0.000	0.000	0.000	0.000
167	A	768	ILE	0	-0.087	-0.053	23.417	0.003	0.003	0.000	0.000	0.000	0.000
168	A	769	GLU	-1	-0.969	-0.968	23.203	-0.125	-0.125	0.000	0.000	0.000	0.000
169	A	770	GLY	0	-0.106	-0.045	20.078	0.004	0.004	0.000	0.000	0.000	0.000

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