FMO DATABASE

FMODB ID: JQ129

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1572923.043305
FMO2-HF: Nuclear repulsion	1506373.345
FMO2-HF: Total energy	-66549.698306
FMO2-MP2: Total energy	-66744.916052

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.
-5.105	-0.325	0.556	-2.583	-2.751	-0.006

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 : 0.024 / q_NPA : 0.016

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	-0.007	-0.005	2.720	-4.864	-0.084	0.556	-2.583	-2.751	-0.006
4	A	530	SER	0	-0.008	-0.004	5.569	0.113	0.113	0.000	0.000	0.000	0.000
5	A	531	SER	0	-0.003	-0.001	9.467	0.075	0.075	0.000	0.000	0.000	0.000
6	A	532	ALA	0	-0.013	-0.007	12.794	0.026	0.026	0.000	0.000	0.000	0.000
7	A	533	ASN	0	0.039	0.029	15.742	-0.005	-0.005	0.000	0.000	0.000	0.000
8	A	534	DLY	1	0.858	0.934	19.172	0.232	0.232	0.000	0.000	0.000	0.000
9	A	535	TYR	0	0.005	-0.016	21.143	0.023	0.023	0.000	0.000	0.000	0.000
10	A	536	ASN	0	-0.033	-0.005	25.598	0.003	0.003	0.000	0.000	0.000	0.000
11	A	537	ILE	0	-0.014	-0.003	23.705	0.000	0.000	0.000	0.000	0.000	0.000
12	A	538	GLN	0	-0.042	-0.030	27.223	0.013	0.013	0.000	0.000	0.000	0.000
13	A	539	VAL	0	0.033	0.015	27.728	-0.014	-0.014	0.000	0.000	0.000	0.000
14	A	540	GLY	0	0.034	0.017	28.031	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	541	ASP	-1	-0.826	-0.911	23.662	-0.234	-0.234	0.000	0.000	0.000	0.000
16	A	542	ILE	0	-0.059	-0.032	22.856	-0.020	-0.020	0.000	0.000	0.000	0.000
17	A	543	MET	0	-0.077	-0.001	24.064	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	544	VAL	0	0.026	0.015	23.365	-0.016	-0.016	0.000	0.000	0.000	0.000
19	A	545	ARG	1	0.811	0.857	25.161	0.224	0.224	0.000	0.000	0.000	0.000
20	A	546	ASP	-1	-0.931	-0.936	24.947	-0.208	-0.208	0.000	0.000	0.000	0.000
21	A	547	VAL	0	-0.030	-0.028	26.862	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	548	THR	0	0.010	0.014	28.748	0.004	0.004	0.000	0.000	0.000	0.000
23	A	549	SER	0	-0.012	-0.012	30.875	0.006	0.006	0.000	0.000	0.000	0.000
24	A	550	ILE	0	0.004	0.014	34.561	0.001	0.001	0.000	0.000	0.000	0.000
25	A	551	ALA	0	0.021	0.018	37.708	0.001	0.001	0.000	0.000	0.000	0.000
26	A	552	SER	0	-0.035	-0.019	40.485	0.004	0.004	0.000	0.000	0.000	0.000
27	A	553	THR	0	0.008	-0.002	42.565	0.002	0.002	0.000	0.000	0.000	0.000
28	A	554	SER	0	-0.056	-0.032	39.097	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	555	THR	0	-0.004	-0.037	39.642	0.005	0.005	0.000	0.000	0.000	0.000
30	A	556	TYR	0	0.051	0.015	40.156	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	557	GLY	0	0.027	0.008	38.698	0.000	0.000	0.000	0.000	0.000	0.000
32	A	558	ASP	-1	-0.852	-0.892	35.785	-0.100	-0.100	0.000	0.000	0.000	0.000
33	A	559	LEU	0	-0.016	-0.009	35.493	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	560	LEU	0	0.003	0.000	36.274	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	561	HIS	0	-0.017	0.000	28.895	0.001	0.001	0.000	0.000	0.000	0.000
36	A	562	VAL	0	0.043	0.007	31.439	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	563	LEU	0	-0.034	0.012	31.546	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	564	ARG	1	0.807	0.865	31.320	0.075	0.075	0.000	0.000	0.000	0.000
39	A	565	GLN	0	-0.086	-0.035	27.323	-0.010	-0.010	0.000	0.000	0.000	0.000
40	A	566	THR	0	-0.028	-0.017	26.661	-0.016	-0.016	0.000	0.000	0.000	0.000
41	A	567	LYS	1	0.949	0.965	23.505	0.156	0.156	0.000	0.000	0.000	0.000
42	A	568	LEU	0	-0.003	0.014	28.462	0.001	0.001	0.000	0.000	0.000	0.000
43	A	569	LYS	1	0.920	0.930	30.733	0.117	0.117	0.000	0.000	0.000	0.000
44	A	570	PHE	0	-0.008	0.005	33.802	0.006	0.006	0.000	0.000	0.000	0.000
45	A	571	PHE	0	0.019	0.018	31.914	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	572	PRO	0	-0.035	0.001	33.742	0.007	0.007	0.000	0.000	0.000	0.000
47	A	573	PHE	0	0.025	0.002	36.711	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	574	VAL	0	-0.012	-0.018	37.490	0.000	0.000	0.000	0.000	0.000	0.000
49	A	575	ASP	-1	-0.780	-0.870	40.652	-0.080	-0.080	0.000	0.000	0.000	0.000
50	A	576	THR	0	-0.015	0.000	41.367	0.004	0.004	0.000	0.000	0.000	0.000
51	A	577	PRO	0	0.012	0.001	36.656	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	578	ASP	-1	-0.870	-0.910	36.587	-0.108	-0.108	0.000	0.000	0.000	0.000
53	A	579	THR	0	-0.047	-0.046	38.587	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	580	ASN	0	-0.053	-0.034	36.030	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	581	THR	0	-0.006	-0.016	38.779	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	582	LEU	0	-0.026	-0.009	37.649	0.000	0.000	0.000	0.000	0.000	0.000
57	A	583	LEU	0	-0.026	-0.016	40.839	0.004	0.004	0.000	0.000	0.000	0.000
58	A	584	GLY	0	0.052	0.041	41.882	0.005	0.005	0.000	0.000	0.000	0.000
59	A	585	SER	0	-0.054	-0.030	38.369	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	586	ILE	0	0.010	0.019	39.052	0.005	0.005	0.000	0.000	0.000	0.000
61	A	587	ASP	-1	-0.757	-0.857	38.252	-0.079	-0.079	0.000	0.000	0.000	0.000
62	A	588	ARG	1	0.809	0.880	31.600	0.098	0.098	0.000	0.000	0.000	0.000
63	A	589	THR	0	0.001	-0.016	37.493	0.003	0.003	0.000	0.000	0.000	0.000
64	A	590	GLU	-1	-0.815	-0.891	40.495	-0.055	-0.055	0.000	0.000	0.000	0.000
65	A	591	VAL	0	-0.005	-0.005	37.814	0.002	0.002	0.000	0.000	0.000	0.000
66	A	592	GLU	-1	-0.829	-0.920	36.608	-0.074	-0.074	0.000	0.000	0.000	0.000
67	A	593	GLY	0	0.034	0.017	40.772	0.003	0.003	0.000	0.000	0.000	0.000
68	A	594	LEU	0	-0.052	-0.038	43.169	0.003	0.003	0.000	0.000	0.000	0.000
69	A	595	LEU	0	-0.014	-0.002	39.185	0.002	0.002	0.000	0.000	0.000	0.000
70	A	596	GLN	0	-0.007	0.004	43.494	0.002	0.002	0.000	0.000	0.000	0.000
71	A	597	ARG	1	0.827	0.909	45.819	0.057	0.057	0.000	0.000	0.000	0.000
72	A	598	ARG	1	0.797	0.875	46.687	0.052	0.052	0.000	0.000	0.000	0.000
73	A	599	ILE	0	0.005	0.007	43.042	0.002	0.002	0.000	0.000	0.000	0.000
74	A	600	SER	0	0.027	-0.001	47.681	0.003	0.003	0.000	0.000	0.000	0.000
75	A	601	ALA	0	-0.018	0.001	50.902	0.002	0.002	0.000	0.000	0.000	0.000
76	A	602	TYR	0	-0.019	-0.006	49.591	0.000	0.000	0.000	0.000	0.000	0.000
77	A	603	ARG	1	0.789	0.875	50.097	0.033	0.033	0.000	0.000	0.000	0.000
78	A	604	ARG	1	0.769	0.862	53.579	0.028	0.028	0.000	0.000	0.000	0.000
79	A	605	DGN	0	0.028	0.005	56.236	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	606	PRO	0	-0.035	0.000	56.418	0.001	0.001	0.000	0.000	0.000	0.000
81	A	607	DAL	0	0.021	-0.005	54.256	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	608	DAL	0	-0.040	-0.021	54.722	0.001	0.001	0.000	0.000	0.000	0.000
83	A	609	DAL	0	0.017	0.006	52.005	0.002	0.002	0.000	0.000	0.000	0.000
84	A	610	DAL	0	-0.052	-0.036	48.936	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	611	GLU	-1	-0.901	-0.945	42.542	-0.045	-0.045	0.000	0.000	0.000	0.000
86	A	612	DAL	0	-0.019	-0.001	42.899	0.001	0.001	0.000	0.000	0.000	0.000
87	A	613	ASP	-1	-0.934	-0.965	41.260	-0.030	-0.030	0.000	0.000	0.000	0.000
88	A	614	GLU	-1	-0.786	-0.889	44.517	-0.027	-0.027	0.000	0.000	0.000	0.000
89	A	615	GLU	-1	-1.056	-1.027	46.914	-0.011	-0.011	0.000	0.000	0.000	0.000
90	A	691	PHE	0	-0.016	-0.017	53.465	0.000	0.000	0.000	0.000	0.000	0.000
91	A	692	GLU	-1	-0.913	-0.953	53.913	-0.017	-0.017	0.000	0.000	0.000	0.000
92	A	693	GLU	-1	-0.898	-0.933	55.439	-0.025	-0.025	0.000	0.000	0.000	0.000
93	A	694	MED	0	-0.016	-0.001	50.823	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	695	LEU	0	-0.041	-0.012	48.415	0.000	0.000	0.000	0.000	0.000	0.000
95	A	696	THR	0	0.039	-0.006	47.487	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	697	LEU	0	0.044	0.017	39.531	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	698	GLU	-1	-0.789	-0.886	43.223	-0.038	-0.038	0.000	0.000	0.000	0.000
98	A	699	GLU	-1	-0.833	-0.871	44.817	-0.032	-0.032	0.000	0.000	0.000	0.000
99	A	700	ILE	0	0.002	0.008	42.012	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	701	TYR	0	0.005	0.006	38.471	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	702	ARG	1	0.737	0.830	42.276	0.036	0.036	0.000	0.000	0.000	0.000
102	A	703	TRP	0	-0.042	-0.017	42.507	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	704	GLU	-1	-0.762	-0.840	38.056	-0.068	-0.068	0.000	0.000	0.000	0.000
104	A	705	GLN	0	-0.045	-0.029	39.866	-0.006	-0.006	0.000	0.000	0.000	0.000
105	A	706	ARG	1	0.872	0.952	42.871	0.041	0.041	0.000	0.000	0.000	0.000
106	A	707	GLU	-1	-0.789	-0.881	45.165	-0.048	-0.048	0.000	0.000	0.000	0.000
107	A	708	LYS	1	0.969	0.994	37.257	0.080	0.080	0.000	0.000	0.000	0.000
108	A	709	ASN	0	-0.027	-0.021	40.932	-0.007	-0.007	0.000	0.000	0.000	0.000
109	A	710	VAL	0	-0.031	-0.002	42.927	0.000	0.000	0.000	0.000	0.000	0.000
110	A	711	VAL	0	0.014	0.000	44.491	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	712	VAL	0	-0.001	-0.005	42.308	0.004	0.004	0.000	0.000	0.000	0.000
112	A	713	ASN	0	-0.044	-0.029	45.594	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	714	PHE	0	0.032	-0.012	41.806	0.001	0.001	0.000	0.000	0.000	0.000
114	A	715	GLU	-1	-0.875	-0.914	47.479	-0.048	-0.048	0.000	0.000	0.000	0.000
115	A	716	THR	0	-0.076	-0.038	49.512	0.001	0.001	0.000	0.000	0.000	0.000
116	A	717	CYS	0	-0.087	-0.015	44.557	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	718	ARG	1	0.778	0.845	42.644	0.067	0.067	0.000	0.000	0.000	0.000
118	A	719	ILE	0	-0.009	0.000	43.680	-0.004	-0.004	0.000	0.000	0.000	0.000
119	A	720	ASP	-1	-0.831	-0.871	42.341	-0.068	-0.068	0.000	0.000	0.000	0.000
120	A	721	GLN	0	-0.009	-0.040	43.460	-0.007	-0.007	0.000	0.000	0.000	0.000
121	A	722	SER	0	0.018	0.019	40.743	0.000	0.000	0.000	0.000	0.000	0.000
122	A	723	PRO	0	-0.029	-0.020	42.382	0.001	0.001	0.000	0.000	0.000	0.000
123	A	724	PHE	0	-0.033	-0.019	37.430	0.001	0.001	0.000	0.000	0.000	0.000
124	A	725	GLN	0	0.029	0.015	40.587	0.001	0.001	0.000	0.000	0.000	0.000
125	A	726	LEU	0	-0.009	0.005	33.304	0.001	0.001	0.000	0.000	0.000	0.000
126	A	727	VAL	0	0.035	0.020	36.021	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	728	GLU	-1	-0.698	-0.831	30.781	-0.172	-0.172	0.000	0.000	0.000	0.000
128	A	729	GLY	0	0.003	0.010	31.984	-0.007	-0.007	0.000	0.000	0.000	0.000
129	A	730	THR	0	-0.054	-0.036	33.942	0.008	0.008	0.000	0.000	0.000	0.000
130	A	731	SER	0	-0.013	-0.012	31.990	-0.006	-0.006	0.000	0.000	0.000	0.000
131	A	732	LEU	0	0.061	0.023	26.537	0.010	0.010	0.000	0.000	0.000	0.000
132	A	733	GLN	0	0.065	0.036	30.686	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	734	LYS	1	0.914	0.970	33.175	0.101	0.101	0.000	0.000	0.000	0.000
134	A	735	THR	0	0.040	0.022	31.537	0.008	0.008	0.000	0.000	0.000	0.000
135	A	736	HIS	0	0.069	0.041	31.006	0.000	0.000	0.000	0.000	0.000	0.000
136	A	737	THR	0	-0.048	-0.028	33.226	0.007	0.007	0.000	0.000	0.000	0.000
137	A	738	LEU	0	-0.008	-0.004	36.748	0.005	0.005	0.000	0.000	0.000	0.000
138	A	739	PHE	0	0.005	-0.016	31.494	0.003	0.003	0.000	0.000	0.000	0.000
139	A	740	SER	0	-0.035	-0.021	35.064	0.004	0.004	0.000	0.000	0.000	0.000
140	A	741	LEU	0	-0.063	-0.040	36.917	0.005	0.005	0.000	0.000	0.000	0.000
141	A	742	LEU	0	-0.034	-0.012	39.247	0.004	0.004	0.000	0.000	0.000	0.000
142	A	743	GLY	0	-0.002	0.017	37.443	0.001	0.001	0.000	0.000	0.000	0.000
143	A	744	LEU	0	-0.060	-0.018	35.172	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	745	ASP	-1	-0.841	-0.902	30.473	-0.132	-0.132	0.000	0.000	0.000	0.000
145	A	746	ARG	1	0.862	0.892	25.928	0.175	0.175	0.000	0.000	0.000	0.000
146	A	747	ALA	0	0.000	0.008	31.999	0.011	0.011	0.000	0.000	0.000	0.000
147	A	748	TYR	0	0.032	0.005	32.337	-0.013	-0.013	0.000	0.000	0.000	0.000
148	A	749	VAL	0	-0.033	-0.006	30.778	0.007	0.007	0.000	0.000	0.000	0.000
149	A	750	THR	0	-0.008	-0.018	33.856	0.002	0.002	0.000	0.000	0.000	0.000
150	A	751	SER	0	-0.004	-0.022	36.401	0.000	0.000	0.000	0.000	0.000	0.000
151	A	752	MET	0	-0.035	-0.025	38.250	0.001	0.001	0.000	0.000	0.000	0.000
152	A	753	GLY	0	0.074	0.050	41.170	0.004	0.004	0.000	0.000	0.000	0.000
153	A	754	LYS	1	0.869	0.941	37.642	0.107	0.107	0.000	0.000	0.000	0.000
154	A	755	LEU	0	0.029	0.005	33.543	-0.001	-0.001	0.000	0.000	0.000	0.000
155	A	756	VAL	0	-0.092	-0.046	31.249	-0.001	-0.001	0.000	0.000	0.000	0.000
156	A	757	GLY	0	0.088	0.022	29.517	-0.013	-0.013	0.000	0.000	0.000	0.000
157	A	758	VAL	0	-0.051	-0.012	28.600	0.015	0.015	0.000	0.000	0.000	0.000
158	A	759	VAL	0	-0.005	0.002	27.302	-0.016	-0.016	0.000	0.000	0.000	0.000
159	A	760	ALA	0	0.018	0.003	26.616	0.015	0.015	0.000	0.000	0.000	0.000
160	A	761	LEU	0	0.033	0.023	27.812	-0.010	-0.010	0.000	0.000	0.000	0.000
161	A	762	ALA	0	0.025	0.010	23.978	-0.002	-0.002	0.000	0.000	0.000	0.000
162	A	763	GLU	-1	-0.797	-0.888	23.126	-0.235	-0.235	0.000	0.000	0.000	0.000
163	A	764	ILE	0	-0.008	-0.015	24.245	-0.011	-0.011	0.000	0.000	0.000	0.000
164	A	765	GLN	0	-0.057	-0.034	25.573	0.003	0.003	0.000	0.000	0.000	0.000
165	A	766	ALA	0	0.047	0.023	20.353	0.000	0.000	0.000	0.000	0.000	0.000
166	A	767	ALA	0	-0.010	0.002	21.781	-0.013	-0.013	0.000	0.000	0.000	0.000
167	A	768	ILE	0	-0.081	-0.037	23.238	0.002	0.002	0.000	0.000	0.000	0.000
168	A	769	GLU	-1	-0.915	-0.944	23.340	-0.143	-0.143	0.000	0.000	0.000	0.000
169	A	770	GLY	0	-0.079	-0.047	20.534	-0.008	-0.008	0.000	0.000	0.000	0.000

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