FMO DATABASE

FMODB ID: 2N3MR

Calculation Name: 2GRR-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GRR

Chain ID: B

ChEMBL ID:

UniProt ID: P46060

Base Structure: X-ray

Registration Date: 2023-09-23

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	157
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1519222.053226
FMO2-HF: Nuclear repulsion	1458835.183296
FMO2-HF: Total energy	-60386.86993
FMO2-MP2: Total energy	-60562.672037

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:431:PRO)

Summations of interaction energy for fragment #1(B:431:PRO)

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.
-3.456	0.993	0.106	-2.074	-2.481	0.001

Interaction energy analysis for fragmet #1(B:431:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.052 / q_NPA : 0.008

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	433	ASP	-1	-0.749	-0.825	3.800	-2.496	-0.409	-0.022	-1.069	-0.996	0.003
4	B	434	VAL	0	0.057	0.007	6.631	0.194	0.194	0.000	0.000	0.000	0.000
5	B	435	SER	0	0.020	0.016	10.026	0.148	0.148	0.000	0.000	0.000	0.000
6	B	436	THR	0	-0.055	-0.083	8.649	0.176	0.176	0.000	0.000	0.000	0.000
7	B	437	PHE	0	-0.040	-0.025	9.270	0.122	0.122	0.000	0.000	0.000	0.000
8	B	438	LEU	0	0.029	0.007	10.914	0.093	0.093	0.000	0.000	0.000	0.000
9	B	439	ALA	0	-0.028	-0.002	13.896	0.057	0.057	0.000	0.000	0.000	0.000
10	B	440	PHE	0	-0.062	-0.032	12.925	0.046	0.046	0.000	0.000	0.000	0.000
11	B	441	PRO	0	-0.006	0.010	13.055	0.010	0.010	0.000	0.000	0.000	0.000
12	B	442	SER	0	-0.016	-0.017	11.221	0.048	0.048	0.000	0.000	0.000	0.000
13	B	443	PRO	0	0.070	0.022	11.858	-0.001	-0.001	0.000	0.000	0.000	0.000
14	B	444	GLU	-1	-0.818	-0.917	9.570	0.531	0.531	0.000	0.000	0.000	0.000
15	B	445	LYS	1	0.843	0.926	7.280	0.364	0.364	0.000	0.000	0.000	0.000
16	B	446	LEU	0	0.019	0.027	7.138	-0.062	-0.062	0.000	0.000	0.000	0.000
17	B	447	LEU	0	0.036	0.011	8.335	0.021	0.021	0.000	0.000	0.000	0.000
18	B	448	ARG	1	0.859	0.921	2.795	-1.510	-0.241	0.043	-0.469	-0.843	0.002
19	B	449	LEU	0	-0.066	-0.014	3.191	-0.878	0.215	0.085	-0.536	-0.642	-0.004
20	B	450	GLY	0	0.003	0.014	5.559	-0.136	-0.136	0.000	0.000	0.000	0.000
21	B	451	PRO	0	0.004	-0.014	6.471	-0.158	-0.158	0.000	0.000	0.000	0.000
22	B	452	LYS	1	0.981	0.987	9.066	-0.124	-0.124	0.000	0.000	0.000	0.000
23	B	453	SER	0	0.024	0.018	8.871	-0.128	-0.128	0.000	0.000	0.000	0.000
24	B	454	SER	0	0.055	0.033	10.202	-0.080	-0.080	0.000	0.000	0.000	0.000
25	B	455	VAL	0	0.044	0.011	12.976	-0.040	-0.040	0.000	0.000	0.000	0.000
26	B	456	LEU	0	-0.028	-0.014	7.409	-0.046	-0.046	0.000	0.000	0.000	0.000
27	B	457	ILE	0	0.031	0.013	11.625	-0.052	-0.052	0.000	0.000	0.000	0.000
28	B	458	ALA	0	0.031	0.034	13.640	-0.018	-0.018	0.000	0.000	0.000	0.000
29	B	459	GLN	0	-0.059	-0.030	12.599	-0.054	-0.054	0.000	0.000	0.000	0.000
30	B	460	GLN	0	-0.068	-0.047	11.640	-0.029	-0.029	0.000	0.000	0.000	0.000
31	B	461	THR	0	-0.020	0.004	14.979	-0.012	-0.012	0.000	0.000	0.000	0.000
32	B	462	ASP	-1	-0.856	-0.914	18.076	-0.112	-0.112	0.000	0.000	0.000	0.000
33	B	463	THR	0	-0.009	-0.034	20.910	0.006	0.006	0.000	0.000	0.000	0.000
34	B	464	SER	0	-0.077	-0.038	23.364	0.014	0.014	0.000	0.000	0.000	0.000
35	B	465	ASP	-1	-0.808	-0.911	25.171	-0.084	-0.084	0.000	0.000	0.000	0.000
36	B	466	PRO	0	0.005	-0.021	25.661	-0.001	-0.001	0.000	0.000	0.000	0.000
37	B	467	GLU	-1	-0.716	-0.817	26.753	-0.053	-0.053	0.000	0.000	0.000	0.000
38	B	468	LYS	1	0.906	0.952	21.759	0.153	0.153	0.000	0.000	0.000	0.000
39	B	469	VAL	0	0.014	0.018	21.922	-0.004	-0.004	0.000	0.000	0.000	0.000
40	B	470	VAL	0	-0.008	0.010	22.796	0.009	0.009	0.000	0.000	0.000	0.000
41	B	471	SER	0	-0.049	-0.023	21.586	0.007	0.007	0.000	0.000	0.000	0.000
42	B	472	ALA	0	0.023	0.008	18.183	0.004	0.004	0.000	0.000	0.000	0.000
43	B	473	PHE	0	0.039	0.010	18.716	0.015	0.015	0.000	0.000	0.000	0.000
44	B	474	LEU	0	0.009	0.000	20.643	0.019	0.019	0.000	0.000	0.000	0.000
45	B	475	LYS	1	0.848	0.935	16.904	0.141	0.141	0.000	0.000	0.000	0.000
46	B	476	VAL	0	0.020	0.027	14.997	0.019	0.019	0.000	0.000	0.000	0.000
47	B	477	SER	0	0.001	-0.006	16.869	0.033	0.033	0.000	0.000	0.000	0.000
48	B	478	SER	0	-0.095	-0.054	18.009	0.019	0.019	0.000	0.000	0.000	0.000
49	B	479	VAL	0	-0.049	-0.018	14.107	0.012	0.012	0.000	0.000	0.000	0.000
50	B	480	PHE	0	0.034	0.013	17.107	0.044	0.044	0.000	0.000	0.000	0.000
51	B	481	LYS	1	0.924	0.950	17.896	-0.182	-0.182	0.000	0.000	0.000	0.000
52	B	482	ASP	-1	-0.906	-0.937	20.170	0.168	0.168	0.000	0.000	0.000	0.000
53	B	483	GLU	-1	-0.758	-0.865	16.896	0.393	0.393	0.000	0.000	0.000	0.000
54	B	484	ALA	0	-0.031	-0.014	18.987	0.001	0.001	0.000	0.000	0.000	0.000
55	B	485	THR	0	-0.040	-0.046	13.836	0.012	0.012	0.000	0.000	0.000	0.000
56	B	486	VAL	0	0.006	-0.006	14.162	0.001	0.001	0.000	0.000	0.000	0.000
57	B	487	ARG	1	0.908	0.970	15.645	-0.222	-0.222	0.000	0.000	0.000	0.000
58	B	488	MET	0	-0.009	-0.006	16.655	-0.019	-0.019	0.000	0.000	0.000	0.000
59	B	489	ALA	0	0.035	0.027	12.596	-0.022	-0.022	0.000	0.000	0.000	0.000
60	B	490	VAL	0	-0.029	-0.025	14.578	-0.047	-0.047	0.000	0.000	0.000	0.000
61	B	491	GLN	0	-0.031	-0.024	16.747	-0.039	-0.039	0.000	0.000	0.000	0.000
62	B	492	ASP	-1	-0.818	-0.904	15.978	0.167	0.167	0.000	0.000	0.000	0.000
63	B	493	ALA	0	-0.048	-0.037	14.463	-0.030	-0.030	0.000	0.000	0.000	0.000
64	B	494	VAL	0	-0.061	-0.021	16.434	-0.033	-0.033	0.000	0.000	0.000	0.000
65	B	495	ASP	-1	-0.722	-0.829	19.910	0.053	0.053	0.000	0.000	0.000	0.000
66	B	496	ALA	0	-0.026	-0.003	17.317	-0.014	-0.014	0.000	0.000	0.000	0.000
67	B	497	LEU	0	-0.052	-0.035	18.511	-0.019	-0.019	0.000	0.000	0.000	0.000
68	B	498	MET	0	0.005	-0.012	19.968	-0.014	-0.014	0.000	0.000	0.000	0.000
69	B	499	GLN	0	0.006	0.026	22.744	-0.007	-0.007	0.000	0.000	0.000	0.000
70	B	500	LYS	1	0.856	0.931	18.915	0.106	0.106	0.000	0.000	0.000	0.000
71	B	501	ALA	0	-0.032	-0.022	23.264	-0.006	-0.006	0.000	0.000	0.000	0.000
72	B	502	PHE	0	-0.001	-0.026	25.240	-0.002	-0.002	0.000	0.000	0.000	0.000
73	B	503	ASN	0	-0.013	0.001	26.554	0.003	0.003	0.000	0.000	0.000	0.000
74	B	504	SER	0	-0.022	0.019	27.661	-0.001	-0.001	0.000	0.000	0.000	0.000
75	B	505	SER	0	0.019	-0.006	29.459	0.000	0.000	0.000	0.000	0.000	0.000
76	B	506	SER	0	-0.025	-0.012	31.123	0.000	0.000	0.000	0.000	0.000	0.000
77	B	507	PHE	0	0.006	0.016	26.998	-0.002	-0.002	0.000	0.000	0.000	0.000
78	B	508	ASN	0	0.044	0.019	30.932	0.009	0.009	0.000	0.000	0.000	0.000
79	B	509	SER	0	0.091	0.017	31.531	-0.001	-0.001	0.000	0.000	0.000	0.000
80	B	510	ASN	0	0.022	0.015	32.607	0.004	0.004	0.000	0.000	0.000	0.000
81	B	511	THR	0	-0.029	-0.010	32.157	0.000	0.000	0.000	0.000	0.000	0.000
82	B	512	PHE	0	0.034	0.019	25.603	-0.001	-0.001	0.000	0.000	0.000	0.000
83	B	513	LEU	0	0.009	0.005	30.374	0.001	0.001	0.000	0.000	0.000	0.000
84	B	514	THR	0	0.006	0.002	32.349	0.002	0.002	0.000	0.000	0.000	0.000
85	B	515	ARG	1	0.760	0.828	30.187	0.048	0.048	0.000	0.000	0.000	0.000
86	B	516	LEU	0	0.022	0.023	26.657	-0.001	-0.001	0.000	0.000	0.000	0.000
87	B	517	LEU	0	0.003	-0.011	29.565	0.003	0.003	0.000	0.000	0.000	0.000
88	B	518	VAL	0	-0.028	-0.002	32.387	0.002	0.002	0.000	0.000	0.000	0.000
89	B	519	HIS	0	-0.072	-0.052	27.527	0.003	0.003	0.000	0.000	0.000	0.000
90	B	520	MET	0	-0.061	-0.023	28.154	0.002	0.002	0.000	0.000	0.000	0.000
91	B	521	GLY	0	0.003	0.000	30.108	0.005	0.005	0.000	0.000	0.000	0.000
92	B	522	LEU	0	-0.074	-0.036	32.907	0.003	0.003	0.000	0.000	0.000	0.000
93	B	523	LEU	0	-0.036	-0.010	35.491	0.002	0.002	0.000	0.000	0.000	0.000
94	B	524	LYS	1	0.946	0.974	36.265	0.011	0.011	0.000	0.000	0.000	0.000
95	B	525	SER	0	-0.010	-0.025	35.980	0.001	0.001	0.000	0.000	0.000	0.000
96	B	526	GLU	-1	-0.948	-0.968	38.043	-0.030	-0.030	0.000	0.000	0.000	0.000
97	B	527	ASP	-1	-0.794	-0.867	33.701	-0.047	-0.047	0.000	0.000	0.000	0.000
98	B	528	LYS	1	0.951	0.977	34.032	0.035	0.035	0.000	0.000	0.000	0.000
99	B	529	VAL	0	0.041	0.024	30.747	-0.006	-0.006	0.000	0.000	0.000	0.000
100	B	530	LYS	1	0.884	0.933	24.536	0.087	0.087	0.000	0.000	0.000	0.000
101	B	531	ALA	0	0.026	0.016	28.187	-0.002	-0.002	0.000	0.000	0.000	0.000
102	B	532	ILE	0	-0.017	-0.002	24.354	0.001	0.001	0.000	0.000	0.000	0.000
103	B	533	ALA	0	0.014	0.007	26.620	0.003	0.003	0.000	0.000	0.000	0.000
104	B	534	ASN	0	0.004	-0.004	24.726	0.002	0.002	0.000	0.000	0.000	0.000
105	B	535	LEU	0	0.067	0.021	25.738	-0.001	-0.001	0.000	0.000	0.000	0.000
106	B	536	TYR	0	0.023	0.006	23.165	0.005	0.005	0.000	0.000	0.000	0.000
107	B	537	GLY	0	0.037	0.019	22.421	0.005	0.005	0.000	0.000	0.000	0.000
108	B	538	PRO	0	0.013	-0.003	23.267	0.002	0.002	0.000	0.000	0.000	0.000
109	B	539	LEU	0	0.017	0.006	24.882	-0.002	-0.002	0.000	0.000	0.000	0.000
110	B	540	MET	0	-0.007	0.001	24.155	-0.003	-0.003	0.000	0.000	0.000	0.000
111	B	541	ALA	0	-0.010	-0.003	22.054	0.004	0.004	0.000	0.000	0.000	0.000
112	B	542	LEU	0	-0.011	-0.011	23.793	-0.003	-0.003	0.000	0.000	0.000	0.000
113	B	543	ASN	0	0.037	0.041	27.165	-0.008	-0.008	0.000	0.000	0.000	0.000
114	B	544	HIS	0	-0.029	-0.021	22.988	0.002	0.002	0.000	0.000	0.000	0.000
115	B	545	MET	0	0.002	0.009	24.429	-0.006	-0.006	0.000	0.000	0.000	0.000
116	B	546	VAL	0	-0.069	-0.037	26.581	-0.004	-0.004	0.000	0.000	0.000	0.000
117	B	547	GLN	0	-0.092	-0.048	29.066	-0.002	-0.002	0.000	0.000	0.000	0.000
118	B	548	GLN	0	-0.049	-0.012	25.462	0.002	0.002	0.000	0.000	0.000	0.000
119	B	549	ASP	-1	-0.895	-0.952	28.854	0.033	0.033	0.000	0.000	0.000	0.000
120	B	550	TYR	0	-0.098	-0.077	24.074	-0.010	-0.010	0.000	0.000	0.000	0.000
121	B	551	PHE	0	-0.018	0.001	29.198	-0.007	-0.007	0.000	0.000	0.000	0.000
122	B	552	PRO	0	0.019	0.010	30.658	0.001	0.001	0.000	0.000	0.000	0.000
123	B	553	LYS	1	1.048	1.006	33.884	-0.023	-0.023	0.000	0.000	0.000	0.000
124	B	554	ALA	0	-0.017	0.001	36.437	0.001	0.001	0.000	0.000	0.000	0.000
125	B	555	LEU	0	0.005	-0.006	32.319	-0.001	-0.001	0.000	0.000	0.000	0.000
126	B	556	ALA	0	0.026	0.021	35.558	0.001	0.001	0.000	0.000	0.000	0.000
127	B	557	PRO	0	0.002	0.000	36.504	0.001	0.001	0.000	0.000	0.000	0.000
128	B	558	LEU	0	0.013	0.013	37.269	0.000	0.000	0.000	0.000	0.000	0.000
129	B	559	LEU	0	0.035	0.006	31.016	0.000	0.000	0.000	0.000	0.000	0.000
130	B	560	LEU	0	0.015	0.013	35.538	0.002	0.002	0.000	0.000	0.000	0.000
131	B	561	ALA	0	0.004	0.001	37.924	0.001	0.001	0.000	0.000	0.000	0.000
132	B	562	PHE	0	-0.044	-0.037	36.539	-0.001	-0.001	0.000	0.000	0.000	0.000
133	B	563	VAL	0	0.029	0.029	33.495	0.001	0.001	0.000	0.000	0.000	0.000
134	B	564	THR	0	-0.036	-0.021	36.281	0.002	0.002	0.000	0.000	0.000	0.000
135	B	565	LYS	1	0.940	0.988	39.792	-0.003	-0.003	0.000	0.000	0.000	0.000
136	B	566	PRO	0	-0.012	-0.014	39.566	0.001	0.001	0.000	0.000	0.000	0.000
137	B	567	ASN	0	0.032	0.003	35.672	0.000	0.000	0.000	0.000	0.000	0.000
138	B	568	SER	0	0.083	0.042	37.577	0.002	0.002	0.000	0.000	0.000	0.000
139	B	569	ALA	0	0.033	0.024	32.231	0.004	0.004	0.000	0.000	0.000	0.000
140	B	570	LEU	0	-0.013	-0.016	32.578	0.006	0.006	0.000	0.000	0.000	0.000
141	B	571	GLU	-1	-0.957	-0.986	34.471	0.027	0.027	0.000	0.000	0.000	0.000
142	B	572	SER	0	-0.041	-0.008	32.930	0.003	0.003	0.000	0.000	0.000	0.000
143	B	573	CYS	0	-0.085	-0.026	30.182	0.007	0.007	0.000	0.000	0.000	0.000
144	B	574	SER	0	0.049	0.021	32.109	0.002	0.002	0.000	0.000	0.000	0.000
145	B	575	PHE	0	0.048	0.032	29.336	-0.002	-0.002	0.000	0.000	0.000	0.000
146	B	576	ALA	0	0.058	0.017	28.852	0.000	0.000	0.000	0.000	0.000	0.000
147	B	577	ARG	1	0.863	0.948	30.662	-0.030	-0.030	0.000	0.000	0.000	0.000
148	B	578	HIS	0	0.023	-0.003	33.502	-0.004	-0.004	0.000	0.000	0.000	0.000
149	B	579	SER	0	-0.030	-0.018	31.402	0.000	0.000	0.000	0.000	0.000	0.000
150	B	580	LEU	0	0.009	0.019	30.359	-0.001	-0.001	0.000	0.000	0.000	0.000
151	B	581	LEU	0	-0.032	-0.018	32.605	-0.004	-0.004	0.000	0.000	0.000	0.000
152	B	582	GLN	0	0.016	0.000	35.988	-0.002	-0.002	0.000	0.000	0.000	0.000
153	B	583	THR	0	-0.082	-0.065	31.624	0.000	0.000	0.000	0.000	0.000	0.000
154	B	584	LEU	0	0.001	-0.010	33.954	-0.003	-0.003	0.000	0.000	0.000	0.000
155	B	585	TYR	0	-0.063	-0.023	36.239	-0.002	-0.002	0.000	0.000	0.000	0.000
156	B	586	LYS	1	0.918	0.964	34.601	-0.056	-0.056	0.000	0.000	0.000	0.000
157	B	587	VAL	0	-0.045	0.008	34.774	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:431:PRO)