FMO DATABASE

FMODB ID: 6YV4Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1520105.800095
FMO2-HF: Nuclear repulsion	1459718.404629
FMO2-HF: Total energy	-60387.395465
FMO2-MP2: Total energy	-60563.180581

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.
-6.455	-1.984	0.091	-2.089	-2.472	0

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 : 0.038 / q_NPA : 0.000

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	-0.752	-0.820	3.800	-2.279	-0.391	-0.023	-0.920	-0.945	0.001
4	B	434	VAL	0	0.054	0.006	6.398	0.239	0.239	0.000	0.000	0.000	0.000
5	B	435	SER	0	0.018	-0.004	9.967	0.129	0.129	0.000	0.000	0.000	0.000
6	B	436	THR	0	-0.049	-0.063	8.639	0.185	0.185	0.000	0.000	0.000	0.000
7	B	437	PHE	0	-0.041	-0.021	9.206	0.133	0.133	0.000	0.000	0.000	0.000
8	B	438	LEU	0	0.032	0.009	10.917	0.074	0.074	0.000	0.000	0.000	0.000
9	B	439	ALA	0	-0.026	0.008	13.891	0.042	0.042	0.000	0.000	0.000	0.000
10	B	440	PHE	0	-0.028	-0.016	13.186	0.036	0.036	0.000	0.000	0.000	0.000
11	B	441	PRO	0	0.019	0.028	13.043	0.055	0.055	0.000	0.000	0.000	0.000
12	B	442	SER	0	-0.035	-0.055	11.885	0.006	0.006	0.000	0.000	0.000	0.000
13	B	443	PRO	0	0.056	0.026	11.845	0.009	0.009	0.000	0.000	0.000	0.000
14	B	444	GLU	-1	-0.778	-0.877	9.642	0.648	0.648	0.000	0.000	0.000	0.000
15	B	445	LYS	1	0.809	0.898	7.256	0.021	0.021	0.000	0.000	0.000	0.000
16	B	446	LEU	0	0.009	0.020	7.133	-0.066	-0.066	0.000	0.000	0.000	0.000
17	B	447	LEU	0	0.029	0.008	8.340	-0.021	-0.021	0.000	0.000	0.000	0.000
18	B	448	ARG	1	0.864	0.916	3.226	-4.377	-2.863	0.031	-0.639	-0.905	0.003
19	B	449	LEU	0	-0.077	-0.016	3.201	-1.105	-0.036	0.083	-0.530	-0.622	-0.004
20	B	450	GLY	0	0.011	0.017	5.579	-0.220	-0.220	0.000	0.000	0.000	0.000
21	B	451	PRO	0	0.004	-0.018	6.492	-0.067	-0.067	0.000	0.000	0.000	0.000
22	B	452	LYS	1	0.972	0.987	8.989	0.116	0.116	0.000	0.000	0.000	0.000
23	B	453	SER	0	0.031	0.019	8.845	-0.099	-0.099	0.000	0.000	0.000	0.000
24	B	454	SER	0	0.050	0.032	10.255	-0.057	-0.057	0.000	0.000	0.000	0.000
25	B	455	VAL	0	0.033	0.005	13.079	-0.027	-0.027	0.000	0.000	0.000	0.000
26	B	456	LEU	0	-0.019	-0.006	7.551	-0.032	-0.032	0.000	0.000	0.000	0.000
27	B	457	ILE	0	0.034	0.012	11.807	-0.035	-0.035	0.000	0.000	0.000	0.000
28	B	458	ALA	0	0.034	0.038	13.849	-0.011	-0.011	0.000	0.000	0.000	0.000
29	B	459	GLN	0	-0.030	-0.009	12.710	-0.041	-0.041	0.000	0.000	0.000	0.000
30	B	460	GLN	0	-0.061	-0.042	11.622	-0.016	-0.016	0.000	0.000	0.000	0.000
31	B	461	THR	0	-0.010	0.006	15.116	0.001	0.001	0.000	0.000	0.000	0.000
32	B	462	ASP	-1	-0.778	-0.867	18.219	-0.098	-0.098	0.000	0.000	0.000	0.000
33	B	463	THR	0	-0.010	-0.031	21.156	0.007	0.007	0.000	0.000	0.000	0.000
34	B	464	SER	0	-0.068	-0.040	23.626	0.011	0.011	0.000	0.000	0.000	0.000
35	B	465	ASP	-1	-0.763	-0.870	25.175	-0.063	-0.063	0.000	0.000	0.000	0.000
36	B	466	PRO	0	0.019	-0.012	25.758	0.001	0.001	0.000	0.000	0.000	0.000
37	B	467	GLU	-1	-0.722	-0.807	26.787	-0.023	-0.023	0.000	0.000	0.000	0.000
38	B	468	LYS	1	0.761	0.853	21.766	0.103	0.103	0.000	0.000	0.000	0.000
39	B	469	VAL	0	0.005	0.012	22.004	-0.001	-0.001	0.000	0.000	0.000	0.000
40	B	470	VAL	0	-0.012	0.010	22.814	0.010	0.010	0.000	0.000	0.000	0.000
41	B	471	SER	0	-0.044	-0.020	21.802	0.012	0.012	0.000	0.000	0.000	0.000
42	B	472	ALA	0	0.021	0.007	18.256	0.010	0.010	0.000	0.000	0.000	0.000
43	B	473	PHE	0	0.048	0.015	18.728	0.019	0.019	0.000	0.000	0.000	0.000
44	B	474	LEU	0	0.012	0.012	20.652	0.020	0.020	0.000	0.000	0.000	0.000
45	B	475	LYS	1	0.838	0.922	16.925	0.055	0.055	0.000	0.000	0.000	0.000
46	B	476	VAL	0	0.021	0.023	15.044	0.030	0.030	0.000	0.000	0.000	0.000
47	B	477	SER	0	-0.004	-0.019	16.875	0.035	0.035	0.000	0.000	0.000	0.000
48	B	478	SER	0	-0.082	-0.040	18.076	0.021	0.021	0.000	0.000	0.000	0.000
49	B	479	VAL	0	-0.051	-0.024	13.885	0.018	0.018	0.000	0.000	0.000	0.000
50	B	480	PHE	0	0.050	0.023	17.096	0.042	0.042	0.000	0.000	0.000	0.000
51	B	481	LYS	1	0.864	0.922	18.025	-0.238	-0.238	0.000	0.000	0.000	0.000
52	B	482	ASP	-1	-0.868	-0.903	20.156	0.167	0.167	0.000	0.000	0.000	0.000
53	B	483	GLU	-1	-0.773	-0.872	16.847	0.380	0.380	0.000	0.000	0.000	0.000
54	B	484	ALA	0	-0.024	-0.005	18.976	0.000	0.000	0.000	0.000	0.000	0.000
55	B	485	THR	0	-0.034	-0.047	13.889	0.013	0.013	0.000	0.000	0.000	0.000
56	B	486	VAL	0	0.003	-0.008	14.072	0.001	0.001	0.000	0.000	0.000	0.000
57	B	487	ARG	1	0.872	0.933	15.636	-0.211	-0.211	0.000	0.000	0.000	0.000
58	B	488	MET	0	0.011	0.007	16.518	-0.018	-0.018	0.000	0.000	0.000	0.000
59	B	489	ALA	0	0.037	0.027	12.568	-0.024	-0.024	0.000	0.000	0.000	0.000
60	B	490	VAL	0	-0.032	-0.027	14.584	-0.042	-0.042	0.000	0.000	0.000	0.000
61	B	491	GLN	0	-0.027	-0.018	16.753	-0.027	-0.027	0.000	0.000	0.000	0.000
62	B	492	ASP	-1	-0.836	-0.914	16.028	0.118	0.118	0.000	0.000	0.000	0.000
63	B	493	ALA	0	-0.046	-0.036	14.472	-0.031	-0.031	0.000	0.000	0.000	0.000
64	B	494	VAL	0	-0.059	-0.025	16.453	-0.029	-0.029	0.000	0.000	0.000	0.000
65	B	495	ASP	-1	-0.733	-0.827	19.926	0.039	0.039	0.000	0.000	0.000	0.000
66	B	496	ALA	0	-0.028	-0.006	17.422	-0.014	-0.014	0.000	0.000	0.000	0.000
67	B	497	LEU	0	-0.052	-0.034	18.627	-0.018	-0.018	0.000	0.000	0.000	0.000
68	B	498	MET	0	-0.001	-0.010	20.134	-0.012	-0.012	0.000	0.000	0.000	0.000
69	B	499	GLN	0	0.003	0.023	22.917	-0.010	-0.010	0.000	0.000	0.000	0.000
70	B	500	LYS	1	0.818	0.911	19.090	0.109	0.109	0.000	0.000	0.000	0.000
71	B	501	ALA	0	-0.040	-0.027	23.434	-0.005	-0.005	0.000	0.000	0.000	0.000
72	B	502	PHE	0	0.000	-0.027	25.443	-0.001	-0.001	0.000	0.000	0.000	0.000
73	B	503	ASN	0	-0.010	0.004	26.955	0.004	0.004	0.000	0.000	0.000	0.000
74	B	504	SER	0	-0.020	0.020	27.903	-0.002	-0.002	0.000	0.000	0.000	0.000
75	B	505	SER	0	0.027	-0.002	29.660	0.002	0.002	0.000	0.000	0.000	0.000
76	B	506	SER	0	-0.030	-0.013	31.321	0.001	0.001	0.000	0.000	0.000	0.000
77	B	507	PHE	0	0.002	0.011	27.221	0.000	0.000	0.000	0.000	0.000	0.000
78	B	508	ASN	0	0.045	0.024	31.169	0.008	0.008	0.000	0.000	0.000	0.000
79	B	509	SER	0	0.092	0.023	31.738	0.001	0.001	0.000	0.000	0.000	0.000
80	B	510	ASN	0	0.027	0.014	32.815	0.005	0.005	0.000	0.000	0.000	0.000
81	B	511	THR	0	-0.012	0.002	32.368	0.002	0.002	0.000	0.000	0.000	0.000
82	B	512	PHE	0	0.023	0.012	25.529	0.001	0.001	0.000	0.000	0.000	0.000
83	B	513	LEU	0	0.007	0.007	30.390	0.003	0.003	0.000	0.000	0.000	0.000
84	B	514	THR	0	-0.001	-0.018	32.365	0.004	0.004	0.000	0.000	0.000	0.000
85	B	515	ARG	1	0.778	0.813	30.168	0.025	0.025	0.000	0.000	0.000	0.000
86	B	516	LEU	0	0.011	0.016	26.577	0.002	0.002	0.000	0.000	0.000	0.000
87	B	517	LEU	0	0.004	-0.008	29.576	0.005	0.005	0.000	0.000	0.000	0.000
88	B	518	VAL	0	-0.031	-0.006	32.327	0.003	0.003	0.000	0.000	0.000	0.000
89	B	519	HIS	0	-0.050	-0.041	27.536	0.007	0.007	0.000	0.000	0.000	0.000
90	B	520	MET	0	-0.064	-0.026	28.117	0.005	0.005	0.000	0.000	0.000	0.000
91	B	521	GLY	0	0.007	0.001	30.110	0.005	0.005	0.000	0.000	0.000	0.000
92	B	522	LEU	0	-0.070	-0.037	32.805	0.002	0.002	0.000	0.000	0.000	0.000
93	B	523	LEU	0	-0.037	-0.012	35.494	0.000	0.000	0.000	0.000	0.000	0.000
94	B	524	LYS	1	0.959	0.979	36.271	-0.002	-0.002	0.000	0.000	0.000	0.000
95	B	525	SER	0	-0.004	-0.020	35.994	0.000	0.000	0.000	0.000	0.000	0.000
96	B	526	GLU	-1	-0.946	-0.967	38.052	-0.014	-0.014	0.000	0.000	0.000	0.000
97	B	527	ASP	-1	-0.811	-0.863	33.724	-0.021	-0.021	0.000	0.000	0.000	0.000
98	B	528	LYS	1	0.911	0.952	34.063	0.003	0.003	0.000	0.000	0.000	0.000
99	B	529	VAL	0	0.063	0.036	30.735	-0.004	-0.004	0.000	0.000	0.000	0.000
100	B	530	LYS	1	0.890	0.936	24.753	0.025	0.025	0.000	0.000	0.000	0.000
101	B	531	ALA	0	0.029	0.022	28.186	0.001	0.001	0.000	0.000	0.000	0.000
102	B	532	ILE	0	-0.010	-0.001	24.186	0.003	0.003	0.000	0.000	0.000	0.000
103	B	533	ALA	0	0.015	0.009	26.601	0.001	0.001	0.000	0.000	0.000	0.000
104	B	534	ASN	0	-0.006	-0.008	24.940	-0.003	-0.003	0.000	0.000	0.000	0.000
105	B	535	LEU	0	0.075	0.026	25.731	0.001	0.001	0.000	0.000	0.000	0.000
106	B	536	TYR	0	0.030	0.010	23.105	0.003	0.003	0.000	0.000	0.000	0.000
107	B	537	GLY	0	0.030	0.015	22.415	0.001	0.001	0.000	0.000	0.000	0.000
108	B	538	PRO	0	0.022	-0.001	23.262	-0.002	-0.002	0.000	0.000	0.000	0.000
109	B	539	LEU	0	0.011	0.006	24.883	-0.005	-0.005	0.000	0.000	0.000	0.000
110	B	540	MET	0	-0.001	0.002	24.185	-0.007	-0.007	0.000	0.000	0.000	0.000
111	B	541	ALA	0	-0.016	-0.007	22.048	0.000	0.000	0.000	0.000	0.000	0.000
112	B	542	LEU	0	-0.004	-0.006	23.797	-0.007	-0.007	0.000	0.000	0.000	0.000
113	B	543	ASN	0	0.019	0.015	27.173	-0.010	-0.010	0.000	0.000	0.000	0.000
114	B	544	HIS	0	-0.027	-0.024	23.101	0.003	0.003	0.000	0.000	0.000	0.000
115	B	545	MET	0	0.008	0.013	24.635	-0.008	-0.008	0.000	0.000	0.000	0.000
116	B	546	VAL	0	-0.057	-0.030	26.594	-0.006	-0.006	0.000	0.000	0.000	0.000
117	B	547	GLN	0	-0.086	-0.053	29.178	-0.004	-0.004	0.000	0.000	0.000	0.000
118	B	548	GLN	0	-0.034	-0.005	25.434	-0.003	-0.003	0.000	0.000	0.000	0.000
119	B	549	ASP	-1	-0.899	-0.953	28.873	0.019	0.019	0.000	0.000	0.000	0.000
120	B	550	TYR	0	-0.092	-0.079	24.141	-0.007	-0.007	0.000	0.000	0.000	0.000
121	B	551	PHE	0	-0.022	-0.002	29.289	-0.004	-0.004	0.000	0.000	0.000	0.000
122	B	552	PRO	0	0.032	0.017	30.735	0.001	0.001	0.000	0.000	0.000	0.000
123	B	553	LYS	1	1.003	0.980	34.004	-0.019	-0.019	0.000	0.000	0.000	0.000
124	B	554	ALA	0	-0.020	-0.002	36.456	0.002	0.002	0.000	0.000	0.000	0.000
125	B	555	LEU	0	0.001	-0.004	32.282	0.000	0.000	0.000	0.000	0.000	0.000
126	B	556	ALA	0	0.023	0.016	35.579	0.002	0.002	0.000	0.000	0.000	0.000
127	B	557	PRO	0	0.008	0.003	36.518	0.002	0.002	0.000	0.000	0.000	0.000
128	B	558	LEU	0	0.010	0.011	37.295	0.001	0.001	0.000	0.000	0.000	0.000
129	B	559	LEU	0	0.019	0.001	30.961	0.001	0.001	0.000	0.000	0.000	0.000
130	B	560	LEU	0	0.026	0.016	35.548	0.003	0.003	0.000	0.000	0.000	0.000
131	B	561	ALA	0	0.005	0.015	37.932	0.002	0.002	0.000	0.000	0.000	0.000
132	B	562	PHE	0	-0.030	-0.029	36.501	0.000	0.000	0.000	0.000	0.000	0.000
133	B	563	VAL	0	0.017	0.019	33.480	0.002	0.002	0.000	0.000	0.000	0.000
134	B	564	THR	0	-0.035	-0.034	36.283	0.003	0.003	0.000	0.000	0.000	0.000
135	B	565	LYS	1	0.913	0.982	39.794	-0.019	-0.019	0.000	0.000	0.000	0.000
136	B	566	PRO	0	-0.007	-0.010	39.565	0.002	0.002	0.000	0.000	0.000	0.000
137	B	567	ASN	0	-0.035	-0.033	36.032	0.000	0.000	0.000	0.000	0.000	0.000
138	B	568	SER	0	0.100	0.050	37.514	0.002	0.002	0.000	0.000	0.000	0.000
139	B	569	ALA	0	0.027	0.023	32.201	0.004	0.004	0.000	0.000	0.000	0.000
140	B	570	LEU	0	-0.007	-0.009	32.511	0.006	0.006	0.000	0.000	0.000	0.000
141	B	571	GLU	-1	-0.825	-0.908	34.465	0.042	0.042	0.000	0.000	0.000	0.000
142	B	572	SER	0	-0.052	-0.014	32.901	0.003	0.003	0.000	0.000	0.000	0.000
143	B	573	CYS	0	-0.080	-0.023	30.094	0.010	0.010	0.000	0.000	0.000	0.000
144	B	574	SER	0	0.052	0.022	32.098	0.001	0.001	0.000	0.000	0.000	0.000
145	B	575	PHE	0	0.048	0.033	29.190	-0.003	-0.003	0.000	0.000	0.000	0.000
146	B	576	ALA	0	0.056	0.021	28.841	-0.002	-0.002	0.000	0.000	0.000	0.000
147	B	577	ARG	1	0.791	0.895	30.656	-0.046	-0.046	0.000	0.000	0.000	0.000
148	B	578	HIS	0	0.031	-0.001	33.498	-0.005	-0.005	0.000	0.000	0.000	0.000
149	B	579	SER	0	-0.024	-0.017	31.360	-0.002	-0.002	0.000	0.000	0.000	0.000
150	B	580	LEU	0	-0.003	0.008	30.347	-0.003	-0.003	0.000	0.000	0.000	0.000
151	B	581	LEU	0	-0.029	-0.013	32.607	-0.005	-0.005	0.000	0.000	0.000	0.000
152	B	582	GLN	0	0.026	0.004	36.011	-0.004	-0.004	0.000	0.000	0.000	0.000
153	B	583	THR	0	-0.072	-0.056	31.571	-0.003	-0.003	0.000	0.000	0.000	0.000
154	B	584	LEU	0	0.000	-0.007	33.859	-0.004	-0.004	0.000	0.000	0.000	0.000
155	B	585	TYR	0	-0.057	-0.021	36.247	-0.003	-0.003	0.000	0.000	0.000	0.000
156	B	586	LYS	1	0.904	0.980	33.756	-0.055	-0.055	0.000	0.000	0.000	0.000
157	B	587	VAL	0	-0.034	0.012	34.657	-0.004	-0.004	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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