FMO DATABASE

FMODB ID: ZV5ZN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1521895.616976
FMO2-HF: Nuclear repulsion	1461508.139605
FMO2-HF: Total energy	-60387.477371
FMO2-MP2: Total energy	-60563.258861

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.
-6.701	-1.373	0.997	-2.863	-3.462	-0.01

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 : 0.045 / q_NPA : 0.006

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	-0.747	-0.806	3.863	-2.010	-0.237	-0.015	-0.905	-0.853	0.001
4	B	434	VAL	0	0.050	0.007	6.437	0.193	0.193	0.000	0.000	0.000	0.000
5	B	435	SER	0	0.008	-0.011	10.013	0.125	0.125	0.000	0.000	0.000	0.000
6	B	436	THR	0	-0.041	-0.062	8.364	0.188	0.188	0.000	0.000	0.000	0.000
7	B	437	PHE	0	-0.036	-0.024	8.960	0.133	0.133	0.000	0.000	0.000	0.000
8	B	438	LEU	0	0.022	0.005	10.683	0.085	0.085	0.000	0.000	0.000	0.000
9	B	439	ALA	0	-0.027	0.004	13.727	0.046	0.046	0.000	0.000	0.000	0.000
10	B	440	PHE	0	-0.031	-0.015	13.031	0.040	0.040	0.000	0.000	0.000	0.000
11	B	441	PRO	0	0.022	0.024	13.171	0.053	0.053	0.000	0.000	0.000	0.000
12	B	442	SER	0	-0.029	-0.058	11.971	-0.006	-0.006	0.000	0.000	0.000	0.000
13	B	443	PRO	0	0.043	0.021	11.334	0.011	0.011	0.000	0.000	0.000	0.000
14	B	444	GLU	-1	-0.767	-0.857	9.320	0.631	0.631	0.000	0.000	0.000	0.000
15	B	445	LYS	1	0.799	0.892	6.920	0.208	0.208	0.000	0.000	0.000	0.000
16	B	446	LEU	0	0.011	0.016	6.713	-0.124	-0.124	0.000	0.000	0.000	0.000
17	B	447	LEU	0	0.032	0.009	7.725	-0.032	-0.032	0.000	0.000	0.000	0.000
18	B	448	ARG	1	0.851	0.920	3.036	-3.426	-1.651	0.138	-0.617	-1.296	0.003
19	B	449	LEU	0	-0.050	-0.004	2.687	-2.748	-0.968	0.874	-1.341	-1.313	-0.014
20	B	450	GLY	0	0.023	0.018	5.422	-0.140	-0.140	0.000	0.000	0.000	0.000
21	B	451	PRO	0	0.011	-0.015	6.316	-0.092	-0.092	0.000	0.000	0.000	0.000
22	B	452	LYS	1	0.959	0.974	8.766	0.089	0.089	0.000	0.000	0.000	0.000
23	B	453	SER	0	0.031	0.026	8.450	-0.094	-0.094	0.000	0.000	0.000	0.000
24	B	454	SER	0	0.044	0.028	9.812	-0.067	-0.067	0.000	0.000	0.000	0.000
25	B	455	VAL	0	0.039	0.012	12.861	-0.028	-0.028	0.000	0.000	0.000	0.000
26	B	456	LEU	0	-0.016	-0.005	7.340	-0.032	-0.032	0.000	0.000	0.000	0.000
27	B	457	ILE	0	0.020	0.001	11.499	-0.031	-0.031	0.000	0.000	0.000	0.000
28	B	458	ALA	0	0.025	0.033	13.503	-0.008	-0.008	0.000	0.000	0.000	0.000
29	B	459	GLN	0	-0.026	-0.006	12.688	-0.040	-0.040	0.000	0.000	0.000	0.000
30	B	460	GLN	0	-0.044	-0.043	11.691	-0.001	-0.001	0.000	0.000	0.000	0.000
31	B	461	THR	0	-0.020	-0.002	15.161	0.005	0.005	0.000	0.000	0.000	0.000
32	B	462	ASP	-1	-0.799	-0.869	18.070	-0.093	-0.093	0.000	0.000	0.000	0.000
33	B	463	THR	0	0.003	-0.015	21.170	0.005	0.005	0.000	0.000	0.000	0.000
34	B	464	SER	0	-0.043	-0.040	23.691	0.011	0.011	0.000	0.000	0.000	0.000
35	B	465	ASP	-1	-0.774	-0.872	25.449	-0.063	-0.063	0.000	0.000	0.000	0.000
36	B	466	PRO	0	0.012	-0.017	25.913	-0.001	-0.001	0.000	0.000	0.000	0.000
37	B	467	GLU	-1	-0.721	-0.807	26.744	-0.029	-0.029	0.000	0.000	0.000	0.000
38	B	468	LYS	1	0.758	0.860	21.961	0.101	0.101	0.000	0.000	0.000	0.000
39	B	469	VAL	0	0.031	0.020	22.149	-0.001	-0.001	0.000	0.000	0.000	0.000
40	B	470	VAL	0	-0.018	0.006	22.840	0.009	0.009	0.000	0.000	0.000	0.000
41	B	471	SER	0	-0.031	-0.014	21.909	0.010	0.010	0.000	0.000	0.000	0.000
42	B	472	ALA	0	0.017	0.004	18.446	0.007	0.007	0.000	0.000	0.000	0.000
43	B	473	PHE	0	0.059	0.020	18.651	0.015	0.015	0.000	0.000	0.000	0.000
44	B	474	LEU	0	-0.010	0.011	20.509	0.019	0.019	0.000	0.000	0.000	0.000
45	B	475	LYS	1	0.831	0.921	16.735	0.081	0.081	0.000	0.000	0.000	0.000
46	B	476	VAL	0	0.027	0.017	15.019	0.026	0.026	0.000	0.000	0.000	0.000
47	B	477	SER	0	-0.007	-0.024	16.716	0.034	0.034	0.000	0.000	0.000	0.000
48	B	478	SER	0	-0.072	-0.037	18.018	0.023	0.023	0.000	0.000	0.000	0.000
49	B	479	VAL	0	-0.017	-0.010	13.570	0.020	0.020	0.000	0.000	0.000	0.000
50	B	480	PHE	0	0.049	0.035	16.769	0.043	0.043	0.000	0.000	0.000	0.000
51	B	481	LYS	1	0.833	0.897	17.934	-0.217	-0.217	0.000	0.000	0.000	0.000
52	B	482	ASP	-1	-0.839	-0.900	19.624	0.168	0.168	0.000	0.000	0.000	0.000
53	B	483	GLU	-1	-0.785	-0.866	16.246	0.388	0.388	0.000	0.000	0.000	0.000
54	B	484	ALA	0	-0.012	-0.007	18.652	-0.007	-0.007	0.000	0.000	0.000	0.000
55	B	485	THR	0	-0.033	-0.047	13.564	0.011	0.011	0.000	0.000	0.000	0.000
56	B	486	VAL	0	-0.023	-0.018	13.822	-0.006	-0.006	0.000	0.000	0.000	0.000
57	B	487	ARG	1	0.850	0.931	15.256	-0.215	-0.215	0.000	0.000	0.000	0.000
58	B	488	MET	0	0.014	0.013	15.972	-0.017	-0.017	0.000	0.000	0.000	0.000
59	B	489	ALA	0	0.044	0.022	12.099	-0.028	-0.028	0.000	0.000	0.000	0.000
60	B	490	VAL	0	-0.040	-0.028	14.178	-0.044	-0.044	0.000	0.000	0.000	0.000
61	B	491	GLN	0	-0.031	-0.020	16.387	-0.022	-0.022	0.000	0.000	0.000	0.000
62	B	492	ASP	-1	-0.834	-0.915	15.560	0.123	0.123	0.000	0.000	0.000	0.000
63	B	493	ALA	0	-0.034	-0.037	14.120	-0.032	-0.032	0.000	0.000	0.000	0.000
64	B	494	VAL	0	-0.064	-0.024	16.120	-0.029	-0.029	0.000	0.000	0.000	0.000
65	B	495	ASP	-1	-0.744	-0.831	19.708	0.035	0.035	0.000	0.000	0.000	0.000
66	B	496	ALA	0	-0.026	-0.010	17.148	-0.014	-0.014	0.000	0.000	0.000	0.000
67	B	497	LEU	0	-0.050	-0.029	18.419	-0.017	-0.017	0.000	0.000	0.000	0.000
68	B	498	MET	0	-0.012	-0.013	19.930	-0.011	-0.011	0.000	0.000	0.000	0.000
69	B	499	GLN	0	0.000	0.014	22.837	-0.008	-0.008	0.000	0.000	0.000	0.000
70	B	500	LYS	1	0.799	0.902	18.730	0.117	0.117	0.000	0.000	0.000	0.000
71	B	501	ALA	0	-0.027	-0.014	23.103	-0.006	-0.006	0.000	0.000	0.000	0.000
72	B	502	PHE	0	-0.010	-0.031	25.414	-0.001	-0.001	0.000	0.000	0.000	0.000
73	B	503	ASN	0	0.012	0.011	26.767	0.005	0.005	0.000	0.000	0.000	0.000
74	B	504	SER	0	-0.002	0.023	27.803	-0.001	-0.001	0.000	0.000	0.000	0.000
75	B	505	SER	0	0.036	0.008	29.543	0.002	0.002	0.000	0.000	0.000	0.000
76	B	506	SER	0	-0.058	-0.028	31.391	0.000	0.000	0.000	0.000	0.000	0.000
77	B	507	PHE	0	0.014	0.017	27.053	-0.001	-0.001	0.000	0.000	0.000	0.000
78	B	508	ASN	0	0.040	0.027	30.897	0.008	0.008	0.000	0.000	0.000	0.000
79	B	509	SER	0	0.068	0.012	31.475	0.001	0.001	0.000	0.000	0.000	0.000
80	B	510	ASN	0	0.033	0.016	32.558	0.003	0.003	0.000	0.000	0.000	0.000
81	B	511	THR	0	-0.002	0.010	32.472	0.002	0.002	0.000	0.000	0.000	0.000
82	B	512	PHE	0	0.011	0.008	25.350	0.000	0.000	0.000	0.000	0.000	0.000
83	B	513	LEU	0	0.017	0.013	30.238	0.003	0.003	0.000	0.000	0.000	0.000
84	B	514	THR	0	-0.001	-0.022	32.172	0.004	0.004	0.000	0.000	0.000	0.000
85	B	515	ARG	1	0.752	0.800	29.982	0.030	0.030	0.000	0.000	0.000	0.000
86	B	516	LEU	0	0.010	0.012	26.474	0.002	0.002	0.000	0.000	0.000	0.000
87	B	517	LEU	0	-0.004	-0.011	29.494	0.005	0.005	0.000	0.000	0.000	0.000
88	B	518	VAL	0	-0.016	0.004	32.106	0.003	0.003	0.000	0.000	0.000	0.000
89	B	519	HIS	0	-0.054	-0.046	27.359	0.007	0.007	0.000	0.000	0.000	0.000
90	B	520	MET	0	-0.036	-0.017	27.888	0.004	0.004	0.000	0.000	0.000	0.000
91	B	521	GLY	0	0.015	0.006	29.951	0.004	0.004	0.000	0.000	0.000	0.000
92	B	522	LEU	0	-0.066	-0.029	32.519	0.001	0.001	0.000	0.000	0.000	0.000
93	B	523	LEU	0	-0.017	-0.004	35.389	0.000	0.000	0.000	0.000	0.000	0.000
94	B	524	LYS	1	0.964	0.982	36.081	0.002	0.002	0.000	0.000	0.000	0.000
95	B	525	SER	0	-0.007	-0.027	35.563	0.000	0.000	0.000	0.000	0.000	0.000
96	B	526	GLU	-1	-0.947	-0.965	37.635	-0.016	-0.016	0.000	0.000	0.000	0.000
97	B	527	ASP	-1	-0.787	-0.857	33.573	-0.025	-0.025	0.000	0.000	0.000	0.000
98	B	528	LYS	1	0.903	0.951	33.825	0.010	0.010	0.000	0.000	0.000	0.000
99	B	529	VAL	0	0.038	0.033	30.731	-0.003	-0.003	0.000	0.000	0.000	0.000
100	B	530	LYS	1	0.888	0.929	25.027	0.037	0.037	0.000	0.000	0.000	0.000
101	B	531	ALA	0	0.039	0.026	27.977	0.000	0.000	0.000	0.000	0.000	0.000
102	B	532	ILE	0	-0.013	0.002	23.894	0.002	0.002	0.000	0.000	0.000	0.000
103	B	533	ALA	0	0.005	-0.001	26.786	0.002	0.002	0.000	0.000	0.000	0.000
104	B	534	ASN	0	-0.023	-0.017	24.978	0.004	0.004	0.000	0.000	0.000	0.000
105	B	535	LEU	0	0.078	0.028	25.784	-0.002	-0.002	0.000	0.000	0.000	0.000
106	B	536	TYR	0	0.033	0.012	22.806	0.003	0.003	0.000	0.000	0.000	0.000
107	B	537	GLY	0	0.034	0.022	22.172	0.002	0.002	0.000	0.000	0.000	0.000
108	B	538	PRO	0	0.023	-0.003	22.849	-0.001	-0.001	0.000	0.000	0.000	0.000
109	B	539	LEU	0	0.007	0.007	24.561	-0.005	-0.005	0.000	0.000	0.000	0.000
110	B	540	MET	0	0.006	0.004	24.020	-0.007	-0.007	0.000	0.000	0.000	0.000
111	B	541	ALA	0	-0.014	-0.003	21.751	0.001	0.001	0.000	0.000	0.000	0.000
112	B	542	LEU	0	-0.015	-0.016	23.537	-0.007	-0.007	0.000	0.000	0.000	0.000
113	B	543	ASN	0	0.021	0.020	26.931	-0.009	-0.009	0.000	0.000	0.000	0.000
114	B	544	HIS	0	-0.009	-0.006	22.853	0.005	0.005	0.000	0.000	0.000	0.000
115	B	545	MET	0	0.007	0.015	24.490	-0.008	-0.008	0.000	0.000	0.000	0.000
116	B	546	VAL	0	-0.048	-0.034	26.315	-0.005	-0.005	0.000	0.000	0.000	0.000
117	B	547	GLN	0	-0.059	-0.036	29.126	-0.004	-0.004	0.000	0.000	0.000	0.000
118	B	548	GLN	0	-0.030	0.001	25.340	-0.001	-0.001	0.000	0.000	0.000	0.000
119	B	549	ASP	-1	-0.906	-0.959	28.804	0.019	0.019	0.000	0.000	0.000	0.000
120	B	550	TYR	0	-0.080	-0.068	23.877	-0.007	-0.007	0.000	0.000	0.000	0.000
121	B	551	PHE	0	-0.008	0.006	28.962	-0.005	-0.005	0.000	0.000	0.000	0.000
122	B	552	PRO	0	0.027	0.004	30.565	0.001	0.001	0.000	0.000	0.000	0.000
123	B	553	LYS	1	0.976	0.974	33.713	-0.019	-0.019	0.000	0.000	0.000	0.000
124	B	554	ALA	0	-0.005	0.004	35.952	0.002	0.002	0.000	0.000	0.000	0.000
125	B	555	LEU	0	0.001	-0.002	32.219	-0.001	-0.001	0.000	0.000	0.000	0.000
126	B	556	ALA	0	0.022	0.018	35.149	0.002	0.002	0.000	0.000	0.000	0.000
127	B	557	PRO	0	0.018	0.003	36.060	0.002	0.002	0.000	0.000	0.000	0.000
128	B	558	LEU	0	0.004	0.011	37.022	0.001	0.001	0.000	0.000	0.000	0.000
129	B	559	LEU	0	0.023	0.002	31.096	0.001	0.001	0.000	0.000	0.000	0.000
130	B	560	LEU	0	0.019	0.016	35.320	0.002	0.002	0.000	0.000	0.000	0.000
131	B	561	ALA	0	0.017	0.024	37.942	0.002	0.002	0.000	0.000	0.000	0.000
132	B	562	PHE	0	-0.025	-0.032	36.328	0.000	0.000	0.000	0.000	0.000	0.000
133	B	563	VAL	0	0.022	0.017	33.251	0.002	0.002	0.000	0.000	0.000	0.000
134	B	564	THR	0	-0.039	-0.037	36.184	0.003	0.003	0.000	0.000	0.000	0.000
135	B	565	LYS	1	0.846	0.947	38.961	-0.016	-0.016	0.000	0.000	0.000	0.000
136	B	566	PRO	0	-0.002	-0.003	39.130	0.002	0.002	0.000	0.000	0.000	0.000
137	B	567	ASN	0	-0.013	-0.020	35.514	0.000	0.000	0.000	0.000	0.000	0.000
138	B	568	SER	0	0.098	0.053	36.832	0.002	0.002	0.000	0.000	0.000	0.000
139	B	569	ALA	0	0.024	0.032	31.635	0.005	0.005	0.000	0.000	0.000	0.000
140	B	570	LEU	0	0.004	0.003	32.296	0.006	0.006	0.000	0.000	0.000	0.000
141	B	571	GLU	-1	-0.813	-0.902	34.194	0.037	0.037	0.000	0.000	0.000	0.000
142	B	572	SER	0	-0.032	-0.031	32.865	0.003	0.003	0.000	0.000	0.000	0.000
143	B	573	CYS	0	-0.072	-0.013	29.811	0.008	0.008	0.000	0.000	0.000	0.000
144	B	574	SER	0	0.024	0.017	31.655	0.004	0.004	0.000	0.000	0.000	0.000
145	B	575	PHE	0	0.049	0.029	28.758	-0.003	-0.003	0.000	0.000	0.000	0.000
146	B	576	ALA	0	0.045	0.023	28.351	0.000	0.000	0.000	0.000	0.000	0.000
147	B	577	ARG	1	0.767	0.877	30.200	-0.042	-0.042	0.000	0.000	0.000	0.000
148	B	578	HIS	0	0.047	0.005	33.086	-0.004	-0.004	0.000	0.000	0.000	0.000
149	B	579	SER	0	-0.013	-0.009	30.730	-0.001	-0.001	0.000	0.000	0.000	0.000
150	B	580	LEU	0	-0.009	0.001	30.093	-0.002	-0.002	0.000	0.000	0.000	0.000
151	B	581	LEU	0	-0.042	-0.018	32.217	-0.004	-0.004	0.000	0.000	0.000	0.000
152	B	582	GLN	0	0.020	-0.006	35.624	-0.004	-0.004	0.000	0.000	0.000	0.000
153	B	583	THR	0	-0.047	-0.042	31.025	-0.002	-0.002	0.000	0.000	0.000	0.000
154	B	584	LEU	0	-0.003	-0.008	33.575	-0.003	-0.003	0.000	0.000	0.000	0.000
155	B	585	TYR	0	-0.041	-0.018	35.846	-0.003	-0.003	0.000	0.000	0.000	0.000
156	B	586	LYS	1	0.858	0.956	33.312	-0.054	-0.054	0.000	0.000	0.000	0.000
157	B	587	VAL	0	-0.049	0.000	34.059	-0.005	-0.005	0.000	0.000	0.000	0.000

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