FMO DATABASE

FMODB ID: 76V1K

Calculation Name: 2VY7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VY7

Chain ID: A

ChEMBL ID:

UniProt ID: P31345

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	-1567871.271841
FMO2-HF: Nuclear repulsion	1505933.857967
FMO2-HF: Total energy	-61937.413874
FMO2-MP2: Total energy	-62118.514056

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:537:GLY)

Summations of interaction energy for fragment #1(A:537:GLY)

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.
-2.975	1.373	3.484	-3.827	-4.003	-0.022

Interaction energy analysis for fragmet #1(A:537:GLY)

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 : 0.014

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	539	ILE	0	0.071	0.019	3.849	-0.081	1.211	-0.002	-0.765	-0.525	0.004
4	A	540	ASN	0	-0.021	-0.014	6.677	0.456	0.456	0.000	0.000	0.000	0.000
5	A	541	GLY	0	0.042	0.021	9.898	0.237	0.237	0.000	0.000	0.000	0.000
6	A	542	PRO	0	0.017	0.000	10.044	-0.089	-0.089	0.000	0.000	0.000	0.000
7	A	543	GLU	-1	-0.763	-0.857	9.377	-0.894	-0.894	0.000	0.000	0.000	0.000
8	A	544	SER	0	-0.023	-0.017	5.831	0.087	0.087	0.000	0.000	0.000	0.000
9	A	545	VAL	0	0.007	0.012	6.308	0.216	0.216	0.000	0.000	0.000	0.000
10	A	546	LEU	0	-0.007	0.007	8.693	0.294	0.294	0.000	0.000	0.000	0.000
11	A	547	VAL	0	-0.014	-0.013	4.533	0.175	0.218	-0.001	-0.004	-0.038	0.000
12	A	548	ASN	0	0.011	-0.007	2.683	-0.195	0.989	1.634	-1.359	-1.460	-0.013
13	A	549	THR	0	0.026	0.012	5.040	0.546	0.586	-0.001	-0.003	-0.035	0.000
14	A	550	TYR	0	-0.054	-0.054	8.621	0.081	0.081	0.000	0.000	0.000	0.000
15	A	551	GLN	0	-0.005	-0.002	2.447	2.242	3.429	1.821	-1.425	-1.582	-0.015
16	A	552	TRP	0	-0.003	0.016	6.584	0.159	0.159	0.000	0.000	0.000	0.000
17	A	553	ILE	0	-0.012	-0.012	8.493	-0.161	-0.161	0.000	0.000	0.000	0.000
18	A	554	ILE	0	-0.014	0.001	9.576	-0.108	-0.108	0.000	0.000	0.000	0.000
19	A	555	ARG	1	0.888	0.942	3.000	-8.985	-8.383	0.033	-0.271	-0.363	0.002
20	A	556	ASN	0	-0.026	-0.006	10.497	-0.210	-0.210	0.000	0.000	0.000	0.000
21	A	557	TRP	0	0.034	0.020	13.503	-0.156	-0.156	0.000	0.000	0.000	0.000
22	A	558	GLU	-1	-0.771	-0.882	15.590	0.413	0.413	0.000	0.000	0.000	0.000
23	A	559	THR	0	-0.001	0.007	17.350	-0.080	-0.080	0.000	0.000	0.000	0.000
24	A	560	VAL	0	-0.051	-0.030	14.747	-0.071	-0.071	0.000	0.000	0.000	0.000
25	A	561	LYS	1	0.880	0.929	18.109	-0.490	-0.490	0.000	0.000	0.000	0.000
26	A	562	ILE	0	0.062	0.046	20.859	-0.048	-0.048	0.000	0.000	0.000	0.000
27	A	563	GLN	0	0.024	-0.003	19.745	-0.032	-0.032	0.000	0.000	0.000	0.000
28	A	564	TRP	0	0.002	-0.014	21.077	-0.029	-0.029	0.000	0.000	0.000	0.000
29	A	565	SER	0	0.024	-0.001	22.996	-0.038	-0.038	0.000	0.000	0.000	0.000
30	A	566	GLN	0	-0.028	0.002	25.864	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	567	ASN	0	-0.037	-0.031	25.810	-0.021	-0.021	0.000	0.000	0.000	0.000
32	A	568	PRO	0	0.075	0.043	23.773	0.019	0.019	0.000	0.000	0.000	0.000
33	A	569	THR	0	-0.015	-0.007	23.519	0.010	0.010	0.000	0.000	0.000	0.000
34	A	570	MET	0	0.003	0.015	22.436	0.017	0.017	0.000	0.000	0.000	0.000
35	A	571	LEU	0	-0.012	0.009	17.574	0.030	0.030	0.000	0.000	0.000	0.000
36	A	572	TYR	0	0.012	-0.014	19.137	0.025	0.025	0.000	0.000	0.000	0.000
37	A	573	ASN	0	0.003	0.005	19.822	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	574	LYS	1	0.879	0.944	16.226	-0.451	-0.451	0.000	0.000	0.000	0.000
39	A	575	MET	0	0.055	0.018	16.323	0.011	0.011	0.000	0.000	0.000	0.000
40	A	576	GLU	-1	-0.924	-0.956	9.529	1.030	1.030	0.000	0.000	0.000	0.000
41	A	577	PHE	0	-0.002	-0.014	12.173	-0.014	-0.014	0.000	0.000	0.000	0.000
42	A	578	GLU	-1	-0.896	-0.943	14.661	0.093	0.093	0.000	0.000	0.000	0.000
43	A	579	PRO	0	0.016	0.013	11.314	-0.081	-0.081	0.000	0.000	0.000	0.000
44	A	580	PHE	0	0.053	0.018	12.021	-0.083	-0.083	0.000	0.000	0.000	0.000
45	A	581	GLN	0	-0.017	-0.034	13.965	-0.082	-0.082	0.000	0.000	0.000	0.000
46	A	582	SER	0	-0.085	-0.048	15.835	-0.028	-0.028	0.000	0.000	0.000	0.000
47	A	583	LEU	0	0.018	0.013	12.365	-0.036	-0.036	0.000	0.000	0.000	0.000
48	A	584	VAL	0	0.010	0.032	17.023	-0.016	-0.016	0.000	0.000	0.000	0.000
49	A	585	PRO	0	0.026	0.017	19.871	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	586	LYS	1	1.004	0.996	23.326	0.039	0.039	0.000	0.000	0.000	0.000
51	A	587	ALA	0	-0.008	0.003	25.008	0.011	0.011	0.000	0.000	0.000	0.000
52	A	588	ILE	0	-0.006	-0.010	24.522	0.007	0.007	0.000	0.000	0.000	0.000
53	A	589	ARG	1	0.890	0.961	20.661	0.030	0.030	0.000	0.000	0.000	0.000
54	A	590	GLY	0	0.081	0.047	24.237	0.015	0.015	0.000	0.000	0.000	0.000
55	A	591	GLN	0	0.028	0.015	26.958	0.013	0.013	0.000	0.000	0.000	0.000
56	A	592	TYR	0	-0.002	-0.003	22.199	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	593	SER	0	0.018	0.007	23.709	0.013	0.013	0.000	0.000	0.000	0.000
58	A	594	GLY	0	0.042	0.010	24.776	0.012	0.012	0.000	0.000	0.000	0.000
59	A	595	PHE	0	-0.013	0.007	25.643	0.005	0.005	0.000	0.000	0.000	0.000
60	A	596	VAL	0	0.018	0.006	21.668	0.003	0.003	0.000	0.000	0.000	0.000
61	A	597	ARG	1	0.807	0.898	23.386	-0.150	-0.150	0.000	0.000	0.000	0.000
62	A	598	THR	0	0.019	-0.001	26.428	0.006	0.006	0.000	0.000	0.000	0.000
63	A	599	LEU	0	-0.023	0.013	25.521	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	600	PHE	0	0.012	-0.009	20.279	0.006	0.006	0.000	0.000	0.000	0.000
65	A	601	GLN	0	-0.101	-0.061	26.602	0.003	0.003	0.000	0.000	0.000	0.000
66	A	602	GLN	0	-0.022	-0.021	29.905	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	603	MET	0	-0.029	-0.006	25.453	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	604	ARG	1	0.868	0.938	25.164	-0.204	-0.204	0.000	0.000	0.000	0.000
69	A	605	ASP	-1	-0.869	-0.929	29.417	0.134	0.134	0.000	0.000	0.000	0.000
70	A	606	VAL	0	-0.056	-0.027	32.527	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	607	LEU	0	-0.047	-0.011	29.284	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	608	GLY	0	0.014	0.020	29.333	0.008	0.008	0.000	0.000	0.000	0.000
73	A	609	THR	0	-0.031	-0.046	24.003	0.002	0.002	0.000	0.000	0.000	0.000
74	A	610	PHE	0	0.021	0.024	24.403	0.019	0.019	0.000	0.000	0.000	0.000
75	A	611	ASP	-1	-0.856	-0.923	24.041	0.177	0.177	0.000	0.000	0.000	0.000
76	A	612	THR	0	-0.007	-0.018	18.307	0.002	0.002	0.000	0.000	0.000	0.000
77	A	613	THR	0	-0.014	-0.033	17.899	0.039	0.039	0.000	0.000	0.000	0.000
78	A	614	GLN	0	-0.037	-0.029	18.252	-0.009	-0.009	0.000	0.000	0.000	0.000
79	A	615	ILE	0	0.004	0.005	19.205	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	616	ILE	0	0.020	0.007	13.522	0.013	0.013	0.000	0.000	0.000	0.000
81	A	617	LYS	1	0.771	0.889	15.278	-0.105	-0.105	0.000	0.000	0.000	0.000
82	A	618	LEU	0	-0.024	-0.013	16.658	-0.024	-0.024	0.000	0.000	0.000	0.000
83	A	619	LEU	0	0.035	0.027	15.813	-0.028	-0.028	0.000	0.000	0.000	0.000
84	A	620	PRO	0	0.042	0.027	13.747	-0.017	-0.017	0.000	0.000	0.000	0.000
85	A	621	PHE	0	-0.009	-0.015	16.316	-0.040	-0.040	0.000	0.000	0.000	0.000
86	A	622	ALA	0	-0.003	0.009	19.523	-0.024	-0.024	0.000	0.000	0.000	0.000
87	A	623	ALA	0	0.049	0.031	18.264	-0.012	-0.012	0.000	0.000	0.000	0.000
88	A	624	ALA	0	-0.036	-0.003	20.334	-0.008	-0.008	0.000	0.000	0.000	0.000
89	A	625	PRO	0	0.033	0.018	22.748	0.007	0.007	0.000	0.000	0.000	0.000
90	A	626	PRO	0	-0.008	0.016	26.410	-0.012	-0.012	0.000	0.000	0.000	0.000
91	A	627	LYS	1	0.858	0.914	28.260	-0.031	-0.031	0.000	0.000	0.000	0.000
92	A	628	GLN	0	0.023	0.004	31.206	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	629	SER	0	-0.032	-0.022	32.208	-0.009	-0.009	0.000	0.000	0.000	0.000
94	A	630	ARG	1	1.017	0.995	34.513	-0.032	-0.032	0.000	0.000	0.000	0.000
95	A	631	MET	0	-0.010	0.017	31.831	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	632	GLN	0	0.018	-0.002	31.062	0.011	0.011	0.000	0.000	0.000	0.000
97	A	633	PHE	0	-0.019	-0.002	26.747	-0.008	-0.008	0.000	0.000	0.000	0.000
98	A	634	SER	0	0.067	0.029	27.357	0.008	0.008	0.000	0.000	0.000	0.000
99	A	635	SER	0	-0.056	-0.026	23.584	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	636	LEU	0	-0.015	0.023	20.834	-0.005	-0.005	0.000	0.000	0.000	0.000
101	A	637	THR	0	-0.018	-0.013	20.856	-0.013	-0.013	0.000	0.000	0.000	0.000
102	A	638	VAL	0	0.036	0.007	15.581	0.018	0.018	0.000	0.000	0.000	0.000
103	A	639	ASN	0	-0.052	-0.037	18.482	-0.020	-0.020	0.000	0.000	0.000	0.000
104	A	640	VAL	0	0.024	0.008	13.602	-0.038	-0.038	0.000	0.000	0.000	0.000
105	A	641	ARG	1	0.832	0.885	12.807	0.628	0.628	0.000	0.000	0.000	0.000
106	A	642	GLY	0	0.055	0.035	17.777	0.004	0.004	0.000	0.000	0.000	0.000
107	A	643	SER	0	-0.017	0.009	21.022	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	644	GLY	0	-0.018	-0.006	21.118	0.023	0.023	0.000	0.000	0.000	0.000
109	A	645	MET	0	-0.037	-0.010	18.125	-0.015	-0.015	0.000	0.000	0.000	0.000
110	A	646	ARG	1	0.950	0.961	19.746	0.070	0.070	0.000	0.000	0.000	0.000
111	A	647	ILE	0	0.039	0.046	15.251	-0.014	-0.014	0.000	0.000	0.000	0.000
112	A	648	LEU	0	0.000	-0.011	19.658	0.008	0.008	0.000	0.000	0.000	0.000
113	A	649	VAL	0	0.044	0.029	21.856	0.015	0.015	0.000	0.000	0.000	0.000
114	A	650	ARG	1	0.973	0.993	23.568	-0.024	-0.024	0.000	0.000	0.000	0.000
115	A	651	GLY	0	0.013	0.005	23.267	-0.014	-0.014	0.000	0.000	0.000	0.000
116	A	652	ASN	0	0.017	0.017	19.377	0.033	0.033	0.000	0.000	0.000	0.000
117	A	653	SER	0	-0.047	-0.059	19.088	-0.009	-0.009	0.000	0.000	0.000	0.000
118	A	654	PRO	0	0.034	0.003	18.372	0.003	0.003	0.000	0.000	0.000	0.000
119	A	655	VAL	0	-0.017	0.001	14.903	-0.047	-0.047	0.000	0.000	0.000	0.000
120	A	656	PHE	0	0.048	0.016	13.939	-0.018	-0.018	0.000	0.000	0.000	0.000
121	A	657	ASN	0	-0.026	-0.028	14.734	0.016	0.016	0.000	0.000	0.000	0.000
122	A	658	TYR	0	0.017	-0.012	15.413	0.006	0.006	0.000	0.000	0.000	0.000
123	A	659	ASN	0	0.037	0.029	16.781	-0.014	-0.014	0.000	0.000	0.000	0.000
124	A	660	LYS	1	0.898	0.926	18.793	-0.075	-0.075	0.000	0.000	0.000	0.000
125	A	661	THR	0	-0.022	-0.017	20.981	0.005	0.005	0.000	0.000	0.000	0.000
126	A	662	THR	0	-0.007	-0.019	16.566	0.014	0.014	0.000	0.000	0.000	0.000
127	A	663	LYS	1	0.919	0.982	17.625	-0.153	-0.153	0.000	0.000	0.000	0.000
128	A	664	ARG	1	0.857	0.903	9.459	-0.476	-0.476	0.000	0.000	0.000	0.000
129	A	665	LEU	0	-0.017	0.004	11.413	-0.087	-0.087	0.000	0.000	0.000	0.000
130	A	666	THR	0	-0.027	-0.006	11.075	0.013	0.013	0.000	0.000	0.000	0.000
131	A	667	ILE	0	-0.023	-0.015	9.172	0.041	0.041	0.000	0.000	0.000	0.000
132	A	668	LEU	0	-0.007	-0.007	10.397	-0.158	-0.158	0.000	0.000	0.000	0.000
133	A	669	GLY	0	-0.007	0.005	12.465	-0.049	-0.049	0.000	0.000	0.000	0.000
134	A	670	LYS	1	0.814	0.916	7.109	1.731	1.731	0.000	0.000	0.000	0.000
135	A	671	ASP	-1	-0.756	-0.853	7.829	0.762	0.762	0.000	0.000	0.000	0.000
136	A	672	ALA	0	-0.011	-0.014	6.464	-0.080	-0.080	0.000	0.000	0.000	0.000
137	A	673	GLY	0	0.039	0.018	7.791	0.504	0.504	0.000	0.000	0.000	0.000
138	A	674	THR	0	-0.035	-0.029	9.962	-0.165	-0.165	0.000	0.000	0.000	0.000
139	A	675	LEU	0	-0.046	-0.015	13.493	0.104	0.104	0.000	0.000	0.000	0.000
140	A	676	ILE	0	0.039	0.015	15.857	-0.009	-0.009	0.000	0.000	0.000	0.000
141	A	677	GLU	-1	-0.833	-0.881	19.036	0.213	0.213	0.000	0.000	0.000	0.000
142	A	678	ASP	-1	-0.847	-0.909	21.786	0.194	0.194	0.000	0.000	0.000	0.000
143	A	679	PRO	0	-0.103	-0.056	23.530	0.027	0.027	0.000	0.000	0.000	0.000
144	A	680	ASP	-1	-0.863	-0.921	24.590	0.232	0.232	0.000	0.000	0.000	0.000
145	A	681	GLU	-1	-0.922	-0.983	20.980	0.316	0.316	0.000	0.000	0.000	0.000
146	A	682	SER	0	-0.014	-0.006	23.359	0.029	0.029	0.000	0.000	0.000	0.000
147	A	683	THR	0	-0.078	-0.054	22.061	0.001	0.001	0.000	0.000	0.000	0.000
148	A	684	SER	0	0.038	0.053	17.652	-0.021	-0.021	0.000	0.000	0.000	0.000
149	A	685	GLY	0	-0.046	-0.031	17.716	0.010	0.010	0.000	0.000	0.000	0.000
150	A	686	VAL	0	-0.054	-0.040	18.631	-0.026	-0.026	0.000	0.000	0.000	0.000
151	A	687	GLU	-1	-0.720	-0.829	20.570	0.118	0.118	0.000	0.000	0.000	0.000
152	A	688	SER	0	0.046	0.008	24.245	-0.012	-0.012	0.000	0.000	0.000	0.000
153	A	689	ALA	0	0.006	0.004	27.288	-0.005	-0.005	0.000	0.000	0.000	0.000
154	A	690	VAL	0	0.004	0.030	22.857	-0.014	-0.014	0.000	0.000	0.000	0.000
155	A	691	LEU	0	-0.013	-0.005	23.970	-0.015	-0.015	0.000	0.000	0.000	0.000
156	A	692	ARG	1	0.846	0.903	26.098	-0.021	-0.021	0.000	0.000	0.000	0.000
157	A	693	GLY	0	0.053	0.040	27.446	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:537:GLY)