FMO DATABASE

FMODB ID: QVY4Y

Calculation Name: 2VSW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VSW

Chain ID: A

ChEMBL ID:

UniProt ID: Q9BY84

Base Structure: X-ray

Registration Date: 2023-09-21

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	134
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1205352.58465
FMO2-HF: Nuclear repulsion	1152378.517957
FMO2-HF: Total energy	-52974.066694
FMO2-MP2: Total energy	-53125.934659

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:5:MET)

Summations of interaction energy for fragment #1(A:5:MET)

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.
-44.225	-38.728	23.983	-9.587	-19.899	-0.036

Interaction energy analysis for fragmet #1(A:5:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.091 / q_NPA : -0.033

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	7	GLY	0	0.024	-0.001	3.364	0.515	3.407	1.806	-1.944	-2.755	-0.004
4	A	8	THR	0	-0.031	-0.004	3.685	0.456	-1.018	0.172	1.641	-0.340	0.000
5	A	9	GLN	0	0.044	0.016	7.405	0.368	0.368	0.000	0.000	0.000	0.000
6	A	10	ILE	0	-0.034	-0.004	10.142	-0.067	-0.067	0.000	0.000	0.000	0.000
7	A	11	VAL	0	0.043	0.021	13.545	0.022	0.022	0.000	0.000	0.000	0.000
8	A	12	THR	0	0.026	-0.023	16.533	0.008	0.008	0.000	0.000	0.000	0.000
9	A	13	GLU	-1	-0.901	-0.957	19.122	-0.082	-0.082	0.000	0.000	0.000	0.000
10	A	14	ARG	1	0.889	0.941	17.937	0.114	0.114	0.000	0.000	0.000	0.000
11	A	15	LEU	0	0.025	0.024	16.384	-0.001	-0.001	0.000	0.000	0.000	0.000
12	A	16	VAL	0	0.012	0.011	18.564	0.008	0.008	0.000	0.000	0.000	0.000
13	A	17	ALA	0	0.017	-0.001	22.356	0.004	0.004	0.000	0.000	0.000	0.000
14	A	18	LEU	0	-0.075	-0.017	16.732	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	19	LEU	0	0.010	-0.001	19.765	0.008	0.008	0.000	0.000	0.000	0.000
16	A	20	GLU	-1	-0.957	-0.971	22.308	-0.031	-0.031	0.000	0.000	0.000	0.000
17	A	21	SER	0	-0.083	-0.030	22.935	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	22	GLY	0	0.007	-0.005	24.418	0.005	0.005	0.000	0.000	0.000	0.000
19	A	23	THR	0	-0.061	-0.044	22.332	0.004	0.004	0.000	0.000	0.000	0.000
20	A	24	GLU	-1	-0.799	-0.900	18.680	-0.055	-0.055	0.000	0.000	0.000	0.000
21	A	25	LYS	1	0.858	0.963	19.224	-0.055	-0.055	0.000	0.000	0.000	0.000
22	A	26	VAL	0	0.026	0.010	15.912	0.004	0.004	0.000	0.000	0.000	0.000
23	A	27	LEU	0	-0.022	-0.009	13.192	0.017	0.017	0.000	0.000	0.000	0.000
24	A	28	LEU	0	0.019	0.012	13.888	0.000	0.000	0.000	0.000	0.000	0.000
25	A	29	ILE	0	-0.019	-0.016	11.151	0.020	0.020	0.000	0.000	0.000	0.000
26	A	30	ASP	-1	-0.719	-0.818	13.619	0.027	0.027	0.000	0.000	0.000	0.000
27	A	31	SER	0	-0.051	-0.054	10.944	0.013	0.013	0.000	0.000	0.000	0.000
28	A	32	ARG	1	0.800	0.873	12.889	-0.023	-0.023	0.000	0.000	0.000	0.000
29	A	33	PRO	0	-0.016	-0.020	15.623	0.021	0.021	0.000	0.000	0.000	0.000
30	A	34	PHE	0	0.036	0.011	18.556	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	35	VAL	0	-0.007	0.007	21.154	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	36	GLU	-1	-0.839	-0.922	18.628	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	37	TYR	0	-0.015	-0.016	19.540	0.000	0.000	0.000	0.000	0.000	0.000
34	A	38	ASN	0	-0.044	-0.030	21.573	0.001	0.001	0.000	0.000	0.000	0.000
35	A	39	THR	0	-0.059	-0.025	24.917	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	40	SER	0	-0.051	-0.047	24.095	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	41	HIS	1	0.795	0.899	20.600	-0.041	-0.041	0.000	0.000	0.000	0.000
38	A	42	ILE	0	0.046	0.030	17.898	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	43	LEU	0	0.014	0.008	21.586	0.010	0.010	0.000	0.000	0.000	0.000
40	A	44	GLU	-1	-0.914	-0.974	21.796	0.051	0.051	0.000	0.000	0.000	0.000
41	A	45	ALA	0	-0.058	0.002	18.196	0.014	0.014	0.000	0.000	0.000	0.000
42	A	46	ILE	0	-0.041	-0.018	16.886	0.004	0.004	0.000	0.000	0.000	0.000
43	A	47	ASN	0	0.014	-0.005	16.372	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	48	ILE	0	-0.023	0.002	12.334	0.018	0.018	0.000	0.000	0.000	0.000
45	A	49	ASN	0	0.023	-0.009	14.025	-0.023	-0.023	0.000	0.000	0.000	0.000
46	A	50	CYS	0	0.039	0.036	13.354	0.023	0.023	0.000	0.000	0.000	0.000
47	A	51	SER	0	-0.058	-0.022	14.401	-0.013	-0.013	0.000	0.000	0.000	0.000
48	A	52	LYN	0	0.100	0.048	12.336	0.039	0.039	0.000	0.000	0.000	0.000
49	A	53	LEU	0	0.017	0.007	15.309	0.035	0.035	0.000	0.000	0.000	0.000
50	A	54	MET	0	0.023	0.025	14.125	0.047	0.047	0.000	0.000	0.000	0.000
51	A	55	LYS	1	0.805	0.887	9.554	-0.067	-0.067	0.000	0.000	0.000	0.000
52	A	56	ARG	1	0.876	0.943	12.299	-0.189	-0.189	0.000	0.000	0.000	0.000
53	A	57	ARG	1	0.944	0.953	14.894	-0.277	-0.277	0.000	0.000	0.000	0.000
54	A	58	LEU	0	0.019	0.029	9.958	0.054	0.054	0.000	0.000	0.000	0.000
55	A	59	GLN	0	-0.024	-0.016	10.189	0.125	0.125	0.000	0.000	0.000	0.000
56	A	60	GLN	0	-0.027	-0.012	11.107	-0.088	-0.088	0.000	0.000	0.000	0.000
57	A	61	ASP	-1	-0.807	-0.870	11.383	1.358	1.358	0.000	0.000	0.000	0.000
58	A	62	LYS	1	0.820	0.889	13.895	-0.647	-0.647	0.000	0.000	0.000	0.000
59	A	63	VAL	0	0.008	0.003	14.374	-0.088	-0.088	0.000	0.000	0.000	0.000
60	A	64	LEU	0	0.015	0.021	13.518	0.120	0.120	0.000	0.000	0.000	0.000
61	A	65	ILE	0	0.028	0.005	9.472	-0.093	-0.093	0.000	0.000	0.000	0.000
62	A	66	THR	0	0.060	0.025	12.254	-0.078	-0.078	0.000	0.000	0.000	0.000
63	A	67	GLU	-1	-0.874	-0.928	15.054	0.344	0.344	0.000	0.000	0.000	0.000
64	A	68	LEU	0	0.006	-0.010	12.902	-0.045	-0.045	0.000	0.000	0.000	0.000
65	A	69	ILE	0	0.013	0.011	12.399	-0.047	-0.047	0.000	0.000	0.000	0.000
66	A	70	GLN	0	-0.030	-0.034	16.224	-0.055	-0.055	0.000	0.000	0.000	0.000
67	A	71	HIS	0	-0.066	-0.037	19.344	-0.021	-0.021	0.000	0.000	0.000	0.000
68	A	72	SER	0	-0.013	-0.001	17.343	-0.020	-0.020	0.000	0.000	0.000	0.000
69	A	73	ALA	0	-0.045	0.002	19.650	-0.023	-0.023	0.000	0.000	0.000	0.000
70	A	74	LYS	1	0.840	0.911	21.658	-0.109	-0.109	0.000	0.000	0.000	0.000
71	A	75	HIS	0	0.078	0.043	22.058	0.003	0.003	0.000	0.000	0.000	0.000
72	A	76	LYS	1	0.958	0.975	24.247	-0.127	-0.127	0.000	0.000	0.000	0.000
73	A	77	VAL	0	-0.015	0.007	18.616	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	78	ASP	-1	-0.807	-0.905	20.678	0.158	0.158	0.000	0.000	0.000	0.000
75	A	79	ILE	0	-0.062	-0.042	16.870	0.006	0.006	0.000	0.000	0.000	0.000
76	A	80	ASP	-1	-0.787	-0.846	17.148	0.168	0.168	0.000	0.000	0.000	0.000
77	A	81	CYS	0	0.007	-0.003	13.355	-0.032	-0.032	0.000	0.000	0.000	0.000
78	A	82	SER	0	-0.040	-0.040	13.487	-0.035	-0.035	0.000	0.000	0.000	0.000
79	A	83	GLN	0	-0.040	-0.027	15.317	-0.054	-0.054	0.000	0.000	0.000	0.000
80	A	84	LYS	1	0.777	0.882	13.183	0.050	0.050	0.000	0.000	0.000	0.000
81	A	85	VAL	0	0.007	0.002	9.650	0.019	0.019	0.000	0.000	0.000	0.000
82	A	86	VAL	0	-0.010	-0.003	10.724	-0.057	-0.057	0.000	0.000	0.000	0.000
83	A	87	VAL	0	-0.006	-0.003	8.271	0.024	0.024	0.000	0.000	0.000	0.000
84	A	88	TYR	0	0.003	-0.018	11.095	-0.009	-0.009	0.000	0.000	0.000	0.000
85	A	89	ASP	-1	-0.741	-0.829	11.077	-0.050	-0.050	0.000	0.000	0.000	0.000
86	A	90	GLN	0	0.093	0.038	13.039	0.006	0.006	0.000	0.000	0.000	0.000
87	A	91	SER	0	-0.058	-0.030	14.561	0.005	0.005	0.000	0.000	0.000	0.000
88	A	92	SER	0	-0.010	-0.021	9.799	-0.033	-0.033	0.000	0.000	0.000	0.000
89	A	93	GLN	0	-0.059	-0.027	11.458	0.023	0.023	0.000	0.000	0.000	0.000
90	A	94	ASP	-1	-0.837	-0.932	8.877	-0.337	-0.337	0.000	0.000	0.000	0.000
91	A	95	VAL	0	0.020	0.009	2.654	-0.734	-0.917	2.814	-0.622	-2.009	0.001
92	A	96	ALA	0	-0.034	-0.003	4.498	-0.642	-0.576	-0.001	-0.013	-0.052	0.000
93	A	97	SER	0	-0.087	-0.052	6.644	0.023	0.023	0.000	0.000	0.000	0.000
94	A	98	LEU	0	0.008	0.009	4.388	0.026	0.125	-0.001	-0.005	-0.093	0.000
95	A	99	SER	0	0.025	0.007	6.463	-0.124	-0.124	0.000	0.000	0.000	0.000
96	A	100	SER	0	0.034	0.006	5.562	-0.067	-0.067	0.000	0.000	0.000	0.000
97	A	101	ASP	-1	-0.804	-0.895	6.130	0.298	0.298	0.000	0.000	0.000	0.000
98	A	102	CYS	0	-0.030	0.011	6.157	0.170	0.170	0.000	0.000	0.000	0.000
99	A	103	PHE	0	0.007	-0.013	6.793	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	104	LEU	0	0.089	0.036	5.830	0.061	0.061	0.000	0.000	0.000	0.000
101	A	105	THR	0	0.046	0.013	2.512	-0.520	-0.311	1.767	-0.420	-1.557	0.000
102	A	106	VAL	0	-0.026	-0.014	2.851	-1.912	-0.705	0.391	-0.558	-1.040	-0.010
103	A	107	LEU	0	-0.033	-0.009	5.419	0.514	0.514	0.000	0.000	0.000	0.000
104	A	108	LEU	0	0.073	0.026	2.900	-1.211	0.172	0.447	-0.362	-1.468	0.000
105	A	109	GLY	0	0.004	0.012	2.144	-1.906	-1.360	4.463	-2.318	-2.692	-0.004
106	A	110	LYS	1	0.792	0.872	2.879	3.579	0.910	0.091	3.102	-0.525	-0.001
107	A	111	LEU	0	0.032	0.021	6.026	-0.033	-0.033	0.000	0.000	0.000	0.000
108	A	112	GLU	-1	-0.729	-0.871	2.309	-14.929	-10.657	5.335	-5.113	-4.494	-0.059
109	A	113	LYS	1	0.764	0.879	2.124	-27.549	-28.400	6.699	-2.975	-2.874	0.041
110	A	114	SER	0	-0.065	-0.031	7.256	-0.275	-0.275	0.000	0.000	0.000	0.000
111	A	115	PHE	0	-0.014	-0.014	9.001	-0.111	-0.111	0.000	0.000	0.000	0.000
112	A	116	ASN	0	-0.044	-0.026	8.698	-0.071	-0.071	0.000	0.000	0.000	0.000
113	A	117	SER	0	-0.042	-0.031	9.543	-0.143	-0.143	0.000	0.000	0.000	0.000
114	A	118	VAL	0	-0.016	0.006	5.719	0.156	0.156	0.000	0.000	0.000	0.000
115	A	119	HIS	0	0.008	0.012	7.181	-0.143	-0.143	0.000	0.000	0.000	0.000
116	A	120	LEU	0	0.016	0.015	7.270	0.052	0.052	0.000	0.000	0.000	0.000
117	A	121	LEU	0	-0.012	-0.015	9.212	-0.067	-0.067	0.000	0.000	0.000	0.000
118	A	122	ALA	0	-0.024	-0.009	12.602	0.003	0.003	0.000	0.000	0.000	0.000
119	A	123	GLY	0	0.047	0.017	13.457	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	124	GLY	0	-0.014	0.001	14.282	0.004	0.004	0.000	0.000	0.000	0.000
121	A	125	PHE	0	-0.004	-0.025	15.156	0.000	0.000	0.000	0.000	0.000	0.000
122	A	126	ALA	0	-0.017	0.014	18.196	0.000	0.000	0.000	0.000	0.000	0.000
123	A	127	GLU	-1	-0.829	-0.873	18.626	-0.089	-0.089	0.000	0.000	0.000	0.000
124	A	128	PHE	0	0.072	0.021	19.042	0.002	0.002	0.000	0.000	0.000	0.000
125	A	129	SER	0	-0.015	-0.029	20.936	0.001	0.001	0.000	0.000	0.000	0.000
126	A	130	ARG	1	0.824	0.903	22.155	0.071	0.071	0.000	0.000	0.000	0.000
127	A	131	CYS	0	-0.100	-0.045	23.052	-0.004	-0.004	0.000	0.000	0.000	0.000
128	A	132	PHE	0	0.033	0.009	23.662	0.000	0.000	0.000	0.000	0.000	0.000
129	A	133	PRO	0	0.067	0.027	26.005	0.006	0.006	0.000	0.000	0.000	0.000
130	A	134	GLY	0	-0.038	-0.019	27.892	0.005	0.005	0.000	0.000	0.000	0.000
131	A	135	LEU	0	-0.015	0.002	24.921	0.002	0.002	0.000	0.000	0.000	0.000
132	A	136	CYS	0	-0.059	-0.019	24.250	0.002	0.002	0.000	0.000	0.000	0.000
133	A	137	GLU	-1	-0.802	-0.881	25.105	0.040	0.040	0.000	0.000	0.000	0.000
134	A	138	GLY	0	0.001	0.012	25.909	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:MET)