FMO DATABASE

FMODB ID: YVGG2

Calculation Name: 2QVG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2QVG

Chain ID: A

ChEMBL ID:

UniProt ID: Q5ZSR0

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	129
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1196323.749243
FMO2-HF: Nuclear repulsion	1144779.819258
FMO2-HF: Total energy	-51543.929985
FMO2-MP2: Total energy	-51696.243492

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:7:LYS)

Summations of interaction energy for fragment #1(A:7:LYS)

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.
-141.709	-136.448	12.079	-7.789	-9.547	-0.082

Interaction energy analysis for fragmet #1(A:7:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.903 / q_NPA : 0.946

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	9	ASP	-1	-0.865	-0.923	3.637	-32.053	-29.965	0.001	-0.965	-1.123	0.005
4	A	10	ILE	0	-0.019	-0.029	5.851	2.887	2.887	0.000	0.000	0.000	0.000
5	A	11	LEU	0	0.007	0.024	8.369	-2.204	-2.204	0.000	0.000	0.000	0.000
6	A	12	TYR	0	-0.033	-0.049	9.914	2.522	2.522	0.000	0.000	0.000	0.000
7	A	13	LEU	0	0.004	0.001	13.055	-0.536	-0.536	0.000	0.000	0.000	0.000
8	A	14	GLH	0	-0.032	-0.060	15.261	1.634	1.634	0.000	0.000	0.000	0.000
9	A	15	ASP	-1	-0.893	-0.958	16.793	-15.658	-15.658	0.000	0.000	0.000	0.000
10	A	16	ASP	-1	-0.823	-0.882	19.359	-12.841	-12.841	0.000	0.000	0.000	0.000
11	A	17	GLU	-1	-0.793	-0.908	18.615	-17.621	-17.621	0.000	0.000	0.000	0.000
12	A	18	VAL	0	-0.024	-0.009	20.435	-0.251	-0.251	0.000	0.000	0.000	0.000
13	A	19	ASP	-1	-0.845	-0.909	20.286	-13.939	-13.939	0.000	0.000	0.000	0.000
14	A	20	ILE	0	-0.017	-0.005	15.118	-0.455	-0.455	0.000	0.000	0.000	0.000
15	A	21	GLN	0	-0.002	0.010	16.927	0.320	0.320	0.000	0.000	0.000	0.000
16	A	22	SER	0	-0.102	-0.065	19.068	0.270	0.270	0.000	0.000	0.000	0.000
17	A	23	VAL	0	0.015	0.006	15.437	0.169	0.169	0.000	0.000	0.000	0.000
18	A	24	GLU	-1	-0.867	-0.936	13.338	-21.340	-21.340	0.000	0.000	0.000	0.000
19	A	25	ARG	1	0.897	0.942	15.598	14.597	14.597	0.000	0.000	0.000	0.000
20	A	26	VAL	0	-0.052	-0.025	18.608	0.417	0.417	0.000	0.000	0.000	0.000
21	A	27	PHE	0	0.045	0.007	13.449	0.318	0.318	0.000	0.000	0.000	0.000
22	A	28	HIS	0	0.015	0.017	14.948	-0.650	-0.650	0.000	0.000	0.000	0.000
23	A	29	LYS	1	0.866	0.928	15.933	13.291	13.291	0.000	0.000	0.000	0.000
24	A	30	ILE	0	-0.058	-0.006	15.037	0.705	0.705	0.000	0.000	0.000	0.000
25	A	31	SER	0	0.004	-0.019	11.639	0.094	0.094	0.000	0.000	0.000	0.000
26	A	32	SER	0	0.029	0.027	13.089	-0.337	-0.337	0.000	0.000	0.000	0.000
27	A	33	LEU	0	-0.081	-0.052	8.942	-1.327	-1.327	0.000	0.000	0.000	0.000
28	A	34	ILE	0	-0.028	0.018	7.656	-1.866	-1.866	0.000	0.000	0.000	0.000
29	A	35	LYS	1	0.934	0.964	3.638	36.706	37.117	0.007	-0.089	-0.328	0.000
30	A	36	ILE	0	-0.006	-0.008	7.029	-1.351	-1.351	0.000	0.000	0.000	0.000
31	A	37	GLU	-1	-0.895	-0.942	4.110	-56.292	-56.044	-0.001	-0.054	-0.193	0.000
32	A	38	ILE	0	-0.003	-0.011	7.890	2.615	2.615	0.000	0.000	0.000	0.000
33	A	39	ALA	0	0.008	0.014	10.857	-1.220	-1.220	0.000	0.000	0.000	0.000
34	A	40	LYS	1	0.819	0.879	12.532	20.269	20.269	0.000	0.000	0.000	0.000
35	A	41	SER	0	0.019	-0.010	15.662	1.364	1.364	0.000	0.000	0.000	0.000
36	A	42	GLY	0	0.080	0.028	15.579	-1.216	-1.216	0.000	0.000	0.000	0.000
37	A	43	ASN	0	0.008	-0.004	15.398	-0.844	-0.844	0.000	0.000	0.000	0.000
38	A	44	GLN	0	0.004	0.004	11.409	0.735	0.735	0.000	0.000	0.000	0.000
39	A	45	ALA	0	0.027	0.013	11.211	-2.632	-2.632	0.000	0.000	0.000	0.000
40	A	46	LEU	0	0.001	0.002	10.532	-2.723	-2.723	0.000	0.000	0.000	0.000
41	A	47	ASP	-1	-0.821	-0.890	10.998	-23.607	-23.607	0.000	0.000	0.000	0.000
42	A	48	MET	0	-0.014	0.000	6.977	-2.289	-2.289	0.000	0.000	0.000	0.000
43	A	49	LEU	0	-0.028	-0.003	6.063	-7.109	-7.109	0.000	0.000	0.000	0.000
44	A	50	TYR	0	-0.097	-0.095	8.266	-0.888	-0.888	0.000	0.000	0.000	0.000
45	A	51	GLY	0	-0.072	-0.020	6.936	-0.270	-0.270	0.000	0.000	0.000	0.000
46	A	52	ARG	1	0.870	0.929	7.607	24.661	24.661	0.000	0.000	0.000	0.000
47	A	53	ASN	0	-0.028	-0.044	10.650	-0.200	-0.200	0.000	0.000	0.000	0.000
48	A	54	LYS	1	0.880	0.932	10.823	20.990	20.990	0.000	0.000	0.000	0.000
49	A	55	GLU	-1	-0.802	-0.862	7.412	-34.216	-34.216	0.000	0.000	0.000	0.000
50	A	56	ASN	0	-0.051	-0.030	2.820	0.742	1.210	0.078	-0.152	-0.393	-0.002
51	A	57	LYS	1	0.947	0.972	4.074	30.211	30.979	0.002	-0.407	-0.363	-0.002
52	A	58	ILE	0	-0.083	-0.021	1.862	-50.737	-50.551	11.952	-5.965	-6.173	-0.081
53	A	59	HIS	0	0.044	0.010	3.087	12.546	13.412	0.040	-0.090	-0.816	-0.002
54	A	60	PRO	0	-0.018	0.009	4.118	-1.174	-0.948	0.000	-0.067	-0.158	0.000
55	A	61	LYS	1	0.914	0.957	5.234	26.977	26.977	0.000	0.000	0.000	0.000
56	A	62	LEU	0	-0.023	-0.011	7.245	2.707	2.707	0.000	0.000	0.000	0.000
57	A	63	ILE	0	0.030	0.017	9.996	-2.147	-2.147	0.000	0.000	0.000	0.000
58	A	64	LEU	0	-0.048	-0.012	12.619	1.736	1.736	0.000	0.000	0.000	0.000
59	A	65	LEU	0	0.040	0.006	15.378	-0.638	-0.638	0.000	0.000	0.000	0.000
60	A	66	ASP	-1	-0.748	-0.816	18.165	-13.207	-13.207	0.000	0.000	0.000	0.000
61	A	67	ILE	0	-0.017	-0.016	20.725	-0.040	-0.040	0.000	0.000	0.000	0.000
62	A	68	ASN	0	-0.068	-0.025	23.638	0.576	0.576	0.000	0.000	0.000	0.000
63	A	69	ILE	0	0.035	0.023	20.814	0.451	0.451	0.000	0.000	0.000	0.000
64	A	70	PRO	0	-0.011	-0.013	24.751	-0.181	-0.181	0.000	0.000	0.000	0.000
65	A	71	LYS	1	0.945	0.973	24.865	11.972	11.972	0.000	0.000	0.000	0.000
66	A	72	MET	0	-0.029	0.018	18.364	-0.638	-0.638	0.000	0.000	0.000	0.000
67	A	73	ASN	0	0.005	-0.003	22.615	-0.072	-0.072	0.000	0.000	0.000	0.000
68	A	74	GLY	0	0.064	0.022	20.934	-0.514	-0.514	0.000	0.000	0.000	0.000
69	A	75	ILE	0	0.002	-0.003	21.454	-0.338	-0.338	0.000	0.000	0.000	0.000
70	A	76	GLU	-1	-0.927	-0.963	23.063	-12.586	-12.586	0.000	0.000	0.000	0.000
71	A	77	PHE	0	0.027	0.015	13.861	-0.199	-0.199	0.000	0.000	0.000	0.000
72	A	78	LEU	0	0.006	-0.013	17.915	-0.538	-0.538	0.000	0.000	0.000	0.000
73	A	79	LYS	1	0.923	0.960	19.898	11.898	11.898	0.000	0.000	0.000	0.000
74	A	80	GLU	-1	-0.861	-0.922	17.389	-17.430	-17.430	0.000	0.000	0.000	0.000
75	A	81	LEU	0	-0.066	-0.032	13.328	-0.517	-0.517	0.000	0.000	0.000	0.000
76	A	82	ARG	1	0.765	0.852	14.965	16.939	16.939	0.000	0.000	0.000	0.000
77	A	83	ASP	-1	-0.900	-0.927	19.482	-13.068	-13.068	0.000	0.000	0.000	0.000
78	A	84	ASP	-1	-0.820	-0.851	15.488	-19.896	-19.896	0.000	0.000	0.000	0.000
79	A	85	SER	0	0.040	0.005	16.716	-0.295	-0.295	0.000	0.000	0.000	0.000
80	A	86	SER	0	-0.116	-0.070	12.439	-0.205	-0.205	0.000	0.000	0.000	0.000
81	A	87	PHE	0	-0.045	-0.040	10.198	-2.236	-2.236	0.000	0.000	0.000	0.000
82	A	88	THR	0	-0.037	-0.017	13.349	0.518	0.518	0.000	0.000	0.000	0.000
83	A	89	ASP	-1	-0.939	-0.969	11.333	-17.946	-17.946	0.000	0.000	0.000	0.000
84	A	90	ILE	0	-0.061	-0.002	9.441	-0.525	-0.525	0.000	0.000	0.000	0.000
85	A	91	GLU	-1	-0.815	-0.889	11.531	-14.503	-14.503	0.000	0.000	0.000	0.000
86	A	92	VAL	0	0.006	-0.003	13.085	-1.104	-1.104	0.000	0.000	0.000	0.000
87	A	93	PHE	0	0.002	-0.005	15.354	1.329	1.329	0.000	0.000	0.000	0.000
88	A	94	VAL	0	0.007	0.015	17.808	-0.601	-0.601	0.000	0.000	0.000	0.000
89	A	95	LEU	0	-0.016	-0.018	19.636	0.499	0.499	0.000	0.000	0.000	0.000
90	A	96	THR	0	0.045	0.022	21.908	0.094	0.094	0.000	0.000	0.000	0.000
91	A	97	ALA	0	0.009	-0.002	25.609	0.102	0.102	0.000	0.000	0.000	0.000
92	A	98	ALA	0	-0.030	-0.030	28.645	0.461	0.461	0.000	0.000	0.000	0.000
93	A	99	TYR	0	0.019	0.023	25.765	-0.043	-0.043	0.000	0.000	0.000	0.000
94	A	100	THR	0	-0.030	-0.048	29.469	0.499	0.499	0.000	0.000	0.000	0.000
95	A	101	SER	0	0.039	-0.003	31.394	-0.230	-0.230	0.000	0.000	0.000	0.000
96	A	102	LYS	1	0.961	0.986	31.934	9.826	9.826	0.000	0.000	0.000	0.000
97	A	103	ASP	-1	-0.792	-0.866	27.694	-11.088	-11.088	0.000	0.000	0.000	0.000
98	A	104	LYS	1	0.835	0.904	28.290	9.456	9.456	0.000	0.000	0.000	0.000
99	A	105	LEU	0	-0.029	-0.032	29.187	-0.095	-0.095	0.000	0.000	0.000	0.000
100	A	106	ALA	0	-0.054	-0.016	28.500	-0.052	-0.052	0.000	0.000	0.000	0.000
101	A	107	PHE	0	0.009	-0.015	23.799	-0.322	-0.322	0.000	0.000	0.000	0.000
102	A	108	GLU	-1	-0.852	-0.885	24.888	-10.523	-10.523	0.000	0.000	0.000	0.000
103	A	109	SER	0	-0.026	-0.014	26.388	-0.142	-0.142	0.000	0.000	0.000	0.000
104	A	110	LEU	0	-0.012	-0.005	22.060	-0.208	-0.208	0.000	0.000	0.000	0.000
105	A	111	ASN	0	0.003	0.006	18.425	-0.269	-0.269	0.000	0.000	0.000	0.000
106	A	112	ILE	0	-0.001	0.015	19.115	-0.835	-0.835	0.000	0.000	0.000	0.000
107	A	113	ARG	1	0.884	0.940	15.656	15.700	15.700	0.000	0.000	0.000	0.000
108	A	114	GLY	0	0.000	-0.010	19.411	0.637	0.637	0.000	0.000	0.000	0.000
109	A	115	HIS	0	-0.018	0.001	20.780	-0.764	-0.764	0.000	0.000	0.000	0.000
110	A	116	LEU	0	-0.059	-0.037	18.323	0.311	0.311	0.000	0.000	0.000	0.000
111	A	117	ILE	0	0.013	0.002	22.861	-0.044	-0.044	0.000	0.000	0.000	0.000
112	A	118	LYS	1	0.823	0.926	22.871	13.373	13.373	0.000	0.000	0.000	0.000
113	A	119	PRO	0	0.011	-0.010	24.908	0.437	0.437	0.000	0.000	0.000	0.000
114	A	120	LEU	0	0.024	0.010	17.698	0.135	0.135	0.000	0.000	0.000	0.000
115	A	121	ASP	-1	-0.860	-0.932	21.396	-12.253	-12.253	0.000	0.000	0.000	0.000
116	A	122	TYR	0	0.056	0.000	20.226	-0.347	-0.347	0.000	0.000	0.000	0.000
117	A	123	GLY	0	0.029	0.022	20.540	-0.299	-0.299	0.000	0.000	0.000	0.000
118	A	124	GLH	0	-0.059	-0.055	20.537	-0.398	-0.398	0.000	0.000	0.000	0.000
119	A	125	ALA	0	0.050	0.024	16.686	-0.468	-0.468	0.000	0.000	0.000	0.000
120	A	126	ILE	0	-0.008	-0.005	15.938	-0.779	-0.779	0.000	0.000	0.000	0.000
121	A	127	LYS	1	0.917	0.974	16.998	12.895	12.895	0.000	0.000	0.000	0.000
122	A	128	LEU	0	-0.002	-0.006	13.909	-0.140	-0.140	0.000	0.000	0.000	0.000
123	A	129	PHE	0	0.020	0.013	11.206	-0.923	-0.923	0.000	0.000	0.000	0.000
124	A	130	TRP	0	0.034	0.001	12.488	-0.600	-0.600	0.000	0.000	0.000	0.000
125	A	131	ILE	0	-0.023	0.005	12.957	0.174	0.174	0.000	0.000	0.000	0.000
126	A	132	LEU	0	0.050	0.024	7.598	-0.239	-0.239	0.000	0.000	0.000	0.000
127	A	133	GLN	0	-0.067	-0.022	9.379	-0.286	-0.286	0.000	0.000	0.000	0.000
128	A	134	SER	0	-0.084	-0.020	11.468	0.350	0.350	0.000	0.000	0.000	0.000
129	A	135	MET	0	-0.041	-0.021	9.599	-1.207	-1.207	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:7:LYS)