FMO DATABASE

FMODB ID: 4363N

Calculation Name: 1VGG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VGG

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SJC3

Base Structure: X-ray

Registration Date: 2023-03-13

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	OptH
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	161
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1468441.022906
FMO2-HF: Nuclear repulsion	1407375.519388
FMO2-HF: Total energy	-61065.503517
FMO2-MP2: Total energy	-61245.788058

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:1:MET)

Summations of interaction energy for fragment #1(A:1: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.
-26.02	-19.903	16.546	-9.685	-12.978	-0.079

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.033 / q_NPA : -0.004

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	3	LEU	0	-0.033	-0.022	2.647	-2.673	-0.077	0.496	-1.235	-1.858	0.003
4	A	4	LYS	1	0.915	0.962	5.125	1.470	1.553	-0.001	-0.008	-0.073	0.000
5	A	5	LEU	0	-0.011	-0.009	8.638	0.151	0.151	0.000	0.000	0.000	0.000
6	A	6	ILE	0	-0.005	-0.010	10.898	-0.011	-0.011	0.000	0.000	0.000	0.000
7	A	7	PRO	0	-0.045	-0.027	14.031	0.046	0.046	0.000	0.000	0.000	0.000
8	A	8	ILE	0	0.005	0.011	17.218	-0.004	-0.004	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.874	-0.918	19.712	-0.033	-0.033	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.828	0.896	22.910	-0.021	-0.021	0.000	0.000	0.000	0.000
11	A	11	PRO	0	0.033	0.034	25.876	0.000	0.000	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.892	-0.954	28.759	0.005	0.005	0.000	0.000	0.000	0.000
13	A	13	ASN	0	-0.035	-0.012	29.898	0.003	0.003	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.051	-0.011	29.019	0.002	0.002	0.000	0.000	0.000	0.000
15	A	15	ASN	0	0.018	-0.002	27.664	0.007	0.007	0.000	0.000	0.000	0.000
16	A	16	VAL	0	-0.010	0.004	22.516	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	17	ILE	0	0.002	-0.007	23.482	0.008	0.008	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.003	0.015	15.944	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.033	0.003	18.623	0.020	0.020	0.000	0.000	0.000	0.000
20	A	20	GLN	0	-0.006	0.033	13.856	0.035	0.035	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.011	0.006	17.747	-0.012	-0.012	0.000	0.000	0.000	0.000
22	A	22	HIS	0	-0.053	-0.035	18.518	0.015	0.015	0.000	0.000	0.000	0.000
23	A	23	PHE	0	0.075	0.031	20.597	-0.014	-0.014	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.064	0.018	23.369	0.002	0.002	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.851	0.926	25.083	-0.063	-0.063	0.000	0.000	0.000	0.000
26	A	26	THR	0	-0.006	-0.010	22.793	0.005	0.005	0.000	0.000	0.000	0.000
27	A	27	VAL	0	-0.046	-0.027	25.196	0.000	0.000	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.897	-0.948	27.251	0.026	0.026	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.703	-0.803	28.908	0.062	0.062	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.020	-0.021	24.609	0.002	0.002	0.000	0.000	0.000	0.000
31	A	31	HIS	0	0.001	0.036	29.138	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.917	-0.970	31.518	0.036	0.036	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.017	-0.008	31.239	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.053	-0.030	29.182	0.000	0.000	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.029	-0.020	33.481	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.040	-0.008	36.474	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.075	-0.027	35.297	0.000	0.000	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.027	-0.017	36.489	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	39	PRO	0	0.018	0.018	38.804	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.012	-0.010	41.030	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	41	ILE	0	-0.040	0.004	33.529	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.889	0.947	35.472	-0.015	-0.015	0.000	0.000	0.000	0.000
43	A	43	PHE	0	0.015	-0.012	29.810	0.003	0.003	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.035	0.027	28.982	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.036	-0.009	24.629	0.007	0.007	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.012	0.006	22.340	-0.010	-0.010	0.000	0.000	0.000	0.000
47	A	47	PHE	0	0.012	-0.014	19.487	0.014	0.014	0.000	0.000	0.000	0.000
48	A	48	SER	0	0.014	0.012	15.441	-0.031	-0.031	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.826	-0.892	17.368	0.012	0.012	0.000	0.000	0.000	0.000
50	A	50	ALA	0	0.022	0.006	14.391	-0.020	-0.020	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.024	-0.004	15.646	-0.019	-0.019	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.064	0.022	18.311	0.003	0.003	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.903	0.941	20.667	0.044	0.044	0.000	0.000	0.000	0.000
54	A	54	ARG	1	0.851	0.937	14.132	0.227	0.227	0.000	0.000	0.000	0.000
55	A	55	LEU	0	0.002	0.002	19.018	-0.013	-0.013	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.031	0.019	19.016	0.015	0.015	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.795	0.890	21.241	0.003	0.003	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.845	0.889	24.123	0.013	0.013	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.011	-0.026	26.795	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.028	0.000	29.427	0.004	0.004	0.000	0.000	0.000	0.000
61	A	61	THR	0	-0.032	-0.022	32.003	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.788	-0.880	33.630	0.006	0.006	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.739	-0.856	32.164	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	64	ALA	0	0.043	0.035	31.640	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.058	-0.019	29.680	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.017	-0.007	28.018	0.003	0.003	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.945	-0.969	26.836	-0.017	-0.017	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.003	0.006	24.954	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.003	-0.005	23.660	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	70	VAL	0	0.005	-0.014	22.083	0.001	0.001	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.855	0.918	21.324	0.034	0.034	0.000	0.000	0.000	0.000
72	A	72	ASN	0	-0.014	-0.018	19.552	-0.019	-0.019	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.018	-0.005	17.452	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.037	-0.008	16.496	-0.013	-0.013	0.000	0.000	0.000	0.000
75	A	75	ASN	0	-0.012	0.004	16.133	-0.044	-0.044	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.017	-0.017	13.185	-0.039	-0.039	0.000	0.000	0.000	0.000
77	A	77	ALA	0	0.006	0.026	11.765	-0.026	-0.026	0.000	0.000	0.000	0.000
78	A	78	CYS	0	-0.002	-0.002	10.605	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	79	GLY	0	0.026	0.007	11.342	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	80	HIS	0	-0.012	-0.033	13.278	0.052	0.052	0.000	0.000	0.000	0.000
81	A	81	VAL	0	0.006	0.033	13.572	0.023	0.023	0.000	0.000	0.000	0.000
82	A	82	PHE	0	-0.028	-0.017	16.408	-0.041	-0.041	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.011	-0.010	19.889	0.018	0.018	0.000	0.000	0.000	0.000
84	A	84	ILE	0	0.012	0.012	21.876	-0.011	-0.011	0.000	0.000	0.000	0.000
85	A	85	VAL	0	0.001	-0.004	25.193	0.005	0.005	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.015	-0.020	27.220	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	87	GLY	0	0.040	-0.001	30.568	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.902	-0.970	33.567	0.017	0.017	0.000	0.000	0.000	0.000
89	A	89	GLY	0	-0.018	0.001	35.513	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	90	PHE	0	0.016	0.022	34.166	0.002	0.002	0.000	0.000	0.000	0.000
91	A	91	TYR	0	0.034	0.000	32.126	0.001	0.001	0.000	0.000	0.000	0.000
92	A	92	PRO	0	0.076	0.026	27.861	0.002	0.002	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.043	-0.014	30.015	0.004	0.004	0.000	0.000	0.000	0.000
94	A	94	ASN	0	-0.026	-0.012	32.376	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	95	VAL	0	0.061	0.020	29.964	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.004	0.000	25.989	0.005	0.005	0.000	0.000	0.000	0.000
97	A	97	HIS	0	-0.049	-0.016	29.001	0.012	0.012	0.000	0.000	0.000	0.000
98	A	98	ALA	0	0.087	0.038	31.096	0.004	0.004	0.000	0.000	0.000	0.000
99	A	99	VAL	0	-0.033	-0.007	25.087	0.003	0.003	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.913	0.936	26.005	-0.104	-0.104	0.000	0.000	0.000	0.000
101	A	101	ALA	0	-0.003	0.011	27.088	0.007	0.007	0.000	0.000	0.000	0.000
102	A	102	CYS	0	-0.017	0.026	27.001	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	103	PRO	0	0.033	0.004	26.811	0.011	0.011	0.000	0.000	0.000	0.000
104	A	104	GLH	0	-0.033	-0.055	24.071	0.006	0.006	0.000	0.000	0.000	0.000
105	A	105	VAL	0	-0.061	-0.024	22.281	0.018	0.018	0.000	0.000	0.000	0.000
106	A	106	VAL	0	-0.023	0.003	17.888	0.004	0.004	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.951	0.964	11.991	-0.593	-0.593	0.000	0.000	0.000	0.000
108	A	108	ILE	0	-0.004	-0.009	19.781	-0.008	-0.008	0.000	0.000	0.000	0.000
109	A	109	TYR	0	-0.079	-0.063	13.530	0.051	0.051	0.000	0.000	0.000	0.000
110	A	110	ALA	0	0.034	0.004	17.853	-0.005	-0.005	0.000	0.000	0.000	0.000
111	A	111	ALA	0	-0.016	0.001	20.441	-0.006	-0.006	0.000	0.000	0.000	0.000
112	A	112	THR	0	-0.052	-0.024	22.276	-0.005	-0.005	0.000	0.000	0.000	0.000
113	A	113	ALA	0	0.077	0.033	25.270	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	114	ASN	0	-0.043	0.002	24.067	-0.015	-0.015	0.000	0.000	0.000	0.000
115	A	115	PRO	0	-0.011	-0.015	23.023	0.002	0.002	0.000	0.000	0.000	0.000
116	A	116	LEU	0	0.037	0.029	18.212	0.007	0.007	0.000	0.000	0.000	0.000
117	A	117	LYS	1	0.929	0.967	15.414	0.003	0.003	0.000	0.000	0.000	0.000
118	A	118	VAL	0	0.017	0.008	11.688	0.032	0.032	0.000	0.000	0.000	0.000
119	A	119	VAL	0	0.013	0.020	7.374	-0.093	-0.093	0.000	0.000	0.000	0.000
120	A	120	VAL	0	0.002	-0.007	7.405	0.243	0.243	0.000	0.000	0.000	0.000
121	A	121	ALA	0	0.026	0.013	2.596	-0.839	-1.534	3.472	-1.007	-1.770	0.003
122	A	122	GLU	-1	-0.859	-0.939	2.985	-0.924	0.010	0.091	-0.261	-0.765	-0.001
123	A	123	GLU	-1	-0.817	-0.921	1.969	-24.419	-21.643	12.474	-7.104	-8.146	-0.084
124	A	124	GLY	0	-0.006	0.007	3.692	1.237	1.410	0.015	-0.040	-0.148	0.000
125	A	125	GLU	-1	-0.906	-0.948	7.002	-0.292	-0.292	0.000	0.000	0.000	0.000
126	A	126	GLN	0	-0.043	-0.022	6.511	0.563	0.563	0.000	0.000	0.000	0.000
127	A	127	ARG	1	0.832	0.894	5.896	0.000	0.000	0.000	0.000	0.000	0.000
128	A	128	ALA	0	-0.031	-0.003	5.881	0.075	0.132	-0.001	-0.003	-0.052	0.000
129	A	129	ILE	0	0.025	0.008	7.621	-0.018	-0.018	0.000	0.000	0.000	0.000
130	A	130	LEU	0	-0.065	-0.043	4.185	-0.070	0.123	0.000	-0.027	-0.166	0.000
131	A	131	GLY	0	0.008	0.001	8.761	-0.088	-0.088	0.000	0.000	0.000	0.000
132	A	132	VAL	0	-0.035	-0.009	12.041	-0.041	-0.041	0.000	0.000	0.000	0.000
133	A	133	MET	0	-0.017	-0.011	12.737	-0.010	-0.010	0.000	0.000	0.000	0.000
134	A	134	ASP	-1	-0.805	-0.904	16.770	0.071	0.071	0.000	0.000	0.000	0.000
135	A	135	GLY	0	0.018	0.012	20.233	0.000	0.000	0.000	0.000	0.000	0.000
136	A	136	PHE	0	-0.049	-0.036	21.492	-0.003	-0.003	0.000	0.000	0.000	0.000
137	A	137	THR	0	0.026	0.014	21.459	0.005	0.005	0.000	0.000	0.000	0.000
138	A	138	PRO	0	-0.021	-0.010	23.869	-0.003	-0.003	0.000	0.000	0.000	0.000
139	A	139	LEU	0	0.021	-0.002	27.209	-0.003	-0.003	0.000	0.000	0.000	0.000
140	A	140	GLY	0	-0.004	0.004	30.214	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	141	VAL	0	-0.073	-0.035	31.462	0.004	0.004	0.000	0.000	0.000	0.000
142	A	142	GLU	-1	-0.768	-0.850	33.732	0.039	0.039	0.000	0.000	0.000	0.000
143	A	143	ASP	-1	-0.794	-0.894	36.415	0.025	0.025	0.000	0.000	0.000	0.000
144	A	144	GLU	-1	-0.901	-0.994	40.014	0.032	0.032	0.000	0.000	0.000	0.000
145	A	145	ALA	0	-0.052	-0.009	42.793	0.000	0.000	0.000	0.000	0.000	0.000
146	A	146	GLU	-1	-0.862	-0.931	38.188	0.026	0.026	0.000	0.000	0.000	0.000
147	A	147	VAL	0	-0.035	-0.001	38.716	0.002	0.002	0.000	0.000	0.000	0.000
148	A	148	ALA	0	-0.045	-0.038	40.312	0.001	0.001	0.000	0.000	0.000	0.000
149	A	149	TRP	0	0.034	0.020	39.765	0.000	0.000	0.000	0.000	0.000	0.000
150	A	150	ARG	1	0.823	0.888	36.220	-0.042	-0.042	0.000	0.000	0.000	0.000
151	A	151	LYS	1	0.868	0.931	39.479	-0.033	-0.033	0.000	0.000	0.000	0.000
152	A	152	ASP	-1	-0.798	-0.889	41.888	0.023	0.023	0.000	0.000	0.000	0.000
153	A	153	LEU	0	0.024	0.019	37.923	0.000	0.000	0.000	0.000	0.000	0.000
154	A	154	LEU	0	-0.006	-0.018	37.270	0.000	0.000	0.000	0.000	0.000	0.000
155	A	155	ARG	1	0.812	0.912	41.298	-0.033	-0.033	0.000	0.000	0.000	0.000
156	A	156	ARG	1	0.859	0.919	44.739	-0.021	-0.021	0.000	0.000	0.000	0.000
157	A	157	LEU	0	-0.032	-0.010	39.026	-0.001	-0.001	0.000	0.000	0.000	0.000
158	A	158	GLY	0	0.026	0.031	43.156	0.000	0.000	0.000	0.000	0.000	0.000
159	A	159	TYR	0	-0.020	-0.006	37.806	0.002	0.002	0.000	0.000	0.000	0.000
160	A	160	LYS	1	0.873	0.931	38.734	-0.044	-0.044	0.000	0.000	0.000	0.000
161	A	161	LEU	0	0.070	0.041	43.484	-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:1:MET)