FMO DATABASE

FMODB ID: 53Y3Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1467894.425961
FMO2-HF: Nuclear repulsion	1406828.51753
FMO2-HF: Total energy	-61065.908431
FMO2-MP2: Total energy	-61246.123893

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.
-25.069	-20.289	18.656	-10.02	-13.416	-0.085

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 : -0.039 / q_NPA : -0.013

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	-0.031	-0.016	2.516	-2.100	0.485	0.658	-1.241	-2.003	0.001
4	A	4	LYS	1	0.826	0.897	5.303	1.013	1.090	-0.001	-0.007	-0.069	0.000
5	A	5	LEU	0	-0.019	-0.013	8.561	0.160	0.160	0.000	0.000	0.000	0.000
6	A	6	ILE	0	0.003	-0.008	10.879	-0.013	-0.013	0.000	0.000	0.000	0.000
7	A	7	PRO	0	-0.041	-0.022	14.033	0.041	0.041	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.004	0.005	17.192	0.002	0.002	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.867	-0.901	19.761	-0.008	-0.008	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.836	0.896	22.950	-0.034	-0.034	0.000	0.000	0.000	0.000
11	A	11	PRO	0	0.028	0.025	25.932	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.905	-0.956	28.897	0.016	0.016	0.000	0.000	0.000	0.000
13	A	13	ASN	0	-0.038	-0.018	30.075	0.003	0.003	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.044	-0.007	29.220	0.002	0.002	0.000	0.000	0.000	0.000
15	A	15	ASN	0	0.006	-0.001	27.831	0.005	0.005	0.000	0.000	0.000	0.000
16	A	16	VAL	0	-0.006	0.001	22.714	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	17	ILE	0	0.004	-0.007	23.574	0.005	0.005	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.004	0.015	16.224	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.037	0.006	18.682	0.015	0.015	0.000	0.000	0.000	0.000
20	A	20	GLN	0	-0.016	0.027	13.871	0.059	0.059	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.016	0.010	17.773	-0.019	-0.019	0.000	0.000	0.000	0.000
22	A	22	HIS	0	-0.049	-0.037	18.665	0.022	0.022	0.000	0.000	0.000	0.000
23	A	23	PHE	0	0.080	0.034	20.749	-0.017	-0.017	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.048	0.016	23.510	0.002	0.002	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.835	0.908	25.175	-0.085	-0.085	0.000	0.000	0.000	0.000
26	A	26	THR	0	-0.008	-0.009	22.776	0.002	0.002	0.000	0.000	0.000	0.000
27	A	27	VAL	0	-0.045	-0.025	25.185	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.888	-0.944	27.295	0.051	0.051	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.701	-0.795	28.973	0.084	0.084	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.008	-0.015	24.698	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	31	HIS	0	-0.001	0.025	29.202	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.914	-0.968	31.547	0.052	0.052	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.034	-0.003	31.293	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.040	-0.024	29.150	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.021	-0.019	33.517	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.049	-0.021	36.522	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.073	-0.025	35.346	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.029	-0.020	36.607	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	39	PRO	0	0.029	0.021	38.837	0.000	0.000	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.003	-0.011	41.005	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	41	ILE	0	-0.044	0.002	33.652	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.871	0.939	35.558	-0.029	-0.029	0.000	0.000	0.000	0.000
43	A	43	PHE	0	0.004	-0.015	29.798	0.003	0.003	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.032	0.024	28.899	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.041	-0.013	24.632	0.007	0.007	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.020	0.009	22.383	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	47	PHE	0	0.015	-0.011	19.402	0.014	0.014	0.000	0.000	0.000	0.000
48	A	48	SER	0	0.037	0.026	16.169	-0.028	-0.028	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.827	-0.877	17.400	0.075	0.075	0.000	0.000	0.000	0.000
50	A	50	ALA	0	0.008	-0.002	14.549	-0.014	-0.014	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.015	-0.001	15.725	-0.012	-0.012	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.070	0.026	18.390	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.885	0.937	20.685	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	54	ARG	1	0.815	0.901	13.411	0.082	0.082	0.000	0.000	0.000	0.000
55	A	55	LEU	0	0.009	0.004	18.959	-0.010	-0.010	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.022	0.011	18.828	0.015	0.015	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.785	0.874	21.173	-0.056	-0.056	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.868	0.882	24.080	-0.020	-0.020	0.000	0.000	0.000	0.000
59	A	59	SER	0	0.000	-0.014	26.742	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.028	0.001	29.384	0.004	0.004	0.000	0.000	0.000	0.000
61	A	61	THR	0	-0.024	-0.023	31.954	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.784	-0.881	33.589	0.024	0.024	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.757	-0.846	32.261	0.026	0.026	0.000	0.000	0.000	0.000
64	A	64	ALA	0	0.049	0.034	31.504	0.000	0.000	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.041	-0.008	29.741	0.000	0.000	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.025	-0.010	27.981	0.005	0.005	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.955	-0.969	26.716	0.015	0.015	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.005	0.004	24.982	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.013	0.006	23.639	0.002	0.002	0.000	0.000	0.000	0.000
70	A	70	VAL	0	0.006	-0.015	21.963	0.007	0.007	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.843	0.903	21.170	0.003	0.003	0.000	0.000	0.000	0.000
72	A	72	ASN	0	-0.024	-0.023	19.637	-0.010	-0.010	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.008	-0.002	17.261	0.005	0.005	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.040	-0.010	16.355	0.000	0.000	0.000	0.000	0.000	0.000
75	A	75	ASN	0	-0.010	0.005	16.033	-0.029	-0.029	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.006	-0.012	13.278	-0.026	-0.026	0.000	0.000	0.000	0.000
77	A	77	ALA	0	0.010	0.029	11.645	0.001	0.001	0.000	0.000	0.000	0.000
78	A	78	CYS	0	-0.012	-0.005	10.466	0.028	0.028	0.000	0.000	0.000	0.000
79	A	79	GLY	0	0.036	0.012	11.361	-0.023	-0.023	0.000	0.000	0.000	0.000
80	A	80	HIS	0	-0.020	-0.040	13.319	0.050	0.050	0.000	0.000	0.000	0.000
81	A	81	VAL	0	0.013	0.035	13.530	0.011	0.011	0.000	0.000	0.000	0.000
82	A	82	PHE	0	-0.026	-0.017	16.441	-0.039	-0.039	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.012	-0.010	19.889	0.016	0.016	0.000	0.000	0.000	0.000
84	A	84	ILE	0	0.010	0.009	21.840	-0.011	-0.011	0.000	0.000	0.000	0.000
85	A	85	VAL	0	0.003	-0.004	25.220	0.003	0.003	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.012	-0.017	27.330	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	87	GLY	0	0.055	0.008	30.699	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.896	-0.961	33.684	0.026	0.026	0.000	0.000	0.000	0.000
89	A	89	GLY	0	-0.017	0.001	35.678	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	90	PHE	0	0.006	0.016	34.323	0.001	0.001	0.000	0.000	0.000	0.000
91	A	91	TYR	0	0.035	0.004	32.255	0.002	0.002	0.000	0.000	0.000	0.000
92	A	92	PRO	0	0.078	0.026	28.012	0.002	0.002	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.049	-0.018	30.142	0.004	0.004	0.000	0.000	0.000	0.000
94	A	94	ASN	0	-0.016	-0.009	32.490	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	95	VAL	0	0.062	0.025	30.096	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.004	0.000	26.098	0.006	0.006	0.000	0.000	0.000	0.000
97	A	97	HIS	0	-0.056	-0.022	29.077	0.012	0.012	0.000	0.000	0.000	0.000
98	A	98	ALA	0	0.075	0.034	31.169	0.004	0.004	0.000	0.000	0.000	0.000
99	A	99	VAL	0	-0.022	-0.006	25.127	0.005	0.005	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.915	0.938	25.945	-0.112	-0.112	0.000	0.000	0.000	0.000
101	A	101	ALA	0	-0.006	0.009	27.163	0.007	0.007	0.000	0.000	0.000	0.000
102	A	102	CYS	0	-0.027	0.023	27.015	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	103	PRO	0	0.046	0.010	26.854	0.012	0.012	0.000	0.000	0.000	0.000
104	A	104	GLH	0	-0.029	-0.058	24.218	0.006	0.006	0.000	0.000	0.000	0.000
105	A	105	VAL	0	-0.060	-0.019	22.321	0.023	0.023	0.000	0.000	0.000	0.000
106	A	106	VAL	0	-0.022	0.002	17.912	0.001	0.001	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.921	0.947	11.952	-0.614	-0.614	0.000	0.000	0.000	0.000
108	A	108	ILE	0	-0.007	-0.013	19.844	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	109	TYR	0	-0.063	-0.045	13.185	0.046	0.046	0.000	0.000	0.000	0.000
110	A	110	ALA	0	0.029	0.008	17.949	-0.011	-0.011	0.000	0.000	0.000	0.000
111	A	111	ALA	0	-0.010	-0.008	20.563	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	112	THR	0	-0.057	-0.039	22.392	-0.008	-0.008	0.000	0.000	0.000	0.000
113	A	113	ALA	0	0.064	0.030	25.413	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	114	ASN	0	-0.060	-0.016	24.164	-0.014	-0.014	0.000	0.000	0.000	0.000
115	A	115	PRO	0	0.000	-0.011	23.021	0.004	0.004	0.000	0.000	0.000	0.000
116	A	116	LEU	0	0.020	0.020	18.438	0.005	0.005	0.000	0.000	0.000	0.000
117	A	117	LYS	1	0.944	0.974	15.726	-0.004	-0.004	0.000	0.000	0.000	0.000
118	A	118	VAL	0	0.015	0.006	11.961	0.025	0.025	0.000	0.000	0.000	0.000
119	A	119	VAL	0	0.011	0.021	7.525	-0.083	-0.083	0.000	0.000	0.000	0.000
120	A	120	VAL	0	0.007	-0.006	7.507	0.224	0.224	0.000	0.000	0.000	0.000
121	A	121	ALA	0	0.019	0.013	2.794	-0.790	-1.604	3.448	-0.948	-1.685	0.003
122	A	122	GLU	-1	-0.801	-0.876	3.044	-0.746	0.202	0.094	-0.259	-0.783	-0.001
123	A	123	GLU	-1	-0.831	-0.930	1.903	-23.357	-21.783	14.438	-7.504	-8.508	-0.088
124	A	124	GLY	0	0.033	0.026	3.643	1.002	1.193	0.021	-0.040	-0.173	0.000
125	A	125	GLU	-1	-0.884	-0.923	6.873	-0.101	-0.101	0.000	0.000	0.000	0.000
126	A	126	GLN	0	-0.050	-0.026	6.605	0.418	0.418	0.000	0.000	0.000	0.000
127	A	127	ARG	1	0.813	0.874	5.822	-0.136	-0.136	0.000	0.000	0.000	0.000
128	A	128	ALA	0	-0.038	-0.010	5.881	0.013	0.067	-0.001	-0.003	-0.049	0.000
129	A	129	ILE	0	0.024	0.011	7.691	-0.008	-0.008	0.000	0.000	0.000	0.000
130	A	130	LEU	0	-0.057	-0.039	4.279	-0.087	0.078	-0.001	-0.018	-0.146	0.000
131	A	131	GLY	0	0.003	-0.002	8.892	-0.110	-0.110	0.000	0.000	0.000	0.000
132	A	132	VAL	0	-0.035	-0.003	12.154	-0.027	-0.027	0.000	0.000	0.000	0.000
133	A	133	MET	0	-0.018	-0.015	12.918	-0.015	-0.015	0.000	0.000	0.000	0.000
134	A	134	ASP	-1	-0.793	-0.879	16.918	0.079	0.079	0.000	0.000	0.000	0.000
135	A	135	GLY	0	0.033	0.020	20.374	-0.003	-0.003	0.000	0.000	0.000	0.000
136	A	136	PHE	0	-0.055	-0.037	21.633	-0.004	-0.004	0.000	0.000	0.000	0.000
137	A	137	THR	0	0.027	0.015	21.639	0.005	0.005	0.000	0.000	0.000	0.000
138	A	138	PRO	0	-0.012	-0.008	23.981	-0.002	-0.002	0.000	0.000	0.000	0.000
139	A	139	LEU	0	0.012	-0.005	27.310	-0.005	-0.005	0.000	0.000	0.000	0.000
140	A	140	GLY	0	-0.002	0.006	30.317	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	141	VAL	0	-0.072	-0.035	31.712	0.004	0.004	0.000	0.000	0.000	0.000
142	A	142	GLU	-1	-0.766	-0.826	33.982	0.033	0.033	0.000	0.000	0.000	0.000
143	A	143	ASP	-1	-0.809	-0.900	36.659	0.017	0.017	0.000	0.000	0.000	0.000
144	A	144	GLU	-1	-0.905	-0.993	40.257	0.026	0.026	0.000	0.000	0.000	0.000
145	A	145	ALA	0	-0.042	-0.005	43.024	0.001	0.001	0.000	0.000	0.000	0.000
146	A	146	GLU	-1	-0.866	-0.941	37.899	0.020	0.020	0.000	0.000	0.000	0.000
147	A	147	VAL	0	-0.022	-0.004	38.810	0.002	0.002	0.000	0.000	0.000	0.000
148	A	148	ALA	0	-0.043	-0.033	40.532	0.002	0.002	0.000	0.000	0.000	0.000
149	A	149	TRP	0	0.043	0.025	39.832	0.001	0.001	0.000	0.000	0.000	0.000
150	A	150	ARG	1	0.814	0.865	36.374	-0.036	-0.036	0.000	0.000	0.000	0.000
151	A	151	LYS	1	0.862	0.937	39.641	-0.027	-0.027	0.000	0.000	0.000	0.000
152	A	152	ASP	-1	-0.792	-0.890	42.086	0.022	0.022	0.000	0.000	0.000	0.000
153	A	153	LEU	0	0.016	0.017	38.205	0.000	0.000	0.000	0.000	0.000	0.000
154	A	154	LEU	0	0.005	-0.011	37.324	0.001	0.001	0.000	0.000	0.000	0.000
155	A	155	ARG	1	0.827	0.922	41.418	-0.031	-0.031	0.000	0.000	0.000	0.000
156	A	156	ARG	1	0.821	0.896	44.803	-0.021	-0.021	0.000	0.000	0.000	0.000
157	A	157	LEU	0	-0.037	-0.012	39.137	0.000	0.000	0.000	0.000	0.000	0.000
158	A	158	GLY	0	0.028	0.030	43.286	0.000	0.000	0.000	0.000	0.000	0.000
159	A	159	TYR	0	-0.023	-0.007	37.697	0.002	0.002	0.000	0.000	0.000	0.000
160	A	160	LYS	1	0.875	0.930	38.644	-0.044	-0.044	0.000	0.000	0.000	0.000
161	A	161	LEU	0	0.086	0.052	43.638	-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)