FMO DATABASE

FMODB ID: VKKG1

Calculation Name: 5VT9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5VT9

Chain ID: A

ChEMBL ID:

UniProt ID: O00934

Base Structure: X-ray

Registration Date: 2023-09-27

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	134
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1098394.804984
FMO2-HF: Nuclear repulsion	1044477.700553
FMO2-HF: Total energy	-53917.104431
FMO2-MP2: Total energy	-54070.928638

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:77:MET)

Summations of interaction energy for fragment #1(A:77: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.
-8.975	-1.352	2.836	-3.131	-7.328	-0.013

Interaction energy analysis for fragmet #1(A:77: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 : -0.032

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	79	GLU	-1	-0.896	-0.931	3.090	-6.665	-4.252	0.118	-1.280	-1.252	-0.003
4	A	80	ALA	0	-0.029	-0.030	4.862	0.772	0.772	0.000	0.000	0.000	0.000
5	A	81	ASP	-1	-0.874	-0.946	5.540	-1.166	-1.166	0.000	0.000	0.000	0.000
6	A	82	GLU	-1	-0.768	-0.878	8.157	-0.918	-0.918	0.000	0.000	0.000	0.000
7	A	83	MET	0	-0.011	-0.005	2.278	-0.273	0.312	1.093	-0.296	-1.381	0.003
8	A	84	TYR	0	-0.047	-0.027	7.099	0.368	0.368	0.000	0.000	0.000	0.000
9	A	85	ALA	0	-0.002	-0.003	9.289	0.197	0.197	0.000	0.000	0.000	0.000
10	A	86	ARG	1	0.831	0.909	10.231	0.769	0.769	0.000	0.000	0.000	0.000
11	A	87	PHE	0	-0.008	-0.004	9.269	0.113	0.113	0.000	0.000	0.000	0.000
12	A	88	ASN	0	-0.021	-0.029	11.259	0.121	0.121	0.000	0.000	0.000	0.000
13	A	89	ALA	0	-0.051	-0.011	14.176	0.057	0.057	0.000	0.000	0.000	0.000
14	A	90	ARG	1	0.847	0.931	14.077	0.213	0.213	0.000	0.000	0.000	0.000
15	A	91	ALA	0	-0.018	0.001	14.454	0.048	0.048	0.000	0.000	0.000	0.000
16	A	92	SER	0	-0.012	-0.004	16.262	0.007	0.007	0.000	0.000	0.000	0.000
17	A	93	GLY	0	-0.010	-0.012	19.326	0.012	0.012	0.000	0.000	0.000	0.000
18	A	94	GLY	0	-0.033	-0.018	16.433	0.007	0.007	0.000	0.000	0.000	0.000
19	A	95	LYS	1	0.933	0.966	14.737	0.112	0.112	0.000	0.000	0.000	0.000
20	A	96	VAL	0	0.040	0.036	11.694	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	97	SER	0	0.018	0.018	14.358	0.032	0.032	0.000	0.000	0.000	0.000
22	A	98	THR	0	0.030	-0.037	12.744	-0.030	-0.030	0.000	0.000	0.000	0.000
23	A	99	GLY	0	-0.015	0.002	13.761	0.044	0.044	0.000	0.000	0.000	0.000
24	A	100	ASP	-1	-0.819	-0.925	14.804	-0.058	-0.058	0.000	0.000	0.000	0.000
25	A	101	ALA	0	-0.026	-0.012	9.808	-0.031	-0.031	0.000	0.000	0.000	0.000
26	A	102	MET	0	0.000	0.015	10.391	0.070	0.070	0.000	0.000	0.000	0.000
27	A	103	ILE	0	-0.041	-0.009	12.468	0.037	0.037	0.000	0.000	0.000	0.000
28	A	104	LEU	0	-0.017	-0.015	9.938	-0.025	-0.025	0.000	0.000	0.000	0.000
29	A	105	ALA	0	0.015	0.008	8.018	-0.097	-0.097	0.000	0.000	0.000	0.000
30	A	106	ARG	1	0.979	0.996	9.004	-0.235	-0.235	0.000	0.000	0.000	0.000
31	A	107	GLN	0	-0.081	-0.043	12.078	-0.095	-0.095	0.000	0.000	0.000	0.000
32	A	108	LEU	0	-0.053	-0.019	5.779	-0.104	-0.104	0.000	0.000	0.000	0.000
33	A	109	GLY	0	0.007	0.019	8.022	-0.342	-0.342	0.000	0.000	0.000	0.000
34	A	110	LEU	0	-0.054	-0.017	4.671	0.175	0.370	0.001	-0.033	-0.164	0.000
35	A	111	ALA	0	0.033	0.004	8.679	-0.302	-0.302	0.000	0.000	0.000	0.000
36	A	112	PRO	0	-0.026	-0.001	10.131	0.078	0.078	0.000	0.000	0.000	0.000
37	A	113	SER	0	0.023	0.019	11.810	-0.185	-0.185	0.000	0.000	0.000	0.000
38	A	114	TYR	0	-0.014	-0.043	14.445	-0.017	-0.017	0.000	0.000	0.000	0.000
39	A	115	ALA	0	0.020	0.013	16.909	-0.029	-0.029	0.000	0.000	0.000	0.000
40	A	116	ASP	-1	-0.796	-0.868	11.300	1.107	1.107	0.000	0.000	0.000	0.000
41	A	117	LYS	1	0.819	0.886	12.770	-0.246	-0.246	0.000	0.000	0.000	0.000
42	A	118	GLN	0	-0.079	-0.054	14.114	-0.037	-0.037	0.000	0.000	0.000	0.000
43	A	119	ALA	0	0.030	0.020	14.067	-0.030	-0.030	0.000	0.000	0.000	0.000
44	A	120	PHE	0	-0.045	-0.027	8.413	-0.035	-0.035	0.000	0.000	0.000	0.000
45	A	121	GLU	-1	-0.801	-0.846	13.053	0.144	0.144	0.000	0.000	0.000	0.000
46	A	122	GLU	-1	-0.905	-0.931	15.961	0.268	0.268	0.000	0.000	0.000	0.000
47	A	123	LYS	1	0.860	0.947	11.177	-0.652	-0.652	0.000	0.000	0.000	0.000
48	A	124	SER	0	-0.094	-0.063	12.750	-0.028	-0.028	0.000	0.000	0.000	0.000
49	A	125	GLY	0	-0.001	0.020	14.768	-0.049	-0.049	0.000	0.000	0.000	0.000
50	A	126	ASP	-1	-0.865	-0.950	15.195	0.086	0.086	0.000	0.000	0.000	0.000
51	A	127	ASN	0	-0.061	-0.050	16.087	-0.048	-0.048	0.000	0.000	0.000	0.000
52	A	128	LEU	0	-0.008	0.006	9.798	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	129	ASP	-1	-0.852	-0.930	12.172	-0.253	-0.253	0.000	0.000	0.000	0.000
54	A	130	TYR	0	0.054	0.018	6.610	-0.039	-0.039	0.000	0.000	0.000	0.000
55	A	131	ALA	0	0.025	0.015	7.850	-0.134	-0.134	0.000	0.000	0.000	0.000
56	A	132	SER	0	-0.038	-0.026	7.387	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	133	PHE	0	0.003	0.009	7.083	0.064	0.064	0.000	0.000	0.000	0.000
58	A	134	GLN	0	0.032	0.005	3.804	-0.052	0.349	0.010	-0.066	-0.345	0.000
59	A	135	LYS	1	0.917	0.965	2.670	-2.693	-1.762	0.595	-0.559	-0.966	-0.008
60	A	136	PHE	0	0.011	0.002	5.145	0.367	0.450	-0.001	-0.002	-0.079	0.000
61	A	137	VAL	0	0.065	0.023	3.026	-0.636	0.200	0.496	-0.223	-1.110	0.000
62	A	138	GLY	0	0.001	0.000	2.851	-0.157	1.280	0.374	-0.607	-1.203	-0.004
63	A	139	THR	0	-0.147	-0.073	3.409	1.075	1.164	0.036	0.138	-0.264	0.000
64	A	140	SER	0	0.023	0.008	6.081	-0.288	-0.288	0.000	0.000	0.000	0.000
65	A	141	THR	0	-0.086	-0.052	3.228	-0.721	-0.068	0.114	-0.203	-0.564	-0.001
66	A	142	HIS	1	0.793	0.876	6.187	-1.877	-1.877	0.000	0.000	0.000	0.000
67	A	143	PRO	0	0.004	0.008	7.349	-0.199	-0.199	0.000	0.000	0.000	0.000
68	A	144	GLU	-1	-0.875	-0.937	9.110	1.435	1.435	0.000	0.000	0.000	0.000
69	A	145	ASP	-1	-0.898	-0.927	11.847	0.964	0.964	0.000	0.000	0.000	0.000
70	A	146	ASN	0	-0.009	-0.019	13.457	-0.100	-0.100	0.000	0.000	0.000	0.000
71	A	147	ILE	0	-0.014	-0.019	16.192	-0.056	-0.056	0.000	0.000	0.000	0.000
72	A	148	GLU	-1	-0.849	-0.936	18.624	0.255	0.255	0.000	0.000	0.000	0.000
73	A	149	ASP	-1	-0.866	-0.927	18.910	0.574	0.574	0.000	0.000	0.000	0.000
74	A	150	LEU	0	-0.017	-0.012	17.217	-0.041	-0.041	0.000	0.000	0.000	0.000
75	A	151	VAL	0	-0.027	-0.026	21.050	-0.049	-0.049	0.000	0.000	0.000	0.000
76	A	152	GLU	-1	-0.916	-0.975	24.060	0.223	0.223	0.000	0.000	0.000	0.000
77	A	153	ALA	0	-0.028	0.005	23.549	-0.018	-0.018	0.000	0.000	0.000	0.000
78	A	154	PHE	0	-0.025	-0.036	22.682	-0.031	-0.031	0.000	0.000	0.000	0.000
79	A	155	ALA	0	0.022	0.017	27.297	-0.024	-0.024	0.000	0.000	0.000	0.000
80	A	156	TYR	0	-0.048	-0.002	29.118	-0.020	-0.020	0.000	0.000	0.000	0.000
81	A	157	PHE	0	-0.027	-0.019	28.274	-0.016	-0.016	0.000	0.000	0.000	0.000
82	A	158	ASP	-1	-0.776	-0.846	32.286	0.126	0.126	0.000	0.000	0.000	0.000
83	A	159	VAL	0	-0.042	-0.032	33.923	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	160	SER	0	-0.085	-0.055	37.208	0.000	0.000	0.000	0.000	0.000	0.000
85	A	161	LYS	1	0.916	0.962	33.595	-0.167	-0.167	0.000	0.000	0.000	0.000
86	A	162	HIS	0	-0.048	-0.022	36.297	-0.009	-0.009	0.000	0.000	0.000	0.000
87	A	163	GLY	0	-0.033	-0.010	32.448	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	164	TYR	0	-0.023	-0.017	31.558	0.000	0.000	0.000	0.000	0.000	0.000
89	A	165	LEU	0	-0.009	-0.001	29.392	0.002	0.002	0.000	0.000	0.000	0.000
90	A	166	THR	0	0.006	0.004	33.038	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	167	ARG	1	1.039	1.016	32.922	-0.060	-0.060	0.000	0.000	0.000	0.000
92	A	168	LYS	1	0.932	0.968	33.237	-0.086	-0.086	0.000	0.000	0.000	0.000
93	A	169	GLN	0	0.014	0.018	33.332	0.001	0.001	0.000	0.000	0.000	0.000
94	A	170	MET	0	0.041	0.030	26.234	0.012	0.012	0.000	0.000	0.000	0.000
95	A	171	GLY	0	0.035	0.005	29.384	0.013	0.013	0.000	0.000	0.000	0.000
96	A	172	ASN	0	-0.045	-0.036	30.939	0.002	0.002	0.000	0.000	0.000	0.000
97	A	173	ILE	0	0.020	0.028	27.055	0.005	0.005	0.000	0.000	0.000	0.000
98	A	174	LEU	0	0.039	0.003	24.094	0.013	0.013	0.000	0.000	0.000	0.000
99	A	175	MET	0	-0.051	0.000	26.676	0.001	0.001	0.000	0.000	0.000	0.000
100	A	176	THR	0	-0.085	-0.040	29.367	-0.012	-0.012	0.000	0.000	0.000	0.000
101	A	177	TYR	0	-0.050	-0.033	27.492	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	178	GLY	0	-0.010	-0.001	24.170	0.005	0.005	0.000	0.000	0.000	0.000
103	A	179	GLU	-1	-0.802	-0.907	18.883	0.456	0.456	0.000	0.000	0.000	0.000
104	A	180	PRO	0	-0.069	-0.022	23.142	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	181	LEU	0	0.034	0.018	22.626	-0.009	-0.009	0.000	0.000	0.000	0.000
106	A	182	THR	0	0.016	0.001	25.853	-0.019	-0.019	0.000	0.000	0.000	0.000
107	A	183	THR	0	0.005	-0.021	28.069	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	184	GLU	-1	-0.966	-0.979	27.754	0.042	0.042	0.000	0.000	0.000	0.000
109	A	185	GLU	-1	-0.844	-0.920	22.337	0.169	0.169	0.000	0.000	0.000	0.000
110	A	186	PHE	0	0.006	0.009	26.169	-0.005	-0.005	0.000	0.000	0.000	0.000
111	A	187	ASN	0	-0.052	-0.042	28.031	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	188	ALA	0	-0.009	0.005	26.088	-0.009	-0.009	0.000	0.000	0.000	0.000
113	A	189	LEU	0	0.011	0.011	23.045	-0.008	-0.008	0.000	0.000	0.000	0.000
114	A	190	ALA	0	-0.042	-0.041	25.947	-0.006	-0.006	0.000	0.000	0.000	0.000
115	A	191	ALA	0	-0.075	-0.035	29.312	-0.006	-0.006	0.000	0.000	0.000	0.000
116	A	192	GLU	-1	-0.941	-0.961	23.704	-0.016	-0.016	0.000	0.000	0.000	0.000
117	A	193	TYR	0	0.037	0.011	20.760	0.006	0.006	0.000	0.000	0.000	0.000
118	A	194	PHE	0	-0.086	-0.026	26.433	0.008	0.008	0.000	0.000	0.000	0.000
119	A	195	THR	0	0.036	0.011	29.615	-0.008	-0.008	0.000	0.000	0.000	0.000
120	A	196	SER	0	-0.052	-0.039	32.541	-0.004	-0.004	0.000	0.000	0.000	0.000
121	A	197	ASP	-1	-0.885	-0.949	34.522	0.082	0.082	0.000	0.000	0.000	0.000
122	A	198	GLN	0	-0.071	-0.038	35.109	0.005	0.005	0.000	0.000	0.000	0.000
123	A	199	ILE	0	-0.003	0.012	28.581	-0.006	-0.006	0.000	0.000	0.000	0.000
124	A	200	ASP	-1	-0.807	-0.918	28.417	0.139	0.139	0.000	0.000	0.000	0.000
125	A	201	TYR	0	0.004	-0.024	26.495	0.005	0.005	0.000	0.000	0.000	0.000
126	A	202	ARG	1	0.882	0.956	23.592	-0.202	-0.202	0.000	0.000	0.000	0.000
127	A	203	GLN	0	-0.051	-0.036	23.258	0.012	0.012	0.000	0.000	0.000	0.000
128	A	204	PHE	0	0.026	0.023	23.124	-0.005	-0.005	0.000	0.000	0.000	0.000
129	A	205	CYS	0	-0.018	-0.013	20.665	0.013	0.013	0.000	0.000	0.000	0.000
130	A	206	LYS	1	0.906	0.953	18.917	-0.131	-0.131	0.000	0.000	0.000	0.000
131	A	207	ALA	0	0.047	0.030	18.008	0.003	0.003	0.000	0.000	0.000	0.000
132	A	208	MET	0	-0.074	-0.032	18.068	-0.010	-0.010	0.000	0.000	0.000	0.000
133	A	209	LEU	0	-0.030	-0.007	14.080	0.030	0.030	0.000	0.000	0.000	0.000
134	A	210	GLU	-1	-1.034	-0.991	13.301	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:77:MET)