FMO DATABASE

FMODB ID: 166LZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1099256.753792
FMO2-HF: Nuclear repulsion	1045339.270359
FMO2-HF: Total energy	-53917.483433
FMO2-MP2: Total energy	-54071.381026

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.
-11.481	-3.499	4.344	-3.808	-8.517	-0.01

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 : -0.032 / q_NPA : -0.005

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	-0.900	-0.939	3.112	-7.220	-4.057	0.095	-1.764	-1.493	0.001
4	A	80	ALA	0	-0.013	-0.020	4.787	0.511	0.667	-0.001	-0.008	-0.147	0.000
5	A	81	ASP	-1	-0.908	-0.965	5.486	-0.938	-0.938	0.000	0.000	0.000	0.000
6	A	82	GLU	-1	-0.746	-0.855	8.310	-0.737	-0.737	0.000	0.000	0.000	0.000
7	A	83	MET	0	-0.006	-0.002	2.362	-0.449	-0.102	1.730	-0.400	-1.677	0.002
8	A	84	TYR	0	-0.047	-0.019	6.802	0.255	0.255	0.000	0.000	0.000	0.000
9	A	85	ALA	0	-0.003	-0.004	9.111	0.155	0.155	0.000	0.000	0.000	0.000
10	A	86	ARG	1	0.816	0.888	9.894	0.684	0.684	0.000	0.000	0.000	0.000
11	A	87	PHE	0	-0.008	-0.007	9.075	0.088	0.088	0.000	0.000	0.000	0.000
12	A	88	ASN	0	-0.031	-0.037	11.065	0.101	0.101	0.000	0.000	0.000	0.000
13	A	89	ALA	0	-0.046	-0.007	14.012	0.048	0.048	0.000	0.000	0.000	0.000
14	A	90	ARG	1	0.832	0.915	13.821	0.218	0.218	0.000	0.000	0.000	0.000
15	A	91	ALA	0	-0.018	-0.001	14.329	0.039	0.039	0.000	0.000	0.000	0.000
16	A	92	SER	0	-0.010	-0.005	16.130	0.009	0.009	0.000	0.000	0.000	0.000
17	A	93	GLY	0	-0.015	-0.013	19.273	0.010	0.010	0.000	0.000	0.000	0.000
18	A	94	GLY	0	-0.029	-0.014	16.400	0.008	0.008	0.000	0.000	0.000	0.000
19	A	95	LYS	1	0.875	0.920	14.727	0.082	0.082	0.000	0.000	0.000	0.000
20	A	96	VAL	0	0.023	0.028	11.511	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	97	SER	0	0.000	-0.016	14.102	0.024	0.024	0.000	0.000	0.000	0.000
22	A	98	THR	0	0.043	-0.036	12.310	-0.035	-0.035	0.000	0.000	0.000	0.000
23	A	99	GLY	0	-0.001	0.010	13.338	0.025	0.025	0.000	0.000	0.000	0.000
24	A	100	ASP	-1	-0.815	-0.884	14.487	-0.103	-0.103	0.000	0.000	0.000	0.000
25	A	101	ALA	0	-0.018	-0.010	9.410	-0.032	-0.032	0.000	0.000	0.000	0.000
26	A	102	MET	0	0.001	0.012	9.827	0.039	0.039	0.000	0.000	0.000	0.000
27	A	103	ILE	0	-0.030	-0.007	11.844	0.018	0.018	0.000	0.000	0.000	0.000
28	A	104	LEU	0	-0.019	-0.015	9.643	-0.023	-0.023	0.000	0.000	0.000	0.000
29	A	105	ALA	0	0.018	0.008	7.605	-0.065	-0.065	0.000	0.000	0.000	0.000
30	A	106	ARG	1	0.959	0.985	8.483	-0.087	-0.087	0.000	0.000	0.000	0.000
31	A	107	GLN	0	-0.070	-0.027	11.687	-0.098	-0.098	0.000	0.000	0.000	0.000
32	A	108	LEU	0	-0.064	-0.025	5.482	-0.097	-0.097	0.000	0.000	0.000	0.000
33	A	109	GLY	0	0.017	0.024	8.027	-0.276	-0.276	0.000	0.000	0.000	0.000
34	A	110	LEU	0	-0.059	-0.020	4.466	-0.081	0.182	0.006	-0.051	-0.218	0.000
35	A	111	ALA	0	0.038	0.006	8.676	-0.183	-0.183	0.000	0.000	0.000	0.000
36	A	112	PRO	0	-0.034	-0.007	9.646	0.070	0.070	0.000	0.000	0.000	0.000
37	A	113	SER	0	0.010	-0.015	11.336	-0.132	-0.132	0.000	0.000	0.000	0.000
38	A	114	TYR	0	-0.018	-0.052	14.066	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	115	ALA	0	0.003	0.010	16.605	-0.013	-0.013	0.000	0.000	0.000	0.000
40	A	116	ASP	-1	-0.790	-0.849	11.027	0.775	0.775	0.000	0.000	0.000	0.000
41	A	117	LYS	1	0.812	0.882	12.594	-0.145	-0.145	0.000	0.000	0.000	0.000
42	A	118	GLN	0	-0.076	-0.042	13.834	-0.031	-0.031	0.000	0.000	0.000	0.000
43	A	119	ALA	0	0.023	0.015	14.038	-0.016	-0.016	0.000	0.000	0.000	0.000
44	A	120	PHE	0	-0.030	-0.022	8.458	-0.028	-0.028	0.000	0.000	0.000	0.000
45	A	121	GLU	-1	-0.765	-0.827	13.028	0.084	0.084	0.000	0.000	0.000	0.000
46	A	122	GLU	-1	-0.923	-0.943	15.889	0.211	0.211	0.000	0.000	0.000	0.000
47	A	123	LYS	1	0.867	0.949	11.898	-0.572	-0.572	0.000	0.000	0.000	0.000
48	A	124	SER	0	-0.083	-0.057	12.694	-0.009	-0.009	0.000	0.000	0.000	0.000
49	A	125	GLY	0	-0.011	0.013	14.897	-0.041	-0.041	0.000	0.000	0.000	0.000
50	A	126	ASP	-1	-0.864	-0.947	15.125	0.039	0.039	0.000	0.000	0.000	0.000
51	A	127	ASN	0	-0.045	-0.033	15.894	-0.041	-0.041	0.000	0.000	0.000	0.000
52	A	128	LEU	0	0.019	0.016	9.657	0.002	0.002	0.000	0.000	0.000	0.000
53	A	129	ASP	-1	-0.810	-0.883	12.337	-0.199	-0.199	0.000	0.000	0.000	0.000
54	A	130	TYR	0	0.065	0.021	6.527	-0.066	-0.066	0.000	0.000	0.000	0.000
55	A	131	ALA	0	0.020	0.013	7.956	-0.143	-0.143	0.000	0.000	0.000	0.000
56	A	132	SER	0	-0.083	-0.063	7.640	-0.010	-0.010	0.000	0.000	0.000	0.000
57	A	133	PHE	0	0.009	0.011	6.915	0.023	0.023	0.000	0.000	0.000	0.000
58	A	134	GLN	0	0.025	0.004	3.779	-0.184	0.173	0.008	-0.055	-0.309	0.000
59	A	135	LYS	1	0.908	0.960	2.848	-2.239	-1.334	0.350	-0.499	-0.756	-0.006
60	A	136	PHE	0	0.000	0.001	5.406	0.390	0.390	0.000	0.000	0.000	0.000
61	A	137	VAL	0	0.055	0.018	2.477	-0.614	-0.040	1.473	-0.348	-1.699	-0.001
62	A	138	GLY	0	0.010	0.007	2.833	-0.275	1.139	0.512	-0.594	-1.333	-0.005
63	A	139	THR	0	-0.071	-0.041	3.500	0.857	0.948	0.027	0.124	-0.242	0.000
64	A	140	SER	0	-0.046	-0.025	5.841	-0.252	-0.252	0.000	0.000	0.000	0.000
65	A	141	THR	0	-0.072	-0.046	3.264	-0.749	-0.037	0.144	-0.213	-0.643	-0.001
66	A	142	HIS	1	0.814	0.890	6.176	-1.518	-1.518	0.000	0.000	0.000	0.000
67	A	143	PRO	0	0.009	0.011	6.822	-0.213	-0.213	0.000	0.000	0.000	0.000
68	A	144	GLU	-1	-0.878	-0.932	8.491	1.081	1.081	0.000	0.000	0.000	0.000
69	A	145	ASP	-1	-0.910	-0.938	11.317	0.495	0.495	0.000	0.000	0.000	0.000
70	A	146	ASN	0	-0.020	-0.022	12.700	-0.100	-0.100	0.000	0.000	0.000	0.000
71	A	147	ILE	0	0.018	0.001	15.453	-0.024	-0.024	0.000	0.000	0.000	0.000
72	A	148	GLU	-1	-0.831	-0.887	17.959	0.110	0.110	0.000	0.000	0.000	0.000
73	A	149	ASP	-1	-0.860	-0.924	18.311	0.351	0.351	0.000	0.000	0.000	0.000
74	A	150	LEU	0	-0.010	-0.005	16.575	-0.021	-0.021	0.000	0.000	0.000	0.000
75	A	151	VAL	0	-0.035	-0.028	20.557	-0.025	-0.025	0.000	0.000	0.000	0.000
76	A	152	GLU	-1	-0.899	-0.974	23.350	0.112	0.112	0.000	0.000	0.000	0.000
77	A	153	ALA	0	-0.019	0.009	23.304	-0.006	-0.006	0.000	0.000	0.000	0.000
78	A	154	PHE	0	-0.014	-0.027	22.541	-0.016	-0.016	0.000	0.000	0.000	0.000
79	A	155	ALA	0	0.006	0.009	26.965	-0.013	-0.013	0.000	0.000	0.000	0.000
80	A	156	TYR	0	-0.049	-0.005	28.697	-0.008	-0.008	0.000	0.000	0.000	0.000
81	A	157	PHE	0	-0.012	-0.012	28.095	-0.008	-0.008	0.000	0.000	0.000	0.000
82	A	158	ASP	-1	-0.790	-0.851	31.746	0.055	0.055	0.000	0.000	0.000	0.000
83	A	159	VAL	0	-0.032	-0.031	33.475	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	160	SER	0	-0.077	-0.047	36.812	0.002	0.002	0.000	0.000	0.000	0.000
85	A	161	LYS	1	0.897	0.952	31.324	-0.095	-0.095	0.000	0.000	0.000	0.000
86	A	162	HIS	0	-0.048	-0.022	35.623	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	163	GLY	0	-0.014	0.003	31.817	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	164	TYR	0	-0.026	-0.021	30.963	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	165	LEU	0	-0.030	-0.010	29.040	0.004	0.004	0.000	0.000	0.000	0.000
90	A	166	THR	0	-0.005	-0.009	32.650	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	167	ARG	1	1.017	0.997	32.816	0.000	0.000	0.000	0.000	0.000	0.000
92	A	168	LYS	1	0.926	0.963	33.222	-0.035	-0.035	0.000	0.000	0.000	0.000
93	A	169	GLN	0	0.038	0.043	33.120	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	170	MET	0	0.031	0.025	26.086	0.011	0.011	0.000	0.000	0.000	0.000
95	A	171	GLY	0	0.041	0.001	29.369	0.007	0.007	0.000	0.000	0.000	0.000
96	A	172	ASN	0	-0.066	-0.043	30.927	0.001	0.001	0.000	0.000	0.000	0.000
97	A	173	ILE	0	0.015	0.022	27.072	0.006	0.006	0.000	0.000	0.000	0.000
98	A	174	LEU	0	0.047	0.009	24.109	0.010	0.010	0.000	0.000	0.000	0.000
99	A	175	MET	0	-0.047	0.002	26.587	0.000	0.000	0.000	0.000	0.000	0.000
100	A	176	THR	0	-0.081	-0.038	29.126	-0.005	-0.005	0.000	0.000	0.000	0.000
101	A	177	TYR	0	-0.055	-0.031	27.592	0.003	0.003	0.000	0.000	0.000	0.000
102	A	178	GLY	0	-0.005	0.002	23.954	0.000	0.000	0.000	0.000	0.000	0.000
103	A	179	GLU	-1	-0.796	-0.899	18.330	0.288	0.288	0.000	0.000	0.000	0.000
104	A	180	PRO	0	-0.062	-0.018	22.722	-0.006	-0.006	0.000	0.000	0.000	0.000
105	A	181	LEU	0	0.015	0.009	22.470	-0.007	-0.007	0.000	0.000	0.000	0.000
106	A	182	THR	0	0.002	-0.031	25.389	-0.009	-0.009	0.000	0.000	0.000	0.000
107	A	183	THR	0	-0.003	-0.027	27.503	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	184	GLU	-1	-0.977	-0.978	27.389	-0.019	-0.019	0.000	0.000	0.000	0.000
109	A	185	GLU	-1	-0.789	-0.873	21.830	0.054	0.054	0.000	0.000	0.000	0.000
110	A	186	PHE	0	0.000	0.007	25.774	-0.007	-0.007	0.000	0.000	0.000	0.000
111	A	187	ASN	0	-0.059	-0.048	28.025	-0.005	-0.005	0.000	0.000	0.000	0.000
112	A	188	ALA	0	-0.006	0.010	26.122	-0.006	-0.006	0.000	0.000	0.000	0.000
113	A	189	LEU	0	0.011	0.010	22.820	-0.008	-0.008	0.000	0.000	0.000	0.000
114	A	190	ALA	0	-0.044	-0.036	25.938	-0.006	-0.006	0.000	0.000	0.000	0.000
115	A	191	ALA	0	-0.068	-0.031	29.301	-0.003	-0.003	0.000	0.000	0.000	0.000
116	A	192	GLU	-1	-0.896	-0.925	23.343	-0.110	-0.110	0.000	0.000	0.000	0.000
117	A	193	TYR	0	-0.014	-0.028	21.090	0.005	0.005	0.000	0.000	0.000	0.000
118	A	194	PHE	0	-0.085	-0.031	26.231	0.009	0.009	0.000	0.000	0.000	0.000
119	A	195	THR	0	0.046	0.015	29.390	-0.005	-0.005	0.000	0.000	0.000	0.000
120	A	196	SER	0	-0.059	-0.038	32.145	0.000	0.000	0.000	0.000	0.000	0.000
121	A	197	ASP	-1	-0.857	-0.929	34.253	0.024	0.024	0.000	0.000	0.000	0.000
122	A	198	GLN	0	-0.061	-0.035	34.574	0.004	0.004	0.000	0.000	0.000	0.000
123	A	199	ILE	0	0.001	0.012	28.182	-0.006	-0.006	0.000	0.000	0.000	0.000
124	A	200	ASP	-1	-0.809	-0.908	27.554	0.034	0.034	0.000	0.000	0.000	0.000
125	A	201	TYR	0	-0.005	-0.033	26.068	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	202	ARG	1	0.839	0.893	23.028	-0.086	-0.086	0.000	0.000	0.000	0.000
127	A	203	GLN	0	-0.030	-0.031	22.719	-0.007	-0.007	0.000	0.000	0.000	0.000
128	A	204	PHE	0	0.013	0.013	22.673	-0.012	-0.012	0.000	0.000	0.000	0.000
129	A	205	CYS	0	-0.029	-0.021	20.031	0.001	0.001	0.000	0.000	0.000	0.000
130	A	206	LYS	1	0.919	0.959	18.408	0.019	0.019	0.000	0.000	0.000	0.000
131	A	207	ALA	0	0.037	0.024	17.574	-0.019	-0.019	0.000	0.000	0.000	0.000
132	A	208	MET	0	-0.062	-0.026	17.671	-0.018	-0.018	0.000	0.000	0.000	0.000
133	A	209	LEU	0	-0.024	-0.007	13.286	0.010	0.010	0.000	0.000	0.000	0.000
134	A	210	GLU	-1	-1.057	-1.000	12.837	-0.297	-0.297	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:77:MET)