FMO DATABASE

FMODB ID: GYY21

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	OptAll
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	-1102039.889385
FMO2-HF: Nuclear repulsion	1048122.204479
FMO2-HF: Total energy	-53917.684906
FMO2-MP2: Total energy	-54071.599537

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.
-11.55	-3.811	6.57	-4.186	-10.124	-0.019

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 : -0.029 / q_NPA : -0.001

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	-0.885	-0.936	2.968	-7.504	-4.321	0.167	-1.736	-1.614	-0.004
4	A	80	ALA	0	-0.005	-0.011	4.738	0.358	0.496	-0.001	-0.007	-0.130	0.000
5	A	81	ASP	-1	-0.914	-0.967	5.548	-0.958	-0.958	0.000	0.000	0.000	0.000
6	A	82	GLU	-1	-0.793	-0.883	8.565	-0.779	-0.779	0.000	0.000	0.000	0.000
7	A	83	MET	0	0.011	0.019	2.319	-0.277	-0.219	2.306	-0.487	-1.877	0.002
8	A	84	TYR	0	-0.042	-0.017	6.746	0.246	0.246	0.000	0.000	0.000	0.000
9	A	85	ALA	0	-0.014	-0.011	9.131	0.166	0.166	0.000	0.000	0.000	0.000
10	A	86	ARG	1	0.848	0.894	9.730	0.726	0.726	0.000	0.000	0.000	0.000
11	A	87	PHE	0	-0.013	0.004	9.107	0.091	0.091	0.000	0.000	0.000	0.000
12	A	88	ASN	0	0.001	-0.026	11.089	0.111	0.111	0.000	0.000	0.000	0.000
13	A	89	ALA	0	-0.057	-0.014	14.134	0.054	0.054	0.000	0.000	0.000	0.000
14	A	90	ARG	1	0.833	0.903	14.047	0.237	0.237	0.000	0.000	0.000	0.000
15	A	91	ALA	0	-0.031	-0.006	14.469	0.040	0.040	0.000	0.000	0.000	0.000
16	A	92	SER	0	-0.010	-0.005	16.167	0.014	0.014	0.000	0.000	0.000	0.000
17	A	93	GLY	0	-0.009	-0.011	19.053	0.007	0.007	0.000	0.000	0.000	0.000
18	A	94	GLY	0	-0.019	-0.005	16.655	0.008	0.008	0.000	0.000	0.000	0.000
19	A	95	LYS	1	0.833	0.889	14.576	0.095	0.095	0.000	0.000	0.000	0.000
20	A	96	VAL	0	0.022	0.031	11.748	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	97	SER	0	0.000	-0.023	14.491	0.028	0.028	0.000	0.000	0.000	0.000
22	A	98	THR	0	0.022	-0.044	12.578	-0.040	-0.040	0.000	0.000	0.000	0.000
23	A	99	GLY	0	0.002	0.012	13.413	0.032	0.032	0.000	0.000	0.000	0.000
24	A	100	ASP	-1	-0.803	-0.870	14.145	-0.130	-0.130	0.000	0.000	0.000	0.000
25	A	101	ALA	0	-0.008	-0.001	9.361	-0.032	-0.032	0.000	0.000	0.000	0.000
26	A	102	MET	0	0.009	0.018	9.638	0.037	0.037	0.000	0.000	0.000	0.000
27	A	103	ILE	0	-0.035	-0.007	11.767	0.017	0.017	0.000	0.000	0.000	0.000
28	A	104	LEU	0	-0.025	-0.020	9.745	-0.023	-0.023	0.000	0.000	0.000	0.000
29	A	105	ALA	0	0.013	0.000	7.342	-0.077	-0.077	0.000	0.000	0.000	0.000
30	A	106	ARG	1	0.871	0.935	8.242	-0.100	-0.100	0.000	0.000	0.000	0.000
31	A	107	GLN	0	-0.051	-0.024	11.552	-0.101	-0.101	0.000	0.000	0.000	0.000
32	A	108	LEU	0	-0.073	-0.023	5.462	-0.112	-0.112	0.000	0.000	0.000	0.000
33	A	109	GLY	0	0.020	0.021	7.624	-0.186	-0.186	0.000	0.000	0.000	0.000
34	A	110	LEU	0	-0.040	-0.009	4.511	-0.082	0.174	0.005	-0.048	-0.213	0.000
35	A	111	ALA	0	0.049	0.014	8.649	-0.182	-0.182	0.000	0.000	0.000	0.000
36	A	112	PRO	0	-0.046	-0.008	9.640	0.057	0.057	0.000	0.000	0.000	0.000
37	A	113	SER	0	0.059	0.001	11.568	-0.150	-0.150	0.000	0.000	0.000	0.000
38	A	114	TYR	0	-0.017	-0.047	14.253	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	115	ALA	0	0.006	0.003	16.646	-0.015	-0.015	0.000	0.000	0.000	0.000
40	A	116	ASP	-1	-0.803	-0.853	11.187	0.787	0.787	0.000	0.000	0.000	0.000
41	A	117	LYS	1	0.831	0.889	12.744	-0.148	-0.148	0.000	0.000	0.000	0.000
42	A	118	GLN	0	-0.075	-0.033	13.730	-0.028	-0.028	0.000	0.000	0.000	0.000
43	A	119	ALA	0	0.025	0.009	14.381	-0.021	-0.021	0.000	0.000	0.000	0.000
44	A	120	PHE	0	-0.041	-0.017	8.400	-0.014	-0.014	0.000	0.000	0.000	0.000
45	A	121	GLU	-1	-0.758	-0.843	13.096	0.080	0.080	0.000	0.000	0.000	0.000
46	A	122	GLU	-1	-0.926	-0.955	16.006	0.215	0.215	0.000	0.000	0.000	0.000
47	A	123	LYS	1	0.895	0.955	12.406	-0.568	-0.568	0.000	0.000	0.000	0.000
48	A	124	SER	0	-0.092	-0.047	12.799	-0.009	-0.009	0.000	0.000	0.000	0.000
49	A	125	GLY	0	-0.015	0.009	14.973	-0.041	-0.041	0.000	0.000	0.000	0.000
50	A	126	ASP	-1	-0.864	-0.949	15.145	0.016	0.016	0.000	0.000	0.000	0.000
51	A	127	ASN	0	-0.026	-0.011	15.908	-0.044	-0.044	0.000	0.000	0.000	0.000
52	A	128	LEU	0	0.012	0.020	9.504	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	129	ASP	-1	-0.814	-0.881	11.971	-0.232	-0.232	0.000	0.000	0.000	0.000
54	A	130	TYR	0	0.076	0.031	6.434	-0.079	-0.079	0.000	0.000	0.000	0.000
55	A	131	ALA	0	0.036	0.023	7.806	-0.162	-0.162	0.000	0.000	0.000	0.000
56	A	132	SER	0	-0.079	-0.074	7.483	0.001	0.001	0.000	0.000	0.000	0.000
57	A	133	PHE	0	0.002	0.017	6.991	0.049	0.049	0.000	0.000	0.000	0.000
58	A	134	GLN	0	0.030	0.003	3.519	-0.231	0.206	0.020	-0.079	-0.377	0.000
59	A	135	LYS	1	0.881	0.953	2.697	-2.393	-1.477	0.674	-0.621	-0.970	-0.008
60	A	136	PHE	0	0.014	0.009	5.453	0.443	0.443	0.000	0.000	0.000	0.000
61	A	137	VAL	0	0.042	0.016	2.430	-0.578	-0.071	1.743	-0.407	-1.843	-0.001
62	A	138	GLY	0	0.013	0.004	2.650	-0.305	1.158	1.182	-0.856	-1.789	-0.006
63	A	139	THR	0	-0.061	-0.037	3.404	1.075	0.957	0.040	0.388	-0.311	0.000
64	A	140	SER	0	-0.045	-0.027	5.864	-0.165	-0.165	0.000	0.000	0.000	0.000
65	A	141	THR	0	-0.077	-0.056	2.946	-0.915	-0.016	0.434	-0.333	-1.000	-0.002
66	A	142	HIS	1	0.798	0.889	5.874	-1.530	-1.530	0.000	0.000	0.000	0.000
67	A	143	PRO	0	0.007	0.013	6.547	-0.255	-0.255	0.000	0.000	0.000	0.000
68	A	144	GLU	-1	-0.876	-0.930	8.277	1.221	1.221	0.000	0.000	0.000	0.000
69	A	145	ASP	-1	-0.916	-0.948	11.182	0.529	0.529	0.000	0.000	0.000	0.000
70	A	146	ASN	0	-0.057	-0.049	12.447	-0.082	-0.082	0.000	0.000	0.000	0.000
71	A	147	ILE	0	0.018	0.007	15.226	-0.029	-0.029	0.000	0.000	0.000	0.000
72	A	148	GLU	-1	-0.849	-0.901	17.803	0.138	0.138	0.000	0.000	0.000	0.000
73	A	149	ASP	-1	-0.853	-0.917	18.572	0.355	0.355	0.000	0.000	0.000	0.000
74	A	150	LEU	0	0.024	0.014	16.131	-0.025	-0.025	0.000	0.000	0.000	0.000
75	A	151	VAL	0	-0.035	-0.019	20.334	-0.030	-0.030	0.000	0.000	0.000	0.000
76	A	152	GLU	-1	-0.855	-0.959	23.059	0.120	0.120	0.000	0.000	0.000	0.000
77	A	153	ALA	0	-0.023	0.006	23.221	-0.009	-0.009	0.000	0.000	0.000	0.000
78	A	154	PHE	0	-0.001	-0.019	22.306	-0.018	-0.018	0.000	0.000	0.000	0.000
79	A	155	ALA	0	-0.013	0.000	26.693	-0.015	-0.015	0.000	0.000	0.000	0.000
80	A	156	TYR	0	-0.026	0.001	28.666	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	157	PHE	0	0.003	-0.005	28.044	-0.010	-0.010	0.000	0.000	0.000	0.000
82	A	158	ASP	-1	-0.777	-0.852	31.572	0.065	0.065	0.000	0.000	0.000	0.000
83	A	159	VAL	0	-0.010	-0.016	33.291	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	160	SER	0	-0.067	-0.039	36.535	0.001	0.001	0.000	0.000	0.000	0.000
85	A	161	LYS	1	0.802	0.909	31.265	-0.107	-0.107	0.000	0.000	0.000	0.000
86	A	162	HIS	0	-0.039	-0.013	35.546	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	163	GLY	0	-0.010	0.007	31.563	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	164	TYR	0	-0.018	-0.010	30.670	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	165	LEU	0	-0.032	-0.014	28.698	0.005	0.005	0.000	0.000	0.000	0.000
90	A	166	THR	0	-0.009	-0.008	32.371	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	167	ARG	1	0.955	0.966	32.303	-0.006	-0.006	0.000	0.000	0.000	0.000
92	A	168	LYS	1	0.926	0.967	33.002	-0.041	-0.041	0.000	0.000	0.000	0.000
93	A	169	GLN	0	0.033	0.035	32.630	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	170	MET	0	0.043	0.030	25.812	0.011	0.011	0.000	0.000	0.000	0.000
95	A	171	GLY	0	0.026	0.002	29.050	0.007	0.007	0.000	0.000	0.000	0.000
96	A	172	ASN	0	-0.079	-0.056	30.888	0.000	0.000	0.000	0.000	0.000	0.000
97	A	173	ILE	0	0.026	0.033	26.736	0.005	0.005	0.000	0.000	0.000	0.000
98	A	174	LEU	0	0.047	0.008	23.904	0.009	0.009	0.000	0.000	0.000	0.000
99	A	175	MET	0	-0.047	0.002	26.574	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	176	THR	0	-0.085	-0.058	29.152	-0.007	-0.007	0.000	0.000	0.000	0.000
101	A	177	TYR	0	-0.044	-0.022	27.392	0.002	0.002	0.000	0.000	0.000	0.000
102	A	178	GLY	0	-0.008	0.001	23.728	0.002	0.002	0.000	0.000	0.000	0.000
103	A	179	GLU	-1	-0.795	-0.894	18.354	0.292	0.292	0.000	0.000	0.000	0.000
104	A	180	PRO	0	-0.076	-0.027	22.701	-0.008	-0.008	0.000	0.000	0.000	0.000
105	A	181	LEU	0	0.039	0.030	22.082	-0.007	-0.007	0.000	0.000	0.000	0.000
106	A	182	THR	0	-0.012	-0.043	25.073	-0.011	-0.011	0.000	0.000	0.000	0.000
107	A	183	THR	0	0.001	-0.026	27.255	-0.002	-0.002	0.000	0.000	0.000	0.000
108	A	184	GLU	-1	-0.966	-0.964	27.339	-0.021	-0.021	0.000	0.000	0.000	0.000
109	A	185	GLU	-1	-0.767	-0.864	21.646	0.058	0.058	0.000	0.000	0.000	0.000
110	A	186	PHE	0	0.021	0.012	25.490	-0.006	-0.006	0.000	0.000	0.000	0.000
111	A	187	ASN	0	-0.067	-0.049	27.726	-0.005	-0.005	0.000	0.000	0.000	0.000
112	A	188	ALA	0	0.000	0.010	25.828	-0.006	-0.006	0.000	0.000	0.000	0.000
113	A	189	LEU	0	0.031	0.017	22.450	-0.007	-0.007	0.000	0.000	0.000	0.000
114	A	190	ALA	0	-0.030	-0.029	25.540	-0.005	-0.005	0.000	0.000	0.000	0.000
115	A	191	ALA	0	-0.073	-0.036	28.992	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	192	GLU	-1	-0.914	-0.921	23.286	-0.105	-0.105	0.000	0.000	0.000	0.000
117	A	193	TYR	0	-0.031	-0.042	21.116	0.002	0.002	0.000	0.000	0.000	0.000
118	A	194	PHE	0	-0.069	-0.024	25.913	0.012	0.012	0.000	0.000	0.000	0.000
119	A	195	THR	0	0.017	-0.004	29.260	-0.007	-0.007	0.000	0.000	0.000	0.000
120	A	196	SER	0	-0.034	-0.016	32.248	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	197	ASP	-1	-0.861	-0.929	33.956	0.030	0.030	0.000	0.000	0.000	0.000
122	A	198	GLN	0	-0.059	-0.045	34.323	0.001	0.001	0.000	0.000	0.000	0.000
123	A	199	ILE	0	0.005	0.012	27.836	-0.005	-0.005	0.000	0.000	0.000	0.000
124	A	200	ASP	-1	-0.797	-0.902	27.164	0.049	0.049	0.000	0.000	0.000	0.000
125	A	201	TYR	0	0.000	-0.036	25.913	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	202	ARG	1	0.814	0.879	23.210	-0.109	-0.109	0.000	0.000	0.000	0.000
127	A	203	GLN	0	0.006	-0.006	22.464	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	204	PHE	0	0.016	0.006	22.167	-0.011	-0.011	0.000	0.000	0.000	0.000
129	A	205	CYS	0	-0.027	-0.020	19.562	0.001	0.001	0.000	0.000	0.000	0.000
130	A	206	LYS	1	0.845	0.943	17.906	0.003	0.003	0.000	0.000	0.000	0.000
131	A	207	ALA	0	0.075	0.046	17.033	-0.012	-0.012	0.000	0.000	0.000	0.000
132	A	208	MET	0	-0.058	-0.033	17.163	-0.020	-0.020	0.000	0.000	0.000	0.000
133	A	209	LEU	0	-0.037	0.000	12.945	0.034	0.034	0.000	0.000	0.000	0.000
134	A	210	GLU	-1	-1.039	-1.014	12.492	-0.246	-0.246	0.000	0.000	0.000	0.000

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