FMO DATABASE

FMODB ID: 9MG82

Calculation Name: 2VYI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VYI

Chain ID: A

ChEMBL ID:

UniProt ID: O43765

Base Structure: X-ray

Registration Date: 2023-09-26

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	131
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1089126.144777
FMO2-HF: Nuclear repulsion	1038101.530136
FMO2-HF: Total energy	-51024.61464
FMO2-MP2: Total energy	-51172.421991

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:80:GLY)

Summations of interaction energy for fragment #1(A:80:GLY)

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.
-2.161	0.733	0.312	-1.47	-1.736	-0.001

Interaction energy analysis for fragmet #1(A:80:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / q_NPA : 0.018

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	82	LEU	0	-0.007	0.012	3.405	0.190	2.027	0.009	-0.955	-0.891	0.002
4	A	83	GLY	0	-0.008	-0.007	2.529	-1.391	-0.625	0.286	-0.439	-0.613	-0.002
5	A	84	SER	0	-0.083	-0.082	3.303	-0.090	0.201	0.017	-0.076	-0.232	-0.001
6	A	85	GLU	-1	-0.781	-0.904	5.735	-0.313	-0.313	0.000	0.000	0.000	0.000
7	A	86	GLU	-1	-0.828	-0.835	5.645	-0.385	-0.385	0.000	0.000	0.000	0.000
8	A	87	ASP	-1	-0.843	-0.935	10.015	-0.304	-0.304	0.000	0.000	0.000	0.000
9	A	88	SER	0	-0.039	-0.040	6.160	-0.225	-0.225	0.000	0.000	0.000	0.000
10	A	89	ALA	0	-0.031	0.007	8.169	-0.140	-0.140	0.000	0.000	0.000	0.000
11	A	90	GLU	-1	-0.826	-0.906	9.518	-0.259	-0.259	0.000	0.000	0.000	0.000
12	A	91	ALA	0	0.000	0.008	10.957	0.033	0.033	0.000	0.000	0.000	0.000
13	A	92	GLU	-1	-0.763	-0.850	9.928	-1.154	-1.154	0.000	0.000	0.000	0.000
14	A	93	ARG	1	0.781	0.864	12.631	0.333	0.333	0.000	0.000	0.000	0.000
15	A	94	LEU	0	0.030	0.023	15.407	0.054	0.054	0.000	0.000	0.000	0.000
16	A	95	LYS	1	0.818	0.899	13.858	0.824	0.824	0.000	0.000	0.000	0.000
17	A	96	THR	0	-0.103	-0.076	15.684	0.016	0.016	0.000	0.000	0.000	0.000
18	A	97	GLU	-1	-0.833	-0.895	18.228	-0.201	-0.201	0.000	0.000	0.000	0.000
19	A	98	GLY	0	0.039	0.009	20.228	0.031	0.031	0.000	0.000	0.000	0.000
20	A	99	ASN	0	-0.029	-0.019	18.631	0.019	0.019	0.000	0.000	0.000	0.000
21	A	100	GLU	-1	-0.804	-0.878	22.142	-0.261	-0.261	0.000	0.000	0.000	0.000
22	A	101	GLN	0	-0.025	-0.029	24.491	0.035	0.035	0.000	0.000	0.000	0.000
23	A	102	MET	0	-0.059	-0.013	24.473	0.020	0.020	0.000	0.000	0.000	0.000
24	A	103	LYS	1	0.751	0.864	23.053	0.292	0.292	0.000	0.000	0.000	0.000
25	A	104	VAL	0	-0.052	-0.014	28.478	0.014	0.014	0.000	0.000	0.000	0.000
26	A	105	GLU	-1	-0.866	-0.944	30.539	-0.153	-0.153	0.000	0.000	0.000	0.000
27	A	106	ASN	0	0.022	0.039	29.734	0.009	0.009	0.000	0.000	0.000	0.000
28	A	107	PHE	0	0.041	-0.023	28.670	-0.019	-0.019	0.000	0.000	0.000	0.000
29	A	108	GLU	-1	-0.857	-0.930	28.321	-0.175	-0.175	0.000	0.000	0.000	0.000
30	A	109	ALA	0	-0.001	0.005	27.344	-0.010	-0.010	0.000	0.000	0.000	0.000
31	A	110	ALA	0	-0.007	-0.006	24.434	-0.018	-0.018	0.000	0.000	0.000	0.000
32	A	111	VAL	0	-0.031	-0.019	23.405	-0.032	-0.032	0.000	0.000	0.000	0.000
33	A	112	HIS	0	-0.033	-0.005	23.742	-0.011	-0.011	0.000	0.000	0.000	0.000
34	A	113	PHE	0	0.022	0.002	20.643	-0.009	-0.009	0.000	0.000	0.000	0.000
35	A	114	TYR	0	-0.005	-0.034	18.783	-0.032	-0.032	0.000	0.000	0.000	0.000
36	A	115	GLY	0	-0.012	-0.005	18.706	-0.039	-0.039	0.000	0.000	0.000	0.000
37	A	116	LYS	1	0.816	0.894	19.106	0.215	0.215	0.000	0.000	0.000	0.000
38	A	117	ALA	0	0.011	0.010	14.888	-0.013	-0.013	0.000	0.000	0.000	0.000
39	A	118	ILE	0	-0.059	-0.038	14.366	-0.081	-0.081	0.000	0.000	0.000	0.000
40	A	119	GLU	-1	-0.873	-0.917	15.855	-0.255	-0.255	0.000	0.000	0.000	0.000
41	A	120	LEU	0	-0.027	0.008	12.688	0.022	0.022	0.000	0.000	0.000	0.000
42	A	121	ASN	0	0.036	0.011	8.760	0.020	0.020	0.000	0.000	0.000	0.000
43	A	122	PRO	0	-0.017	-0.005	11.705	-0.056	-0.056	0.000	0.000	0.000	0.000
44	A	123	ALA	0	0.003	0.000	10.200	0.091	0.091	0.000	0.000	0.000	0.000
45	A	124	ASN	0	0.044	0.035	10.875	-0.045	-0.045	0.000	0.000	0.000	0.000
46	A	125	ALA	0	0.072	0.025	12.508	0.151	0.151	0.000	0.000	0.000	0.000
47	A	126	VAL	0	-0.038	-0.025	14.716	0.136	0.136	0.000	0.000	0.000	0.000
48	A	127	TYR	0	-0.023	-0.045	11.196	0.113	0.113	0.000	0.000	0.000	0.000
49	A	128	PHE	0	0.013	0.020	15.856	0.086	0.086	0.000	0.000	0.000	0.000
50	A	129	CYS	0	-0.009	0.020	19.477	0.070	0.070	0.000	0.000	0.000	0.000
51	A	130	ASN	0	-0.030	-0.014	19.767	0.054	0.054	0.000	0.000	0.000	0.000
52	A	131	ARG	1	0.890	0.924	21.352	0.359	0.359	0.000	0.000	0.000	0.000
53	A	132	ALA	0	0.015	0.019	23.219	0.036	0.036	0.000	0.000	0.000	0.000
54	A	133	ALA	0	-0.041	-0.022	24.905	0.029	0.029	0.000	0.000	0.000	0.000
55	A	134	ALA	0	0.042	0.015	25.844	0.023	0.023	0.000	0.000	0.000	0.000
56	A	135	TYR	0	-0.001	-0.013	25.723	0.019	0.019	0.000	0.000	0.000	0.000
57	A	136	SER	0	-0.035	-0.029	29.190	0.019	0.019	0.000	0.000	0.000	0.000
58	A	137	LYS	1	0.782	0.910	30.612	0.199	0.199	0.000	0.000	0.000	0.000
59	A	138	LEU	0	-0.017	0.000	30.146	0.011	0.011	0.000	0.000	0.000	0.000
60	A	139	GLY	0	0.004	0.018	33.587	0.010	0.010	0.000	0.000	0.000	0.000
61	A	140	ASN	0	-0.036	-0.013	30.405	0.012	0.012	0.000	0.000	0.000	0.000
62	A	141	TYR	0	0.051	0.003	31.361	-0.012	-0.012	0.000	0.000	0.000	0.000
63	A	142	ALA	0	0.025	0.016	31.512	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	143	GLY	0	0.027	0.012	29.256	-0.009	-0.009	0.000	0.000	0.000	0.000
65	A	144	ALA	0	0.001	-0.003	27.289	-0.022	-0.022	0.000	0.000	0.000	0.000
66	A	145	VAL	0	0.015	-0.003	26.940	-0.022	-0.022	0.000	0.000	0.000	0.000
67	A	146	GLN	0	0.038	0.023	25.707	0.000	0.000	0.000	0.000	0.000	0.000
68	A	147	ASP	-1	-0.786	-0.867	22.959	-0.354	-0.354	0.000	0.000	0.000	0.000
69	A	148	CYS	0	-0.071	-0.046	22.363	-0.044	-0.044	0.000	0.000	0.000	0.000
70	A	149	GLU	-1	-0.899	-0.944	23.370	-0.256	-0.256	0.000	0.000	0.000	0.000
71	A	150	ARG	1	0.911	0.974	16.844	0.442	0.442	0.000	0.000	0.000	0.000
72	A	151	ALA	0	-0.032	-0.029	18.625	-0.046	-0.046	0.000	0.000	0.000	0.000
73	A	152	ILE	0	-0.002	0.001	18.802	-0.047	-0.047	0.000	0.000	0.000	0.000
74	A	153	CYS	0	-0.063	-0.034	20.406	0.005	0.005	0.000	0.000	0.000	0.000
75	A	154	ILE	0	-0.088	-0.028	14.039	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	155	ASP	-1	-0.866	-0.945	15.351	-0.751	-0.751	0.000	0.000	0.000	0.000
77	A	156	PRO	0	0.020	0.009	17.131	0.042	0.042	0.000	0.000	0.000	0.000
78	A	157	ALA	0	-0.005	0.017	18.861	0.058	0.058	0.000	0.000	0.000	0.000
79	A	158	TYR	0	0.071	0.028	18.513	0.006	0.006	0.000	0.000	0.000	0.000
80	A	159	SER	0	0.034	0.007	20.241	0.023	0.023	0.000	0.000	0.000	0.000
81	A	160	LYS	1	0.905	0.955	19.876	0.525	0.525	0.000	0.000	0.000	0.000
82	A	161	ALA	0	0.001	-0.003	21.524	0.023	0.023	0.000	0.000	0.000	0.000
83	A	162	TYR	0	-0.018	-0.027	23.120	0.043	0.043	0.000	0.000	0.000	0.000
84	A	163	GLY	0	0.023	0.008	26.535	0.026	0.026	0.000	0.000	0.000	0.000
85	A	164	ARG	1	0.832	0.887	22.507	0.384	0.384	0.000	0.000	0.000	0.000
86	A	165	MET	0	0.024	0.044	26.827	0.020	0.020	0.000	0.000	0.000	0.000
87	A	166	GLY	0	0.031	0.012	29.024	0.019	0.019	0.000	0.000	0.000	0.000
88	A	167	LEU	0	-0.028	-0.013	30.316	0.015	0.015	0.000	0.000	0.000	0.000
89	A	168	ALA	0	0.010	0.018	30.728	0.014	0.014	0.000	0.000	0.000	0.000
90	A	169	LEU	0	0.030	0.004	32.035	0.014	0.014	0.000	0.000	0.000	0.000
91	A	170	SER	0	-0.021	-0.004	34.713	0.015	0.015	0.000	0.000	0.000	0.000
92	A	171	SER	0	-0.060	-0.031	35.609	0.012	0.012	0.000	0.000	0.000	0.000
93	A	172	LEU	0	-0.059	-0.021	34.388	0.007	0.007	0.000	0.000	0.000	0.000
94	A	173	ASN	0	-0.068	-0.044	38.383	0.007	0.007	0.000	0.000	0.000	0.000
95	A	174	LYS	1	0.852	0.930	35.153	0.161	0.161	0.000	0.000	0.000	0.000
96	A	175	HIS	0	0.055	0.006	37.704	-0.014	-0.014	0.000	0.000	0.000	0.000
97	A	176	VAL	0	0.010	0.011	38.980	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	177	GLU	-1	-0.797	-0.898	33.976	-0.166	-0.166	0.000	0.000	0.000	0.000
99	A	178	ALA	0	0.014	0.016	34.299	-0.011	-0.011	0.000	0.000	0.000	0.000
100	A	179	VAL	0	-0.014	-0.008	34.358	-0.009	-0.009	0.000	0.000	0.000	0.000
101	A	180	ALA	0	-0.028	-0.006	34.193	-0.005	-0.005	0.000	0.000	0.000	0.000
102	A	181	TYR	0	0.041	0.014	27.495	-0.013	-0.013	0.000	0.000	0.000	0.000
103	A	182	TYR	0	-0.007	-0.010	30.368	-0.014	-0.014	0.000	0.000	0.000	0.000
104	A	183	LYS	1	0.860	0.929	31.945	0.136	0.136	0.000	0.000	0.000	0.000
105	A	184	LYS	1	0.887	0.937	26.264	0.256	0.256	0.000	0.000	0.000	0.000
106	A	185	ALA	0	0.027	-0.003	27.307	-0.013	-0.013	0.000	0.000	0.000	0.000
107	A	186	LEU	0	-0.044	-0.027	28.119	-0.009	-0.009	0.000	0.000	0.000	0.000
108	A	187	GLU	-1	-0.901	-0.912	28.671	-0.215	-0.215	0.000	0.000	0.000	0.000
109	A	188	LEU	0	-0.069	-0.024	23.695	-0.005	-0.005	0.000	0.000	0.000	0.000
110	A	189	ASP	-1	-0.893	-0.950	25.558	-0.305	-0.305	0.000	0.000	0.000	0.000
111	A	190	PRO	0	-0.003	-0.006	27.380	0.011	0.011	0.000	0.000	0.000	0.000
112	A	191	ASP	-1	-0.906	-0.949	29.771	-0.190	-0.190	0.000	0.000	0.000	0.000
113	A	192	ASN	0	-0.039	-0.030	27.711	0.030	0.030	0.000	0.000	0.000	0.000
114	A	193	GLU	-1	-0.760	-0.877	31.060	-0.146	-0.146	0.000	0.000	0.000	0.000
115	A	194	THR	0	-0.024	-0.007	31.121	0.012	0.012	0.000	0.000	0.000	0.000
116	A	195	TYR	0	-0.010	-0.011	26.312	0.007	0.007	0.000	0.000	0.000	0.000
117	A	196	LYS	1	0.878	0.938	33.207	0.169	0.169	0.000	0.000	0.000	0.000
118	A	197	SER	0	-0.019	-0.011	36.412	0.012	0.012	0.000	0.000	0.000	0.000
119	A	198	ASN	0	-0.019	-0.034	34.923	0.012	0.012	0.000	0.000	0.000	0.000
120	A	199	LEU	0	-0.008	0.025	36.010	0.004	0.004	0.000	0.000	0.000	0.000
121	A	200	LYS	1	0.880	0.925	37.616	0.132	0.132	0.000	0.000	0.000	0.000
122	A	201	ILE	0	0.001	0.003	39.520	0.007	0.007	0.000	0.000	0.000	0.000
123	A	202	ALA	0	0.012	0.008	38.405	0.005	0.005	0.000	0.000	0.000	0.000
124	A	203	GLU	-1	-0.808	-0.910	40.490	-0.123	-0.123	0.000	0.000	0.000	0.000
125	A	204	LEU	0	-0.070	-0.033	42.752	0.007	0.007	0.000	0.000	0.000	0.000
126	A	205	LYS	1	0.988	0.990	41.758	0.126	0.126	0.000	0.000	0.000	0.000
127	A	206	LEU	0	-0.045	-0.010	42.051	0.003	0.003	0.000	0.000	0.000	0.000
128	A	207	ARG	1	0.890	0.951	45.021	0.084	0.084	0.000	0.000	0.000	0.000
129	A	208	GLU	-1	-0.927	-0.967	47.747	-0.091	-0.091	0.000	0.000	0.000	0.000
130	A	209	ALA	0	-0.045	-0.004	46.963	0.003	0.003	0.000	0.000	0.000	0.000
131	A	210	PRO	0	-0.011	-0.002	49.081	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:80:GLY)