FMO DATABASE

FMODB ID: LJYZ9

Calculation Name: 2VVX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VVX

Chain ID: A

ChEMBL ID:

UniProt ID: Q01220

Base Structure: X-ray

Registration Date: 2023-06-19

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	153
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1681737.620826
FMO2-HF: Nuclear repulsion	1616398.532578
FMO2-HF: Total energy	-65339.088248
FMO2-MP2: Total energy	-65526.878542

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:40:ILE)

Summations of interaction energy for fragment #1(A:40:ILE)

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.
-4.246	-1.283	0.93	-1.739	-2.153	-0.006

Interaction energy analysis for fragmet #1(A:40:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : -0.025

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	42	PRO	0	-0.042	-0.018	2.626	-4.655	-1.788	0.931	-1.736	-2.062	-0.006
4	A	43	ASP	-1	-0.774	-0.855	5.012	-0.471	-0.375	-0.001	-0.003	-0.091	0.000
5	A	44	TYR	0	-0.069	-0.091	7.329	0.105	0.105	0.000	0.000	0.000	0.000
6	A	45	LEU	0	-0.014	0.024	10.703	0.104	0.104	0.000	0.000	0.000	0.000
7	A	46	GLU	-1	-0.889	-0.971	12.154	-0.392	-0.392	0.000	0.000	0.000	0.000
8	A	47	TYR	0	-0.047	-0.002	9.325	-0.074	-0.074	0.000	0.000	0.000	0.000
9	A	48	ASP	-1	-0.881	-0.952	12.701	-0.275	-0.275	0.000	0.000	0.000	0.000
10	A	49	ASP	-1	-0.926	-0.949	13.588	-0.325	-0.325	0.000	0.000	0.000	0.000
11	A	50	LEU	0	-0.019	-0.039	14.282	-0.001	-0.001	0.000	0.000	0.000	0.000
12	A	51	LEU	0	-0.001	0.006	11.295	0.054	0.054	0.000	0.000	0.000	0.000
13	A	52	ASP	-1	-0.808	-0.917	14.158	0.144	0.144	0.000	0.000	0.000	0.000
14	A	53	ARG	1	0.900	0.962	7.734	0.719	0.719	0.000	0.000	0.000	0.000
15	A	54	ASP	-1	-0.785	-0.866	9.826	-0.171	-0.171	0.000	0.000	0.000	0.000
16	A	55	GLU	-1	-0.885	-0.960	10.207	0.682	0.682	0.000	0.000	0.000	0.000
17	A	56	MET	0	0.043	0.030	11.993	-0.097	-0.097	0.000	0.000	0.000	0.000
18	A	57	PHE	0	0.031	0.002	14.283	-0.061	-0.061	0.000	0.000	0.000	0.000
19	A	58	THR	0	0.042	0.024	8.399	0.031	0.031	0.000	0.000	0.000	0.000
20	A	59	ILE	0	0.014	0.019	11.810	-0.097	-0.097	0.000	0.000	0.000	0.000
21	A	60	LEU	0	-0.026	-0.016	13.254	-0.047	-0.047	0.000	0.000	0.000	0.000
22	A	61	GLU	-1	-0.956	-0.992	12.011	0.280	0.280	0.000	0.000	0.000	0.000
23	A	62	GLU	-1	-0.824	-0.927	8.054	-0.606	-0.606	0.000	0.000	0.000	0.000
24	A	63	TYR	0	0.030	0.032	12.883	-0.030	-0.030	0.000	0.000	0.000	0.000
25	A	64	PHE	0	-0.009	-0.030	16.180	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	65	MET	0	-0.049	-0.001	11.144	0.028	0.028	0.000	0.000	0.000	0.000
27	A	66	TYR	0	-0.005	-0.051	10.338	0.056	0.056	0.000	0.000	0.000	0.000
28	A	67	ARG	1	0.752	0.847	16.663	0.081	0.081	0.000	0.000	0.000	0.000
29	A	68	GLY	0	0.010	-0.012	19.669	0.009	0.009	0.000	0.000	0.000	0.000
30	A	69	LEU	0	-0.087	-0.042	16.875	0.012	0.012	0.000	0.000	0.000	0.000
31	A	70	LEU	0	-0.015	-0.007	16.600	0.002	0.002	0.000	0.000	0.000	0.000
32	A	71	GLY	0	-0.036	-0.006	20.742	0.008	0.008	0.000	0.000	0.000	0.000
33	A	72	LEU	0	0.019	-0.006	21.602	-0.018	-0.018	0.000	0.000	0.000	0.000
34	A	73	ARG	1	0.873	0.948	23.792	0.112	0.112	0.000	0.000	0.000	0.000
35	A	74	ILE	0	0.033	0.007	18.462	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	75	LYS	1	0.864	0.943	16.293	0.422	0.422	0.000	0.000	0.000	0.000
37	A	76	TYR	0	0.016	0.009	17.141	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	77	GLY	0	0.019	0.022	15.970	0.008	0.008	0.000	0.000	0.000	0.000
39	A	78	ARG	1	0.922	0.936	16.969	0.286	0.286	0.000	0.000	0.000	0.000
40	A	79	LEU	0	0.016	0.029	13.530	0.039	0.039	0.000	0.000	0.000	0.000
41	A	80	PHE	0	0.060	0.015	13.692	0.040	0.040	0.000	0.000	0.000	0.000
42	A	81	ASN	0	-0.036	-0.019	18.099	0.038	0.038	0.000	0.000	0.000	0.000
43	A	82	GLU	-1	-0.826	-0.914	20.706	-0.077	-0.077	0.000	0.000	0.000	0.000
44	A	83	ILE	0	-0.012	-0.005	17.569	0.019	0.019	0.000	0.000	0.000	0.000
45	A	84	LYS	1	0.906	0.963	21.737	0.135	0.135	0.000	0.000	0.000	0.000
46	A	85	LYS	1	0.821	0.908	23.648	0.108	0.108	0.000	0.000	0.000	0.000
47	A	86	PHE	0	-0.002	-0.012	22.724	0.008	0.008	0.000	0.000	0.000	0.000
48	A	87	ASP	-1	-0.798	-0.899	26.507	-0.051	-0.051	0.000	0.000	0.000	0.000
49	A	88	ASN	0	-0.040	-0.024	28.793	0.004	0.004	0.000	0.000	0.000	0.000
50	A	89	ASP	-1	-0.900	-0.936	29.912	-0.014	-0.014	0.000	0.000	0.000	0.000
51	A	90	ALA	0	-0.029	-0.022	29.693	0.005	0.005	0.000	0.000	0.000	0.000
52	A	91	GLU	-1	-0.969	-0.970	31.776	-0.025	-0.025	0.000	0.000	0.000	0.000
53	A	92	GLU	-1	-0.982	-0.985	34.678	-0.012	-0.012	0.000	0.000	0.000	0.000
54	A	93	GLN	0	-0.085	-0.036	34.063	0.001	0.001	0.000	0.000	0.000	0.000
55	A	94	PHE	0	-0.065	-0.061	31.298	0.005	0.005	0.000	0.000	0.000	0.000
56	A	95	GLY	0	0.045	0.046	36.006	0.001	0.001	0.000	0.000	0.000	0.000
57	A	96	THR	0	0.043	0.022	35.808	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	97	ILE	0	0.040	0.012	31.555	0.004	0.004	0.000	0.000	0.000	0.000
59	A	98	GLU	-1	-0.894	-0.969	34.865	-0.025	-0.025	0.000	0.000	0.000	0.000
60	A	99	GLU	-1	-0.937	-0.944	37.931	0.002	0.002	0.000	0.000	0.000	0.000
61	A	100	LEU	0	0.035	0.016	33.516	0.003	0.003	0.000	0.000	0.000	0.000
62	A	101	LYS	1	0.920	0.974	35.235	0.026	0.026	0.000	0.000	0.000	0.000
63	A	102	GLN	0	-0.091	-0.064	36.422	0.003	0.003	0.000	0.000	0.000	0.000
64	A	103	LYS	1	0.941	0.961	39.762	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	104	LEU	0	0.009	0.007	33.709	0.003	0.003	0.000	0.000	0.000	0.000
66	A	105	ARG	1	0.908	0.969	36.468	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	106	LEU	0	0.034	0.032	31.494	0.001	0.001	0.000	0.000	0.000	0.000
68	A	107	ASN	0	0.031	-0.009	32.562	0.002	0.002	0.000	0.000	0.000	0.000
69	A	108	SER	0	-0.054	-0.011	34.191	0.000	0.000	0.000	0.000	0.000	0.000
70	A	109	GLU	-1	-0.884	-0.952	34.325	0.019	0.019	0.000	0.000	0.000	0.000
71	A	110	GLU	-1	-0.835	-0.924	33.924	0.020	0.020	0.000	0.000	0.000	0.000
72	A	111	GLY	0	-0.040	-0.002	33.259	0.003	0.003	0.000	0.000	0.000	0.000
73	A	112	ALA	0	-0.018	-0.028	28.460	0.001	0.001	0.000	0.000	0.000	0.000
74	A	113	ASP	-1	-0.889	-0.953	30.406	0.054	0.054	0.000	0.000	0.000	0.000
75	A	114	ASN	0	-0.013	-0.011	32.476	0.006	0.006	0.000	0.000	0.000	0.000
76	A	115	PHE	0	0.017	-0.006	26.696	0.002	0.002	0.000	0.000	0.000	0.000
77	A	116	ILE	0	-0.059	-0.032	27.026	0.005	0.005	0.000	0.000	0.000	0.000
78	A	117	ASP	-1	-0.921	-0.957	30.812	0.052	0.052	0.000	0.000	0.000	0.000
79	A	118	TYR	0	0.053	0.025	33.198	0.001	0.001	0.000	0.000	0.000	0.000
80	A	119	ILE	0	-0.009	-0.003	28.519	0.001	0.001	0.000	0.000	0.000	0.000
81	A	120	LYS	1	0.897	0.937	30.959	-0.076	-0.076	0.000	0.000	0.000	0.000
82	A	121	VAL	0	0.017	0.015	33.163	0.002	0.002	0.000	0.000	0.000	0.000
83	A	122	GLN	0	0.006	0.006	33.298	0.000	0.000	0.000	0.000	0.000	0.000
84	A	123	LYS	1	0.854	0.939	29.062	-0.093	-0.093	0.000	0.000	0.000	0.000
85	A	124	GLN	0	-0.101	-0.049	33.582	0.005	0.005	0.000	0.000	0.000	0.000
86	A	125	ASP	-1	-0.887	-0.937	36.885	0.038	0.038	0.000	0.000	0.000	0.000
87	A	126	ILE	0	-0.077	-0.021	34.078	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	127	VAL	0	-0.002	0.004	37.201	0.004	0.004	0.000	0.000	0.000	0.000
89	A	128	LYS	1	0.925	0.945	35.059	-0.058	-0.058	0.000	0.000	0.000	0.000
90	A	129	LEU	0	0.005	0.020	29.593	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	130	THR	0	-0.035	-0.020	32.149	0.003	0.003	0.000	0.000	0.000	0.000
92	A	131	VAL	0	0.037	-0.012	26.258	0.002	0.002	0.000	0.000	0.000	0.000
93	A	132	TYR	0	0.016	-0.008	28.187	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	133	ASP	-1	-0.691	-0.808	30.693	0.031	0.031	0.000	0.000	0.000	0.000
95	A	134	CYS	0	-0.088	-0.042	25.855	0.003	0.003	0.000	0.000	0.000	0.000
96	A	135	ILE	0	-0.014	-0.007	25.489	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	136	SER	0	0.092	0.040	27.017	-0.010	-0.010	0.000	0.000	0.000	0.000
98	A	137	MET	0	-0.044	-0.002	25.598	-0.004	-0.004	0.000	0.000	0.000	0.000
99	A	138	ILE	0	0.007	-0.005	21.859	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	139	GLY	0	0.044	0.021	24.982	-0.009	-0.009	0.000	0.000	0.000	0.000
101	A	140	LEU	0	0.001	0.009	26.792	-0.006	-0.006	0.000	0.000	0.000	0.000
102	A	141	CYS	0	-0.060	-0.032	24.173	0.001	0.001	0.000	0.000	0.000	0.000
103	A	142	ALA	0	-0.043	-0.008	23.925	-0.006	-0.006	0.000	0.000	0.000	0.000
104	A	143	CYS	0	0.037	0.016	24.809	-0.008	-0.008	0.000	0.000	0.000	0.000
105	A	144	VAL	0	0.003	-0.002	27.613	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	145	VAL	0	-0.049	-0.028	22.112	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	146	ASP	-1	-0.787	-0.863	25.490	-0.079	-0.079	0.000	0.000	0.000	0.000
108	A	147	VAL	0	-0.055	-0.018	27.178	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	148	TRP	0	-0.001	-0.020	25.652	0.001	0.001	0.000	0.000	0.000	0.000
110	A	149	ARG	1	0.836	0.932	23.447	0.085	0.085	0.000	0.000	0.000	0.000
111	A	150	ASN	0	-0.063	-0.041	26.416	-0.009	-0.009	0.000	0.000	0.000	0.000
112	A	151	GLU	-1	-0.924	-0.946	29.800	-0.026	-0.026	0.000	0.000	0.000	0.000
113	A	152	LYS	1	0.889	0.944	27.607	0.059	0.059	0.000	0.000	0.000	0.000
114	A	153	LEU	0	-0.009	0.010	27.860	0.004	0.004	0.000	0.000	0.000	0.000
115	A	154	PHE	0	0.056	0.006	22.612	0.004	0.004	0.000	0.000	0.000	0.000
116	A	155	SER	0	-0.032	-0.013	22.054	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	156	ARG	1	0.866	0.935	22.883	0.006	0.006	0.000	0.000	0.000	0.000
118	A	157	TRP	0	0.096	0.050	15.132	0.015	0.015	0.000	0.000	0.000	0.000
119	A	158	LYS	1	0.908	0.964	17.394	-0.055	-0.055	0.000	0.000	0.000	0.000
120	A	159	TYR	0	-0.008	-0.011	20.884	0.020	0.020	0.000	0.000	0.000	0.000
121	A	160	CYS	0	0.028	0.033	21.486	0.008	0.008	0.000	0.000	0.000	0.000
122	A	161	LEU	0	0.028	0.038	16.411	0.009	0.009	0.000	0.000	0.000	0.000
123	A	162	ARG	1	0.909	0.953	20.512	-0.074	-0.074	0.000	0.000	0.000	0.000
124	A	163	ALA	0	0.039	0.016	23.256	0.009	0.009	0.000	0.000	0.000	0.000
125	A	164	ILE	0	0.039	0.009	20.429	0.005	0.005	0.000	0.000	0.000	0.000
126	A	165	LYS	1	0.915	0.964	17.461	-0.247	-0.247	0.000	0.000	0.000	0.000
127	A	166	LEU	0	-0.064	-0.013	22.636	0.006	0.006	0.000	0.000	0.000	0.000
128	A	167	PHE	0	-0.014	-0.026	25.955	0.000	0.000	0.000	0.000	0.000	0.000
129	A	168	ILE	0	-0.015	-0.016	22.906	-0.005	-0.005	0.000	0.000	0.000	0.000
130	A	169	ASN	0	0.015	0.021	22.994	0.016	0.016	0.000	0.000	0.000	0.000
131	A	170	ASP	-1	-0.779	-0.917	19.334	0.288	0.288	0.000	0.000	0.000	0.000
132	A	171	HIS	0	-0.037	-0.013	21.585	-0.020	-0.020	0.000	0.000	0.000	0.000
133	A	172	MET	0	-0.029	-0.026	24.336	-0.015	-0.015	0.000	0.000	0.000	0.000
134	A	173	LEU	0	0.017	0.007	17.994	-0.021	-0.021	0.000	0.000	0.000	0.000
135	A	174	ASP	-1	-0.860	-0.919	19.560	0.204	0.204	0.000	0.000	0.000	0.000
136	A	175	LYS	1	0.867	0.932	21.240	-0.103	-0.103	0.000	0.000	0.000	0.000
137	A	176	ILE	0	0.010	0.001	21.231	-0.018	-0.018	0.000	0.000	0.000	0.000
138	A	177	LYS	1	0.903	0.950	14.701	-0.237	-0.237	0.000	0.000	0.000	0.000
139	A	178	SER	0	-0.002	-0.002	20.061	-0.025	-0.025	0.000	0.000	0.000	0.000
140	A	179	ILE	0	-0.040	-0.011	22.743	-0.018	-0.018	0.000	0.000	0.000	0.000
141	A	180	LEU	0	0.004	-0.010	19.079	-0.016	-0.016	0.000	0.000	0.000	0.000
142	A	181	GLN	0	-0.039	-0.017	17.479	-0.007	-0.007	0.000	0.000	0.000	0.000
143	A	182	ASN	0	0.003	0.000	21.107	-0.017	-0.017	0.000	0.000	0.000	0.000
144	A	183	ARG	1	0.924	0.961	23.925	0.024	0.024	0.000	0.000	0.000	0.000
145	A	184	LEU	0	0.017	0.008	18.137	-0.008	-0.008	0.000	0.000	0.000	0.000
146	A	185	VAL	0	0.024	0.024	22.359	-0.013	-0.013	0.000	0.000	0.000	0.000
147	A	186	TYR	0	-0.004	-0.001	24.210	-0.002	-0.002	0.000	0.000	0.000	0.000
148	A	187	VAL	0	-0.010	-0.001	23.573	-0.004	-0.004	0.000	0.000	0.000	0.000
149	A	188	GLU	-1	-0.843	-0.910	22.368	-0.192	-0.192	0.000	0.000	0.000	0.000
150	A	189	MET	0	-0.043	-0.035	25.062	0.002	0.002	0.000	0.000	0.000	0.000
151	A	190	SER	0	-0.059	-0.032	28.557	0.004	0.004	0.000	0.000	0.000	0.000
152	A	191	LYS	1	0.747	0.888	22.625	0.191	0.191	0.000	0.000	0.000	0.000
153	A	192	HIS	0	-0.035	-0.004	25.168	0.009	0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:40:ILE)