FMO DATABASE

FMODB ID: 3Q1LL

Calculation Name: 3VEA-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VEA

Chain ID: B

ChEMBL ID:

UniProt ID: Q8ZG78

Base Structure: X-ray

Registration Date: 2023-06-20

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	149
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1222801.673314
FMO2-HF: Nuclear repulsion	1160755.738963
FMO2-HF: Total energy	-62045.934352
FMO2-MP2: Total energy	-62227.002906

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(B:14:MET)

Summations of interaction energy for fragment #1(B:14: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.
-10.598	-9.976	9.672	-4.623	-5.672	0.01

Interaction energy analysis for fragmet #1(B:14: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 : 0.015

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	B	16	TYR	0	-0.001	0.004	3.086	-2.374	0.863	0.001	-1.615	-1.623	0.001
4	B	17	GLN	0	0.062	0.046	3.049	-1.284	-0.158	0.138	-0.516	-0.748	-0.005
5	B	18	GLN	0	0.026	-0.020	2.447	-3.731	-7.590	9.534	-2.487	-3.189	0.014
6	B	19	LEU	0	0.028	0.031	6.624	-0.184	-0.184	0.000	0.000	0.000	0.000
7	B	20	GLU	-1	-0.896	-0.950	10.040	0.285	0.285	0.000	0.000	0.000	0.000
8	B	21	ASN	0	0.067	0.028	11.540	-0.089	-0.089	0.000	0.000	0.000	0.000
9	B	22	LEU	0	0.011	0.015	13.105	-0.041	-0.041	0.000	0.000	0.000	0.000
10	B	23	GLU	-1	-0.835	-0.931	8.357	1.229	1.229	0.000	0.000	0.000	0.000
11	B	24	SER	0	0.032	0.015	13.006	-0.049	-0.049	0.000	0.000	0.000	0.000
12	B	25	GLY	0	0.081	0.054	15.738	-0.040	-0.040	0.000	0.000	0.000	0.000
13	B	26	TRP	0	-0.079	-0.056	11.178	0.003	0.003	0.000	0.000	0.000	0.000
14	B	27	LYS	1	0.880	0.920	10.748	-0.446	-0.446	0.000	0.000	0.000	0.000
15	B	28	TRP	0	0.027	0.030	16.943	-0.016	-0.016	0.000	0.000	0.000	0.000
16	B	29	ALA	0	0.041	0.014	20.279	-0.017	-0.017	0.000	0.000	0.000	0.000
17	B	30	TYR	0	-0.104	-0.056	18.590	-0.015	-0.015	0.000	0.000	0.000	0.000
18	B	31	LEU	0	0.043	0.010	19.635	-0.011	-0.011	0.000	0.000	0.000	0.000
19	B	32	VAL	0	0.051	0.033	22.605	-0.014	-0.014	0.000	0.000	0.000	0.000
20	B	33	LYS	1	0.867	0.943	23.595	-0.170	-0.170	0.000	0.000	0.000	0.000
21	B	34	LYS	1	0.851	0.909	22.631	-0.159	-0.159	0.000	0.000	0.000	0.000
22	B	35	HIS	0	0.027	0.013	25.683	-0.004	-0.004	0.000	0.000	0.000	0.000
23	B	36	ARG	1	0.939	0.970	28.260	-0.108	-0.108	0.000	0.000	0.000	0.000
24	B	37	GLU	-1	-0.884	-0.937	25.997	0.141	0.141	0.000	0.000	0.000	0.000
25	B	38	GLY	0	0.027	0.030	30.044	-0.003	-0.003	0.000	0.000	0.000	0.000
26	B	39	GLU	-1	-0.805	-0.877	24.919	0.117	0.117	0.000	0.000	0.000	0.000
27	B	40	ALA	0	0.031	0.018	27.951	-0.001	-0.001	0.000	0.000	0.000	0.000
28	B	41	ILE	0	-0.022	-0.025	23.472	0.000	0.000	0.000	0.000	0.000	0.000
29	B	42	THR	0	0.034	0.035	23.832	0.004	0.004	0.000	0.000	0.000	0.000
30	B	43	ARG	1	0.728	0.864	20.354	-0.020	-0.020	0.000	0.000	0.000	0.000
31	B	44	HIS	0	0.000	-0.001	26.015	-0.009	-0.009	0.000	0.000	0.000	0.000
32	B	45	ILE	0	0.004	-0.006	29.598	0.004	0.004	0.000	0.000	0.000	0.000
33	B	46	GLU	-1	-0.830	-0.904	32.496	0.028	0.028	0.000	0.000	0.000	0.000
34	B	47	ASN	0	0.006	-0.015	33.804	0.005	0.005	0.000	0.000	0.000	0.000
35	B	48	SER	0	-0.019	0.005	35.089	0.003	0.003	0.000	0.000	0.000	0.000
36	B	49	ALA	0	0.035	0.014	31.508	0.003	0.003	0.000	0.000	0.000	0.000
37	B	50	ALA	0	-0.030	-0.014	30.128	0.003	0.003	0.000	0.000	0.000	0.000
38	B	51	GLN	0	-0.009	-0.027	30.477	0.008	0.008	0.000	0.000	0.000	0.000
39	B	52	ASP	-1	-0.841	-0.925	32.315	0.036	0.036	0.000	0.000	0.000	0.000
40	B	53	ALA	0	-0.039	-0.008	27.048	0.003	0.003	0.000	0.000	0.000	0.000
41	B	54	VAL	0	0.004	-0.001	27.796	0.009	0.009	0.000	0.000	0.000	0.000
42	B	55	GLU	-1	-0.833	-0.906	29.044	0.057	0.057	0.000	0.000	0.000	0.000
43	B	56	GLN	0	-0.087	-0.032	27.359	0.001	0.001	0.000	0.000	0.000	0.000
44	B	57	LEU	0	0.011	0.015	22.295	0.008	0.008	0.000	0.000	0.000	0.000
45	B	58	MET	0	-0.019	-0.017	25.953	0.014	0.014	0.000	0.000	0.000	0.000
46	B	59	LYS	1	0.883	0.932	27.970	-0.062	-0.062	0.000	0.000	0.000	0.000
47	B	60	LEU	0	-0.018	-0.007	22.394	-0.001	-0.001	0.000	0.000	0.000	0.000
48	B	61	GLU	-1	-0.916	-0.951	23.206	0.149	0.149	0.000	0.000	0.000	0.000
49	B	62	ASN	0	-0.074	-0.043	22.327	0.010	0.010	0.000	0.000	0.000	0.000
50	B	63	GLU	-1	-0.787	-0.875	22.272	0.086	0.086	0.000	0.000	0.000	0.000
51	B	64	PRO	0	-0.015	-0.020	16.581	-0.003	-0.003	0.000	0.000	0.000	0.000
52	B	65	VAL	0	0.012	0.000	17.271	0.009	0.009	0.000	0.000	0.000	0.000
53	B	66	LYS	1	0.915	0.940	18.321	-0.085	-0.085	0.000	0.000	0.000	0.000
54	B	67	VAL	0	-0.073	-0.023	17.387	-0.006	-0.006	0.000	0.000	0.000	0.000
55	B	68	GLN	0	-0.022	-0.020	13.178	0.068	0.068	0.000	0.000	0.000	0.000
56	B	69	GLU	-1	-0.849	-0.918	16.608	0.040	0.040	0.000	0.000	0.000	0.000
57	B	70	TRP	0	0.005	-0.004	19.624	-0.010	-0.010	0.000	0.000	0.000	0.000
58	B	71	ILE	0	-0.090	-0.058	15.294	-0.003	-0.003	0.000	0.000	0.000	0.000
59	B	72	ASP	-1	-0.855	-0.930	15.379	0.019	0.019	0.000	0.000	0.000	0.000
60	B	73	ALA	0	-0.010	0.014	18.214	-0.019	-0.019	0.000	0.000	0.000	0.000
61	B	74	HIS	0	0.029	0.002	21.941	-0.003	-0.003	0.000	0.000	0.000	0.000
62	B	75	MET	0	-0.044	0.005	18.109	0.004	0.004	0.000	0.000	0.000	0.000
63	B	76	ASN	0	-0.017	-0.015	21.447	-0.016	-0.016	0.000	0.000	0.000	0.000
64	B	77	VAL	0	0.072	0.020	19.821	0.014	0.014	0.000	0.000	0.000	0.000
65	B	78	ASN	0	0.020	0.023	19.389	0.020	0.020	0.000	0.000	0.000	0.000
66	B	79	LEU	0	0.059	0.018	19.748	0.018	0.018	0.000	0.000	0.000	0.000
67	B	80	ALA	0	0.055	0.037	16.527	0.029	0.029	0.000	0.000	0.000	0.000
68	B	81	THR	0	-0.040	-0.021	14.943	0.015	0.015	0.000	0.000	0.000	0.000
69	B	82	ARG	1	0.797	0.865	15.132	-0.092	-0.092	0.000	0.000	0.000	0.000
70	B	83	MET	0	0.058	0.058	14.108	0.049	0.049	0.000	0.000	0.000	0.000
71	B	84	LYS	1	0.896	0.944	10.346	-0.010	-0.010	0.000	0.000	0.000	0.000
72	B	85	GLN	0	-0.020	-0.010	10.950	0.075	0.075	0.000	0.000	0.000	0.000
73	B	86	THR	0	-0.033	-0.022	12.829	0.053	0.053	0.000	0.000	0.000	0.000
74	B	87	ILE	0	0.027	0.009	9.750	0.020	0.020	0.000	0.000	0.000	0.000
75	B	88	ARG	1	0.921	0.970	7.676	-0.480	-0.480	0.000	0.000	0.000	0.000
76	B	89	ALA	0	-0.006	-0.002	9.461	0.055	0.055	0.000	0.000	0.000	0.000
77	B	90	ARG	1	0.922	0.971	12.336	-0.335	-0.335	0.000	0.000	0.000	0.000
78	B	91	ARG	1	0.867	0.926	4.606	-1.718	-1.600	-0.001	-0.005	-0.112	0.000
79	B	92	LYS	1	0.863	0.934	8.725	-0.851	-0.851	0.000	0.000	0.000	0.000
80	B	93	ARG	1	0.915	0.941	10.151	-0.433	-0.433	0.000	0.000	0.000	0.000
81	B	94	HIS	0	0.013	0.013	12.344	-0.020	-0.020	0.000	0.000	0.000	0.000
82	B	95	PHE	0	0.028	0.001	8.214	-0.048	-0.048	0.000	0.000	0.000	0.000
83	B	96	ASN	0	-0.020	-0.004	11.739	0.062	0.062	0.000	0.000	0.000	0.000
84	B	97	ALA	0	-0.053	-0.026	14.180	-0.028	-0.028	0.000	0.000	0.000	0.000
85	B	98	GLU	-1	-0.829	-0.909	13.623	0.188	0.188	0.000	0.000	0.000	0.000
86	B	99	HIS	0	-0.012	-0.007	16.122	-0.042	-0.042	0.000	0.000	0.000	0.000
87	B	100	GLN	0	0.045	0.018	18.078	0.024	0.024	0.000	0.000	0.000	0.000
88	B	101	HIS	0	0.055	0.031	18.304	0.035	0.035	0.000	0.000	0.000	0.000
89	B	102	THR	0	-0.008	0.001	14.222	0.032	0.032	0.000	0.000	0.000	0.000
90	B	103	ARG	1	0.928	0.995	15.624	-0.155	-0.155	0.000	0.000	0.000	0.000
91	B	104	LYS	1	0.856	0.904	14.989	-0.334	-0.334	0.000	0.000	0.000	0.000
92	B	105	LYS	1	0.951	0.961	19.710	-0.156	-0.156	0.000	0.000	0.000	0.000
93	B	106	SER	0	0.011	0.007	23.297	0.007	0.007	0.000	0.000	0.000	0.000
94	B	107	ILE	0	-0.014	-0.001	24.515	-0.010	-0.010	0.000	0.000	0.000	0.000
95	B	108	ASP	-1	-0.882	-0.923	27.525	0.142	0.142	0.000	0.000	0.000	0.000
96	B	109	LEU	0	-0.042	-0.036	29.430	-0.004	-0.004	0.000	0.000	0.000	0.000
97	B	110	GLU	-1	-0.869	-0.926	32.357	0.080	0.080	0.000	0.000	0.000	0.000
98	B	111	PHE	0	0.027	0.006	32.351	0.003	0.003	0.000	0.000	0.000	0.000
99	B	112	LEU	0	0.081	0.027	34.030	0.004	0.004	0.000	0.000	0.000	0.000
100	B	113	VAL	0	0.006	0.006	33.277	0.000	0.000	0.000	0.000	0.000	0.000
101	B	114	TRP	0	0.006	0.006	26.553	0.000	0.000	0.000	0.000	0.000	0.000
102	B	115	GLN	0	0.007	0.006	30.529	0.004	0.004	0.000	0.000	0.000	0.000
103	B	116	ARG	1	0.943	0.965	32.286	-0.075	-0.075	0.000	0.000	0.000	0.000
104	B	117	LEU	0	0.022	0.021	27.733	0.000	0.000	0.000	0.000	0.000	0.000
105	B	118	ALA	0	0.047	0.009	27.642	0.006	0.006	0.000	0.000	0.000	0.000
106	B	119	VAL	0	-0.073	-0.039	28.470	0.003	0.003	0.000	0.000	0.000	0.000
107	B	120	LEU	0	-0.014	-0.006	30.530	-0.002	-0.002	0.000	0.000	0.000	0.000
108	B	121	ALA	0	0.030	0.024	25.097	-0.001	-0.001	0.000	0.000	0.000	0.000
109	B	122	ARG	1	0.906	0.947	25.674	-0.116	-0.116	0.000	0.000	0.000	0.000
110	B	123	ARG	1	0.910	0.966	26.843	-0.082	-0.082	0.000	0.000	0.000	0.000
111	B	124	ARG	1	0.839	0.917	27.408	-0.111	-0.111	0.000	0.000	0.000	0.000
112	B	125	GLY	0	0.018	0.038	24.174	0.001	0.001	0.000	0.000	0.000	0.000
113	B	126	ASN	0	-0.033	-0.013	21.681	0.006	0.006	0.000	0.000	0.000	0.000
114	B	127	THR	0	-0.034	-0.052	18.361	0.000	0.000	0.000	0.000	0.000	0.000
115	B	128	LEU	0	0.030	0.007	21.632	-0.021	-0.021	0.000	0.000	0.000	0.000
116	B	129	SER	0	-0.003	-0.006	20.507	-0.020	-0.020	0.000	0.000	0.000	0.000
117	B	130	ASP	-1	-0.782	-0.853	20.785	0.229	0.229	0.000	0.000	0.000	0.000
118	B	131	THR	0	-0.014	-0.019	23.702	-0.020	-0.020	0.000	0.000	0.000	0.000
119	B	132	VAL	0	-0.029	-0.020	26.597	-0.013	-0.013	0.000	0.000	0.000	0.000
120	B	133	VAL	0	-0.015	-0.002	24.822	-0.009	-0.009	0.000	0.000	0.000	0.000
121	B	134	GLN	0	0.068	0.019	25.967	-0.011	-0.011	0.000	0.000	0.000	0.000
122	B	135	LEU	0	-0.031	-0.016	29.249	-0.009	-0.009	0.000	0.000	0.000	0.000
123	B	136	ILE	0	-0.021	0.002	29.948	-0.007	-0.007	0.000	0.000	0.000	0.000
124	B	137	GLU	-1	-0.896	-0.947	29.017	0.089	0.089	0.000	0.000	0.000	0.000
125	B	138	ASP	-1	-0.853	-0.929	32.921	0.076	0.076	0.000	0.000	0.000	0.000
126	B	139	ALA	0	-0.063	-0.030	35.102	-0.006	-0.006	0.000	0.000	0.000	0.000
127	B	140	GLU	-1	-0.767	-0.870	36.017	0.055	0.055	0.000	0.000	0.000	0.000
128	B	141	ARG	1	0.854	0.917	36.779	-0.049	-0.049	0.000	0.000	0.000	0.000
129	B	142	LYS	1	0.814	0.896	38.862	-0.061	-0.061	0.000	0.000	0.000	0.000
130	B	143	GLU	-1	-0.832	-0.913	40.524	0.056	0.056	0.000	0.000	0.000	0.000
131	B	144	LYS	1	0.806	0.893	38.510	-0.054	-0.054	0.000	0.000	0.000	0.000
132	B	145	TYR	0	0.028	0.012	40.743	-0.002	-0.002	0.000	0.000	0.000	0.000
133	B	146	ALA	0	0.024	0.018	45.016	-0.002	-0.002	0.000	0.000	0.000	0.000
134	B	147	SER	0	-0.006	0.006	45.827	-0.002	-0.002	0.000	0.000	0.000	0.000
135	B	148	GLN	0	0.065	0.034	44.175	0.000	0.000	0.000	0.000	0.000	0.000
136	B	149	MET	0	-0.012	-0.010	48.401	-0.001	-0.001	0.000	0.000	0.000	0.000
137	B	150	SER	0	-0.040	-0.031	50.752	-0.001	-0.001	0.000	0.000	0.000	0.000
138	B	151	SER	0	-0.033	-0.018	50.246	-0.001	-0.001	0.000	0.000	0.000	0.000
139	B	152	LEU	0	0.048	0.031	52.481	-0.001	-0.001	0.000	0.000	0.000	0.000
140	B	153	LYS	1	0.910	0.950	54.300	-0.028	-0.028	0.000	0.000	0.000	0.000
141	B	154	GLN	0	-0.040	-0.020	56.209	0.000	0.000	0.000	0.000	0.000	0.000
142	B	155	ASP	-1	-0.880	-0.946	54.073	0.022	0.022	0.000	0.000	0.000	0.000
143	B	156	LEU	0	-0.042	-0.030	57.643	-0.001	-0.001	0.000	0.000	0.000	0.000
144	B	157	LYS	1	0.768	0.871	60.208	-0.019	-0.019	0.000	0.000	0.000	0.000
145	B	158	ASP	-1	-0.756	-0.877	60.293	0.019	0.019	0.000	0.000	0.000	0.000
146	B	159	ILE	0	-0.062	-0.019	61.270	-0.001	-0.001	0.000	0.000	0.000	0.000
147	B	160	LEU	0	-0.026	-0.002	63.905	-0.001	-0.001	0.000	0.000	0.000	0.000
148	B	161	ASP	-1	-0.813	-0.867	66.207	0.017	0.017	0.000	0.000	0.000	0.000
149	B	162	LYS	1	0.787	0.881	64.138	-0.016	-0.016	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(B:14:MET)