FMO DATABASE

FMODB ID: QVL2Y

Calculation Name: 3EPU-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EPU

Chain ID: B

ChEMBL ID:

UniProt ID: Q8ZNP3

Base Structure: X-ray

Registration Date: 2023-09-23

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	133
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1127113.164435
FMO2-HF: Nuclear repulsion	1072541.248178
FMO2-HF: Total energy	-54571.916257
FMO2-MP2: Total energy	-54729.081053

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:3:SER)

Summations of interaction energy for fragment #1(B:3:SER)

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.
-27.481	-30.225	20.68	-10.839	-7.097	-0.066

Interaction energy analysis for fragmet #1(B:3:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / 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	B	5	ALA	0	0.044	0.029	3.153	-1.079	1.015	0.017	-1.040	-1.071	0.003
4	B	6	ASP	-1	-0.710	-0.822	1.643	-26.854	-32.434	20.663	-9.552	-5.531	-0.069
5	B	7	ARG	1	0.967	0.989	3.927	-3.478	-2.818	0.001	-0.238	-0.424	0.000
6	B	8	LEU	0	0.006	0.010	5.995	0.275	0.275	0.000	0.000	0.000	0.000
7	B	9	LEU	0	0.050	0.021	6.363	0.254	0.254	0.000	0.000	0.000	0.000
8	B	10	ARG	1	0.807	0.880	7.570	1.159	1.159	0.000	0.000	0.000	0.000
9	B	11	GLN	0	-0.015	-0.019	9.611	0.265	0.265	0.000	0.000	0.000	0.000
10	B	12	PHE	0	-0.002	0.000	11.721	0.078	0.078	0.000	0.000	0.000	0.000
11	B	13	SER	0	0.021	-0.001	11.624	0.045	0.045	0.000	0.000	0.000	0.000
12	B	14	LEU	0	-0.005	-0.006	13.238	0.070	0.070	0.000	0.000	0.000	0.000
13	B	15	LYS	1	0.734	0.863	15.768	0.174	0.174	0.000	0.000	0.000	0.000
14	B	16	LEU	0	0.043	0.019	16.166	0.029	0.029	0.000	0.000	0.000	0.000
15	B	17	ASN	0	0.054	0.018	17.878	0.019	0.019	0.000	0.000	0.000	0.000
16	B	18	THR	0	-0.098	-0.049	19.681	0.042	0.042	0.000	0.000	0.000	0.000
17	B	19	ASP	-1	-0.854	-0.893	21.704	-0.126	-0.126	0.000	0.000	0.000	0.000
18	B	20	SER	0	-0.047	-0.029	23.430	0.005	0.005	0.000	0.000	0.000	0.000
19	B	21	ILE	0	-0.062	-0.019	20.982	-0.003	-0.003	0.000	0.000	0.000	0.000
20	B	22	VAL	0	0.032	0.007	20.457	-0.023	-0.023	0.000	0.000	0.000	0.000
21	B	23	PHE	0	-0.067	-0.033	14.394	-0.010	-0.010	0.000	0.000	0.000	0.000
22	B	24	ASP	-1	-0.866	-0.917	17.659	-0.396	-0.396	0.000	0.000	0.000	0.000
23	B	25	GLU	-1	-0.833	-0.894	11.620	-0.945	-0.945	0.000	0.000	0.000	0.000
24	B	26	ASN	0	0.048	-0.006	12.651	0.065	0.065	0.000	0.000	0.000	0.000
25	B	27	ARG	1	0.816	0.910	3.736	3.757	3.839	-0.001	-0.009	-0.071	0.000
26	B	28	LEU	0	0.020	0.011	10.750	0.173	0.173	0.000	0.000	0.000	0.000
27	B	29	CYS	0	-0.032	-0.019	10.882	-0.227	-0.227	0.000	0.000	0.000	0.000
28	B	30	SER	0	-0.041	0.003	12.936	0.138	0.138	0.000	0.000	0.000	0.000
29	B	31	PHE	0	0.029	0.013	15.941	-0.044	-0.044	0.000	0.000	0.000	0.000
30	B	32	ILE	0	-0.007	-0.004	18.419	0.013	0.013	0.000	0.000	0.000	0.000
31	B	33	ILE	0	0.021	0.031	20.832	0.002	0.002	0.000	0.000	0.000	0.000
32	B	34	ASP	-1	-0.829	-0.929	23.782	-0.164	-0.164	0.000	0.000	0.000	0.000
33	B	35	ASN	0	-0.118	-0.065	25.291	-0.004	-0.004	0.000	0.000	0.000	0.000
34	B	36	ARG	1	0.826	0.885	26.550	0.153	0.153	0.000	0.000	0.000	0.000
35	B	37	TYR	0	0.025	-0.011	25.703	-0.003	-0.003	0.000	0.000	0.000	0.000
36	B	38	ARG	1	0.888	0.947	18.458	0.450	0.450	0.000	0.000	0.000	0.000
37	B	39	ILE	0	0.023	0.017	19.476	0.013	0.013	0.000	0.000	0.000	0.000
38	B	40	LEU	0	-0.040	-0.030	16.404	-0.057	-0.057	0.000	0.000	0.000	0.000
39	B	41	LEU	0	0.030	0.019	15.248	0.046	0.046	0.000	0.000	0.000	0.000
40	B	42	THR	0	-0.025	-0.029	14.819	-0.087	-0.087	0.000	0.000	0.000	0.000
41	B	43	SER	0	-0.033	-0.003	13.013	0.081	0.081	0.000	0.000	0.000	0.000
42	B	44	THR	0	0.038	0.009	13.662	-0.120	-0.120	0.000	0.000	0.000	0.000
43	B	45	ASN	0	0.033	0.015	15.981	-0.003	-0.003	0.000	0.000	0.000	0.000
44	B	46	SER	0	-0.015	-0.004	16.327	-0.023	-0.023	0.000	0.000	0.000	0.000
45	B	47	GLU	-1	-0.937	-0.959	17.263	-0.162	-0.162	0.000	0.000	0.000	0.000
46	B	48	TYR	0	0.011	0.002	18.893	0.041	0.041	0.000	0.000	0.000	0.000
47	B	49	ILE	0	-0.032	-0.004	14.821	-0.065	-0.065	0.000	0.000	0.000	0.000
48	B	50	MET	0	-0.028	0.017	17.899	0.059	0.059	0.000	0.000	0.000	0.000
49	B	51	ILE	0	0.009	-0.003	18.765	-0.060	-0.060	0.000	0.000	0.000	0.000
50	B	52	TYR	0	0.016	-0.004	20.047	0.047	0.047	0.000	0.000	0.000	0.000
51	B	53	GLY	0	0.091	0.013	22.546	-0.024	-0.024	0.000	0.000	0.000	0.000
52	B	54	PHE	0	-0.052	-0.033	21.956	0.012	0.012	0.000	0.000	0.000	0.000
53	B	55	CYS	0	-0.025	0.004	25.771	0.007	0.007	0.000	0.000	0.000	0.000
54	B	56	GLY	0	0.091	0.044	29.339	0.009	0.009	0.000	0.000	0.000	0.000
55	B	57	LYS	1	0.861	0.939	29.119	0.247	0.247	0.000	0.000	0.000	0.000
56	B	58	PRO	0	-0.011	0.006	32.644	0.009	0.009	0.000	0.000	0.000	0.000
57	B	59	PRO	0	0.009	-0.006	36.117	-0.002	-0.002	0.000	0.000	0.000	0.000
58	B	60	ASP	-1	-0.857	-0.931	37.113	-0.169	-0.169	0.000	0.000	0.000	0.000
59	B	61	ASN	0	-0.017	-0.008	39.576	0.010	0.010	0.000	0.000	0.000	0.000
60	B	62	ASN	0	0.031	0.004	41.705	-0.005	-0.005	0.000	0.000	0.000	0.000
61	B	63	ASN	0	0.015	-0.004	42.980	-0.002	-0.002	0.000	0.000	0.000	0.000
62	B	64	LEU	0	0.003	0.016	39.931	0.003	0.003	0.000	0.000	0.000	0.000
63	B	65	ALA	0	0.037	0.019	38.850	-0.003	-0.003	0.000	0.000	0.000	0.000
64	B	66	PHE	0	-0.012	-0.016	39.839	-0.001	-0.001	0.000	0.000	0.000	0.000
65	B	67	GLU	-1	-0.819	-0.888	41.547	-0.101	-0.101	0.000	0.000	0.000	0.000
66	B	68	PHE	0	0.006	-0.008	36.512	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	69	LEU	0	-0.014	-0.003	37.602	-0.002	-0.002	0.000	0.000	0.000	0.000
68	B	70	ASN	0	-0.053	-0.031	39.537	0.004	0.004	0.000	0.000	0.000	0.000
69	B	71	ALA	0	0.015	0.004	38.409	0.002	0.002	0.000	0.000	0.000	0.000
70	B	72	ASN	0	-0.049	-0.048	34.716	-0.005	-0.005	0.000	0.000	0.000	0.000
71	B	73	LEU	0	-0.026	0.004	37.475	0.001	0.001	0.000	0.000	0.000	0.000
72	B	74	TRP	0	0.026	0.026	35.736	0.000	0.000	0.000	0.000	0.000	0.000
73	B	75	PHE	0	0.041	0.004	33.548	0.001	0.001	0.000	0.000	0.000	0.000
74	B	76	ALA	0	-0.012	0.001	35.461	-0.001	-0.001	0.000	0.000	0.000	0.000
75	B	77	GLU	-1	-0.942	-0.965	36.801	-0.081	-0.081	0.000	0.000	0.000	0.000
76	B	78	ASN	0	-0.127	-0.072	37.196	0.007	0.007	0.000	0.000	0.000	0.000
77	B	79	ASN	0	-0.103	-0.045	33.633	-0.002	-0.002	0.000	0.000	0.000	0.000
78	B	80	GLY	0	0.040	0.029	31.516	-0.004	-0.004	0.000	0.000	0.000	0.000
79	B	81	PRO	0	-0.056	-0.040	28.029	-0.003	-0.003	0.000	0.000	0.000	0.000
80	B	82	HIS	0	0.009	0.012	29.461	0.004	0.004	0.000	0.000	0.000	0.000
81	B	83	LEU	0	0.008	0.023	30.025	-0.016	-0.016	0.000	0.000	0.000	0.000
82	B	84	CYS	0	-0.048	-0.023	29.210	0.008	0.008	0.000	0.000	0.000	0.000
83	B	85	TYR	0	-0.003	-0.018	30.958	-0.005	-0.005	0.000	0.000	0.000	0.000
84	B	86	ASP	-1	-0.773	-0.841	25.939	-0.325	-0.325	0.000	0.000	0.000	0.000
85	B	87	ASN	0	-0.014	-0.028	28.607	0.010	0.010	0.000	0.000	0.000	0.000
86	B	88	ASN	0	-0.103	-0.050	25.598	0.007	0.007	0.000	0.000	0.000	0.000
87	B	89	SER	0	-0.045	-0.057	25.271	-0.001	-0.001	0.000	0.000	0.000	0.000
88	B	90	GLN	0	-0.029	-0.012	27.379	0.004	0.004	0.000	0.000	0.000	0.000
89	B	91	SER	0	-0.010	0.002	27.516	0.014	0.014	0.000	0.000	0.000	0.000
90	B	92	LEU	0	-0.014	-0.004	29.660	-0.004	-0.004	0.000	0.000	0.000	0.000
91	B	93	LEU	0	-0.049	-0.036	24.587	-0.011	-0.011	0.000	0.000	0.000	0.000
92	B	94	LEU	0	0.004	0.015	27.406	0.016	0.016	0.000	0.000	0.000	0.000
93	B	95	ALA	0	0.006	0.000	25.322	-0.020	-0.020	0.000	0.000	0.000	0.000
94	B	96	LEU	0	0.031	0.013	24.521	0.021	0.021	0.000	0.000	0.000	0.000
95	B	97	ASN	0	-0.030	-0.030	23.001	-0.018	-0.018	0.000	0.000	0.000	0.000
96	B	98	PHE	0	0.017	0.017	18.506	0.024	0.024	0.000	0.000	0.000	0.000
97	B	99	SER	0	0.046	0.018	20.499	-0.016	-0.016	0.000	0.000	0.000	0.000
98	B	100	LEU	0	0.018	-0.003	16.113	0.006	0.006	0.000	0.000	0.000	0.000
99	B	101	ASN	0	-0.053	-0.021	20.004	0.040	0.040	0.000	0.000	0.000	0.000
100	B	102	GLU	-1	-0.959	-0.981	23.353	-0.048	-0.048	0.000	0.000	0.000	0.000
101	B	103	SER	0	-0.079	-0.024	19.271	-0.004	-0.004	0.000	0.000	0.000	0.000
102	B	104	SER	0	-0.021	-0.051	19.443	0.019	0.019	0.000	0.000	0.000	0.000
103	B	105	VAL	0	0.012	0.003	16.886	-0.034	-0.034	0.000	0.000	0.000	0.000
104	B	106	GLU	-1	-0.766	-0.861	18.633	-0.061	-0.061	0.000	0.000	0.000	0.000
105	B	107	LYS	1	0.842	0.914	22.307	0.112	0.112	0.000	0.000	0.000	0.000
106	B	108	LEU	0	0.001	-0.003	16.345	-0.016	-0.016	0.000	0.000	0.000	0.000
107	B	109	GLU	-1	-0.925	-0.975	20.049	-0.159	-0.159	0.000	0.000	0.000	0.000
108	B	110	CYS	0	-0.072	-0.036	21.990	0.005	0.005	0.000	0.000	0.000	0.000
109	B	111	GLU	-1	-0.789	-0.886	22.988	-0.149	-0.149	0.000	0.000	0.000	0.000
110	B	112	ILE	0	-0.029	-0.019	18.540	-0.016	-0.016	0.000	0.000	0.000	0.000
111	B	113	GLU	-1	-0.790	-0.873	23.151	-0.139	-0.139	0.000	0.000	0.000	0.000
112	B	114	VAL	0	-0.014	0.002	26.456	0.007	0.007	0.000	0.000	0.000	0.000
113	B	115	VAL	0	-0.011	0.002	24.472	0.005	0.005	0.000	0.000	0.000	0.000
114	B	116	ILE	0	0.029	0.010	23.883	0.002	0.002	0.000	0.000	0.000	0.000
115	B	117	ARG	1	0.842	0.893	27.795	0.123	0.123	0.000	0.000	0.000	0.000
116	B	118	SER	0	-0.025	-0.012	30.017	0.012	0.012	0.000	0.000	0.000	0.000
117	B	119	MET	0	-0.062	-0.017	26.545	-0.001	-0.001	0.000	0.000	0.000	0.000
118	B	120	GLU	-1	-0.775	-0.825	30.909	-0.134	-0.134	0.000	0.000	0.000	0.000
119	B	121	ASN	0	-0.012	-0.009	33.348	0.008	0.008	0.000	0.000	0.000	0.000
120	B	122	LEU	0	0.004	0.005	32.763	0.006	0.006	0.000	0.000	0.000	0.000
121	B	123	TYR	0	-0.034	-0.042	30.012	0.002	0.002	0.000	0.000	0.000	0.000
122	B	124	HIS	0	-0.024	-0.007	35.700	0.010	0.010	0.000	0.000	0.000	0.000
123	B	125	ILE	0	-0.003	-0.004	38.803	0.006	0.006	0.000	0.000	0.000	0.000
124	B	126	LEU	0	-0.051	-0.024	35.903	0.004	0.004	0.000	0.000	0.000	0.000
125	B	127	GLN	0	-0.067	-0.030	39.380	0.000	0.000	0.000	0.000	0.000	0.000
126	B	128	ASP	-1	-0.894	-0.943	41.008	-0.090	-0.090	0.000	0.000	0.000	0.000
127	B	129	LYS	1	0.805	0.901	42.898	0.108	0.108	0.000	0.000	0.000	0.000
128	B	130	GLY	0	-0.027	-0.002	43.986	0.002	0.002	0.000	0.000	0.000	0.000
129	B	131	ILE	0	-0.090	-0.050	40.051	-0.001	-0.001	0.000	0.000	0.000	0.000
130	B	132	THR	0	0.041	0.016	37.392	-0.003	-0.003	0.000	0.000	0.000	0.000
131	B	133	LEU	0	-0.033	-0.012	32.886	0.002	0.002	0.000	0.000	0.000	0.000
132	B	134	ASP	-1	-0.881	-0.930	32.015	-0.209	-0.209	0.000	0.000	0.000	0.000
133	B	135	THR	0	-0.023	-0.003	27.729	-0.014	-0.014	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:3:SER)