FMO DATABASE

FMODB ID: 3QMKL

Calculation Name: 3DLV-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DLV

Chain ID: B

ChEMBL ID:

UniProt ID: Q8TZT9

Base Structure: X-ray

Registration Date: 2023-03-14

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	104
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-801459.263831
FMO2-HF: Nuclear repulsion	760389.907182
FMO2-HF: Total energy	-41069.356649
FMO2-MP2: Total energy	-41192.088982

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:2:GLY)

Summations of interaction energy for fragment #1(B:2: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.
-6.482	-4.632	6.842	-4.295	-4.396	-0.027

Interaction energy analysis for fragmet #1(B:2:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.059 / q_NPA : 0.029

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	4	PHE	0	-0.053	-0.032	2.776	0.471	2.474	0.086	-0.942	-1.146	0.004
4	B	5	VAL	0	0.043	0.027	6.402	0.038	0.038	0.000	0.000	0.000	0.000
5	B	6	VAL	0	-0.034	-0.015	9.210	0.073	0.073	0.000	0.000	0.000	0.000
6	B	7	TRP	0	0.126	0.054	11.563	0.037	0.037	0.000	0.000	0.000	0.000
7	B	8	PRO	0	0.058	0.018	15.277	0.020	0.020	0.000	0.000	0.000	0.000
8	B	9	SER	0	0.033	0.013	17.612	0.016	0.016	0.000	0.000	0.000	0.000
9	B	10	GLU	-1	-0.803	-0.879	12.647	-0.562	-0.562	0.000	0.000	0.000	0.000
10	B	11	LEU	0	-0.030	-0.036	14.025	0.036	0.036	0.000	0.000	0.000	0.000
11	B	12	ASP	-1	-0.684	-0.829	16.935	-0.198	-0.198	0.000	0.000	0.000	0.000
12	B	13	SER	0	-0.043	-0.038	20.698	0.018	0.018	0.000	0.000	0.000	0.000
13	B	14	ARG	1	0.863	0.928	23.043	0.194	0.194	0.000	0.000	0.000	0.000
14	B	15	LEU	0	-0.002	0.033	21.607	0.014	0.014	0.000	0.000	0.000	0.000
15	B	16	SER	0	0.012	-0.005	23.525	0.008	0.008	0.000	0.000	0.000	0.000
16	B	17	ARG	1	0.876	0.911	16.673	0.031	0.031	0.000	0.000	0.000	0.000
17	B	18	LYS	1	0.937	0.971	21.088	0.027	0.027	0.000	0.000	0.000	0.000
18	B	19	TYR	0	-0.043	-0.045	23.350	-0.002	-0.002	0.000	0.000	0.000	0.000
19	B	20	GLY	0	0.065	0.038	19.125	-0.021	-0.021	0.000	0.000	0.000	0.000
20	B	21	ARG	1	0.771	0.915	17.401	0.111	0.111	0.000	0.000	0.000	0.000
21	B	22	ILE	0	0.021	0.010	12.281	0.049	0.049	0.000	0.000	0.000	0.000
22	B	23	VAL	0	-0.007	0.006	13.985	0.063	0.063	0.000	0.000	0.000	0.000
23	B	24	PRO	0	0.018	-0.004	16.224	0.015	0.015	0.000	0.000	0.000	0.000
24	B	25	ARG	1	1.005	0.988	19.305	0.009	0.009	0.000	0.000	0.000	0.000
25	B	26	SER	0	0.034	0.027	22.337	-0.011	-0.011	0.000	0.000	0.000	0.000
26	B	27	ILE	0	-0.030	-0.009	16.406	-0.004	-0.004	0.000	0.000	0.000	0.000
27	B	28	ALA	0	-0.009	0.011	18.601	-0.033	-0.033	0.000	0.000	0.000	0.000
28	B	29	VAL	0	0.013	0.002	19.400	0.023	0.023	0.000	0.000	0.000	0.000
29	B	30	GLU	-1	-0.854	-0.918	21.786	-0.161	-0.161	0.000	0.000	0.000	0.000
30	B	31	SER	0	0.022	0.013	23.657	-0.006	-0.006	0.000	0.000	0.000	0.000
31	B	32	PRO	0	-0.063	-0.008	18.747	-0.005	-0.005	0.000	0.000	0.000	0.000
32	B	33	ARG	1	0.862	0.910	20.737	0.285	0.285	0.000	0.000	0.000	0.000
33	B	34	VAL	0	0.057	0.022	17.699	-0.040	-0.040	0.000	0.000	0.000	0.000
34	B	35	GLU	-1	-0.736	-0.844	17.961	-0.395	-0.395	0.000	0.000	0.000	0.000
35	B	36	GLU	-1	-0.753	-0.837	19.348	-0.326	-0.326	0.000	0.000	0.000	0.000
36	B	37	ILE	0	-0.005	-0.011	13.456	-0.029	-0.029	0.000	0.000	0.000	0.000
37	B	38	VAL	0	-0.011	0.006	14.242	-0.119	-0.119	0.000	0.000	0.000	0.000
38	B	39	ARG	1	0.948	0.963	15.099	0.296	0.296	0.000	0.000	0.000	0.000
39	B	40	ALA	0	-0.036	-0.018	14.915	0.007	0.007	0.000	0.000	0.000	0.000
40	B	41	ALA	0	-0.032	-0.019	10.995	-0.029	-0.029	0.000	0.000	0.000	0.000
41	B	42	GLU	-1	-0.839	-0.923	11.905	-0.666	-0.666	0.000	0.000	0.000	0.000
42	B	43	GLU	-1	-0.874	-0.932	14.360	-0.304	-0.304	0.000	0.000	0.000	0.000
43	B	44	LEU	0	-0.073	-0.045	11.014	0.070	0.070	0.000	0.000	0.000	0.000
44	B	45	LYS	1	0.831	0.923	10.865	0.494	0.494	0.000	0.000	0.000	0.000
45	B	46	PHE	0	-0.050	-0.023	7.647	-0.219	-0.219	0.000	0.000	0.000	0.000
46	B	47	LYS	1	0.899	0.946	7.746	1.628	1.628	0.000	0.000	0.000	0.000
47	B	48	VAL	0	0.042	0.002	9.055	-0.400	-0.400	0.000	0.000	0.000	0.000
48	B	49	ILE	0	-0.085	-0.032	8.620	0.123	0.123	0.000	0.000	0.000	0.000
49	B	50	ARG	1	0.850	0.875	11.915	0.651	0.651	0.000	0.000	0.000	0.000
50	B	51	VAL	0	-0.008	-0.007	14.172	-0.116	-0.116	0.000	0.000	0.000	0.000
51	B	52	GLU	-1	-0.780	-0.837	16.961	-0.407	-0.407	0.000	0.000	0.000	0.000
52	B	53	GLU	-1	-0.850	-0.942	19.544	-0.351	-0.351	0.000	0.000	0.000	0.000
53	B	54	ASP	-1	-0.862	-0.904	22.350	-0.208	-0.208	0.000	0.000	0.000	0.000
54	B	55	LYS	1	0.731	0.824	25.423	0.273	0.273	0.000	0.000	0.000	0.000
55	B	56	LEU	0	0.111	0.068	28.420	0.013	0.013	0.000	0.000	0.000	0.000
56	B	57	ASN	0	-0.010	-0.021	31.059	-0.001	-0.001	0.000	0.000	0.000	0.000
57	B	58	PRO	0	-0.040	0.016	32.396	0.008	0.008	0.000	0.000	0.000	0.000
58	B	59	ARG	1	0.857	0.874	31.333	0.118	0.118	0.000	0.000	0.000	0.000
59	B	60	LEU	0	-0.004	0.005	35.921	0.005	0.005	0.000	0.000	0.000	0.000
60	B	61	SER	0	0.020	0.017	37.550	0.004	0.004	0.000	0.000	0.000	0.000
61	B	62	GLY	0	0.004	0.012	38.592	0.004	0.004	0.000	0.000	0.000	0.000
62	B	63	ILE	0	-0.038	-0.030	36.339	0.001	0.001	0.000	0.000	0.000	0.000
63	B	64	ASP	-1	-0.844	-0.919	31.853	-0.130	-0.130	0.000	0.000	0.000	0.000
64	B	65	GLU	-1	-0.858	-0.932	32.296	-0.103	-0.103	0.000	0.000	0.000	0.000
65	B	66	GLU	-1	-0.913	-0.930	27.517	-0.145	-0.145	0.000	0.000	0.000	0.000
66	B	67	LEU	0	0.001	0.001	26.054	-0.019	-0.019	0.000	0.000	0.000	0.000
67	B	68	ARG	1	0.927	0.995	28.150	0.169	0.169	0.000	0.000	0.000	0.000
68	B	69	THR	0	-0.085	-0.058	24.410	-0.004	-0.004	0.000	0.000	0.000	0.000
69	B	70	PHE	0	0.036	0.032	19.461	-0.008	-0.008	0.000	0.000	0.000	0.000
70	B	71	GLY	0	0.039	0.009	19.865	0.001	0.001	0.000	0.000	0.000	0.000
71	B	72	MET	0	-0.069	-0.024	14.606	0.003	0.003	0.000	0.000	0.000	0.000
72	B	73	ILE	0	0.012	0.009	12.029	0.016	0.016	0.000	0.000	0.000	0.000
73	B	74	VAL	0	-0.014	-0.001	9.379	-0.165	-0.165	0.000	0.000	0.000	0.000
74	B	75	LEU	0	-0.003	-0.001	7.167	0.185	0.185	0.000	0.000	0.000	0.000
75	B	76	GLU	-1	-0.722	-0.837	4.521	-2.842	-2.623	-0.001	-0.067	-0.152	0.000
76	B	77	SER	0	-0.007	-0.001	3.041	1.742	2.540	0.017	-0.315	-0.501	0.001
77	B	78	PRO	0	0.045	0.026	1.934	-6.778	-8.799	6.686	-2.623	-2.041	-0.031
78	B	79	TYR	0	0.001	-0.002	3.915	1.755	2.049	0.003	-0.073	-0.224	0.000
79	B	80	GLY	0	0.089	0.042	3.188	-2.012	-1.499	0.052	-0.277	-0.288	-0.001
80	B	81	LYS	1	0.840	0.895	4.061	0.196	0.240	-0.001	0.002	-0.044	0.000
81	B	82	SER	0	0.021	0.006	6.067	0.008	0.008	0.000	0.000	0.000	0.000
82	B	83	LYS	1	0.936	0.981	7.777	-0.363	-0.363	0.000	0.000	0.000	0.000
83	B	84	SER	0	0.052	0.023	5.117	0.050	0.050	0.000	0.000	0.000	0.000
84	B	85	LEU	0	0.033	0.019	8.146	0.042	0.042	0.000	0.000	0.000	0.000
85	B	86	LYS	1	0.847	0.925	10.938	0.078	0.078	0.000	0.000	0.000	0.000
86	B	87	LEU	0	0.035	0.024	9.748	0.029	0.029	0.000	0.000	0.000	0.000
87	B	88	ILE	0	0.039	0.022	10.221	0.036	0.036	0.000	0.000	0.000	0.000
88	B	89	ALA	0	0.018	0.006	13.681	0.057	0.057	0.000	0.000	0.000	0.000
89	B	90	GLN	0	-0.053	-0.040	15.585	0.024	0.024	0.000	0.000	0.000	0.000
90	B	91	LYS	1	0.848	0.907	16.206	0.369	0.369	0.000	0.000	0.000	0.000
91	B	92	ILE	0	0.039	0.022	16.840	0.025	0.025	0.000	0.000	0.000	0.000
92	B	93	ARG	1	0.819	0.892	19.733	0.220	0.220	0.000	0.000	0.000	0.000
93	B	94	GLU	-1	-0.848	-0.885	20.482	-0.238	-0.238	0.000	0.000	0.000	0.000
94	B	95	PHE	0	-0.030	-0.016	18.504	0.024	0.024	0.000	0.000	0.000	0.000
95	B	96	ARG	1	0.780	0.853	23.015	0.273	0.273	0.000	0.000	0.000	0.000
96	B	97	ARG	1	0.967	0.984	25.754	0.144	0.144	0.000	0.000	0.000	0.000
97	B	98	ARG	1	0.859	0.913	22.208	0.239	0.239	0.000	0.000	0.000	0.000
98	B	99	SER	0	-0.048	-0.036	26.696	0.003	0.003	0.000	0.000	0.000	0.000
99	B	100	ALA	0	-0.012	-0.001	29.258	0.008	0.008	0.000	0.000	0.000	0.000
100	B	101	GLY	0	0.016	0.019	31.267	0.009	0.009	0.000	0.000	0.000	0.000
101	B	102	THR	0	-0.005	-0.009	32.707	0.011	0.011	0.000	0.000	0.000	0.000
102	B	103	LEU	0	-0.067	-0.031	31.961	-0.009	-0.009	0.000	0.000	0.000	0.000
103	B	104	VAL	0	-0.013	-0.011	32.867	-0.002	-0.002	0.000	0.000	0.000	0.000
104	B	105	PRO	0	0.031	0.031	34.635	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:GLY)