FMO DATABASE

FMODB ID: QYK1Y

Calculation Name: 5AN3-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5AN3

Chain ID: D

ChEMBL ID:

UniProt ID: Q08446

Base Structure: X-ray

Registration Date: 2023-06-22

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	102
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-793511.504753
FMO2-HF: Nuclear repulsion	752318.821238
FMO2-HF: Total energy	-41192.683515
FMO2-MP2: Total energy	-41312.397637

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(D:4:SER)

Summations of interaction energy for fragment #1(D:4: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.
-7.801	-2.253	0.226	-2.82	-2.956	0.002

Interaction energy analysis for fragmet #1(D:4:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.024

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

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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	D	6	VAL	0	0.002	0.006	3.897	-0.286	1.958	-0.016	-1.205	-1.024	0.006
4	D	7	VAL	0	-0.020	-0.013	6.972	-0.023	-0.023	0.000	0.000	0.000	0.000
5	D	8	LEU	0	-0.001	0.006	10.735	0.195	0.195	0.000	0.000	0.000	0.000
6	D	9	VAL	0	-0.020	-0.026	13.389	0.006	0.006	0.000	0.000	0.000	0.000
7	D	10	SER	0	0.014	0.002	16.963	0.054	0.054	0.000	0.000	0.000	0.000
8	D	11	GLY	0	0.062	0.027	19.783	0.025	0.025	0.000	0.000	0.000	0.000
9	D	12	GLU	-1	-0.895	-0.943	23.247	-0.338	-0.338	0.000	0.000	0.000	0.000
10	D	13	GLY	0	-0.013	0.001	21.843	0.025	0.025	0.000	0.000	0.000	0.000
11	D	14	GLU	-1	-0.972	-0.973	18.992	-0.530	-0.530	0.000	0.000	0.000	0.000
12	D	15	ARG	1	0.922	0.956	13.018	0.600	0.600	0.000	0.000	0.000	0.000
13	D	16	PHE	0	0.049	0.023	14.004	0.010	0.010	0.000	0.000	0.000	0.000
14	D	17	THR	0	-0.024	-0.014	7.861	-0.010	-0.010	0.000	0.000	0.000	0.000
15	D	18	VAL	0	0.040	0.025	8.163	0.095	0.095	0.000	0.000	0.000	0.000
16	D	19	ASP	-1	-0.852	-0.946	3.232	-14.167	-12.575	0.073	-0.902	-0.764	-0.006
17	D	20	LYS	1	0.951	0.971	2.863	0.087	1.618	0.170	-0.696	-1.005	0.002
18	D	21	LYS	1	0.849	0.907	4.328	2.707	2.888	-0.001	-0.017	-0.163	0.000
19	D	22	ILE	0	-0.052	-0.026	6.432	0.664	0.664	0.000	0.000	0.000	0.000
20	D	23	ALA	0	0.036	0.017	7.614	0.526	0.526	0.000	0.000	0.000	0.000
21	D	24	GLU	-1	-0.879	-0.948	7.029	0.511	0.511	0.000	0.000	0.000	0.000
22	D	25	ARG	1	0.867	0.952	9.742	0.854	0.854	0.000	0.000	0.000	0.000
23	D	26	SER	0	-0.045	-0.038	12.568	0.141	0.141	0.000	0.000	0.000	0.000
24	D	27	LEU	0	0.001	-0.018	13.419	0.019	0.019	0.000	0.000	0.000	0.000
25	D	28	LEU	0	-0.044	0.003	15.671	0.058	0.058	0.000	0.000	0.000	0.000
26	D	29	LEU	0	0.030	-0.002	11.301	0.054	0.054	0.000	0.000	0.000	0.000
27	D	30	LYS	1	0.927	0.974	10.591	0.119	0.119	0.000	0.000	0.000	0.000
28	D	31	ASN	0	-0.041	-0.031	11.891	0.150	0.150	0.000	0.000	0.000	0.000
29	D	32	TYR	0	0.019	0.034	11.854	0.059	0.059	0.000	0.000	0.000	0.000
30	D	33	LEU	0	-0.001	-0.014	6.962	0.073	0.073	0.000	0.000	0.000	0.000
31	D	34	ASN	0	-0.093	-0.054	9.575	0.316	0.316	0.000	0.000	0.000	0.000
32	D	35	ASP	-1	-0.937	-0.952	11.742	0.326	0.326	0.000	0.000	0.000	0.000
33	D	36	ALA	0	-0.090	-0.036	8.353	0.115	0.115	0.000	0.000	0.000	0.000
34	D	74	GLU	-1	-0.942	-0.978	6.573	0.328	0.328	0.000	0.000	0.000	0.000
35	D	75	ILE	0	-0.006	0.000	6.641	0.061	0.061	0.000	0.000	0.000	0.000
36	D	76	VAL	0	-0.037	-0.028	9.144	-0.321	-0.321	0.000	0.000	0.000	0.000
37	D	77	MET	0	0.016	0.013	8.823	0.170	0.170	0.000	0.000	0.000	0.000
38	D	78	PRO	0	-0.016	0.004	13.787	-0.083	-0.083	0.000	0.000	0.000	0.000
39	D	79	VAL	0	-0.002	-0.015	15.682	0.025	0.025	0.000	0.000	0.000	0.000
40	D	80	PRO	0	0.005	0.002	18.469	0.001	0.001	0.000	0.000	0.000	0.000
41	D	81	ASN	0	-0.040	-0.031	22.181	0.004	0.004	0.000	0.000	0.000	0.000
42	D	82	VAL	0	0.015	0.017	20.104	0.009	0.009	0.000	0.000	0.000	0.000
43	D	83	ARG	1	0.891	0.963	22.328	0.273	0.273	0.000	0.000	0.000	0.000
44	D	84	SER	0	0.055	0.007	21.052	-0.052	-0.052	0.000	0.000	0.000	0.000
45	D	85	SER	0	0.023	0.008	21.079	-0.048	-0.048	0.000	0.000	0.000	0.000
46	D	86	VAL	0	0.012	0.018	21.952	-0.026	-0.026	0.000	0.000	0.000	0.000
47	D	87	LEU	0	0.020	0.007	15.729	-0.028	-0.028	0.000	0.000	0.000	0.000
48	D	88	GLN	0	0.008	0.008	17.445	-0.157	-0.157	0.000	0.000	0.000	0.000
49	D	89	LYS	1	0.893	0.949	18.116	0.419	0.419	0.000	0.000	0.000	0.000
50	D	90	VAL	0	-0.014	-0.027	16.490	-0.016	-0.016	0.000	0.000	0.000	0.000
51	D	91	ILE	0	0.009	0.001	12.661	-0.056	-0.056	0.000	0.000	0.000	0.000
52	D	92	GLU	-1	-0.845	-0.908	14.290	-0.655	-0.655	0.000	0.000	0.000	0.000
53	D	93	TRP	0	-0.003	-0.006	16.549	-0.023	-0.023	0.000	0.000	0.000	0.000
54	D	94	ALA	0	-0.047	-0.042	12.946	0.041	0.041	0.000	0.000	0.000	0.000
55	D	95	GLU	-1	-0.958	-0.971	11.020	-1.456	-1.456	0.000	0.000	0.000	0.000
56	D	96	HIS	1	0.904	0.977	12.727	0.545	0.545	0.000	0.000	0.000	0.000
57	D	97	HIS	1	0.760	0.890	15.670	0.566	0.566	0.000	0.000	0.000	0.000
58	D	98	ARG	1	0.984	0.991	5.579	2.186	2.186	0.000	0.000	0.000	0.000
59	D	99	ASP	-1	-0.855	-0.902	11.259	-0.761	-0.761	0.000	0.000	0.000	0.000
60	D	116	VAL	0	0.032	0.002	28.440	-0.005	-0.005	0.000	0.000	0.000	0.000
61	D	117	ASP	-1	-0.852	-0.935	23.708	-0.284	-0.284	0.000	0.000	0.000	0.000
62	D	118	SER	0	-0.068	-0.033	26.941	-0.006	-0.006	0.000	0.000	0.000	0.000
63	D	119	TRP	0	0.038	0.015	19.305	-0.006	-0.006	0.000	0.000	0.000	0.000
64	D	120	ASP	-1	-0.830	-0.938	22.923	-0.395	-0.395	0.000	0.000	0.000	0.000
65	D	121	ARG	1	0.895	0.937	25.015	0.202	0.202	0.000	0.000	0.000	0.000
66	D	122	GLU	-1	-0.837	-0.896	26.115	-0.241	-0.241	0.000	0.000	0.000	0.000
67	D	123	PHE	0	-0.036	-0.013	20.886	-0.001	-0.001	0.000	0.000	0.000	0.000
68	D	124	LEU	0	0.031	0.007	25.065	-0.007	-0.007	0.000	0.000	0.000	0.000
69	D	125	LYS	1	0.800	0.920	27.726	0.259	0.259	0.000	0.000	0.000	0.000
70	D	126	VAL	0	-0.053	-0.032	27.268	-0.011	-0.011	0.000	0.000	0.000	0.000
71	D	127	ASP	-1	-0.874	-0.936	30.550	-0.219	-0.219	0.000	0.000	0.000	0.000
72	D	128	GLN	0	0.019	-0.013	31.849	-0.003	-0.003	0.000	0.000	0.000	0.000
73	D	129	GLU	-1	-0.854	-0.924	31.575	-0.211	-0.211	0.000	0.000	0.000	0.000
74	D	130	MET	0	-0.020	0.000	26.440	-0.022	-0.022	0.000	0.000	0.000	0.000
75	D	131	LEU	0	0.025	0.006	27.625	-0.020	-0.020	0.000	0.000	0.000	0.000
76	D	132	TYR	0	-0.015	-0.011	28.392	-0.002	-0.002	0.000	0.000	0.000	0.000
77	D	133	GLU	-1	-0.812	-0.911	26.523	-0.273	-0.273	0.000	0.000	0.000	0.000
78	D	134	ILE	0	-0.038	-0.032	22.686	-0.028	-0.028	0.000	0.000	0.000	0.000
79	D	135	ILE	0	-0.041	0.000	23.685	-0.020	-0.020	0.000	0.000	0.000	0.000
80	D	136	LEU	0	0.025	0.018	25.273	0.001	0.001	0.000	0.000	0.000	0.000
81	D	137	ALA	0	0.008	0.001	21.046	0.000	0.000	0.000	0.000	0.000	0.000
82	D	138	ALA	0	-0.019	-0.013	20.509	-0.027	-0.027	0.000	0.000	0.000	0.000
83	D	139	ASN	0	-0.031	-0.014	21.388	0.017	0.017	0.000	0.000	0.000	0.000
84	D	140	TYR	0	-0.005	0.006	19.541	-0.001	-0.001	0.000	0.000	0.000	0.000
85	D	141	LEU	0	0.012	0.002	15.901	0.006	0.006	0.000	0.000	0.000	0.000
86	D	142	ASN	0	0.024	0.034	17.292	-0.015	-0.015	0.000	0.000	0.000	0.000
87	D	143	ILE	0	-0.001	0.006	16.198	-0.013	-0.013	0.000	0.000	0.000	0.000
88	D	144	LYS	1	1.006	0.991	18.870	0.170	0.170	0.000	0.000	0.000	0.000
89	D	145	PRO	0	-0.009	-0.004	19.486	0.010	0.010	0.000	0.000	0.000	0.000
90	D	146	LEU	0	0.055	0.043	19.378	0.013	0.013	0.000	0.000	0.000	0.000
91	D	147	LEU	0	0.033	0.018	22.087	0.018	0.018	0.000	0.000	0.000	0.000
92	D	148	ASP	-1	-0.841	-0.911	24.725	-0.181	-0.181	0.000	0.000	0.000	0.000
93	D	149	ALA	0	0.019	-0.001	24.742	0.016	0.016	0.000	0.000	0.000	0.000
94	D	150	GLY	0	0.020	-0.009	26.089	0.013	0.013	0.000	0.000	0.000	0.000
95	D	151	CYS	0	-0.080	-0.044	27.765	0.016	0.016	0.000	0.000	0.000	0.000
96	D	152	LYS	1	0.832	0.882	28.287	0.195	0.195	0.000	0.000	0.000	0.000
97	D	153	VAL	0	0.024	0.023	29.230	0.007	0.007	0.000	0.000	0.000	0.000
98	D	154	VAL	0	-0.039	-0.010	31.759	0.006	0.006	0.000	0.000	0.000	0.000
99	D	155	ALA	0	-0.033	-0.012	33.519	0.010	0.010	0.000	0.000	0.000	0.000
100	D	156	GLU	-1	-1.003	-0.990	34.064	-0.161	-0.161	0.000	0.000	0.000	0.000
101	D	157	MET	0	-0.047	-0.009	34.933	0.003	0.003	0.000	0.000	0.000	0.000
102	D	158	ILE	0	-0.032	-0.012	37.554	0.008	0.008	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:4:SER)