FMO DATABASE

FMODB ID: 6YK5Z

Calculation Name: 6B9X-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 6B9X

Chain ID: B

ChEMBL ID:

UniProt ID: Q6IAA8

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	OptHSide
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	126
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-993584.487736
FMO2-HF: Nuclear repulsion	945021.07218
FMO2-HF: Total energy	-48563.415555
FMO2-MP2: Total energy	-48701.587222

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:0:ALA)

Summations of interaction energy for fragment #1(B:0:ALA)

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.
-4.993	-1.806	0.502	-1.583	-2.108	0

Interaction energy analysis for fragmet #1(B:0:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : 0.003

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	B	2	LEU	0	0.064	0.040	3.806	-0.785	0.883	-0.024	-0.860	-0.783	0.005
4	B	3	ARG	1	0.963	0.973	6.491	0.071	0.071	0.000	0.000	0.000	0.000
5	B	4	PRO	0	0.100	0.036	9.687	-0.030	-0.030	0.000	0.000	0.000	0.000
6	B	5	LYS	1	0.968	0.975	12.594	-0.073	-0.073	0.000	0.000	0.000	0.000
7	B	6	ALA	0	-0.010	0.000	11.600	0.009	0.009	0.000	0.000	0.000	0.000
8	B	7	LEU	0	0.053	0.040	11.372	0.000	0.000	0.000	0.000	0.000	0.000
9	B	8	THR	0	-0.005	-0.010	13.214	0.004	0.004	0.000	0.000	0.000	0.000
10	B	9	GLN	0	0.005	0.009	16.448	0.001	0.001	0.000	0.000	0.000	0.000
11	B	10	VAL	0	0.049	0.037	13.624	0.008	0.008	0.000	0.000	0.000	0.000
12	B	11	LEU	0	0.004	0.006	16.200	0.007	0.007	0.000	0.000	0.000	0.000
13	B	12	SER	0	-0.078	-0.057	18.528	0.017	0.017	0.000	0.000	0.000	0.000
14	B	13	GLN	0	-0.053	-0.030	18.274	0.009	0.009	0.000	0.000	0.000	0.000
15	B	14	ALA	0	0.013	0.017	21.981	0.007	0.007	0.000	0.000	0.000	0.000
16	B	15	ASN	0	-0.001	0.023	23.512	-0.001	-0.001	0.000	0.000	0.000	0.000
17	B	16	THR	0	0.049	0.012	26.126	0.008	0.008	0.000	0.000	0.000	0.000
18	B	17	GLY	0	0.008	-0.009	29.089	-0.005	-0.005	0.000	0.000	0.000	0.000
19	B	18	GLY	0	0.032	0.016	32.108	-0.001	-0.001	0.000	0.000	0.000	0.000
20	B	19	VAL	0	-0.050	-0.029	26.111	-0.002	-0.002	0.000	0.000	0.000	0.000
21	B	20	GLN	0	-0.031	-0.013	28.932	0.008	0.008	0.000	0.000	0.000	0.000
22	B	21	SER	0	-0.057	-0.029	24.877	0.001	0.001	0.000	0.000	0.000	0.000
23	B	22	THR	0	0.018	-0.003	20.099	-0.006	-0.006	0.000	0.000	0.000	0.000
24	B	23	LEU	0	-0.032	-0.026	20.317	0.002	0.002	0.000	0.000	0.000	0.000
25	B	24	LEU	0	0.025	0.016	12.997	-0.008	-0.008	0.000	0.000	0.000	0.000
26	B	25	LEU	0	0.000	-0.002	17.657	0.015	0.015	0.000	0.000	0.000	0.000
27	B	26	ASN	0	0.063	0.026	16.511	-0.001	-0.001	0.000	0.000	0.000	0.000
28	B	27	ASN	0	0.014	-0.013	17.973	0.053	0.053	0.000	0.000	0.000	0.000
29	B	28	GLU	-1	-0.883	-0.938	20.644	-0.179	-0.179	0.000	0.000	0.000	0.000
30	B	29	GLY	0	-0.030	-0.005	21.750	0.021	0.021	0.000	0.000	0.000	0.000
31	B	30	SER	0	-0.070	-0.029	19.156	0.018	0.018	0.000	0.000	0.000	0.000
32	B	31	LEU	0	-0.032	-0.019	19.225	-0.029	-0.029	0.000	0.000	0.000	0.000
33	B	32	LEU	0	-0.032	-0.016	12.994	0.000	0.000	0.000	0.000	0.000	0.000
34	B	33	ALA	0	-0.034	-0.021	14.972	0.011	0.011	0.000	0.000	0.000	0.000
35	B	34	TYR	0	-0.015	-0.006	17.065	-0.006	-0.006	0.000	0.000	0.000	0.000
36	B	35	SER	0	0.024	0.013	20.075	0.019	0.019	0.000	0.000	0.000	0.000
37	B	36	GLY	0	0.031	0.021	22.073	-0.007	-0.007	0.000	0.000	0.000	0.000
38	B	37	TYR	0	-0.024	-0.031	25.800	-0.001	-0.001	0.000	0.000	0.000	0.000
39	B	38	GLY	0	0.038	0.026	28.670	0.002	0.002	0.000	0.000	0.000	0.000
40	B	39	ASP	-1	-0.877	-0.932	31.559	-0.045	-0.045	0.000	0.000	0.000	0.000
41	B	40	THR	0	-0.077	-0.027	30.567	0.001	0.001	0.000	0.000	0.000	0.000
42	B	41	ASP	-1	-0.797	-0.865	27.902	-0.085	-0.085	0.000	0.000	0.000	0.000
43	B	42	ALA	0	0.067	0.021	24.077	-0.006	-0.006	0.000	0.000	0.000	0.000
44	B	43	ARG	1	0.862	0.882	24.438	0.065	0.065	0.000	0.000	0.000	0.000
45	B	44	VAL	0	0.006	0.013	25.951	-0.006	-0.006	0.000	0.000	0.000	0.000
46	B	45	THR	0	0.007	0.000	26.350	-0.001	-0.001	0.000	0.000	0.000	0.000
47	B	46	ALA	0	-0.007	0.000	22.859	-0.006	-0.006	0.000	0.000	0.000	0.000
48	B	47	ALA	0	0.047	0.027	24.721	-0.010	-0.010	0.000	0.000	0.000	0.000
49	B	48	ILE	0	0.014	0.018	26.934	-0.002	-0.002	0.000	0.000	0.000	0.000
50	B	49	ALA	0	0.003	-0.004	25.080	-0.001	-0.001	0.000	0.000	0.000	0.000
51	B	50	SER	0	0.024	0.011	23.740	0.000	0.000	0.000	0.000	0.000	0.000
52	B	51	ASN	0	-0.048	-0.037	25.413	0.004	0.004	0.000	0.000	0.000	0.000
53	B	52	ILE	0	-0.006	-0.008	29.006	0.003	0.003	0.000	0.000	0.000	0.000
54	B	53	TRP	0	-0.009	-0.011	23.545	0.003	0.003	0.000	0.000	0.000	0.000
55	B	54	ALA	0	0.036	0.013	26.366	0.000	0.000	0.000	0.000	0.000	0.000
56	B	55	ALA	0	-0.021	0.005	27.591	0.004	0.004	0.000	0.000	0.000	0.000
57	B	56	TYR	0	-0.019	-0.022	30.243	0.006	0.006	0.000	0.000	0.000	0.000
58	B	57	ASP	-1	-0.833	-0.887	25.060	-0.207	-0.207	0.000	0.000	0.000	0.000
59	B	58	ARG	1	0.918	0.950	25.870	0.166	0.166	0.000	0.000	0.000	0.000
60	B	59	ASN	0	-0.038	-0.025	30.305	0.003	0.003	0.000	0.000	0.000	0.000
61	B	60	GLY	0	-0.009	0.009	32.047	0.007	0.007	0.000	0.000	0.000	0.000
62	B	61	ASN	0	-0.017	0.007	29.499	-0.006	-0.006	0.000	0.000	0.000	0.000
63	B	62	GLN	0	-0.037	-0.017	31.624	0.012	0.012	0.000	0.000	0.000	0.000
64	B	63	ALA	0	0.004	-0.002	32.521	-0.006	-0.006	0.000	0.000	0.000	0.000
65	B	64	PHE	0	-0.052	-0.039	32.734	0.004	0.004	0.000	0.000	0.000	0.000
66	B	65	ASN	0	-0.001	-0.003	31.813	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	66	GLU	-1	-0.837	-0.896	25.230	-0.208	-0.208	0.000	0.000	0.000	0.000
68	B	67	ASP	-1	-0.966	-0.969	28.187	-0.142	-0.142	0.000	0.000	0.000	0.000
69	B	68	ASN	0	-0.034	-0.030	24.284	0.013	0.013	0.000	0.000	0.000	0.000
70	B	69	LEU	0	0.021	0.020	26.691	0.006	0.006	0.000	0.000	0.000	0.000
71	B	70	LYS	1	0.870	0.922	24.585	0.147	0.147	0.000	0.000	0.000	0.000
72	B	71	PHE	0	-0.010	-0.030	23.874	-0.011	-0.011	0.000	0.000	0.000	0.000
73	B	72	ILE	0	0.013	0.030	26.635	0.010	0.010	0.000	0.000	0.000	0.000
74	B	73	LEU	0	-0.043	-0.020	28.350	-0.004	-0.004	0.000	0.000	0.000	0.000
75	B	74	MET	0	-0.007	0.002	31.053	0.001	0.001	0.000	0.000	0.000	0.000
76	B	75	ASP	-1	-0.777	-0.867	33.426	-0.073	-0.073	0.000	0.000	0.000	0.000
77	B	76	CYS	0	-0.041	-0.017	35.909	0.000	0.000	0.000	0.000	0.000	0.000
78	B	77	MET	0	0.024	-0.002	37.946	0.002	0.002	0.000	0.000	0.000	0.000
79	B	78	GLU	-1	-0.937	-0.959	38.893	-0.047	-0.047	0.000	0.000	0.000	0.000
80	B	79	GLY	0	-0.008	-0.008	34.802	0.000	0.000	0.000	0.000	0.000	0.000
81	B	80	ARG	1	0.729	0.859	32.791	0.072	0.072	0.000	0.000	0.000	0.000
82	B	81	VAL	0	0.011	-0.010	28.065	-0.002	-0.002	0.000	0.000	0.000	0.000
83	B	82	ALA	0	-0.009	-0.004	26.144	0.003	0.003	0.000	0.000	0.000	0.000
84	B	83	ILE	0	-0.006	-0.010	23.852	-0.005	-0.005	0.000	0.000	0.000	0.000
85	B	84	THR	0	0.002	-0.008	20.642	0.003	0.003	0.000	0.000	0.000	0.000
86	B	85	ARG	1	0.855	0.916	18.731	0.249	0.249	0.000	0.000	0.000	0.000
87	B	86	VAL	0	-0.034	-0.011	13.646	0.018	0.018	0.000	0.000	0.000	0.000
88	B	87	ALA	0	0.040	0.029	11.489	-0.045	-0.045	0.000	0.000	0.000	0.000
89	B	88	ASN	0	-0.075	-0.039	11.858	0.036	0.036	0.000	0.000	0.000	0.000
90	B	89	LEU	0	-0.075	-0.043	12.189	0.045	0.045	0.000	0.000	0.000	0.000
91	B	90	LEU	0	0.014	0.008	15.951	0.026	0.026	0.000	0.000	0.000	0.000
92	B	91	LEU	0	-0.016	-0.001	17.631	-0.006	-0.006	0.000	0.000	0.000	0.000
93	B	92	CYS	0	-0.041	-0.018	19.708	0.022	0.022	0.000	0.000	0.000	0.000
94	B	93	MET	0	-0.018	0.008	22.520	0.004	0.004	0.000	0.000	0.000	0.000
95	B	94	TYR	0	0.042	0.017	24.933	0.006	0.006	0.000	0.000	0.000	0.000
96	B	95	ALA	0	-0.010	-0.008	28.540	0.003	0.003	0.000	0.000	0.000	0.000
97	B	96	LYS	1	0.931	0.950	31.166	0.053	0.053	0.000	0.000	0.000	0.000
98	B	97	GLU	-1	-0.762	-0.861	34.636	-0.059	-0.059	0.000	0.000	0.000	0.000
99	B	98	THR	0	-0.023	-0.016	36.994	0.000	0.000	0.000	0.000	0.000	0.000
100	B	99	VAL	0	-0.066	-0.009	31.025	0.002	0.002	0.000	0.000	0.000	0.000
101	B	100	GLY	0	0.027	0.010	34.502	-0.002	-0.002	0.000	0.000	0.000	0.000
102	B	101	PHE	0	0.084	0.013	31.912	-0.005	-0.005	0.000	0.000	0.000	0.000
103	B	102	GLY	0	-0.035	-0.008	30.949	-0.007	-0.007	0.000	0.000	0.000	0.000
104	B	103	MET	0	0.015	0.009	29.476	-0.007	-0.007	0.000	0.000	0.000	0.000
105	B	104	LEU	0	0.028	0.015	27.662	-0.006	-0.006	0.000	0.000	0.000	0.000
106	B	105	LYS	1	0.955	0.983	26.404	0.110	0.110	0.000	0.000	0.000	0.000
107	B	106	ALA	0	-0.001	0.007	25.243	-0.012	-0.012	0.000	0.000	0.000	0.000
108	B	107	LYS	1	0.865	0.923	24.014	0.080	0.080	0.000	0.000	0.000	0.000
109	B	108	ALA	0	0.019	0.009	21.962	-0.012	-0.012	0.000	0.000	0.000	0.000
110	B	109	GLN	0	0.021	-0.012	20.535	-0.009	-0.009	0.000	0.000	0.000	0.000
111	B	110	ALA	0	-0.017	0.003	20.056	-0.015	-0.015	0.000	0.000	0.000	0.000
112	B	111	LEU	0	-0.009	-0.008	17.429	-0.014	-0.014	0.000	0.000	0.000	0.000
113	B	112	VAL	0	0.003	0.001	15.843	-0.034	-0.034	0.000	0.000	0.000	0.000
114	B	113	GLN	0	-0.026	-0.014	15.430	-0.053	-0.053	0.000	0.000	0.000	0.000
115	B	114	TYR	0	-0.045	-0.014	12.319	-0.023	-0.023	0.000	0.000	0.000	0.000
116	B	115	LEU	0	-0.003	-0.026	11.431	-0.033	-0.033	0.000	0.000	0.000	0.000
117	B	116	GLU	-1	-0.786	-0.879	10.706	-0.586	-0.586	0.000	0.000	0.000	0.000
118	B	117	GLU	-1	-0.904	-0.944	8.462	-0.607	-0.607	0.000	0.000	0.000	0.000
119	B	118	PRO	0	-0.014	-0.012	6.083	-0.220	-0.220	0.000	0.000	0.000	0.000
120	B	119	LEU	0	-0.028	-0.027	5.733	-0.400	-0.400	0.000	0.000	0.000	0.000
121	B	120	THR	0	0.005	-0.006	7.946	-0.118	-0.118	0.000	0.000	0.000	0.000
122	B	121	GLN	0	-0.098	-0.036	3.346	-0.485	-0.142	0.033	-0.072	-0.306	0.000
123	B	122	VAL	0	-0.082	-0.045	2.608	-2.331	-1.207	0.492	-0.643	-0.973	-0.005
124	B	123	ALA	0	-0.008	0.012	4.050	0.244	0.296	0.001	-0.008	-0.046	0.000
125	B	124	ALA	0	-0.010	0.009	7.337	0.198	0.198	0.000	0.000	0.000	0.000
126	B	125	SER	0	0.031	0.022	9.404	0.182	0.182	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:0:ALA)