FMO DATABASE

FMODB ID: 2K17R

Calculation Name: 1B9W-A-Xray308

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B9W

Chain ID: A

ChEMBL ID:

UniProt ID: Q25659

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	87
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-613486.960873
FMO2-HF: Nuclear repulsion	574417.039627
FMO2-HF: Total energy	-39069.921246
FMO2-MP2: Total energy	-39172.808848

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(A:1:MET )

Summations of interaction energy for fragment #1(A:1: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.
-9.638	0.575	5.316	-4.232	-11.297	-0.022

Interaction energy analysis for fragmet #1(A:1:MET )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.007

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	A	3	SER	0	0.008	-0.022	2.768	-3.834	-1.301	0.423	-1.377	-1.579	-0.008
4	A	4	GLU	-1	-0.909	-0.960	5.429	-1.078	-1.078	0.000	0.000	0.000	0.000
5	A	5	HIS	0	-0.055	-0.017	2.771	-0.447	0.504	0.275	-0.209	-1.017	0.000
6	A	6	ARG	1	0.923	0.972	2.453	1.724	3.669	0.912	-0.703	-2.155	-0.001
7	A	18	CYS	0	-0.111	-0.053	3.505	1.267	1.482	0.023	0.106	-0.344	0.000
8	A	8	ILE	0	-0.059	-0.029	6.243	-0.101	-0.101	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.899	-0.942	9.728	-0.433	-0.433	0.000	0.000	0.000	0.000
10	A	10	THR	0	-0.078	-0.039	9.503	0.157	0.157	0.000	0.000	0.000	0.000
11	A	11	ASN	0	-0.080	-0.048	10.572	-0.156	-0.156	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.001	-0.007	7.320	0.083	0.083	0.000	0.000	0.000	0.000
13	A	13	PRO	0	0.010	0.021	10.660	0.018	0.018	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.931	-0.980	11.774	-0.296	-0.296	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.048	-0.021	12.683	0.038	0.038	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.020	0.008	10.115	0.109	0.109	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.018	0.007	5.307	-0.163	-0.163	0.000	0.000	0.000	0.000
18	A	19	TYR	0	-0.004	0.005	2.817	-5.123	-3.254	2.532	-1.441	-2.959	-0.011
19	A	20	ARG	1	0.907	0.947	4.509	0.504	0.599	0.000	-0.017	-0.079	0.000
20	A	21	TYR	0	-0.045	-0.033	6.909	0.416	0.416	0.000	0.000	0.000	0.000
21	A	22	LEU	0	0.011	-0.012	9.331	-0.154	-0.154	0.000	0.000	0.000	0.000
22	A	23	ASP	-1	-0.900	-0.923	11.684	-0.066	-0.066	0.000	0.000	0.000	0.000
23	A	24	GLY	0	-0.053	-0.024	12.424	-0.019	-0.019	0.000	0.000	0.000	0.000
24	A	25	THR	0	-0.054	-0.031	12.485	-0.048	-0.048	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.675	-0.841	8.284	-0.950	-0.950	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.820	-0.889	8.119	0.293	0.293	0.000	0.000	0.000	0.000
27	A	28	TRP	0	-0.004	-0.026	7.630	-0.053	-0.053	0.000	0.000	0.000	0.000
28	A	29	ARG	1	0.884	0.933	8.776	-0.402	-0.402	0.000	0.000	0.000	0.000
29	A	41	CYS	0	-0.028	0.005	9.962	-0.046	-0.046	0.000	0.000	0.000	0.000
30	A	31	LEU	0	0.013	0.011	8.629	0.095	0.095	0.000	0.000	0.000	0.000
31	A	32	LEU	0	0.075	0.020	12.042	-0.015	-0.015	0.000	0.000	0.000	0.000
32	A	33	TYR	0	0.012	0.019	14.937	-0.042	-0.042	0.000	0.000	0.000	0.000
33	A	34	PHE	0	-0.029	-0.004	15.384	-0.045	-0.045	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.820	0.885	17.128	-0.016	-0.016	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.919	-0.964	15.603	-0.051	-0.051	0.000	0.000	0.000	0.000
36	A	37	ASP	-1	-1.008	-1.009	17.935	-0.027	-0.027	0.000	0.000	0.000	0.000
37	A	38	ALA	0	0.009	0.009	20.649	-0.017	-0.017	0.000	0.000	0.000	0.000
38	A	39	GLY	0	0.014	0.010	16.882	-0.014	-0.014	0.000	0.000	0.000	0.000
39	A	40	LYS	1	0.941	0.976	16.912	0.074	0.074	0.000	0.000	0.000	0.000
40	A	42	VAL	0	-0.037	-0.023	16.880	-0.011	-0.011	0.000	0.000	0.000	0.000
41	A	43	PRO	0	0.025	0.011	19.759	0.018	0.018	0.000	0.000	0.000	0.000
42	A	44	ALA	0	-0.024	-0.015	20.433	0.001	0.001	0.000	0.000	0.000	0.000
43	A	45	PRO	0	0.015	-0.003	21.574	0.019	0.019	0.000	0.000	0.000	0.000
44	A	46	ASN	0	0.006	0.006	22.995	0.021	0.021	0.000	0.000	0.000	0.000
45	A	47	MET	0	-0.033	0.012	18.988	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	48	THR	0	0.057	0.009	23.332	0.014	0.014	0.000	0.000	0.000	0.000
47	A	62	CYS	0	0.049	0.019	18.389	0.023	0.023	0.000	0.000	0.000	0.000
48	A	50	LYS	1	0.900	0.954	22.889	-0.092	-0.092	0.000	0.000	0.000	0.000
49	A	51	ASP	-1	-0.860	-0.904	22.973	0.064	0.064	0.000	0.000	0.000	0.000
50	A	52	LYS	1	0.957	0.964	19.197	-0.058	-0.058	0.000	0.000	0.000	0.000
51	A	53	ASN	0	0.018	0.011	17.047	-0.011	-0.011	0.000	0.000	0.000	0.000
52	A	54	GLY	0	0.008	-0.005	18.507	0.032	0.032	0.000	0.000	0.000	0.000
53	A	55	GLY	0	0.016	0.016	16.154	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	72	CYS	0	-0.074	-0.019	13.984	0.010	0.010	0.000	0.000	0.000	0.000
55	A	57	ALA	0	0.052	0.025	11.240	-0.042	-0.042	0.000	0.000	0.000	0.000
56	A	58	PRO	0	-0.025	-0.026	13.102	-0.043	-0.043	0.000	0.000	0.000	0.000
57	A	59	GLU	-1	-0.919	-0.956	12.177	0.578	0.578	0.000	0.000	0.000	0.000
58	A	60	ALA	0	-0.043	-0.022	14.157	0.013	0.013	0.000	0.000	0.000	0.000
59	A	61	GLU	-1	-0.911	-0.943	16.107	0.236	0.236	0.000	0.000	0.000	0.000
60	A	63	LYS	1	0.869	0.920	20.052	-0.313	-0.313	0.000	0.000	0.000	0.000
61	A	64	MET	0	0.022	0.015	21.638	0.013	0.013	0.000	0.000	0.000	0.000
62	A	65	ASN	0	-0.007	0.021	21.303	-0.017	-0.017	0.000	0.000	0.000	0.000
63	A	66	ASP	-1	-0.915	-0.984	24.401	0.123	0.123	0.000	0.000	0.000	0.000
64	A	67	LYS	1	0.892	0.943	24.965	-0.158	-0.158	0.000	0.000	0.000	0.000
65	A	68	ASN	0	-0.057	-0.029	25.977	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	69	GLU	-1	-0.930	-0.956	20.039	0.212	0.212	0.000	0.000	0.000	0.000
67	A	70	ILE	0	-0.021	-0.016	17.597	0.005	0.005	0.000	0.000	0.000	0.000
68	A	71	VAL	0	-0.012	-0.002	17.629	0.021	0.021	0.000	0.000	0.000	0.000
69	A	73	LYS	1	0.931	0.949	15.299	-0.406	-0.406	0.000	0.000	0.000	0.000
70	A	88	CYS	0	-0.027	0.016	8.189	0.025	0.025	0.000	0.000	0.000	0.000
71	A	75	THR	0	0.017	-0.002	14.039	0.002	0.002	0.000	0.000	0.000	0.000
72	A	76	LYS	1	0.962	0.989	14.500	-0.381	-0.381	0.000	0.000	0.000	0.000
73	A	77	GLU	-1	-0.898	-0.950	14.999	0.377	0.377	0.000	0.000	0.000	0.000
74	A	78	GLY	0	-0.047	-0.015	13.683	-0.011	-0.011	0.000	0.000	0.000	0.000
75	A	79	SER	0	-0.070	-0.038	10.838	0.060	0.060	0.000	0.000	0.000	0.000
76	A	80	GLU	-1	-0.906	-0.984	8.047	1.459	1.459	0.000	0.000	0.000	0.000
77	A	81	PRO	0	-0.018	-0.007	8.058	0.104	0.104	0.000	0.000	0.000	0.000
78	A	82	LEU	0	0.041	0.013	2.750	-1.169	0.293	0.571	-0.295	-1.738	-0.001
79	A	83	PHE	0	-0.026	-0.036	2.602	-1.495	-0.426	0.580	-0.291	-1.358	-0.001
80	A	84	GLU	-1	-0.915	-0.959	7.427	0.230	0.230	0.000	0.000	0.000	0.000
81	A	85	GLY	0	0.016	-0.003	9.374	-0.100	-0.100	0.000	0.000	0.000	0.000
82	A	86	VAL	0	-0.011	0.019	9.085	-0.053	-0.053	0.000	0.000	0.000	0.000
83	A	87	PHE	0	0.026	0.011	6.066	0.096	0.096	0.000	0.000	0.000	0.000
84	A	89	SER	0	0.005	-0.001	5.385	0.020	0.020	0.000	0.000	0.000	0.000
85	A	90	HIS	0	-0.041	-0.018	7.350	-0.049	-0.049	0.000	0.000	0.000	0.000
86	A	91	HIS	0	-0.005	0.004	7.716	-0.032	-0.032	0.000	0.000	0.000	0.000
87	A	92	NME	0	0.030	0.032	4.630	-0.138	-0.064	0.000	-0.005	-0.068	0.000

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