FMO DATABASE

FMODB ID: 2NVRR

Calculation Name: 1B9W-A-Xray372

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: 2023-09-24

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	86
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-613089.389819
FMO2-HF: Nuclear repulsion	574037.646375
FMO2-HF: Total energy	-39051.743444
FMO2-MP2: Total energy	-39154.51691

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.
-15.957	-6.782	10.448	-5.241	-14.377	-0.044

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 : 0.001 / q_NPA : 0.004

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	0.011	-0.022	2.656	-3.977	-1.597	0.677	-1.505	-1.552	-0.012
4	A	4	GLU	-1	-0.875	-0.926	5.263	-1.805	-1.805	0.000	0.000	0.000	0.000
5	A	5	HIS	0	0.003	0.001	2.614	-0.601	0.430	1.479	-0.567	-1.943	-0.001
6	A	6	ARG	1	0.846	0.942	2.524	-3.668	-1.215	2.482	-1.555	-3.378	-0.010
7	A	7	CYS	0	-0.069	-0.043	3.117	1.654	1.139	0.066	0.846	-0.397	-0.001
8	A	8	ILE	0	-0.076	-0.038	5.903	0.138	0.138	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.854	-0.896	9.494	-0.286	-0.286	0.000	0.000	0.000	0.000
10	A	10	THR	0	-0.085	-0.065	9.227	0.137	0.137	0.000	0.000	0.000	0.000
11	A	11	ASN	0	-0.049	-0.028	10.296	-0.068	-0.068	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.011	-0.016	7.285	0.042	0.042	0.000	0.000	0.000	0.000
13	A	13	PRO	0	-0.015	0.006	10.698	0.039	0.039	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.882	-0.940	12.145	0.132	0.132	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.080	-0.052	13.449	0.022	0.022	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.012	0.010	10.404	0.036	0.036	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.015	0.008	5.803	0.040	0.040	0.000	0.000	0.000	0.000
18	A	19	TYR	0	-0.022	-0.003	2.625	-5.821	-3.826	3.111	-1.716	-3.390	-0.017
19	A	20	ARG	1	0.823	0.883	3.898	1.013	1.154	0.001	-0.018	-0.123	0.000
20	A	21	TYR	0	-0.028	-0.034	6.290	0.437	0.437	0.000	0.000	0.000	0.000
21	A	22	LEU	0	-0.002	-0.022	9.181	-0.136	-0.136	0.000	0.000	0.000	0.000
22	A	23	ASP	-1	-0.882	-0.905	11.696	-0.082	-0.082	0.000	0.000	0.000	0.000
23	A	24	GLY	0	-0.049	-0.019	11.489	-0.008	-0.008	0.000	0.000	0.000	0.000
24	A	25	THR	0	-0.057	-0.046	11.769	-0.037	-0.037	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.664	-0.815	7.686	-0.864	-0.864	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.802	-0.849	7.680	0.506	0.506	0.000	0.000	0.000	0.000
27	A	28	TRP	0	0.001	-0.015	7.088	-0.111	-0.111	0.000	0.000	0.000	0.000
28	A	29	ARG	1	0.808	0.879	8.875	-0.576	-0.576	0.000	0.000	0.000	0.000
29	A	30	CYS	0	-0.022	0.005	10.094	0.011	0.011	0.000	0.000	0.000	0.000
30	A	31	LEU	0	0.017	0.014	9.452	0.083	0.083	0.000	0.000	0.000	0.000
31	A	32	LEU	0	0.066	0.025	12.636	-0.064	-0.064	0.000	0.000	0.000	0.000
32	A	33	TYR	0	-0.012	-0.005	15.371	-0.031	-0.031	0.000	0.000	0.000	0.000
33	A	34	PHE	0	-0.019	0.002	15.871	-0.037	-0.037	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.807	0.877	17.235	-0.118	-0.118	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.923	-0.967	16.018	0.099	0.099	0.000	0.000	0.000	0.000
36	A	37	ASP	-1	-0.956	-0.984	18.178	0.066	0.066	0.000	0.000	0.000	0.000
37	A	38	ALA	0	-0.038	-0.018	20.340	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	39	GLY	0	0.029	0.028	17.018	-0.012	-0.012	0.000	0.000	0.000	0.000
39	A	40	LYS	1	0.931	0.960	16.954	-0.081	-0.081	0.000	0.000	0.000	0.000
40	A	42	VAL	0	-0.004	-0.002	17.045	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	43	PRO	0	0.003	-0.001	20.041	0.015	0.015	0.000	0.000	0.000	0.000
42	A	44	ALA	0	-0.020	-0.011	20.675	-0.017	-0.017	0.000	0.000	0.000	0.000
43	A	45	PRO	0	0.021	-0.004	22.175	0.011	0.011	0.000	0.000	0.000	0.000
44	A	46	ASN	0	-0.031	-0.011	23.371	0.001	0.001	0.000	0.000	0.000	0.000
45	A	47	MET	0	-0.031	0.012	19.010	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	48	THR	0	0.033	-0.007	23.240	0.003	0.003	0.000	0.000	0.000	0.000
47	A	49	CYS	0	0.078	0.030	17.871	0.027	0.027	0.000	0.000	0.000	0.000
48	A	50	LYS	1	0.899	0.955	22.777	-0.105	-0.105	0.000	0.000	0.000	0.000
49	A	51	ASP	-1	-0.829	-0.895	23.479	0.137	0.137	0.000	0.000	0.000	0.000
50	A	52	LYS	1	0.961	0.968	18.656	-0.124	-0.124	0.000	0.000	0.000	0.000
51	A	53	ASN	0	0.001	0.006	17.025	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	54	GLY	0	0.023	0.005	18.446	0.023	0.023	0.000	0.000	0.000	0.000
53	A	55	GLY	0	0.012	0.004	15.910	0.004	0.004	0.000	0.000	0.000	0.000
54	A	56	CYS	0	-0.046	-0.003	13.926	0.042	0.042	0.000	0.000	0.000	0.000
55	A	57	ALA	0	0.026	0.017	11.310	-0.045	-0.045	0.000	0.000	0.000	0.000
56	A	58	PRO	0	-0.035	-0.021	13.155	-0.064	-0.064	0.000	0.000	0.000	0.000
57	A	59	GLU	-1	-0.849	-0.933	11.296	0.623	0.623	0.000	0.000	0.000	0.000
58	A	60	ALA	0	-0.054	-0.021	13.802	-0.015	-0.015	0.000	0.000	0.000	0.000
59	A	61	GLU	-1	-0.845	-0.907	15.863	0.150	0.150	0.000	0.000	0.000	0.000
60	A	63	LYS	1	0.786	0.871	19.969	-0.196	-0.196	0.000	0.000	0.000	0.000
61	A	64	MET	0	0.019	0.022	21.540	0.018	0.018	0.000	0.000	0.000	0.000
62	A	65	ASN	0	-0.048	-0.036	22.565	-0.018	-0.018	0.000	0.000	0.000	0.000
63	A	66	ASP	-1	-0.865	-0.926	24.579	0.095	0.095	0.000	0.000	0.000	0.000
64	A	67	LYS	1	0.833	0.902	25.149	-0.114	-0.114	0.000	0.000	0.000	0.000
65	A	68	ASN	0	-0.075	-0.036	26.077	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	69	GLU	-1	-0.851	-0.907	20.592	0.180	0.180	0.000	0.000	0.000	0.000
67	A	70	ILE	0	-0.008	-0.006	17.940	-0.014	-0.014	0.000	0.000	0.000	0.000
68	A	71	VAL	0	-0.006	-0.006	17.647	0.017	0.017	0.000	0.000	0.000	0.000
69	A	73	LYS	1	0.889	0.935	15.277	-0.218	-0.218	0.000	0.000	0.000	0.000
70	A	74	CYS	0	-0.015	0.029	8.297	-0.054	-0.054	0.000	0.000	0.000	0.000
71	A	75	THR	0	0.007	-0.001	14.326	-0.048	-0.048	0.000	0.000	0.000	0.000
72	A	76	LYS	1	0.931	0.977	14.527	-0.205	-0.205	0.000	0.000	0.000	0.000
73	A	77	GLU	-1	-0.875	-0.929	15.242	0.088	0.088	0.000	0.000	0.000	0.000
74	A	78	GLY	0	-0.006	-0.012	14.071	0.004	0.004	0.000	0.000	0.000	0.000
75	A	79	SER	0	-0.079	-0.048	10.756	0.005	0.005	0.000	0.000	0.000	0.000
76	A	80	GLU	-1	-0.836	-0.888	8.216	-0.107	-0.107	0.000	0.000	0.000	0.000
77	A	81	PRO	0	0.018	-0.017	8.467	0.215	0.215	0.000	0.000	0.000	0.000
78	A	82	LEU	0	0.014	0.013	2.735	-0.927	-0.349	1.730	-0.372	-1.935	-0.002
79	A	83	PHE	0	0.001	-0.020	2.626	-1.501	-0.389	0.902	-0.354	-1.659	-0.001
80	A	84	GLU	-1	-0.906	-0.954	7.245	0.326	0.326	0.000	0.000	0.000	0.000
81	A	85	GLY	0	0.010	-0.005	9.354	-0.136	-0.136	0.000	0.000	0.000	0.000
82	A	86	VAL	0	-0.016	0.016	9.328	-0.056	-0.056	0.000	0.000	0.000	0.000
83	A	87	PHE	0	0.020	0.000	6.223	0.039	0.039	0.000	0.000	0.000	0.000
84	A	89	SER	0	0.043	0.030	5.304	0.196	0.196	0.000	0.000	0.000	0.000
85	A	90	HIS	0	-0.086	-0.049	7.459	-0.196	-0.196	0.000	0.000	0.000	0.000
86	A	91	HIS	0	-0.049	-0.045	6.152	-0.066	-0.066	0.000	0.000	0.000	0.000

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