FMO DATABASE

FMODB ID: 43ZYN

Calculation Name: 2OB9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2OB9

Chain ID: A

ChEMBL ID:

UniProt ID: Q9MCS5

Base Structure: X-ray

Registration Date: 2023-06-20

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	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	107
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-808137.572212
FMO2-HF: Nuclear repulsion	765256.223886
FMO2-HF: Total energy	-42881.348325
FMO2-MP2: Total energy	-43006.219611

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:2:SER)

Summations of interaction energy for fragment #1(A:2: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.
-7.542	-2.713	0.601	-2.423	-3.006	0.013

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : -0.011

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	A	4	THR	0	0.014	0.015	2.609	-6.565	-1.976	0.600	-2.378	-2.811	0.013
4	A	5	LEU	0	0.056	0.030	4.391	-1.113	-0.873	0.001	-0.045	-0.195	0.000
5	A	6	LYS	1	0.983	0.987	6.088	-0.029	-0.029	0.000	0.000	0.000	0.000
6	A	7	GLN	0	0.001	-0.005	7.302	0.328	0.328	0.000	0.000	0.000	0.000
7	A	8	LEU	0	-0.021	-0.016	8.112	-0.057	-0.057	0.000	0.000	0.000	0.000
8	A	9	ALA	0	-0.009	-0.001	10.315	-0.031	-0.031	0.000	0.000	0.000	0.000
9	A	10	MET	0	-0.027	-0.014	11.975	-0.010	-0.010	0.000	0.000	0.000	0.000
10	A	11	ALA	0	0.005	0.026	13.518	0.060	0.060	0.000	0.000	0.000	0.000
11	A	12	LYS	1	0.943	0.958	14.993	-0.202	-0.202	0.000	0.000	0.000	0.000
12	A	13	MET	0	-0.025	-0.019	18.625	0.000	0.000	0.000	0.000	0.000	0.000
13	A	14	ALA	0	-0.008	0.011	15.389	-0.017	-0.017	0.000	0.000	0.000	0.000
14	A	15	GLY	0	-0.063	-0.021	17.150	-0.040	-0.040	0.000	0.000	0.000	0.000
15	A	16	PHE	0	-0.001	0.008	20.005	-0.010	-0.010	0.000	0.000	0.000	0.000
16	A	17	ARG	1	0.910	0.955	21.342	0.149	0.149	0.000	0.000	0.000	0.000
17	A	18	HIS	0	-0.028	-0.043	19.514	0.030	0.030	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.876	0.954	23.806	0.029	0.029	0.000	0.000	0.000	0.000
19	A	20	THR	0	-0.006	0.000	25.654	0.010	0.010	0.000	0.000	0.000	0.000
20	A	21	VAL	0	-0.026	-0.008	27.963	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	22	VAL	0	0.006	0.005	31.626	0.006	0.006	0.000	0.000	0.000	0.000
22	A	23	VAL	0	-0.015	-0.018	34.527	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	24	PRO	0	-0.012	-0.003	37.665	0.003	0.003	0.000	0.000	0.000	0.000
24	A	25	GLU	-1	-0.838	-0.915	40.792	0.005	0.005	0.000	0.000	0.000	0.000
25	A	26	TRP	0	-0.048	-0.029	37.155	0.000	0.000	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.895	-0.957	40.137	0.036	0.036	0.000	0.000	0.000	0.000
27	A	28	GLY	0	-0.038	-0.002	38.798	0.003	0.003	0.000	0.000	0.000	0.000
28	A	29	VAL	0	-0.010	0.016	35.190	0.004	0.004	0.000	0.000	0.000	0.000
29	A	30	LYS	1	0.938	0.949	29.877	-0.074	-0.074	0.000	0.000	0.000	0.000
30	A	31	VAL	0	0.037	0.028	31.609	0.005	0.005	0.000	0.000	0.000	0.000
31	A	32	VAL	0	-0.051	-0.043	25.456	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	33	LEU	0	-0.035	0.001	28.534	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	34	ARG	1	0.791	0.881	25.675	0.004	0.004	0.000	0.000	0.000	0.000
34	A	35	GLU	-1	-0.826	-0.915	23.949	-0.098	-0.098	0.000	0.000	0.000	0.000
35	A	36	PRO	0	0.031	0.006	27.818	0.006	0.006	0.000	0.000	0.000	0.000
36	A	37	SER	0	0.016	0.027	27.419	-0.013	-0.013	0.000	0.000	0.000	0.000
37	A	38	GLY	0	0.024	-0.013	27.713	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.930	-0.972	28.656	-0.034	-0.034	0.000	0.000	0.000	0.000
39	A	40	ALA	0	0.001	0.014	31.497	0.005	0.005	0.000	0.000	0.000	0.000
40	A	41	TRP	0	-0.014	-0.035	30.270	0.003	0.003	0.000	0.000	0.000	0.000
41	A	42	LEU	0	-0.057	-0.009	33.375	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	43	ARG	1	1.024	1.011	35.124	0.013	0.013	0.000	0.000	0.000	0.000
43	A	44	TRP	0	-0.011	0.009	37.051	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	45	GLN	0	-0.054	-0.043	38.169	0.003	0.003	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.950	-0.952	39.900	-0.028	-0.028	0.000	0.000	0.000	0.000
46	A	47	VAL	0	-0.091	-0.041	41.362	0.003	0.003	0.000	0.000	0.000	0.000
47	A	48	VAL	0	-0.088	-0.037	41.691	0.001	0.001	0.000	0.000	0.000	0.000
48	A	56	ASN	0	-0.005	-0.024	57.116	0.001	0.001	0.000	0.000	0.000	0.000
49	A	57	VAL	0	0.007	0.027	53.027	0.001	0.001	0.000	0.000	0.000	0.000
50	A	58	SER	0	0.082	0.044	56.030	0.000	0.000	0.000	0.000	0.000	0.000
51	A	59	VAL	0	0.020	-0.019	55.543	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	60	SER	0	0.011	-0.003	54.476	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	61	GLU	-1	-0.894	-0.932	53.223	-0.018	-0.018	0.000	0.000	0.000	0.000
54	A	62	LYS	1	0.938	0.961	48.882	0.029	0.029	0.000	0.000	0.000	0.000
55	A	63	ALA	0	-0.028	-0.017	49.754	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	64	HIS	0	0.056	0.036	49.412	0.000	0.000	0.000	0.000	0.000	0.000
57	A	65	ARG	1	1.017	1.012	47.255	0.029	0.029	0.000	0.000	0.000	0.000
58	A	66	ASN	0	-0.051	-0.047	45.203	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	67	LEU	0	0.039	0.046	44.290	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	68	CYS	0	-0.045	-0.026	44.302	0.002	0.002	0.000	0.000	0.000	0.000
61	A	69	ALA	0	0.022	0.016	41.634	0.001	0.001	0.000	0.000	0.000	0.000
62	A	70	ASP	-1	-0.920	-0.969	40.194	-0.027	-0.027	0.000	0.000	0.000	0.000
63	A	71	VAL	0	-0.045	-0.037	39.563	0.001	0.001	0.000	0.000	0.000	0.000
64	A	72	VAL	0	0.034	0.030	37.592	0.002	0.002	0.000	0.000	0.000	0.000
65	A	73	LEU	0	0.003	0.001	34.125	0.000	0.000	0.000	0.000	0.000	0.000
66	A	74	PHE	0	-0.062	-0.037	34.780	0.002	0.002	0.000	0.000	0.000	0.000
67	A	75	ILE	0	0.002	0.005	35.252	0.003	0.003	0.000	0.000	0.000	0.000
68	A	76	ASP	-1	-0.758	-0.853	30.992	-0.015	-0.015	0.000	0.000	0.000	0.000
69	A	77	VAL	0	-0.067	-0.036	30.600	0.001	0.001	0.000	0.000	0.000	0.000
70	A	78	LEU	0	-0.029	-0.001	30.536	0.002	0.002	0.000	0.000	0.000	0.000
71	A	79	CYS	0	-0.011	-0.009	28.291	0.004	0.004	0.000	0.000	0.000	0.000
72	A	80	ASP	-1	-0.723	-0.871	29.028	0.076	0.076	0.000	0.000	0.000	0.000
73	A	81	THR	0	-0.018	-0.037	27.724	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	82	ASP	-1	-0.999	-0.979	25.475	0.135	0.135	0.000	0.000	0.000	0.000
75	A	83	LYS	1	0.808	0.891	21.074	-0.083	-0.083	0.000	0.000	0.000	0.000
76	A	84	GLN	0	0.003	0.010	25.560	0.003	0.003	0.000	0.000	0.000	0.000
77	A	85	PRO	0	0.025	0.025	28.234	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	86	VAL	0	-0.012	-0.007	31.119	0.006	0.006	0.000	0.000	0.000	0.000
79	A	87	PHE	0	-0.006	0.004	34.395	0.001	0.001	0.000	0.000	0.000	0.000
80	A	88	SER	0	-0.035	-0.016	34.923	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	89	VAL	0	0.003	-0.025	35.206	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	90	ASP	-1	-0.920	-0.962	37.530	0.014	0.014	0.000	0.000	0.000	0.000
83	A	91	GLU	-1	-0.866	-0.919	39.013	0.030	0.030	0.000	0.000	0.000	0.000
84	A	92	GLU	-1	-0.819	-0.919	41.173	-0.008	-0.008	0.000	0.000	0.000	0.000
85	A	93	GLU	-1	-0.953	-0.990	42.263	0.003	0.003	0.000	0.000	0.000	0.000
86	A	94	GLN	0	0.019	0.011	44.151	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	95	VAL	0	-0.001	0.002	40.382	0.000	0.000	0.000	0.000	0.000	0.000
88	A	96	ARG	1	0.841	0.867	43.784	0.002	0.002	0.000	0.000	0.000	0.000
89	A	97	GLU	-1	-1.000	-0.981	46.085	0.008	0.008	0.000	0.000	0.000	0.000
90	A	98	ILE	0	-0.040	-0.002	43.481	0.000	0.000	0.000	0.000	0.000	0.000
91	A	99	TYR	0	-0.031	-0.005	40.341	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	100	GLY	0	0.053	0.017	44.788	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	101	PRO	0	-0.029	-0.033	44.273	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	102	VAL	0	0.016	0.017	40.446	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	103	HIS	0	0.095	0.049	39.799	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	104	SER	0	-0.016	0.009	39.289	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	105	ARG	1	0.832	0.908	37.195	0.000	0.000	0.000	0.000	0.000	0.000
98	A	106	LEU	0	-0.018	-0.008	34.997	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	107	LEU	0	0.033	0.021	34.987	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	108	LYS	1	0.948	0.966	35.083	0.027	0.027	0.000	0.000	0.000	0.000
101	A	109	GLN	0	0.070	0.035	32.955	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	110	ALA	0	-0.017	-0.010	30.874	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	111	LEU	0	-0.010	-0.015	30.443	-0.008	-0.008	0.000	0.000	0.000	0.000
104	A	112	ASP	-1	-0.884	-0.942	31.782	-0.056	-0.056	0.000	0.000	0.000	0.000
105	A	113	LEU	0	-0.153	-0.058	25.830	-0.007	-0.007	0.000	0.000	0.000	0.000
106	A	114	ILE	0	0.000	0.018	26.866	-0.013	-0.013	0.000	0.000	0.000	0.000
107	A	115	ASN	0	-0.047	-0.014	28.513	-0.007	-0.007	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)