FMO DATABASE

FMODB ID: 7GNLK

Calculation Name: 2OB5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2OB5

Chain ID: A

ChEMBL ID:

UniProt ID: A9CIE0

Base Structure: X-ray

Registration Date: 2023-03-13

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	151
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1402801.440963
FMO2-HF: Nuclear repulsion	1344304.21252
FMO2-HF: Total energy	-58497.228444
FMO2-MP2: Total energy	-58664.779612

3D Structure Molmil

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:-3:TYR)

Summations of interaction energy for fragment #1(A:-3:TYR)

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.
-4.676	-0.443	4.245	-3.052	-5.427	-0.012

Interaction energy analysis for fragmet #1(A:-3:TYR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.016

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	-1	GLN	0	-0.015	-0.012	2.189	-3.592	0.575	4.246	-3.042	-5.372	-0.012
4	A	0	GLY	0	0.020	0.004	4.304	-0.394	-0.328	-0.001	-0.010	-0.055	0.000
5	A	1	MET	0	-0.031	0.005	6.926	0.100	0.100	0.000	0.000	0.000	0.000
6	A	2	LEU	0	0.030	0.014	8.456	0.211	0.211	0.000	0.000	0.000	0.000
7	A	3	LYS	1	0.948	0.959	12.189	0.108	0.108	0.000	0.000	0.000	0.000
8	A	4	ASN	0	-0.028	-0.016	14.719	0.007	0.007	0.000	0.000	0.000	0.000
9	A	5	ILE	0	0.046	0.034	11.967	0.004	0.004	0.000	0.000	0.000	0.000
10	A	6	ASP	-1	-0.750	-0.851	8.937	-0.300	-0.300	0.000	0.000	0.000	0.000
11	A	7	PRO	0	0.006	-0.005	5.600	-0.083	-0.083	0.000	0.000	0.000	0.000
12	A	8	ALA	0	-0.036	-0.014	5.316	-0.750	-0.750	0.000	0.000	0.000	0.000
13	A	9	LEU	0	-0.030	-0.004	6.358	-0.220	-0.220	0.000	0.000	0.000	0.000
14	A	10	ASN	0	0.006	0.004	6.591	0.249	0.249	0.000	0.000	0.000	0.000
15	A	11	ALA	0	0.051	0.008	8.242	0.235	0.235	0.000	0.000	0.000	0.000
16	A	12	ASP	-1	-0.809	-0.890	11.024	-0.576	-0.576	0.000	0.000	0.000	0.000
17	A	13	VAL	0	-0.002	-0.002	11.337	0.114	0.114	0.000	0.000	0.000	0.000
18	A	14	LEU	0	0.000	-0.001	11.977	0.130	0.130	0.000	0.000	0.000	0.000
19	A	15	HIS	0	-0.035	-0.008	14.248	0.079	0.079	0.000	0.000	0.000	0.000
20	A	16	ALA	0	0.048	0.015	16.315	0.062	0.062	0.000	0.000	0.000	0.000
21	A	17	LEU	0	0.012	0.001	14.832	0.052	0.052	0.000	0.000	0.000	0.000
22	A	18	ARG	1	0.880	0.945	18.372	0.285	0.285	0.000	0.000	0.000	0.000
23	A	19	ALA	0	-0.032	-0.022	20.307	0.039	0.039	0.000	0.000	0.000	0.000
24	A	20	MET	0	-0.051	0.009	21.406	0.009	0.009	0.000	0.000	0.000	0.000
25	A	21	GLY	0	0.011	0.008	23.851	0.009	0.009	0.000	0.000	0.000	0.000
26	A	22	HIS	0	-0.123	-0.080	26.831	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	23	GLY	0	0.028	0.006	28.181	0.006	0.006	0.000	0.000	0.000	0.000
28	A	24	ASP	-1	-0.866	-0.907	25.345	-0.219	-0.219	0.000	0.000	0.000	0.000
29	A	25	THR	0	-0.004	-0.017	24.823	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	26	LEU	0	-0.015	-0.010	18.247	-0.018	-0.018	0.000	0.000	0.000	0.000
31	A	27	VAL	0	0.011	0.008	20.378	0.026	0.026	0.000	0.000	0.000	0.000
32	A	28	ILE	0	-0.004	0.014	15.442	-0.055	-0.055	0.000	0.000	0.000	0.000
33	A	29	SER	0	-0.004	-0.037	17.007	0.034	0.034	0.000	0.000	0.000	0.000
34	A	30	ASP	-1	-0.751	-0.889	16.401	-0.392	-0.392	0.000	0.000	0.000	0.000
35	A	31	THR	0	0.018	-0.017	14.690	-0.017	-0.017	0.000	0.000	0.000	0.000
36	A	32	ASN	0	-0.160	-0.075	17.371	0.015	0.015	0.000	0.000	0.000	0.000
37	A	33	PHE	0	0.013	0.000	20.525	0.030	0.030	0.000	0.000	0.000	0.000
38	A	34	PRO	0	0.018	0.029	20.851	-0.032	-0.032	0.000	0.000	0.000	0.000
39	A	35	SER	0	0.063	0.009	18.271	0.015	0.015	0.000	0.000	0.000	0.000
40	A	36	ASP	-1	-0.895	-0.950	18.278	-0.506	-0.506	0.000	0.000	0.000	0.000
41	A	37	SER	0	-0.057	-0.046	20.678	0.020	0.020	0.000	0.000	0.000	0.000
42	A	38	VAL	0	-0.018	0.000	23.189	0.018	0.018	0.000	0.000	0.000	0.000
43	A	39	ALA	0	0.056	0.021	20.150	0.013	0.013	0.000	0.000	0.000	0.000
44	A	40	ARG	1	0.900	0.983	22.139	0.305	0.305	0.000	0.000	0.000	0.000
45	A	41	GLN	0	-0.050	-0.031	24.557	0.020	0.020	0.000	0.000	0.000	0.000
46	A	42	THR	0	-0.035	-0.006	22.629	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	43	THR	0	-0.001	-0.005	24.210	0.005	0.005	0.000	0.000	0.000	0.000
48	A	44	VAL	0	-0.056	-0.019	18.044	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	45	GLY	0	0.019	0.028	21.500	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	46	LYS	1	0.828	0.894	14.786	0.602	0.602	0.000	0.000	0.000	0.000
51	A	47	VAL	0	-0.014	0.005	14.906	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	48	LEU	0	-0.028	-0.005	13.486	-0.060	-0.060	0.000	0.000	0.000	0.000
53	A	49	HIS	1	0.928	0.956	9.577	1.139	1.139	0.000	0.000	0.000	0.000
54	A	50	ILE	0	0.006	0.017	7.879	-0.120	-0.120	0.000	0.000	0.000	0.000
55	A	51	ASP	-1	-0.841	-0.946	6.456	-1.438	-1.438	0.000	0.000	0.000	0.000
56	A	52	ASN	0	-0.060	-0.039	4.875	0.216	0.216	0.000	0.000	0.000	0.000
57	A	53	VAL	0	-0.056	0.000	7.110	0.363	0.363	0.000	0.000	0.000	0.000
58	A	54	SER	0	0.090	0.041	9.651	-0.060	-0.060	0.000	0.000	0.000	0.000
59	A	55	ALA	0	0.076	0.026	12.974	-0.042	-0.042	0.000	0.000	0.000	0.000
60	A	56	ALA	0	0.045	0.030	15.438	-0.012	-0.012	0.000	0.000	0.000	0.000
61	A	57	ARG	1	0.804	0.880	7.833	0.010	0.010	0.000	0.000	0.000	0.000
62	A	58	ALA	0	0.027	0.001	11.481	-0.031	-0.031	0.000	0.000	0.000	0.000
63	A	59	MET	0	0.024	0.023	12.416	-0.027	-0.027	0.000	0.000	0.000	0.000
64	A	60	LYS	1	0.963	0.993	13.103	-0.059	-0.059	0.000	0.000	0.000	0.000
65	A	61	ALA	0	-0.029	-0.020	10.475	0.008	0.008	0.000	0.000	0.000	0.000
66	A	62	ILE	0	0.007	0.009	12.404	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	63	LEU	0	0.011	0.001	14.967	0.014	0.014	0.000	0.000	0.000	0.000
68	A	64	SER	0	-0.111	-0.052	14.168	0.028	0.028	0.000	0.000	0.000	0.000
69	A	65	VAL	0	-0.053	-0.035	15.133	0.011	0.011	0.000	0.000	0.000	0.000
70	A	66	LEU	0	-0.049	-0.020	17.793	0.012	0.012	0.000	0.000	0.000	0.000
71	A	67	PRO	0	-0.006	0.021	19.959	0.016	0.016	0.000	0.000	0.000	0.000
72	A	68	LEU	0	0.082	0.035	22.428	-0.019	-0.019	0.000	0.000	0.000	0.000
73	A	69	ASP	-1	-0.754	-0.870	25.111	-0.116	-0.116	0.000	0.000	0.000	0.000
74	A	70	THR	0	-0.026	-0.037	27.174	0.006	0.006	0.000	0.000	0.000	0.000
75	A	71	PRO	0	-0.081	-0.038	29.686	0.008	0.008	0.000	0.000	0.000	0.000
76	A	72	LEU	0	-0.063	-0.032	32.383	0.008	0.008	0.000	0.000	0.000	0.000
77	A	73	GLN	0	-0.057	-0.033	31.112	0.005	0.005	0.000	0.000	0.000	0.000
78	A	74	PRO	0	0.031	0.018	30.846	-0.005	-0.005	0.000	0.000	0.000	0.000
79	A	75	SER	0	-0.001	-0.002	26.663	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	76	VAL	0	0.010	-0.003	22.944	-0.020	-0.020	0.000	0.000	0.000	0.000
81	A	77	GLY	0	-0.008	0.013	25.662	0.017	0.017	0.000	0.000	0.000	0.000
82	A	78	ARG	1	0.898	0.933	25.107	0.093	0.093	0.000	0.000	0.000	0.000
83	A	79	MET	0	-0.029	-0.026	25.026	0.009	0.009	0.000	0.000	0.000	0.000
84	A	80	GLU	-1	-0.928	-0.962	27.944	-0.102	-0.102	0.000	0.000	0.000	0.000
85	A	81	VAL	0	0.014	0.012	29.805	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	82	MET	0	-0.056	-0.044	31.198	0.007	0.007	0.000	0.000	0.000	0.000
87	A	83	GLY	0	-0.001	0.002	34.608	0.005	0.005	0.000	0.000	0.000	0.000
88	A	84	ALA	0	0.001	-0.001	34.913	0.007	0.007	0.000	0.000	0.000	0.000
89	A	85	PRO	0	0.037	0.025	34.493	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	86	ASP	-1	-0.875	-0.931	33.952	-0.076	-0.076	0.000	0.000	0.000	0.000
91	A	87	GLN	0	-0.114	-0.039	31.204	0.007	0.007	0.000	0.000	0.000	0.000
92	A	88	LEU	0	-0.018	-0.014	27.906	-0.010	-0.010	0.000	0.000	0.000	0.000
93	A	89	GLU	-1	-0.880	-0.952	25.785	-0.104	-0.104	0.000	0.000	0.000	0.000
94	A	90	PRO	0	0.007	-0.009	23.716	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	91	VAL	0	0.023	0.015	19.142	0.005	0.005	0.000	0.000	0.000	0.000
96	A	92	GLN	0	0.024	0.012	21.045	0.003	0.003	0.000	0.000	0.000	0.000
97	A	93	VAL	0	-0.006	-0.002	23.610	0.002	0.002	0.000	0.000	0.000	0.000
98	A	94	GLU	-1	-0.837	-0.892	18.688	-0.075	-0.075	0.000	0.000	0.000	0.000
99	A	95	VAL	0	-0.010	-0.012	18.379	0.004	0.004	0.000	0.000	0.000	0.000
100	A	96	GLN	0	0.013	0.007	20.361	-0.008	-0.008	0.000	0.000	0.000	0.000
101	A	97	GLN	0	-0.017	-0.005	21.191	0.021	0.021	0.000	0.000	0.000	0.000
102	A	98	GLU	-1	-0.904	-0.966	16.825	-0.015	-0.015	0.000	0.000	0.000	0.000
103	A	99	ILE	0	-0.024	-0.010	19.899	-0.008	-0.008	0.000	0.000	0.000	0.000
104	A	100	ASP	-1	-0.836	-0.920	22.412	-0.062	-0.062	0.000	0.000	0.000	0.000
105	A	101	ALA	0	-0.055	-0.029	20.831	0.009	0.009	0.000	0.000	0.000	0.000
106	A	102	ALA	0	-0.056	-0.022	20.158	0.007	0.007	0.000	0.000	0.000	0.000
107	A	103	GLU	-1	-0.862	-0.916	22.006	-0.108	-0.108	0.000	0.000	0.000	0.000
108	A	104	GLY	0	-0.036	-0.010	25.441	0.007	0.007	0.000	0.000	0.000	0.000
109	A	105	LYS	1	0.853	0.925	27.221	0.073	0.073	0.000	0.000	0.000	0.000
110	A	106	SER	0	-0.015	0.007	28.249	-0.005	-0.005	0.000	0.000	0.000	0.000
111	A	107	ALA	0	0.021	-0.001	27.197	0.000	0.000	0.000	0.000	0.000	0.000
112	A	108	PRO	0	-0.026	-0.009	27.843	-0.010	-0.010	0.000	0.000	0.000	0.000
113	A	109	MET	0	-0.028	-0.002	23.909	-0.013	-0.013	0.000	0.000	0.000	0.000
114	A	110	TYR	0	-0.013	0.004	28.184	0.006	0.006	0.000	0.000	0.000	0.000
115	A	111	GLY	0	0.021	0.010	29.540	-0.012	-0.012	0.000	0.000	0.000	0.000
116	A	112	ILE	0	-0.053	-0.025	28.060	0.003	0.003	0.000	0.000	0.000	0.000
117	A	113	GLU	-1	-0.851	-0.919	30.911	-0.117	-0.117	0.000	0.000	0.000	0.000
118	A	114	ARG	1	0.999	0.989	27.389	0.179	0.179	0.000	0.000	0.000	0.000
119	A	115	PHE	0	0.013	-0.002	30.714	-0.013	-0.013	0.000	0.000	0.000	0.000
120	A	116	ALA	0	0.085	0.036	32.491	-0.006	-0.006	0.000	0.000	0.000	0.000
121	A	117	PHE	0	-0.020	-0.007	23.470	-0.006	-0.006	0.000	0.000	0.000	0.000
122	A	118	TYR	0	-0.026	-0.028	26.677	-0.022	-0.022	0.000	0.000	0.000	0.000
123	A	119	GLU	-1	-0.915	-0.959	28.752	-0.184	-0.184	0.000	0.000	0.000	0.000
124	A	120	LYS	1	0.961	0.981	28.821	0.148	0.148	0.000	0.000	0.000	0.000
125	A	121	ALA	0	-0.018	-0.008	24.702	-0.010	-0.010	0.000	0.000	0.000	0.000
126	A	122	LYS	1	0.845	0.921	25.695	0.183	0.183	0.000	0.000	0.000	0.000
127	A	123	GLN	0	-0.045	-0.015	27.867	0.002	0.002	0.000	0.000	0.000	0.000
128	A	124	ALA	0	-0.002	0.031	23.731	0.005	0.005	0.000	0.000	0.000	0.000
129	A	125	TYR	0	0.037	0.002	20.403	-0.015	-0.015	0.000	0.000	0.000	0.000
130	A	126	CYS	0	-0.039	-0.027	18.704	-0.032	-0.032	0.000	0.000	0.000	0.000
131	A	127	VAL	0	0.055	0.027	18.014	0.025	0.025	0.000	0.000	0.000	0.000
132	A	128	ILE	0	-0.035	-0.021	13.116	-0.060	-0.060	0.000	0.000	0.000	0.000
133	A	129	THR	0	-0.010	0.010	12.957	0.032	0.032	0.000	0.000	0.000	0.000
134	A	130	THR	0	-0.029	-0.033	11.577	-0.116	-0.116	0.000	0.000	0.000	0.000
135	A	131	GLY	0	-0.006	-0.001	11.400	-0.047	-0.047	0.000	0.000	0.000	0.000
136	A	132	GLU	-1	-0.789	-0.876	12.165	-0.159	-0.159	0.000	0.000	0.000	0.000
137	A	133	THR	0	0.051	0.022	15.501	0.003	0.003	0.000	0.000	0.000	0.000
138	A	134	ARG	1	0.708	0.815	17.769	0.183	0.183	0.000	0.000	0.000	0.000
139	A	135	PHE	0	0.003	-0.001	21.166	-0.017	-0.017	0.000	0.000	0.000	0.000
140	A	136	TYR	0	0.009	-0.006	23.942	0.011	0.011	0.000	0.000	0.000	0.000
141	A	137	GLY	0	0.028	0.022	20.220	0.016	0.016	0.000	0.000	0.000	0.000
142	A	138	CYS	0	-0.111	-0.025	19.420	-0.049	-0.049	0.000	0.000	0.000	0.000
143	A	139	PHE	0	0.014	-0.009	19.496	0.034	0.034	0.000	0.000	0.000	0.000
144	A	140	LEU	0	-0.023	-0.003	21.636	-0.031	-0.031	0.000	0.000	0.000	0.000
145	A	141	LEU	0	0.013	0.008	19.085	0.021	0.021	0.000	0.000	0.000	0.000
146	A	142	THR	0	0.003	0.004	23.271	-0.009	-0.009	0.000	0.000	0.000	0.000
147	A	143	LYS	1	0.804	0.901	22.322	0.256	0.256	0.000	0.000	0.000	0.000
148	A	144	GLY	0	0.038	0.017	25.017	0.013	0.013	0.000	0.000	0.000	0.000
149	A	145	VAL	0	-0.018	-0.026	27.269	-0.010	-0.010	0.000	0.000	0.000	0.000
150	A	146	ILE	0	-0.009	-0.006	23.936	0.009	0.009	0.000	0.000	0.000	0.000
151	A	147	PRO	0	-0.011	0.004	28.485	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-3:TYR)