FMO DATABASE

FMODB ID: JMZJ9

Calculation Name: 2OB5-A-Xray311

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: 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:

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. 1.20200116
Remarks	Structural optimization was performed under the unconstrained condition of hydrogen and heavy atoms fixed using MOE with Auto-FMO protocol as OptH.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	152
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1404445.745259
FMO2-HF: Nuclear repulsion	1345929.412581
FMO2-HF: Total energy	-58516.332678
FMO2-MP2: Total energy	-58683.98361

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.
-4.724	-0.528	4.251	-3.049	-5.399	-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	-0.016	-0.012	2.189	-3.647	0.485	4.251	-3.038	-5.345	-0.012
4	A	0	GLY	0	0.021	0.004	4.304	-0.387	-0.323	0.000	-0.011	-0.054	0.000
5	A	1	MET	0	-0.032	0.005	6.939	0.094	0.094	0.000	0.000	0.000	0.000
6	A	2	LEU	0	0.031	0.014	8.457	0.215	0.215	0.000	0.000	0.000	0.000
7	A	3	LYS	1	0.949	0.959	12.189	0.104	0.104	0.000	0.000	0.000	0.000
8	A	4	ASN	0	-0.029	-0.016	14.719	0.006	0.006	0.000	0.000	0.000	0.000
9	A	5	ILE	0	0.045	0.033	11.966	0.000	0.000	0.000	0.000	0.000	0.000
10	A	6	ASP	-1	-0.749	-0.851	8.935	-0.278	-0.278	0.000	0.000	0.000	0.000
11	A	7	PRO	0	0.005	-0.005	5.599	-0.095	-0.095	0.000	0.000	0.000	0.000
12	A	8	ALA	0	-0.036	-0.015	5.315	-0.759	-0.759	0.000	0.000	0.000	0.000
13	A	9	LEU	0	-0.033	-0.005	6.357	-0.227	-0.227	0.000	0.000	0.000	0.000
14	A	10	ASN	0	0.008	0.004	6.591	0.245	0.245	0.000	0.000	0.000	0.000
15	A	11	ALA	0	0.052	0.009	8.242	0.246	0.246	0.000	0.000	0.000	0.000
16	A	12	ASP	-1	-0.811	-0.891	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	0.115	0.115	0.000	0.000	0.000	0.000
18	A	14	LEU	0	0.002	0.000	11.977	0.133	0.133	0.000	0.000	0.000	0.000
19	A	15	HIS	0	-0.035	-0.007	14.248	0.082	0.082	0.000	0.000	0.000	0.000
20	A	16	ALA	0	0.050	0.016	16.315	0.063	0.063	0.000	0.000	0.000	0.000
21	A	17	LEU	0	0.011	0.001	14.832	0.053	0.053	0.000	0.000	0.000	0.000
22	A	18	ARG	1	0.879	0.945	18.372	0.283	0.283	0.000	0.000	0.000	0.000
23	A	19	ALA	0	-0.035	-0.023	20.307	0.040	0.040	0.000	0.000	0.000	0.000
24	A	20	MET	0	-0.050	0.009	21.408	0.009	0.009	0.000	0.000	0.000	0.000
25	A	21	GLY	0	0.013	0.009	23.851	0.010	0.010	0.000	0.000	0.000	0.000
26	A	22	HIS	0	-0.124	-0.080	26.831	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	23	GLY	0	0.028	0.005	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	-0.002	-0.017	24.823	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	26	LEU	0	-0.017	-0.010	18.248	-0.019	-0.019	0.000	0.000	0.000	0.000
31	A	27	VAL	0	0.010	0.006	20.379	0.026	0.026	0.000	0.000	0.000	0.000
32	A	28	ILE	0	-0.003	0.015	15.443	-0.056	-0.056	0.000	0.000	0.000	0.000
33	A	29	SER	0	-0.004	-0.038	17.008	0.034	0.034	0.000	0.000	0.000	0.000
34	A	30	ASP	-1	-0.752	-0.890	16.402	-0.394	-0.394	0.000	0.000	0.000	0.000
35	A	31	THR	0	0.011	-0.018	14.691	-0.018	-0.018	0.000	0.000	0.000	0.000
36	A	32	ASN	0	-0.153	-0.073	17.371	0.017	0.017	0.000	0.000	0.000	0.000
37	A	33	PHE	0	0.010	-0.001	20.525	0.031	0.031	0.000	0.000	0.000	0.000
38	A	34	PRO	0	0.023	0.030	20.851	-0.033	-0.033	0.000	0.000	0.000	0.000
39	A	35	SER	0	0.062	0.007	18.271	0.015	0.015	0.000	0.000	0.000	0.000
40	A	36	ASP	-1	-0.897	-0.950	18.278	-0.511	-0.511	0.000	0.000	0.000	0.000
41	A	37	SER	0	-0.054	-0.045	20.678	0.021	0.021	0.000	0.000	0.000	0.000
42	A	38	VAL	0	-0.018	-0.001	23.189	0.019	0.019	0.000	0.000	0.000	0.000
43	A	39	ALA	0	0.055	0.020	20.150	0.013	0.013	0.000	0.000	0.000	0.000
44	A	40	ARG	1	0.903	0.984	22.139	0.309	0.309	0.000	0.000	0.000	0.000
45	A	41	GLN	0	-0.054	-0.032	24.557	0.021	0.021	0.000	0.000	0.000	0.000
46	A	42	THR	0	-0.034	-0.006	22.629	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	43	THR	0	0.000	-0.005	24.210	0.005	0.005	0.000	0.000	0.000	0.000
48	A	44	VAL	0	-0.059	-0.020	18.044	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	45	GLY	0	0.020	0.029	21.500	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	46	LYS	1	0.830	0.895	14.786	0.604	0.604	0.000	0.000	0.000	0.000
51	A	47	VAL	0	-0.018	0.003	14.906	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	48	LEU	0	-0.026	-0.003	13.486	-0.064	-0.064	0.000	0.000	0.000	0.000
53	A	49	HIS	1	0.928	0.957	9.577	1.141	1.141	0.000	0.000	0.000	0.000
54	A	50	ILE	0	0.006	0.017	7.877	-0.125	-0.125	0.000	0.000	0.000	0.000
55	A	51	ASP	-1	-0.841	-0.946	6.456	-1.453	-1.453	0.000	0.000	0.000	0.000
56	A	52	ASN	0	-0.060	-0.039	4.874	0.224	0.224	0.000	0.000	0.000	0.000
57	A	53	VAL	0	-0.056	0.000	7.111	0.378	0.378	0.000	0.000	0.000	0.000
58	A	54	SER	0	0.088	0.040	9.651	-0.057	-0.057	0.000	0.000	0.000	0.000
59	A	55	ALA	0	0.075	0.026	12.974	-0.042	-0.042	0.000	0.000	0.000	0.000
60	A	56	ALA	0	0.050	0.032	15.437	-0.010	-0.010	0.000	0.000	0.000	0.000
61	A	57	ARG	1	0.802	0.880	7.830	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	58	ALA	0	0.025	0.000	11.481	-0.033	-0.033	0.000	0.000	0.000	0.000
63	A	59	MET	0	0.027	0.024	12.416	-0.024	-0.024	0.000	0.000	0.000	0.000
64	A	60	LYS	1	0.963	0.994	13.101	-0.065	-0.065	0.000	0.000	0.000	0.000
65	A	61	ALA	0	-0.029	-0.021	10.474	0.007	0.007	0.000	0.000	0.000	0.000
66	A	62	ILE	0	0.006	0.009	12.403	-0.009	-0.009	0.000	0.000	0.000	0.000
67	A	63	LEU	0	0.013	0.003	14.967	0.016	0.016	0.000	0.000	0.000	0.000
68	A	64	SER	0	-0.112	-0.052	14.167	0.030	0.030	0.000	0.000	0.000	0.000
69	A	65	VAL	0	-0.053	-0.035	15.132	0.011	0.011	0.000	0.000	0.000	0.000
70	A	66	LEU	0	-0.050	-0.022	17.791	0.012	0.012	0.000	0.000	0.000	0.000
71	A	67	PRO	0	-0.005	0.021	19.958	0.017	0.017	0.000	0.000	0.000	0.000
72	A	68	LEU	0	0.084	0.035	22.428	-0.019	-0.019	0.000	0.000	0.000	0.000
73	A	69	ASP	-1	-0.755	-0.872	25.110	-0.114	-0.114	0.000	0.000	0.000	0.000
74	A	70	THR	0	-0.027	-0.035	27.173	0.006	0.006	0.000	0.000	0.000	0.000
75	A	71	PRO	0	-0.082	-0.038	29.685	0.008	0.008	0.000	0.000	0.000	0.000
76	A	72	LEU	0	-0.064	-0.031	32.382	0.008	0.008	0.000	0.000	0.000	0.000
77	A	73	GLN	0	-0.055	-0.034	31.112	0.004	0.004	0.000	0.000	0.000	0.000
78	A	74	PRO	0	0.031	0.018	30.845	-0.005	-0.005	0.000	0.000	0.000	0.000
79	A	75	SER	0	-0.003	-0.001	26.662	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	76	VAL	0	0.014	-0.003	22.940	-0.020	-0.020	0.000	0.000	0.000	0.000
81	A	77	GLY	0	-0.011	0.012	25.662	0.017	0.017	0.000	0.000	0.000	0.000
82	A	78	ARG	1	0.897	0.932	25.107	0.092	0.092	0.000	0.000	0.000	0.000
83	A	79	MET	0	-0.031	-0.027	25.057	0.009	0.009	0.000	0.000	0.000	0.000
84	A	80	GLU	-1	-0.926	-0.961	27.944	-0.101	-0.101	0.000	0.000	0.000	0.000
85	A	81	VAL	0	0.013	0.012	29.805	-0.009	-0.009	0.000	0.000	0.000	0.000
86	A	82	MET	0	-0.057	-0.044	31.229	0.007	0.007	0.000	0.000	0.000	0.000
87	A	83	GLY	0	-0.001	0.003	34.610	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	0.034	0.024	34.493	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	86	ASP	-1	-0.872	-0.929	33.952	-0.075	-0.075	0.000	0.000	0.000	0.000
91	A	87	GLN	0	-0.113	-0.038	31.204	0.007	0.007	0.000	0.000	0.000	0.000
92	A	88	LEU	0	-0.024	-0.016	27.905	-0.010	-0.010	0.000	0.000	0.000	0.000
93	A	89	GLU	-1	-0.876	-0.953	25.785	-0.104	-0.104	0.000	0.000	0.000	0.000
94	A	90	PRO	0	0.007	-0.008	23.716	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	91	VAL	0	0.025	0.016	19.142	0.005	0.005	0.000	0.000	0.000	0.000
96	A	92	GLN	0	0.023	0.012	21.044	0.003	0.003	0.000	0.000	0.000	0.000
97	A	93	VAL	0	-0.008	-0.002	23.610	0.003	0.003	0.000	0.000	0.000	0.000
98	A	94	GLU	-1	-0.835	-0.891	18.688	-0.072	-0.072	0.000	0.000	0.000	0.000
99	A	95	VAL	0	-0.013	-0.014	18.377	0.003	0.003	0.000	0.000	0.000	0.000
100	A	96	GLN	0	0.015	0.007	20.360	-0.007	-0.007	0.000	0.000	0.000	0.000
101	A	97	GLN	0	-0.018	-0.004	21.189	0.022	0.022	0.000	0.000	0.000	0.000
102	A	98	GLU	-1	-0.907	-0.967	16.824	-0.008	-0.008	0.000	0.000	0.000	0.000
103	A	99	ILE	0	-0.025	-0.011	19.897	-0.008	-0.008	0.000	0.000	0.000	0.000
104	A	100	ASP	-1	-0.834	-0.918	22.411	-0.059	-0.059	0.000	0.000	0.000	0.000
105	A	101	ALA	0	-0.056	-0.029	20.829	0.009	0.009	0.000	0.000	0.000	0.000
106	A	102	ALA	0	-0.055	-0.021	20.157	0.007	0.007	0.000	0.000	0.000	0.000
107	A	103	GLU	-1	-0.861	-0.916	22.004	-0.104	-0.104	0.000	0.000	0.000	0.000
108	A	104	GLY	0	-0.036	-0.010	25.439	0.007	0.007	0.000	0.000	0.000	0.000
109	A	105	LYS	1	0.852	0.924	27.219	0.070	0.070	0.000	0.000	0.000	0.000
110	A	106	SER	0	-0.015	0.007	28.248	-0.006	-0.006	0.000	0.000	0.000	0.000
111	A	107	ALA	0	0.022	-0.001	27.196	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	108	PRO	0	-0.027	-0.008	27.842	-0.010	-0.010	0.000	0.000	0.000	0.000
113	A	109	MET	0	-0.025	-0.001	24.023	-0.013	-0.013	0.000	0.000	0.000	0.000
114	A	110	TYR	0	-0.017	0.002	28.185	0.006	0.006	0.000	0.000	0.000	0.000
115	A	111	GLY	0	0.026	0.012	29.540	-0.012	-0.012	0.000	0.000	0.000	0.000
116	A	112	ILE	0	-0.053	-0.025	28.061	0.003	0.003	0.000	0.000	0.000	0.000
117	A	113	GLU	-1	-0.852	-0.919	30.911	-0.118	-0.118	0.000	0.000	0.000	0.000
118	A	114	ARG	1	0.999	0.989	27.389	0.180	0.180	0.000	0.000	0.000	0.000
119	A	115	PHE	0	0.014	-0.001	30.714	-0.013	-0.013	0.000	0.000	0.000	0.000
120	A	116	ALA	0	0.086	0.036	32.491	-0.006	-0.006	0.000	0.000	0.000	0.000
121	A	117	PHE	0	-0.021	-0.008	23.471	-0.006	-0.006	0.000	0.000	0.000	0.000
122	A	118	TYR	0	-0.027	-0.028	26.677	-0.022	-0.022	0.000	0.000	0.000	0.000
123	A	119	GLU	-1	-0.914	-0.959	28.752	-0.184	-0.184	0.000	0.000	0.000	0.000
124	A	120	LYS	1	0.964	0.982	28.822	0.148	0.148	0.000	0.000	0.000	0.000
125	A	121	ALA	0	-0.020	-0.009	24.702	-0.010	-0.010	0.000	0.000	0.000	0.000
126	A	122	LYS	1	0.844	0.921	25.696	0.184	0.184	0.000	0.000	0.000	0.000
127	A	123	GLN	0	-0.044	-0.014	27.867	0.002	0.002	0.000	0.000	0.000	0.000
128	A	124	ALA	0	-0.003	0.030	23.731	0.005	0.005	0.000	0.000	0.000	0.000
129	A	125	TYR	0	0.036	0.002	20.403	-0.016	-0.016	0.000	0.000	0.000	0.000
130	A	126	CYS	0	-0.038	-0.026	18.704	-0.033	-0.033	0.000	0.000	0.000	0.000
131	A	127	VAL	0	0.060	0.028	18.014	0.025	0.025	0.000	0.000	0.000	0.000
132	A	128	ILE	0	-0.035	-0.021	13.117	-0.063	-0.063	0.000	0.000	0.000	0.000
133	A	129	THR	0	-0.013	0.008	12.953	0.031	0.031	0.000	0.000	0.000	0.000
134	A	130	THR	0	-0.027	-0.031	11.578	-0.119	-0.119	0.000	0.000	0.000	0.000
135	A	131	GLY	0	-0.009	-0.003	11.400	-0.047	-0.047	0.000	0.000	0.000	0.000
136	A	132	GLU	-1	-0.787	-0.875	12.165	-0.153	-0.153	0.000	0.000	0.000	0.000
137	A	133	THR	0	0.050	0.022	15.499	0.004	0.004	0.000	0.000	0.000	0.000
138	A	134	ARG	1	0.709	0.815	17.769	0.183	0.183	0.000	0.000	0.000	0.000
139	A	135	PHE	0	0.001	-0.002	21.166	-0.017	-0.017	0.000	0.000	0.000	0.000
140	A	136	TYR	0	0.010	-0.005	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	0.015	0.015	0.000	0.000	0.000	0.000
142	A	138	CYS	0	-0.109	-0.024	19.420	-0.049	-0.049	0.000	0.000	0.000	0.000
143	A	139	PHE	0	0.011	-0.010	19.496	0.035	0.035	0.000	0.000	0.000	0.000
144	A	140	LEU	0	-0.022	-0.002	21.636	-0.031	-0.031	0.000	0.000	0.000	0.000
145	A	141	LEU	0	0.013	0.007	19.083	0.022	0.022	0.000	0.000	0.000	0.000
146	A	142	THR	0	0.005	0.004	23.271	-0.009	-0.009	0.000	0.000	0.000	0.000
147	A	143	LYS	1	0.803	0.901	22.322	0.254	0.254	0.000	0.000	0.000	0.000
148	A	144	GLY	0	0.038	0.017	25.017	0.014	0.014	0.000	0.000	0.000	0.000
149	A	145	VAL	0	-0.020	-0.026	27.269	-0.010	-0.010	0.000	0.000	0.000	0.000
150	A	146	ILE	0	-0.010	-0.011	23.934	0.009	0.009	0.000	0.000	0.000	0.000
151	A	147	PRO	0	-0.004	0.004	28.484	0.001	0.001	0.000	0.000	0.000	0.000
152	A	148	NME	0	-0.007	0.004	30.303	-0.002	-0.002	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:-3:TYR )