FMO DATABASE

FMODB ID: 63QVZ

Calculation Name: 2DBO-A-Xray310

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2DBO

Chain ID: A

ChEMBL ID:

UniProt ID: O66742

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	148
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1441342.141385
FMO2-HF: Nuclear repulsion	1382617.060818
FMO2-HF: Total energy	-58725.080567
FMO2-MP2: Total energy	-58899.116978

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: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.
-233.742	-232.741	63.282	-25.784	-38.499	-0.255

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 : 1 / q_Mulliken : 0.675 / q_NPA : 0.838

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	3	ALA	0	0.040	0.009	3.580	3.683	6.097	-0.010	-1.205	-1.199	-0.003
4	A	4	VAL	0	-0.028	-0.002	5.582	1.936	1.936	0.000	0.000	0.000	0.000
5	A	5	ILE	0	0.024	0.008	8.803	0.856	0.856	0.000	0.000	0.000	0.000
6	A	6	GLN	0	-0.021	-0.021	11.112	1.600	1.600	0.000	0.000	0.000	0.000
7	A	7	ARG	1	0.829	0.906	14.797	13.359	13.359	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.029	-0.012	16.862	0.445	0.445	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.906	0.967	19.506	11.136	11.136	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.964	0.980	22.094	11.386	11.386	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.039	-0.027	17.777	-0.631	-0.631	0.000	0.000	0.000	0.000
12	A	12	TRP	0	-0.002	-0.008	19.339	-0.036	-0.036	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.046	0.036	15.942	-0.301	-0.301	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.872	-0.931	19.287	-10.908	-10.908	0.000	0.000	0.000	0.000
15	A	15	VAL	0	-0.049	-0.027	20.129	-0.323	-0.323	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.892	-0.955	22.792	-11.059	-11.059	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.025	0.024	25.588	0.432	0.432	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.879	0.957	22.467	12.206	12.206	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.014	-0.009	22.601	-0.517	-0.517	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.093	-0.062	18.486	0.204	0.204	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.051	0.034	18.461	-0.392	-0.392	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.051	-0.045	19.534	0.062	0.062	0.000	0.000	0.000	0.000
23	A	23	ILE	0	-0.064	-0.009	16.771	0.031	0.031	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.074	-0.046	20.717	0.404	0.404	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.898	-0.960	21.128	-12.081	-12.081	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.026	0.008	18.560	-0.030	-0.030	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.035	-0.022	12.832	-0.205	-0.205	0.000	0.000	0.000	0.000
28	A	28	ASN	0	-0.004	0.018	13.261	-0.984	-0.984	0.000	0.000	0.000	0.000
29	A	29	VAL	0	0.009	-0.018	7.306	-0.910	-0.910	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.005	0.005	8.683	0.068	0.068	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.025	0.006	2.990	-4.632	-4.042	1.646	-0.427	-1.809	0.002
32	A	32	GLY	0	0.031	0.019	4.007	4.170	4.406	0.000	-0.056	-0.180	0.000
33	A	33	VAL	0	-0.015	0.001	2.096	-18.625	-16.404	4.311	-2.326	-4.207	-0.018
34	A	34	ARG	1	0.836	0.895	2.675	57.864	59.440	0.458	-0.488	-1.545	-0.006
35	A	35	LYS	1	0.937	0.994	4.213	27.730	27.856	0.001	-0.012	-0.114	0.000
36	A	36	GLY	0	-0.053	-0.042	5.887	-4.230	-4.230	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.784	-0.906	1.704	-125.906	-137.991	33.355	-10.836	-10.434	-0.126
38	A	38	THR	0	-0.022	-0.029	4.112	11.540	11.875	0.000	-0.134	-0.202	-0.001
39	A	39	GLU	-1	-0.790	-0.933	4.027	-30.392	-30.165	0.001	-0.046	-0.183	0.000
40	A	40	GLU	-1	-0.892	-0.944	6.352	-29.088	-29.088	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.831	-0.890	2.360	-73.485	-71.746	1.012	-1.115	-1.636	-0.004
42	A	42	ILE	0	0.040	0.021	2.554	-1.850	-0.246	1.114	-0.578	-2.140	-0.002
43	A	43	GLU	-1	-0.858	-0.904	4.403	-20.325	-20.405	0.010	0.195	-0.125	0.000
44	A	44	LYS	1	0.847	0.939	6.277	39.049	39.049	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.033	-0.009	2.488	-0.728	0.124	1.783	-0.506	-2.130	-0.003
46	A	46	VAL	0	-0.001	-0.017	5.705	3.025	3.104	0.000	-0.009	-0.070	0.000
47	A	47	ASN	0	0.025	0.023	7.762	3.098	3.098	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.958	0.959	9.171	24.477	24.477	0.000	0.000	0.000	0.000
49	A	49	ILE	0	-0.032	-0.008	7.063	1.371	1.371	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.033	0.011	10.772	1.675	1.675	0.000	0.000	0.000	0.000
51	A	51	ASN	0	-0.008	-0.005	13.649	1.945	1.945	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.016	-0.014	12.332	0.800	0.800	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.936	0.984	15.635	13.930	13.930	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.009	0.005	15.320	0.186	0.186	0.000	0.000	0.000	0.000
55	A	55	PHE	0	-0.013	-0.005	17.286	0.440	0.440	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.864	-0.921	21.625	-11.549	-11.549	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.760	-0.847	25.301	-10.043	-10.043	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.909	-0.974	28.806	-9.175	-9.175	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.850	0.919	31.422	8.945	8.945	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.006	-0.001	29.287	0.082	0.082	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.923	0.953	24.988	10.726	10.726	0.000	0.000	0.000	0.000
62	A	62	PHE	0	-0.060	-0.026	19.854	-0.012	-0.012	0.000	0.000	0.000	0.000
63	A	63	GLN	0	-0.038	-0.016	22.723	0.062	0.062	0.000	0.000	0.000	0.000
64	A	64	TYR	0	-0.054	-0.028	22.253	-0.085	-0.085	0.000	0.000	0.000	0.000
65	A	65	SER	0	-0.040	-0.012	17.310	-0.523	-0.523	0.000	0.000	0.000	0.000
66	A	66	VAL	0	0.027	0.006	14.621	0.568	0.568	0.000	0.000	0.000	0.000
67	A	67	LEU	0	0.045	0.024	16.238	0.641	0.641	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.856	-0.910	19.118	-12.542	-12.542	0.000	0.000	0.000	0.000
69	A	69	ILE	0	-0.054	-0.014	20.334	0.517	0.517	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.860	0.926	21.157	11.457	11.457	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.018	0.003	19.693	0.327	0.327	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.855	-0.936	18.397	-12.600	-12.600	0.000	0.000	0.000	0.000
73	A	73	ILE	0	0.005	-0.003	11.813	-0.582	-0.582	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.004	0.024	14.071	0.322	0.322	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.015	0.009	8.003	-1.050	-1.050	0.000	0.000	0.000	0.000
76	A	76	VAL	0	0.029	-0.002	10.147	1.137	1.137	0.000	0.000	0.000	0.000
77	A	77	SER	0	-0.041	-0.013	8.290	-2.692	-2.692	0.000	0.000	0.000	0.000
78	A	78	GLN	0	0.062	0.020	7.817	2.255	2.255	0.000	0.000	0.000	0.000
79	A	79	PHE	0	0.026	0.000	7.780	-2.720	-2.720	0.000	0.000	0.000	0.000
80	A	80	THR	0	-0.046	-0.018	8.779	-1.701	-1.701	0.000	0.000	0.000	0.000
81	A	81	LEU	0	0.021	0.018	6.215	1.210	1.210	0.000	0.000	0.000	0.000
82	A	82	TYR	0	-0.115	-0.068	2.081	-16.910	-16.744	4.432	-1.551	-3.047	-0.034
83	A	83	ALA	0	0.005	-0.008	8.108	2.315	2.315	0.000	0.000	0.000	0.000
84	A	84	ASN	0	-0.017	0.002	11.881	1.129	1.129	0.000	0.000	0.000	0.000
85	A	85	VAL	0	0.053	0.002	13.801	1.114	1.114	0.000	0.000	0.000	0.000
86	A	86	LYS	1	0.934	0.970	14.702	20.770	20.770	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.927	0.968	16.897	18.536	18.536	0.000	0.000	0.000	0.000
88	A	88	GLY	0	-0.004	0.004	21.111	0.482	0.482	0.000	0.000	0.000	0.000
89	A	89	ARG	1	1.010	0.999	21.696	10.631	10.631	0.000	0.000	0.000	0.000
90	A	90	ARG	1	0.953	0.987	18.718	15.085	15.085	0.000	0.000	0.000	0.000
91	A	91	PRO	0	0.001	0.013	15.674	-0.013	-0.013	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.123	-0.090	15.106	0.103	0.103	0.000	0.000	0.000	0.000
93	A	93	PHE	0	0.079	0.027	11.324	-0.453	-0.453	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.821	-0.886	11.396	-22.573	-22.573	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.853	-0.923	6.873	-34.747	-34.747	0.000	0.000	0.000	0.000
96	A	96	ALA	0	-0.010	0.024	6.957	-5.457	-5.457	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.883	-0.947	6.384	-30.415	-30.415	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.887	-0.952	8.219	-19.996	-19.996	0.000	0.000	0.000	0.000
99	A	99	PRO	0	0.016	-0.020	9.362	-1.228	-1.228	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.940	0.971	10.027	15.770	15.770	0.000	0.000	0.000	0.000
101	A	101	ARG	1	0.999	1.024	6.952	30.304	30.304	0.000	0.000	0.000	0.000
102	A	102	ALA	0	-0.011	-0.015	5.663	-1.727	-1.727	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.897	0.952	5.917	17.257	17.257	0.000	0.000	0.000	0.000
104	A	104	GLU	-1	-0.849	-0.934	7.482	-24.293	-24.293	0.000	0.000	0.000	0.000
105	A	105	LEU	0	-0.013	-0.014	2.384	-0.894	-0.226	0.848	-0.292	-1.224	0.000
106	A	106	TYR	0	-0.031	-0.004	3.411	-2.114	-1.256	0.034	-0.427	-0.465	-0.003
107	A	107	GLU	-1	-0.905	-0.976	5.049	-17.719	-17.678	0.000	-0.001	-0.039	0.000
108	A	108	LYS	1	0.902	0.971	5.312	24.207	24.207	0.000	0.000	0.000	0.000
109	A	109	PHE	0	0.014	-0.005	3.097	-0.155	0.914	1.300	-0.516	-1.852	-0.003
110	A	110	VAL	0	-0.038	-0.033	5.109	1.450	1.483	0.000	-0.006	-0.027	0.000
111	A	111	ASP	-1	-0.898	-0.947	8.471	-16.927	-16.927	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.831	0.897	7.972	22.717	22.717	0.000	0.000	0.000	0.000
113	A	113	ILE	0	-0.004	-0.013	8.755	0.978	0.978	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.923	0.971	10.647	17.377	17.377	0.000	0.000	0.000	0.000
115	A	115	GLU	-1	-0.925	-0.954	12.715	-17.049	-17.049	0.000	0.000	0.000	0.000
116	A	116	SER	0	-0.084	-0.018	14.015	0.950	0.950	0.000	0.000	0.000	0.000
117	A	117	GLY	0	-0.013	-0.010	15.780	0.711	0.711	0.000	0.000	0.000	0.000
118	A	118	LEU	0	-0.078	-0.030	15.925	0.655	0.655	0.000	0.000	0.000	0.000
119	A	119	LYS	1	0.917	0.982	17.669	12.198	12.198	0.000	0.000	0.000	0.000
120	A	120	VAL	0	-0.007	-0.018	12.172	-0.383	-0.383	0.000	0.000	0.000	0.000
121	A	121	GLU	-1	-0.871	-0.926	15.563	-13.221	-13.221	0.000	0.000	0.000	0.000
122	A	122	THR	0	-0.019	-0.046	12.098	-0.951	-0.951	0.000	0.000	0.000	0.000
123	A	123	GLY	0	0.022	0.022	13.267	0.973	0.973	0.000	0.000	0.000	0.000
124	A	124	ILE	0	-0.048	-0.041	14.273	-0.059	-0.059	0.000	0.000	0.000	0.000
125	A	125	PHE	0	0.023	-0.008	7.866	-0.405	-0.405	0.000	0.000	0.000	0.000
126	A	126	GLY	0	-0.039	-0.023	12.834	0.888	0.888	0.000	0.000	0.000	0.000
127	A	127	ALA	0	-0.013	-0.001	14.514	0.643	0.643	0.000	0.000	0.000	0.000
128	A	128	MET	0	-0.024	-0.022	16.505	-0.772	-0.772	0.000	0.000	0.000	0.000
129	A	129	MET	0	-0.032	0.022	13.529	0.417	0.417	0.000	0.000	0.000	0.000
130	A	130	ASP	-1	-0.856	-0.904	19.009	-12.826	-12.826	0.000	0.000	0.000	0.000
131	A	131	VAL	0	-0.076	-0.055	15.432	0.072	0.072	0.000	0.000	0.000	0.000
132	A	132	PHE	0	0.012	0.017	18.644	0.086	0.086	0.000	0.000	0.000	0.000
133	A	133	ILE	0	-0.016	-0.020	15.847	-0.336	-0.336	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.917	-0.941	19.823	-10.776	-10.776	0.000	0.000	0.000	0.000
135	A	135	ASN	0	0.024	0.014	18.078	0.274	0.274	0.000	0.000	0.000	0.000
136	A	136	TRP	0	0.043	0.015	20.699	0.509	0.509	0.000	0.000	0.000	0.000
137	A	137	GLY	0	-0.003	0.018	21.999	-0.398	-0.398	0.000	0.000	0.000	0.000
138	A	138	PRO	0	-0.056	-0.026	20.494	0.476	0.476	0.000	0.000	0.000	0.000
139	A	139	VAL	0	0.014	-0.015	17.114	-0.056	-0.056	0.000	0.000	0.000	0.000
140	A	140	THR	0	-0.010	-0.014	14.012	-0.244	-0.244	0.000	0.000	0.000	0.000
141	A	141	ILE	0	-0.002	0.012	11.833	0.381	0.381	0.000	0.000	0.000	0.000
142	A	142	ILE	0	-0.008	-0.003	9.231	-1.079	-1.079	0.000	0.000	0.000	0.000
143	A	143	ILE	0	0.008	0.003	6.502	1.728	1.728	0.000	0.000	0.000	0.000
144	A	144	ASP	-1	-0.675	-0.835	3.481	-78.637	-77.858	0.011	-0.489	-0.301	-0.003
145	A	145	SER	0	0.004	-0.050	1.791	-13.963	-17.559	12.854	-4.666	-4.592	-0.049
146	A	146	ARG	1	0.788	0.876	2.883	72.221	73.264	0.122	-0.287	-0.878	-0.002
147	A	147	GLU	-1	-0.958	-0.977	4.952	-26.327	-26.221	0.000	-0.006	-0.100	0.000
148	A	148	ILE	-1	-0.959	-0.906	5.949	-28.491	-28.491	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:1:MET )