FMO DATABASE

FMODB ID: Q1MZY

Calculation Name: 2DBO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DBO

Chain ID: A

ChEMBL ID:

UniProt ID: O66742

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

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. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1441262.553281
FMO2-HF: Nuclear repulsion	1382537.425912
FMO2-HF: Total energy	-58725.127368
FMO2-MP2: Total energy	-58899.171167

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.
-24.174	-38.08	75.493	-25.167	-36.412	-0.128

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 : -0.092 / q_NPA : -0.057

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	0.017	-0.006	3.577	-1.321	1.321	-0.021	-1.379	-1.242	0.002
4	A	4	VAL	0	-0.037	-0.007	5.581	-0.017	-0.017	0.000	0.000	0.000	0.000
5	A	5	ILE	0	0.022	0.007	8.803	0.104	0.104	0.000	0.000	0.000	0.000
6	A	6	GLN	0	-0.022	-0.021	11.111	-0.081	-0.081	0.000	0.000	0.000	0.000
7	A	7	ARG	1	0.830	0.906	14.796	-0.099	-0.099	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.032	-0.013	16.862	-0.024	-0.024	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.906	0.967	19.506	-0.105	-0.105	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.965	0.979	22.092	-0.131	-0.131	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.041	-0.029	17.775	0.011	0.011	0.000	0.000	0.000	0.000
12	A	12	TRP	0	-0.002	-0.007	19.338	0.019	0.019	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.048	0.037	15.940	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.874	-0.932	19.284	0.096	0.096	0.000	0.000	0.000	0.000
15	A	15	VAL	0	-0.048	-0.026	20.135	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.893	-0.955	22.799	0.048	0.048	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.025	0.024	25.594	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.879	0.957	22.471	-0.080	-0.080	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.011	-0.010	22.599	0.007	0.007	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.093	-0.064	18.491	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.053	0.035	18.467	0.016	0.016	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.084	-0.055	19.540	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	23	ILE	0	-0.016	0.008	16.771	0.011	0.011	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.073	-0.045	20.717	-0.027	-0.027	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.901	-0.962	21.128	0.162	0.162	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.024	0.007	18.561	0.011	0.011	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.036	-0.022	12.834	-0.022	-0.022	0.000	0.000	0.000	0.000
28	A	28	ASN	0	-0.008	0.017	13.259	0.055	0.055	0.000	0.000	0.000	0.000
29	A	29	VAL	0	0.005	-0.021	7.305	-0.029	-0.029	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.001	0.006	8.680	0.073	0.073	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.022	0.003	2.986	-2.049	-1.439	1.704	-0.463	-1.851	0.004
32	A	32	GLY	0	0.027	0.016	3.995	-0.259	-0.005	-0.001	-0.057	-0.196	0.000
33	A	33	VAL	0	-0.013	0.004	2.100	-3.520	-1.766	4.498	-2.139	-4.113	-0.014
34	A	34	ARG	1	0.863	0.911	2.696	-2.336	-0.538	0.439	-0.602	-1.635	0.000
35	A	35	LYS	1	0.924	0.985	4.222	-1.069	-0.971	0.000	-0.009	-0.088	0.000
36	A	36	GLY	0	-0.061	-0.046	5.830	0.543	0.543	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.778	-0.900	1.651	-9.723	-29.554	40.183	-10.649	-9.703	-0.096
38	A	38	THR	0	-0.039	-0.038	4.109	1.066	1.412	0.000	-0.133	-0.212	0.000
39	A	39	GLU	-1	-0.793	-0.933	4.031	-1.156	-0.954	0.000	-0.042	-0.160	0.000
40	A	40	GLU	-1	-0.898	-0.949	6.357	-0.031	-0.031	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.838	-0.894	2.371	-6.272	-4.424	0.976	-1.101	-1.723	0.001
42	A	42	ILE	0	0.053	0.030	2.554	0.316	1.901	1.136	-0.584	-2.137	0.000
43	A	43	GLU	-1	-0.860	-0.904	4.403	0.279	0.213	0.008	0.213	-0.155	0.000
44	A	44	LYS	1	0.846	0.933	6.269	0.932	0.932	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.023	-0.005	2.499	-1.579	-0.749	1.782	-0.483	-2.128	0.000
46	A	46	VAL	0	0.007	-0.011	5.705	-0.417	-0.330	-0.001	-0.008	-0.078	0.000
47	A	47	ASN	0	0.022	0.021	7.762	-0.321	-0.321	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.942	0.951	9.175	-0.132	-0.132	0.000	0.000	0.000	0.000
49	A	49	ILE	0	-0.020	-0.002	7.067	-0.117	-0.117	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.035	0.013	10.775	-0.085	-0.085	0.000	0.000	0.000	0.000
51	A	51	ASN	0	-0.012	-0.007	13.649	-0.067	-0.067	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.019	-0.015	12.334	-0.059	-0.059	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.930	0.983	15.639	-0.102	-0.102	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.016	0.007	15.321	-0.021	-0.021	0.000	0.000	0.000	0.000
55	A	55	PHE	0	-0.009	-0.003	17.288	-0.010	-0.010	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.868	-0.923	21.628	0.085	0.085	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.759	-0.846	25.303	0.087	0.087	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.908	-0.975	28.808	0.069	0.069	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.850	0.918	31.424	-0.066	-0.066	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.005	-0.001	29.290	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.925	0.954	24.990	-0.064	-0.064	0.000	0.000	0.000	0.000
62	A	62	PHE	0	-0.061	-0.027	19.856	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	63	GLN	0	-0.039	-0.017	22.725	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	64	TYR	0	-0.054	-0.027	22.257	0.003	0.003	0.000	0.000	0.000	0.000
65	A	65	SER	0	-0.041	-0.012	17.313	0.011	0.011	0.000	0.000	0.000	0.000
66	A	66	VAL	0	0.029	0.008	14.624	-0.013	-0.013	0.000	0.000	0.000	0.000
67	A	67	LEU	0	0.042	0.022	16.238	-0.013	-0.013	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.856	-0.911	19.118	0.137	0.137	0.000	0.000	0.000	0.000
69	A	69	ILE	0	-0.053	-0.014	20.336	-0.013	-0.013	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.860	0.925	21.157	-0.160	-0.160	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.017	0.004	19.696	-0.011	-0.011	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.856	-0.937	18.397	0.233	0.233	0.000	0.000	0.000	0.000
73	A	73	ILE	0	0.004	-0.003	11.813	0.016	0.016	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.001	0.025	14.072	-0.008	-0.008	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.013	0.009	8.003	0.033	0.033	0.000	0.000	0.000	0.000
76	A	76	VAL	0	0.029	-0.002	10.145	-0.122	-0.122	0.000	0.000	0.000	0.000
77	A	77	SER	0	-0.043	-0.013	8.295	0.046	0.046	0.000	0.000	0.000	0.000
78	A	78	GLN	0	0.056	0.017	7.822	-0.078	-0.078	0.000	0.000	0.000	0.000
79	A	79	PHE	0	0.030	0.002	7.782	-0.075	-0.075	0.000	0.000	0.000	0.000
80	A	80	THR	0	-0.051	-0.021	8.772	0.025	0.025	0.000	0.000	0.000	0.000
81	A	81	LEU	0	0.021	0.017	6.210	0.037	0.037	0.000	0.000	0.000	0.000
82	A	82	TYR	0	-0.113	-0.061	2.552	2.648	2.427	2.557	-0.210	-2.125	-0.002
83	A	83	ALA	0	-0.001	-0.011	8.102	-0.030	-0.030	0.000	0.000	0.000	0.000
84	A	84	ASN	0	-0.020	0.001	11.875	0.008	0.008	0.000	0.000	0.000	0.000
85	A	85	VAL	0	0.052	0.001	14.235	-0.026	-0.026	0.000	0.000	0.000	0.000
86	A	86	LYS	1	0.933	0.969	15.683	-0.127	-0.127	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.924	0.967	17.627	-0.062	-0.062	0.000	0.000	0.000	0.000
88	A	88	GLY	0	-0.003	0.006	21.782	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	89	ARG	1	1.008	0.998	21.932	-0.015	-0.015	0.000	0.000	0.000	0.000
90	A	90	ARG	1	0.952	0.986	18.714	0.005	0.005	0.000	0.000	0.000	0.000
91	A	91	PRO	0	0.003	0.014	15.668	0.000	0.000	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.126	-0.091	15.391	-0.016	-0.016	0.000	0.000	0.000	0.000
93	A	93	PHE	0	0.081	0.028	11.322	0.017	0.017	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.825	-0.888	11.398	0.057	0.057	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.857	-0.926	7.713	0.556	0.556	0.000	0.000	0.000	0.000
96	A	96	ALA	0	-0.004	0.028	6.958	0.049	0.049	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.884	-0.946	6.384	-1.034	-1.034	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.891	-0.954	8.226	-0.335	-0.335	0.000	0.000	0.000	0.000
99	A	99	PRO	0	0.016	-0.020	9.364	-0.112	-0.112	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.935	0.968	10.030	0.190	0.190	0.000	0.000	0.000	0.000
101	A	101	ARG	1	0.997	1.023	6.952	1.261	1.261	0.000	0.000	0.000	0.000
102	A	102	ALA	0	-0.006	-0.011	5.666	-0.198	-0.198	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.894	0.951	5.922	0.070	0.070	0.000	0.000	0.000	0.000
104	A	104	GLU	-1	-0.850	-0.935	7.483	-0.622	-0.622	0.000	0.000	0.000	0.000
105	A	105	LEU	0	-0.008	-0.011	2.381	-0.622	0.056	0.857	-0.293	-1.241	0.001
106	A	106	TYR	0	-0.032	-0.003	3.412	-0.553	0.263	0.036	-0.405	-0.447	-0.003
107	A	107	GLU	-1	-0.908	-0.977	5.052	0.492	0.540	-0.001	0.000	-0.045	0.000
108	A	108	LYS	1	0.901	0.970	5.311	0.485	0.485	0.000	0.000	0.000	0.000
109	A	109	PHE	0	0.014	-0.004	3.088	-0.466	0.502	1.420	-0.520	-1.868	-0.001
110	A	110	VAL	0	-0.039	-0.033	5.113	-0.005	0.029	-0.001	-0.005	-0.029	0.000
111	A	111	ASP	-1	-0.900	-0.948	8.476	0.179	0.179	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.833	0.898	7.975	-0.466	-0.466	0.000	0.000	0.000	0.000
113	A	113	ILE	0	0.000	-0.012	8.755	-0.119	-0.119	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.918	0.970	10.647	-0.531	-0.531	0.000	0.000	0.000	0.000
115	A	115	GLU	-1	-0.925	-0.955	12.717	0.256	0.256	0.000	0.000	0.000	0.000
116	A	116	SER	0	-0.082	-0.018	14.015	-0.082	-0.082	0.000	0.000	0.000	0.000
117	A	117	GLY	0	-0.018	-0.012	15.780	-0.050	-0.050	0.000	0.000	0.000	0.000
118	A	118	LEU	0	-0.076	-0.030	15.925	-0.035	-0.035	0.000	0.000	0.000	0.000
119	A	119	LYS	1	0.915	0.981	17.669	-0.202	-0.202	0.000	0.000	0.000	0.000
120	A	120	VAL	0	-0.006	-0.019	12.172	0.022	0.022	0.000	0.000	0.000	0.000
121	A	121	GLU	-1	-0.870	-0.925	15.563	0.223	0.223	0.000	0.000	0.000	0.000
122	A	122	THR	0	-0.019	-0.046	12.104	0.088	0.088	0.000	0.000	0.000	0.000
123	A	123	GLY	0	0.022	0.021	13.273	-0.065	-0.065	0.000	0.000	0.000	0.000
124	A	124	ILE	0	-0.050	-0.042	14.278	0.005	0.005	0.000	0.000	0.000	0.000
125	A	125	PHE	0	0.026	-0.007	7.872	0.004	0.004	0.000	0.000	0.000	0.000
126	A	126	GLY	0	-0.040	-0.023	12.840	-0.026	-0.026	0.000	0.000	0.000	0.000
127	A	127	ALA	0	-0.015	-0.002	14.519	-0.015	-0.015	0.000	0.000	0.000	0.000
128	A	128	MET	0	-0.022	-0.022	16.511	0.016	0.016	0.000	0.000	0.000	0.000
129	A	129	MET	0	-0.032	0.022	13.535	0.020	0.020	0.000	0.000	0.000	0.000
130	A	130	ASP	-1	-0.859	-0.904	19.015	0.079	0.079	0.000	0.000	0.000	0.000
131	A	131	VAL	0	-0.072	-0.055	15.428	0.012	0.012	0.000	0.000	0.000	0.000
132	A	132	PHE	0	0.012	0.016	18.641	-0.011	-0.011	0.000	0.000	0.000	0.000
133	A	133	ILE	0	-0.018	-0.021	15.845	0.021	0.021	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.916	-0.940	19.821	0.096	0.096	0.000	0.000	0.000	0.000
135	A	135	ASN	0	0.029	0.015	18.078	0.010	0.010	0.000	0.000	0.000	0.000
136	A	136	TRP	0	0.038	0.014	20.698	-0.016	-0.016	0.000	0.000	0.000	0.000
137	A	137	GLY	0	-0.004	0.017	21.999	0.006	0.006	0.000	0.000	0.000	0.000
138	A	138	PRO	0	-0.056	-0.026	20.493	-0.009	-0.009	0.000	0.000	0.000	0.000
139	A	139	VAL	0	0.016	-0.014	17.114	-0.009	-0.009	0.000	0.000	0.000	0.000
140	A	140	THR	0	-0.014	-0.014	14.011	0.027	0.027	0.000	0.000	0.000	0.000
141	A	141	ILE	0	-0.004	0.010	11.834	-0.022	-0.022	0.000	0.000	0.000	0.000
142	A	142	ILE	0	-0.002	0.001	9.228	0.024	0.024	0.000	0.000	0.000	0.000
143	A	143	ILE	0	-0.011	-0.007	6.508	0.095	0.095	0.000	0.000	0.000	0.000
144	A	144	ASP	-1	-0.677	-0.831	3.868	0.454	0.902	0.010	-0.209	-0.249	0.000
145	A	145	SER	0	-0.001	-0.050	1.743	0.226	-10.070	19.796	-5.644	-3.855	-0.022
146	A	146	ARG	1	0.822	0.888	2.955	1.176	2.528	0.117	-0.441	-1.028	0.002
147	A	147	GLU	-1	-0.935	-0.960	5.004	0.132	0.242	-0.001	-0.004	-0.104	0.000
148	A	148	ILE	0	-0.105	0.027	5.938	0.102	0.102	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)