FMO DATABASE

FMODB ID: K38J3

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:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
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
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1443723.338923
FMO2-HF: Nuclear repulsion	1384996.655003
FMO2-HF: Total energy	-58726.68392
FMO2-MP2: Total energy	-58900.644941

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.
-29.802	-26.399	52.964	-21.611	-34.757	-0.116

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 : -0.046

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	0.027	-0.001	3.606	-1.827	0.918	-0.024	-1.471	-1.249	0.002
4	A	4	VAL	0	-0.036	-0.007	5.688	0.064	0.064	0.000	0.000	0.000	0.000
5	A	5	ILE	0	0.011	-0.001	8.804	0.091	0.091	0.000	0.000	0.000	0.000
6	A	6	GLN	0	-0.003	0.004	11.230	-0.056	-0.056	0.000	0.000	0.000	0.000
7	A	7	ARG	1	0.816	0.885	14.901	-0.079	-0.079	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.044	-0.019	17.291	-0.019	-0.019	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.882	0.934	19.596	-0.089	-0.089	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.936	0.971	22.160	-0.114	-0.114	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.042	-0.039	17.913	0.007	0.007	0.000	0.000	0.000	0.000
12	A	12	TRP	0	0.008	-0.012	19.373	0.017	0.017	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.035	0.031	15.841	-0.008	-0.008	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.860	-0.921	19.222	0.086	0.086	0.000	0.000	0.000	0.000
15	A	15	VAL	0	-0.010	-0.009	20.229	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.860	-0.921	22.946	0.046	0.046	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.034	0.033	25.693	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.806	0.897	24.192	-0.062	-0.062	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.004	-0.017	22.580	0.006	0.006	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.061	-0.045	18.904	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.037	0.030	18.576	0.018	0.018	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.057	-0.053	19.646	-0.014	-0.014	0.000	0.000	0.000	0.000
23	A	23	ILE	0	-0.029	0.009	16.847	0.009	0.009	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.096	-0.060	20.744	-0.024	-0.024	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.903	-0.957	21.196	0.135	0.135	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.019	0.001	18.652	0.011	0.011	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.043	-0.019	12.949	-0.020	-0.020	0.000	0.000	0.000	0.000
28	A	28	ASN	0	-0.014	0.003	13.300	0.051	0.051	0.000	0.000	0.000	0.000
29	A	29	VAL	0	0.009	-0.018	7.332	-0.033	-0.033	0.000	0.000	0.000	0.000
30	A	30	PHE	0	0.017	0.011	8.676	0.076	0.076	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.021	0.006	2.742	-2.036	-1.265	1.590	-0.441	-1.920	0.002
32	A	32	GLY	0	0.030	0.017	3.908	-0.050	0.184	-0.001	-0.051	-0.182	0.000
33	A	33	VAL	0	-0.023	-0.003	2.292	-4.398	-1.780	3.478	-2.167	-3.929	-0.013
34	A	34	ARG	1	0.805	0.876	2.705	-1.608	-0.069	0.426	-0.415	-1.550	0.000
35	A	35	LYS	1	0.859	0.926	4.211	-0.893	-0.787	0.000	-0.009	-0.097	0.000
36	A	36	GLY	0	-0.066	-0.034	5.771	0.546	0.546	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.690	-0.819	1.684	-12.111	-24.267	29.998	-9.262	-8.580	-0.083
38	A	38	THR	0	-0.029	-0.025	4.066	0.833	1.348	0.001	-0.235	-0.281	-0.001
39	A	39	GLU	-1	-0.751	-0.877	3.725	-1.437	-1.124	0.007	-0.101	-0.218	-0.001
40	A	40	GLU	-1	-0.849	-0.922	6.104	-0.249	-0.249	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.806	-0.873	2.494	-4.768	-3.483	0.803	-0.620	-1.468	0.001
42	A	42	ILE	0	0.047	0.031	2.357	0.373	1.290	2.583	-0.758	-2.743	-0.001
43	A	43	GLU	-1	-0.853	-0.923	4.411	0.356	0.346	0.009	0.182	-0.181	0.000
44	A	44	LYS	1	0.757	0.872	5.684	1.360	1.360	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.017	-0.008	2.547	-1.572	-0.562	1.296	-0.427	-1.880	-0.002
46	A	46	VAL	0	0.012	-0.005	5.764	-0.381	-0.294	-0.001	-0.007	-0.078	0.000
47	A	47	ASN	0	0.029	0.023	7.866	-0.291	-0.291	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.949	0.967	9.152	-0.061	-0.061	0.000	0.000	0.000	0.000
49	A	49	ILE	0	-0.004	-0.004	7.454	-0.100	-0.100	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.032	0.015	10.965	-0.072	-0.072	0.000	0.000	0.000	0.000
51	A	51	ASN	0	-0.060	-0.033	13.772	-0.078	-0.078	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.014	-0.007	12.164	-0.049	-0.049	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.869	0.942	15.803	-0.094	-0.094	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.023	0.008	15.428	-0.017	-0.017	0.000	0.000	0.000	0.000
55	A	55	PHE	0	0.003	0.008	17.382	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.821	-0.865	21.800	0.070	0.070	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.739	-0.853	25.480	0.073	0.073	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.885	-0.946	28.980	0.057	0.057	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.822	0.903	31.510	-0.057	-0.057	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.009	0.006	29.482	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.855	0.895	25.142	-0.059	-0.059	0.000	0.000	0.000	0.000
62	A	62	PHE	0	-0.060	-0.030	19.713	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	63	GLN	0	-0.021	-0.004	22.925	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	64	TYR	0	-0.079	-0.049	22.445	0.003	0.003	0.000	0.000	0.000	0.000
65	A	65	SER	0	-0.020	-0.034	17.392	0.009	0.009	0.000	0.000	0.000	0.000
66	A	66	VAL	0	0.031	0.008	14.694	-0.011	-0.011	0.000	0.000	0.000	0.000
67	A	67	LEU	0	0.070	0.040	16.455	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.811	-0.848	19.236	0.117	0.117	0.000	0.000	0.000	0.000
69	A	69	ILE	0	-0.022	-0.014	20.744	-0.013	-0.013	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.789	0.893	21.229	-0.144	-0.144	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.018	0.017	19.849	-0.009	-0.009	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.792	-0.885	18.525	0.205	0.205	0.000	0.000	0.000	0.000
73	A	73	ILE	0	0.012	0.001	11.914	0.009	0.009	0.000	0.000	0.000	0.000
74	A	74	LEU	0	0.005	0.024	14.109	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.007	0.011	8.003	0.014	0.014	0.000	0.000	0.000	0.000
76	A	76	VAL	0	0.029	0.001	10.106	-0.092	-0.092	0.000	0.000	0.000	0.000
77	A	77	SER	0	-0.028	-0.007	8.410	0.020	0.020	0.000	0.000	0.000	0.000
78	A	78	GLN	0	0.029	0.022	7.932	-0.080	-0.080	0.000	0.000	0.000	0.000
79	A	79	PHE	0	0.051	0.013	7.805	-0.095	-0.095	0.000	0.000	0.000	0.000
80	A	80	THR	0	-0.068	-0.051	8.775	0.019	0.019	0.000	0.000	0.000	0.000
81	A	81	LEU	0	0.026	0.027	6.119	0.054	0.054	0.000	0.000	0.000	0.000
82	A	82	TYR	0	-0.084	-0.049	2.543	2.271	3.146	1.274	-0.608	-1.541	0.000
83	A	83	ALA	0	-0.009	0.004	8.101	-0.023	-0.023	0.000	0.000	0.000	0.000
84	A	84	ASN	0	-0.069	-0.050	11.874	0.018	0.018	0.000	0.000	0.000	0.000
85	A	85	VAL	0	0.055	0.004	14.231	-0.028	-0.028	0.000	0.000	0.000	0.000
86	A	86	LYS	1	0.943	0.977	15.365	-0.160	-0.160	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.878	0.931	17.263	-0.072	-0.072	0.000	0.000	0.000	0.000
88	A	88	GLY	0	0.000	0.013	21.777	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	89	ARG	1	1.006	0.996	21.930	-0.016	-0.016	0.000	0.000	0.000	0.000
90	A	90	ARG	1	0.943	0.982	18.434	0.008	0.008	0.000	0.000	0.000	0.000
91	A	91	PRO	0	0.019	0.022	15.611	0.002	0.002	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.107	-0.090	15.673	-0.022	-0.022	0.000	0.000	0.000	0.000
93	A	93	PHE	0	0.088	0.031	11.286	0.021	0.021	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.757	-0.828	11.392	0.059	0.059	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.804	-0.888	7.622	0.773	0.773	0.000	0.000	0.000	0.000
96	A	96	ALA	0	0.022	0.038	6.950	0.009	0.009	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.867	-0.934	6.125	-1.004	-1.004	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.860	-0.930	8.219	-0.251	-0.251	0.000	0.000	0.000	0.000
99	A	99	PRO	0	0.033	-0.008	9.416	-0.106	-0.106	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.926	0.967	10.171	0.194	0.194	0.000	0.000	0.000	0.000
101	A	101	ARG	1	0.866	0.923	6.738	1.493	1.493	0.000	0.000	0.000	0.000
102	A	102	ALA	0	-0.001	0.000	5.738	-0.184	-0.184	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.807	0.888	6.124	0.118	0.118	0.000	0.000	0.000	0.000
104	A	104	GLU	-1	-0.798	-0.894	7.531	-0.808	-0.808	0.000	0.000	0.000	0.000
105	A	105	LEU	0	0.003	-0.011	2.475	-0.782	0.008	0.761	-0.265	-1.287	0.001
106	A	106	TYR	0	-0.003	-0.003	3.804	0.241	0.677	0.005	-0.136	-0.305	-0.001
107	A	107	GLU	-1	-0.822	-0.908	5.696	0.487	0.487	0.000	0.000	0.000	0.000
108	A	108	LYS	1	0.844	0.918	5.428	0.510	0.510	0.000	0.000	0.000	0.000
109	A	109	PHE	0	0.010	-0.002	3.134	-0.881	0.170	1.143	-0.512	-1.683	-0.002
110	A	110	VAL	0	-0.017	-0.025	5.432	-0.095	-0.095	0.000	0.000	0.000	0.000
111	A	111	ASP	-1	-0.903	-0.950	8.910	0.177	0.177	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.777	0.881	7.970	-0.430	-0.430	0.000	0.000	0.000	0.000
113	A	113	ILE	0	0.019	0.004	8.889	-0.124	-0.124	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.886	0.965	10.717	-0.519	-0.519	0.000	0.000	0.000	0.000
115	A	115	GLU	-1	-0.877	-0.919	12.963	0.244	0.244	0.000	0.000	0.000	0.000
116	A	116	SER	0	-0.093	-0.051	14.193	-0.073	-0.073	0.000	0.000	0.000	0.000
117	A	117	GLY	0	-0.025	-0.014	15.861	-0.046	-0.046	0.000	0.000	0.000	0.000
118	A	118	LEU	0	-0.066	-0.020	15.900	-0.034	-0.034	0.000	0.000	0.000	0.000
119	A	119	LYS	1	0.814	0.909	17.747	-0.187	-0.187	0.000	0.000	0.000	0.000
120	A	120	VAL	0	0.000	-0.011	12.194	0.017	0.017	0.000	0.000	0.000	0.000
121	A	121	GLU	-1	-0.808	-0.888	15.640	0.205	0.205	0.000	0.000	0.000	0.000
122	A	122	THR	0	-0.034	-0.044	12.126	0.083	0.083	0.000	0.000	0.000	0.000
123	A	123	GLY	0	0.035	0.024	13.516	-0.062	-0.062	0.000	0.000	0.000	0.000
124	A	124	ILE	0	-0.036	-0.029	14.908	0.012	0.012	0.000	0.000	0.000	0.000
125	A	125	PHE	0	0.026	-0.003	8.045	-0.005	-0.005	0.000	0.000	0.000	0.000
126	A	126	GLY	0	-0.035	-0.020	13.271	-0.026	-0.026	0.000	0.000	0.000	0.000
127	A	127	ALA	0	-0.019	-0.003	14.910	-0.016	-0.016	0.000	0.000	0.000	0.000
128	A	128	MET	0	-0.028	-0.023	16.648	0.012	0.012	0.000	0.000	0.000	0.000
129	A	129	MET	0	-0.021	0.017	13.612	0.020	0.020	0.000	0.000	0.000	0.000
130	A	130	ASP	-1	-0.880	-0.914	19.129	0.062	0.062	0.000	0.000	0.000	0.000
131	A	131	VAL	0	-0.062	-0.053	15.350	0.011	0.011	0.000	0.000	0.000	0.000
132	A	132	PHE	0	0.027	0.023	18.589	-0.012	-0.012	0.000	0.000	0.000	0.000
133	A	133	ILE	0	-0.031	-0.009	15.702	0.018	0.018	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.843	-0.896	19.844	0.082	0.082	0.000	0.000	0.000	0.000
135	A	135	ASN	0	0.013	-0.011	17.914	0.009	0.009	0.000	0.000	0.000	0.000
136	A	136	TRP	0	0.016	0.014	20.783	-0.012	-0.012	0.000	0.000	0.000	0.000
137	A	137	GLY	0	-0.001	0.014	22.127	0.005	0.005	0.000	0.000	0.000	0.000
138	A	138	PRO	0	-0.044	-0.016	20.543	-0.007	-0.007	0.000	0.000	0.000	0.000
139	A	139	VAL	0	0.009	-0.022	17.496	-0.007	-0.007	0.000	0.000	0.000	0.000
140	A	140	THR	0	-0.002	-0.005	14.104	0.021	0.021	0.000	0.000	0.000	0.000
141	A	141	ILE	0	-0.009	0.006	12.157	-0.012	-0.012	0.000	0.000	0.000	0.000
142	A	142	ILE	0	-0.005	-0.002	9.396	0.008	0.008	0.000	0.000	0.000	0.000
143	A	143	ILE	0	0.000	-0.001	6.466	0.098	0.098	0.000	0.000	0.000	0.000
144	A	144	ASP	-1	-0.703	-0.815	4.486	0.919	1.185	0.000	-0.093	-0.173	0.000
145	A	145	SER	0	-0.028	-0.058	1.939	-3.814	-6.328	8.904	-2.870	-3.519	-0.022
146	A	146	ARG	1	0.770	0.858	2.344	-0.003	2.419	0.713	-1.341	-1.794	0.004
147	A	147	GLU	-1	-0.937	-0.960	5.037	0.205	0.308	-0.001	-0.004	-0.099	0.000
148	A	148	ILE	0	-0.096	-0.010	6.078	0.096	0.096	0.000	0.000	0.000	0.000

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