FMO DATABASE

FMODB ID: R9JR8

Calculation Name: 3U2R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3U2R

Chain ID: A

ChEMBL ID:

UniProt ID: D5SNV8

Base Structure: X-ray

Registration Date: 2023-09-20

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	OptAll
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	138
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1207729.043718
FMO2-HF: Nuclear repulsion	1151119.944962
FMO2-HF: Total energy	-56609.098757
FMO2-MP2: Total energy	-56774.885259

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:9:ARG)

Summations of interaction energy for fragment #1(A:9:ARG)

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.
-107.657	-105.138	10.059	-6.347	-6.231	-0.069

Interaction energy analysis for fragmet #1(A:9:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.933 / q_NPA : 0.958

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	11	ASP	-1	-0.821	-0.895	1.834	-95.426	-93.106	10.058	-6.311	-6.067	-0.069
4	A	12	SER	0	-0.050	-0.045	3.853	7.340	7.539	0.001	-0.036	-0.164	0.000
5	A	13	LEU	0	-0.039	-0.002	6.757	4.374	4.374	0.000	0.000	0.000	0.000
6	A	14	THR	0	-0.007	-0.020	9.433	-0.662	-0.662	0.000	0.000	0.000	0.000
7	A	15	GLN	0	0.013	0.001	12.009	-0.464	-0.464	0.000	0.000	0.000	0.000
8	A	16	GLU	-1	-0.805	-0.899	13.412	-19.204	-19.204	0.000	0.000	0.000	0.000
9	A	17	ALA	0	0.016	0.012	12.784	0.285	0.285	0.000	0.000	0.000	0.000
10	A	18	TYR	0	-0.014	-0.001	6.641	-1.300	-1.300	0.000	0.000	0.000	0.000
11	A	19	LEU	0	0.010	-0.004	11.219	-0.097	-0.097	0.000	0.000	0.000	0.000
12	A	20	GLN	0	0.028	0.014	14.129	0.732	0.732	0.000	0.000	0.000	0.000
13	A	21	LEU	0	0.005	0.009	7.832	0.347	0.347	0.000	0.000	0.000	0.000
14	A	22	TRP	0	-0.058	-0.026	8.154	0.591	0.591	0.000	0.000	0.000	0.000
15	A	23	ARG	1	0.913	0.958	12.599	15.656	15.656	0.000	0.000	0.000	0.000
16	A	24	THR	0	0.007	-0.002	13.527	0.643	0.643	0.000	0.000	0.000	0.000
17	A	25	TYR	0	-0.033	-0.018	10.868	0.801	0.801	0.000	0.000	0.000	0.000
18	A	26	ASP	-1	-0.866	-0.951	13.193	-17.490	-17.490	0.000	0.000	0.000	0.000
19	A	27	ARG	1	0.810	0.888	16.199	13.765	13.765	0.000	0.000	0.000	0.000
20	A	28	MET	0	-0.037	-0.020	12.879	0.853	0.853	0.000	0.000	0.000	0.000
21	A	29	LYS	1	0.796	0.882	14.992	15.952	15.952	0.000	0.000	0.000	0.000
22	A	30	ALA	0	0.035	0.012	16.920	0.605	0.605	0.000	0.000	0.000	0.000
23	A	31	ILE	0	-0.004	-0.005	20.491	0.595	0.595	0.000	0.000	0.000	0.000
24	A	32	GLU	-1	-0.837	-0.935	17.677	-14.133	-14.133	0.000	0.000	0.000	0.000
25	A	33	GLU	-1	-0.848	-0.898	19.800	-13.576	-13.576	0.000	0.000	0.000	0.000
26	A	34	GLU	-1	-0.835	-0.885	22.179	-9.967	-9.967	0.000	0.000	0.000	0.000
27	A	35	ILE	0	0.015	0.022	23.590	0.404	0.404	0.000	0.000	0.000	0.000
28	A	36	PHE	0	-0.026	-0.029	20.053	0.309	0.309	0.000	0.000	0.000	0.000
29	A	37	SER	0	0.006	-0.008	25.090	0.263	0.263	0.000	0.000	0.000	0.000
30	A	38	GLN	0	-0.095	-0.045	27.209	0.548	0.548	0.000	0.000	0.000	0.000
31	A	39	PHE	0	-0.001	0.003	28.216	0.319	0.319	0.000	0.000	0.000	0.000
32	A	40	GLU	-1	-0.911	-0.943	28.618	-8.936	-8.936	0.000	0.000	0.000	0.000
33	A	41	LEU	0	-0.069	-0.034	24.398	-0.101	-0.101	0.000	0.000	0.000	0.000
34	A	42	SER	0	0.037	-0.002	20.301	-0.300	-0.300	0.000	0.000	0.000	0.000
35	A	43	ALA	0	0.095	0.043	17.158	0.144	0.144	0.000	0.000	0.000	0.000
36	A	44	GLN	0	0.001	0.006	15.315	-0.616	-0.616	0.000	0.000	0.000	0.000
37	A	45	GLN	0	0.031	0.041	17.931	-0.056	-0.056	0.000	0.000	0.000	0.000
38	A	46	TYR	0	0.078	0.054	20.316	0.194	0.194	0.000	0.000	0.000	0.000
39	A	47	ASN	0	0.037	-0.001	15.504	0.686	0.686	0.000	0.000	0.000	0.000
40	A	48	THR	0	-0.011	-0.009	19.137	-0.047	-0.047	0.000	0.000	0.000	0.000
41	A	49	LEU	0	0.011	0.006	20.935	0.263	0.263	0.000	0.000	0.000	0.000
42	A	50	ARG	1	0.919	0.946	20.520	12.171	12.171	0.000	0.000	0.000	0.000
43	A	51	LEU	0	-0.025	0.002	17.938	0.156	0.156	0.000	0.000	0.000	0.000
44	A	52	LEU	0	0.016	0.021	20.877	0.210	0.210	0.000	0.000	0.000	0.000
45	A	53	ARG	1	0.833	0.890	24.464	10.148	10.148	0.000	0.000	0.000	0.000
46	A	54	SER	0	-0.129	-0.073	21.984	0.093	0.093	0.000	0.000	0.000	0.000
47	A	55	VAL	0	-0.006	-0.005	23.802	-0.035	-0.035	0.000	0.000	0.000	0.000
48	A	56	HIS	0	0.030	0.048	26.438	0.125	0.125	0.000	0.000	0.000	0.000
49	A	57	PRO	0	-0.046	-0.034	29.494	0.037	0.037	0.000	0.000	0.000	0.000
50	A	58	GLU	-1	-0.941	-0.964	29.194	-8.921	-8.921	0.000	0.000	0.000	0.000
51	A	59	GLY	0	0.012	-0.011	27.982	-0.104	-0.104	0.000	0.000	0.000	0.000
52	A	60	MET	0	-0.034	-0.008	21.216	-0.328	-0.328	0.000	0.000	0.000	0.000
53	A	61	ALA	0	0.018	0.007	23.910	0.097	0.097	0.000	0.000	0.000	0.000
54	A	62	THR	0	0.037	-0.014	22.239	-0.421	-0.421	0.000	0.000	0.000	0.000
55	A	63	LEU	0	-0.025	-0.025	19.906	-0.433	-0.433	0.000	0.000	0.000	0.000
56	A	64	GLN	0	0.023	0.015	18.479	-0.259	-0.259	0.000	0.000	0.000	0.000
57	A	65	ILE	0	0.015	0.003	18.468	-0.441	-0.441	0.000	0.000	0.000	0.000
58	A	66	ALA	0	-0.035	-0.024	16.510	-0.455	-0.455	0.000	0.000	0.000	0.000
59	A	67	ASP	-1	-0.941	-0.967	14.201	-16.842	-16.842	0.000	0.000	0.000	0.000
60	A	68	ARG	1	0.935	0.960	13.492	12.887	12.887	0.000	0.000	0.000	0.000
61	A	69	LEU	0	-0.068	-0.022	14.157	-0.126	-0.126	0.000	0.000	0.000	0.000
62	A	70	ILE	0	0.043	0.032	7.923	-1.334	-1.334	0.000	0.000	0.000	0.000
63	A	71	SER	0	-0.065	-0.039	8.416	-0.626	-0.626	0.000	0.000	0.000	0.000
64	A	72	ARG	1	0.873	0.950	10.211	18.380	18.380	0.000	0.000	0.000	0.000
65	A	73	ALA	0	0.054	0.015	14.060	0.181	0.181	0.000	0.000	0.000	0.000
66	A	74	PRO	0	-0.014	-0.003	17.163	0.675	0.675	0.000	0.000	0.000	0.000
67	A	75	ASP	-1	-0.802	-0.926	17.059	-14.836	-14.836	0.000	0.000	0.000	0.000
68	A	76	ILE	0	0.020	0.008	17.602	0.471	0.471	0.000	0.000	0.000	0.000
69	A	77	THR	0	-0.012	0.005	20.528	0.539	0.539	0.000	0.000	0.000	0.000
70	A	78	ARG	1	0.994	0.994	23.566	11.179	11.179	0.000	0.000	0.000	0.000
71	A	79	LEU	0	-0.092	-0.025	19.826	0.208	0.208	0.000	0.000	0.000	0.000
72	A	80	ILE	0	0.034	0.005	22.931	0.270	0.270	0.000	0.000	0.000	0.000
73	A	81	ASP	-1	-0.821	-0.894	25.884	-9.815	-9.815	0.000	0.000	0.000	0.000
74	A	82	ARG	1	0.934	0.960	23.083	11.355	11.355	0.000	0.000	0.000	0.000
75	A	83	LEU	0	-0.037	-0.013	24.547	0.109	0.109	0.000	0.000	0.000	0.000
76	A	84	ASP	-1	-0.796	-0.902	29.017	-8.924	-8.924	0.000	0.000	0.000	0.000
77	A	85	ASP	-1	-0.935	-0.959	31.904	-8.556	-8.556	0.000	0.000	0.000	0.000
78	A	86	ARG	1	0.768	0.880	29.734	9.399	9.399	0.000	0.000	0.000	0.000
79	A	87	GLY	0	0.030	0.026	33.476	0.111	0.111	0.000	0.000	0.000	0.000
80	A	88	LEU	0	-0.045	-0.008	29.111	0.051	0.051	0.000	0.000	0.000	0.000
81	A	89	VAL	0	-0.037	-0.034	27.222	-0.198	-0.198	0.000	0.000	0.000	0.000
82	A	90	LEU	0	0.023	0.022	30.700	0.240	0.240	0.000	0.000	0.000	0.000
83	A	91	ARG	1	0.776	0.868	26.867	9.683	9.683	0.000	0.000	0.000	0.000
84	A	92	THR	0	-0.002	0.000	31.226	0.388	0.388	0.000	0.000	0.000	0.000
85	A	93	ARG	1	0.866	0.932	30.856	8.689	8.689	0.000	0.000	0.000	0.000
86	A	94	LYS	1	0.840	0.903	29.704	9.416	9.416	0.000	0.000	0.000	0.000
87	A	95	PRO	0	-0.002	-0.007	33.611	-0.041	-0.041	0.000	0.000	0.000	0.000
88	A	96	GLU	-1	-0.872	-0.938	35.389	-7.534	-7.534	0.000	0.000	0.000	0.000
89	A	97	ASN	0	-0.034	-0.023	29.652	-0.089	-0.089	0.000	0.000	0.000	0.000
90	A	98	ARG	1	1.025	1.020	31.905	7.505	7.505	0.000	0.000	0.000	0.000
91	A	99	ARG	1	0.961	0.989	25.549	10.616	10.616	0.000	0.000	0.000	0.000
92	A	100	VAL	0	-0.023	-0.008	26.854	-0.318	-0.318	0.000	0.000	0.000	0.000
93	A	101	VAL	0	0.001	-0.001	27.391	0.367	0.367	0.000	0.000	0.000	0.000
94	A	102	GLU	-1	-0.812	-0.876	26.681	-9.910	-9.910	0.000	0.000	0.000	0.000
95	A	103	VAL	0	0.001	-0.006	26.156	0.241	0.241	0.000	0.000	0.000	0.000
96	A	104	ALA	0	0.085	0.057	27.488	-0.243	-0.243	0.000	0.000	0.000	0.000
97	A	105	LEU	0	-0.008	-0.008	26.722	-0.036	-0.036	0.000	0.000	0.000	0.000
98	A	106	THR	0	0.004	-0.009	30.126	0.188	0.188	0.000	0.000	0.000	0.000
99	A	107	ASP	-1	-0.864	-0.951	32.835	-7.904	-7.904	0.000	0.000	0.000	0.000
100	A	108	ALA	0	0.003	0.007	34.880	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	109	GLY	0	0.046	0.025	30.591	-0.132	-0.132	0.000	0.000	0.000	0.000
102	A	110	LEU	0	-0.069	-0.038	29.918	-0.253	-0.253	0.000	0.000	0.000	0.000
103	A	111	LYS	1	0.765	0.866	31.496	7.772	7.772	0.000	0.000	0.000	0.000
104	A	112	LEU	0	0.047	0.021	29.165	-0.050	-0.050	0.000	0.000	0.000	0.000
105	A	113	LEU	0	-0.028	-0.026	24.942	-0.218	-0.218	0.000	0.000	0.000	0.000
106	A	114	LYS	1	0.926	0.968	28.387	8.100	8.100	0.000	0.000	0.000	0.000
107	A	115	ASP	-1	-0.817	-0.882	31.005	-8.120	-8.120	0.000	0.000	0.000	0.000
108	A	116	LEU	0	-0.002	0.000	26.113	-0.088	-0.088	0.000	0.000	0.000	0.000
109	A	117	GLU	-1	-0.853	-0.904	26.918	-9.773	-9.773	0.000	0.000	0.000	0.000
110	A	118	GLU	-1	-0.786	-0.849	27.429	-9.090	-9.090	0.000	0.000	0.000	0.000
111	A	119	PRO	0	0.024	0.006	28.117	-0.202	-0.202	0.000	0.000	0.000	0.000
112	A	120	VAL	0	0.004	-0.002	22.326	-0.319	-0.319	0.000	0.000	0.000	0.000
113	A	121	ARG	1	0.735	0.834	23.828	9.017	9.017	0.000	0.000	0.000	0.000
114	A	122	GLN	0	0.024	-0.006	25.284	-0.295	-0.295	0.000	0.000	0.000	0.000
115	A	123	CYS	0	-0.085	-0.010	22.299	-0.212	-0.212	0.000	0.000	0.000	0.000
116	A	124	HIS	1	0.865	0.909	18.442	12.988	12.988	0.000	0.000	0.000	0.000
117	A	125	GLU	-1	-0.819	-0.894	22.247	-10.089	-10.089	0.000	0.000	0.000	0.000
118	A	126	ARG	1	0.830	0.897	25.118	10.318	10.318	0.000	0.000	0.000	0.000
119	A	127	GLN	0	-0.048	-0.019	18.257	-0.171	-0.171	0.000	0.000	0.000	0.000
120	A	128	LEU	0	0.021	0.011	19.605	-0.232	-0.232	0.000	0.000	0.000	0.000
121	A	129	GLY	0	0.017	0.015	22.174	-0.027	-0.027	0.000	0.000	0.000	0.000
122	A	130	HIS	0	-0.017	-0.024	22.992	-0.137	-0.137	0.000	0.000	0.000	0.000
123	A	131	LEU	0	-0.006	0.011	17.383	-0.073	-0.073	0.000	0.000	0.000	0.000
124	A	132	ALA	0	0.040	0.025	20.947	-0.139	-0.139	0.000	0.000	0.000	0.000
125	A	133	ALA	0	-0.004	-0.001	23.499	0.144	0.144	0.000	0.000	0.000	0.000
126	A	134	ASP	-1	-0.813	-0.882	21.013	-13.341	-13.341	0.000	0.000	0.000	0.000
127	A	135	GLU	-1	-0.925	-0.971	17.967	-15.829	-15.829	0.000	0.000	0.000	0.000
128	A	136	LEU	0	-0.014	-0.008	22.052	0.138	0.138	0.000	0.000	0.000	0.000
129	A	137	HIS	0	-0.008	-0.001	25.781	0.344	0.344	0.000	0.000	0.000	0.000
130	A	138	GLU	-1	-0.807	-0.862	21.134	-13.627	-13.627	0.000	0.000	0.000	0.000
131	A	139	LEU	0	-0.008	-0.005	24.475	0.118	0.118	0.000	0.000	0.000	0.000
132	A	140	ILE	0	0.008	-0.001	25.727	0.250	0.250	0.000	0.000	0.000	0.000
133	A	141	ARG	1	0.816	0.878	23.059	13.057	13.057	0.000	0.000	0.000	0.000
134	A	142	LEU	0	-0.043	-0.034	22.018	0.157	0.157	0.000	0.000	0.000	0.000
135	A	143	MET	0	-0.051	-0.016	26.697	0.189	0.189	0.000	0.000	0.000	0.000
136	A	144	GLU	-1	-0.916	-0.962	29.777	-9.117	-9.117	0.000	0.000	0.000	0.000
137	A	145	LEU	0	-0.104	-0.036	26.561	0.221	0.221	0.000	0.000	0.000	0.000
138	A	146	ALA	0	-0.090	-0.036	29.905	0.320	0.320	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:9:ARG)