FMO DATABASE

FMODB ID: 6NQ9Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1204190.462616
FMO2-HF: Nuclear repulsion	1147582.677182
FMO2-HF: Total energy	-56607.785434
FMO2-MP2: Total energy	-56773.537456

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.
-59.844	-57.516	-0.005	-0.991	-1.331	-0.003

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 : 0.970 / q_NPA : 0.953

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	-0.880	-0.927	3.642	-52.159	-49.909	-0.004	-0.989	-1.257	-0.003
4	A	12	SER	0	-0.055	-0.033	5.245	4.025	4.103	-0.001	-0.002	-0.074	0.000
5	A	13	LEU	0	-0.007	0.017	7.449	2.695	2.695	0.000	0.000	0.000	0.000
6	A	14	THR	0	0.041	0.015	10.390	-0.536	-0.536	0.000	0.000	0.000	0.000
7	A	15	GLN	0	0.046	0.010	12.757	0.047	0.047	0.000	0.000	0.000	0.000
8	A	16	GLU	-1	-0.879	-0.946	13.766	-17.415	-17.415	0.000	0.000	0.000	0.000
9	A	17	ALA	0	0.015	0.012	13.387	0.250	0.250	0.000	0.000	0.000	0.000
10	A	18	TYR	0	-0.016	-0.008	6.963	-1.378	-1.378	0.000	0.000	0.000	0.000
11	A	19	LEU	0	0.013	-0.006	11.552	-0.184	-0.184	0.000	0.000	0.000	0.000
12	A	20	GLN	0	0.020	0.015	14.437	0.847	0.847	0.000	0.000	0.000	0.000
13	A	21	LEU	0	0.013	0.009	7.507	0.476	0.476	0.000	0.000	0.000	0.000
14	A	22	TRP	0	-0.030	-0.016	7.901	0.749	0.749	0.000	0.000	0.000	0.000
15	A	23	ARG	1	0.957	0.980	12.685	15.490	15.490	0.000	0.000	0.000	0.000
16	A	24	THR	0	0.037	0.022	13.507	0.884	0.884	0.000	0.000	0.000	0.000
17	A	25	TYR	0	-0.038	-0.026	11.220	0.757	0.757	0.000	0.000	0.000	0.000
18	A	26	ASP	-1	-0.871	-0.955	13.468	-17.202	-17.202	0.000	0.000	0.000	0.000
19	A	27	ARG	1	0.779	0.882	16.396	13.413	13.413	0.000	0.000	0.000	0.000
20	A	28	MET	0	-0.025	-0.017	13.072	0.764	0.764	0.000	0.000	0.000	0.000
21	A	29	LYS	1	0.958	0.983	14.767	16.871	16.871	0.000	0.000	0.000	0.000
22	A	30	ALA	0	0.041	0.013	17.406	0.542	0.542	0.000	0.000	0.000	0.000
23	A	31	ILE	0	-0.047	-0.009	20.836	0.622	0.622	0.000	0.000	0.000	0.000
24	A	32	GLU	-1	-0.893	-0.966	17.650	-14.080	-14.080	0.000	0.000	0.000	0.000
25	A	33	GLU	-1	-0.993	-0.981	20.353	-13.173	-13.173	0.000	0.000	0.000	0.000
26	A	34	GLU	-1	-0.951	-0.963	22.418	-9.604	-9.604	0.000	0.000	0.000	0.000
27	A	35	ILE	0	0.015	0.005	24.145	0.408	0.408	0.000	0.000	0.000	0.000
28	A	36	PHE	0	-0.025	-0.036	20.517	0.245	0.245	0.000	0.000	0.000	0.000
29	A	37	SER	0	0.006	-0.012	25.396	0.248	0.248	0.000	0.000	0.000	0.000
30	A	38	GLN	0	-0.050	-0.010	27.288	0.547	0.547	0.000	0.000	0.000	0.000
31	A	39	PHE	0	-0.002	0.000	28.477	0.305	0.305	0.000	0.000	0.000	0.000
32	A	40	GLU	-1	-0.951	-0.967	28.851	-9.151	-9.151	0.000	0.000	0.000	0.000
33	A	41	LEU	0	-0.094	-0.035	24.718	-0.147	-0.147	0.000	0.000	0.000	0.000
34	A	42	SER	0	0.021	0.007	20.295	-0.341	-0.341	0.000	0.000	0.000	0.000
35	A	43	ALA	0	0.117	0.043	17.771	0.195	0.195	0.000	0.000	0.000	0.000
36	A	44	GLN	0	-0.007	-0.004	15.433	-0.798	-0.798	0.000	0.000	0.000	0.000
37	A	45	GLN	0	0.004	0.010	18.458	0.049	0.049	0.000	0.000	0.000	0.000
38	A	46	TYR	0	0.081	0.049	20.384	0.170	0.170	0.000	0.000	0.000	0.000
39	A	47	ASN	0	-0.001	-0.013	15.697	0.669	0.669	0.000	0.000	0.000	0.000
40	A	48	THR	0	-0.004	-0.010	19.397	-0.031	-0.031	0.000	0.000	0.000	0.000
41	A	49	LEU	0	0.022	0.015	21.393	0.266	0.266	0.000	0.000	0.000	0.000
42	A	50	ARG	1	0.922	0.957	20.326	12.508	12.508	0.000	0.000	0.000	0.000
43	A	51	LEU	0	-0.023	-0.001	18.411	0.151	0.151	0.000	0.000	0.000	0.000
44	A	52	LEU	0	0.010	0.008	21.740	0.219	0.219	0.000	0.000	0.000	0.000
45	A	53	ARG	1	0.926	0.964	25.149	10.316	10.316	0.000	0.000	0.000	0.000
46	A	54	SER	0	-0.137	-0.077	23.025	0.132	0.132	0.000	0.000	0.000	0.000
47	A	55	VAL	0	0.035	0.016	24.145	-0.026	-0.026	0.000	0.000	0.000	0.000
48	A	56	HIS	0	0.027	0.061	26.925	0.122	0.122	0.000	0.000	0.000	0.000
49	A	57	PRO	0	-0.059	-0.046	30.082	0.062	0.062	0.000	0.000	0.000	0.000
50	A	58	GLU	-1	-0.954	-0.973	29.324	-9.248	-9.248	0.000	0.000	0.000	0.000
51	A	59	GLY	0	-0.001	-0.013	28.524	-0.152	-0.152	0.000	0.000	0.000	0.000
52	A	60	MET	0	-0.003	0.004	21.524	-0.390	-0.390	0.000	0.000	0.000	0.000
53	A	61	ALA	0	0.000	0.004	23.713	0.081	0.081	0.000	0.000	0.000	0.000
54	A	62	THR	0	0.044	-0.007	22.182	-0.402	-0.402	0.000	0.000	0.000	0.000
55	A	63	LEU	0	-0.017	-0.018	19.632	-0.438	-0.438	0.000	0.000	0.000	0.000
56	A	64	GLN	0	0.025	0.021	18.592	-0.326	-0.326	0.000	0.000	0.000	0.000
57	A	65	ILE	0	0.015	0.009	18.279	-0.504	-0.504	0.000	0.000	0.000	0.000
58	A	66	ALA	0	-0.034	-0.018	16.274	-0.482	-0.482	0.000	0.000	0.000	0.000
59	A	67	ASP	-1	-0.959	-0.973	14.332	-18.283	-18.283	0.000	0.000	0.000	0.000
60	A	68	ARG	1	0.953	0.966	13.366	13.142	13.142	0.000	0.000	0.000	0.000
61	A	69	LEU	0	-0.085	-0.028	14.000	-0.243	-0.243	0.000	0.000	0.000	0.000
62	A	70	ILE	0	0.087	0.052	7.884	-1.394	-1.394	0.000	0.000	0.000	0.000
63	A	71	SER	0	-0.072	-0.033	8.474	0.385	0.385	0.000	0.000	0.000	0.000
64	A	72	ARG	1	0.874	0.943	9.919	20.351	20.351	0.000	0.000	0.000	0.000
65	A	73	ALA	0	0.072	0.014	13.653	0.257	0.257	0.000	0.000	0.000	0.000
66	A	74	PRO	0	-0.013	-0.007	16.877	0.810	0.810	0.000	0.000	0.000	0.000
67	A	75	ASP	-1	-0.834	-0.931	16.388	-15.981	-15.981	0.000	0.000	0.000	0.000
68	A	76	ILE	0	-0.019	-0.017	17.722	0.429	0.429	0.000	0.000	0.000	0.000
69	A	77	THR	0	0.018	0.011	20.350	0.593	0.593	0.000	0.000	0.000	0.000
70	A	78	ARG	1	1.002	1.004	23.441	11.705	11.705	0.000	0.000	0.000	0.000
71	A	79	LEU	0	-0.082	-0.021	19.691	0.359	0.359	0.000	0.000	0.000	0.000
72	A	80	ILE	0	0.047	0.004	22.846	0.303	0.303	0.000	0.000	0.000	0.000
73	A	81	ASP	-1	-0.823	-0.896	25.626	-10.017	-10.017	0.000	0.000	0.000	0.000
74	A	82	ARG	1	0.963	0.991	22.729	11.744	11.744	0.000	0.000	0.000	0.000
75	A	83	LEU	0	-0.037	-0.018	24.794	0.210	0.210	0.000	0.000	0.000	0.000
76	A	84	ASP	-1	-0.915	-0.971	28.991	-8.814	-8.814	0.000	0.000	0.000	0.000
77	A	85	ASP	-1	-0.886	-0.939	31.522	-8.731	-8.731	0.000	0.000	0.000	0.000
78	A	86	ARG	1	0.786	0.897	29.507	9.572	9.572	0.000	0.000	0.000	0.000
79	A	87	GLY	0	0.023	0.021	33.812	0.155	0.155	0.000	0.000	0.000	0.000
80	A	88	LEU	0	-0.054	-0.026	29.595	0.031	0.031	0.000	0.000	0.000	0.000
81	A	89	VAL	0	-0.046	-0.039	27.517	-0.207	-0.207	0.000	0.000	0.000	0.000
82	A	90	LEU	0	0.048	0.030	30.920	0.193	0.193	0.000	0.000	0.000	0.000
83	A	91	ARG	1	0.799	0.890	26.608	9.925	9.925	0.000	0.000	0.000	0.000
84	A	92	THR	0	0.024	0.013	31.493	0.394	0.394	0.000	0.000	0.000	0.000
85	A	93	ARG	1	0.858	0.948	30.975	8.901	8.901	0.000	0.000	0.000	0.000
86	A	94	LYS	1	0.994	0.983	29.814	9.716	9.716	0.000	0.000	0.000	0.000
87	A	95	PRO	0	-0.007	-0.012	33.525	-0.030	-0.030	0.000	0.000	0.000	0.000
88	A	96	GLU	-1	-0.889	-0.939	35.679	-7.733	-7.733	0.000	0.000	0.000	0.000
89	A	97	ASN	0	-0.056	-0.021	29.469	-0.055	-0.055	0.000	0.000	0.000	0.000
90	A	98	ARG	1	1.043	1.010	31.888	7.850	7.850	0.000	0.000	0.000	0.000
91	A	99	ARG	1	0.974	0.983	24.969	11.204	11.204	0.000	0.000	0.000	0.000
92	A	100	VAL	0	-0.031	-0.008	26.916	-0.343	-0.343	0.000	0.000	0.000	0.000
93	A	101	VAL	0	0.007	0.003	27.445	0.405	0.405	0.000	0.000	0.000	0.000
94	A	102	GLU	-1	-0.935	-0.961	27.017	-10.202	-10.202	0.000	0.000	0.000	0.000
95	A	103	VAL	0	-0.008	-0.012	26.273	0.298	0.298	0.000	0.000	0.000	0.000
96	A	104	ALA	0	0.092	0.051	27.456	-0.276	-0.276	0.000	0.000	0.000	0.000
97	A	105	LEU	0	-0.008	-0.001	27.876	0.027	0.027	0.000	0.000	0.000	0.000
98	A	106	THR	0	0.001	0.005	30.396	0.156	0.156	0.000	0.000	0.000	0.000
99	A	107	ASP	-1	-0.850	-0.941	33.397	-7.845	-7.845	0.000	0.000	0.000	0.000
100	A	108	ALA	0	-0.014	-0.005	35.229	-0.028	-0.028	0.000	0.000	0.000	0.000
101	A	109	GLY	0	0.055	0.025	30.917	-0.112	-0.112	0.000	0.000	0.000	0.000
102	A	110	LEU	0	-0.034	-0.021	30.317	-0.248	-0.248	0.000	0.000	0.000	0.000
103	A	111	LYS	1	0.828	0.903	31.990	7.740	7.740	0.000	0.000	0.000	0.000
104	A	112	LEU	0	0.027	0.022	29.102	-0.033	-0.033	0.000	0.000	0.000	0.000
105	A	113	LEU	0	-0.040	-0.032	25.554	-0.184	-0.184	0.000	0.000	0.000	0.000
106	A	114	LYS	1	0.930	0.963	29.057	8.066	8.066	0.000	0.000	0.000	0.000
107	A	115	ASP	-1	-0.842	-0.904	31.875	-8.126	-8.126	0.000	0.000	0.000	0.000
108	A	116	LEU	0	-0.039	-0.022	26.491	-0.092	-0.092	0.000	0.000	0.000	0.000
109	A	117	GLU	-1	-0.955	-0.974	27.729	-9.471	-9.471	0.000	0.000	0.000	0.000
110	A	118	GLU	-1	-0.828	-0.907	28.044	-8.713	-8.713	0.000	0.000	0.000	0.000
111	A	119	PRO	0	0.015	0.008	28.510	-0.185	-0.185	0.000	0.000	0.000	0.000
112	A	120	VAL	0	0.011	0.009	22.819	-0.303	-0.303	0.000	0.000	0.000	0.000
113	A	121	ARG	1	0.859	0.931	24.414	8.789	8.789	0.000	0.000	0.000	0.000
114	A	122	GLN	0	0.022	0.001	25.850	-0.033	-0.033	0.000	0.000	0.000	0.000
115	A	123	CYS	0	-0.027	0.005	22.280	-0.197	-0.197	0.000	0.000	0.000	0.000
116	A	124	HIS	1	0.855	0.919	19.512	12.385	12.385	0.000	0.000	0.000	0.000
117	A	125	GLU	-1	-0.868	-0.935	22.622	-9.930	-9.930	0.000	0.000	0.000	0.000
118	A	126	ARG	1	0.923	0.958	25.164	10.124	10.124	0.000	0.000	0.000	0.000
119	A	127	GLN	0	-0.063	-0.028	18.467	-0.064	-0.064	0.000	0.000	0.000	0.000
120	A	128	LEU	0	0.026	0.015	19.629	-0.266	-0.266	0.000	0.000	0.000	0.000
121	A	129	GLY	0	0.004	0.013	22.087	-0.026	-0.026	0.000	0.000	0.000	0.000
122	A	130	HIS	0	-0.023	-0.033	23.170	-0.022	-0.022	0.000	0.000	0.000	0.000
123	A	131	LEU	0	-0.022	0.008	17.433	-0.127	-0.127	0.000	0.000	0.000	0.000
124	A	132	ALA	0	0.055	0.039	21.000	-0.092	-0.092	0.000	0.000	0.000	0.000
125	A	133	ALA	0	-0.029	-0.014	23.350	0.139	0.139	0.000	0.000	0.000	0.000
126	A	134	ASP	-1	-0.825	-0.900	21.577	-12.656	-12.656	0.000	0.000	0.000	0.000
127	A	135	GLU	-1	-0.919	-0.966	18.639	-14.454	-14.454	0.000	0.000	0.000	0.000
128	A	136	LEU	0	-0.013	-0.012	22.417	0.165	0.165	0.000	0.000	0.000	0.000
129	A	137	HIS	0	-0.033	-0.004	25.928	0.352	0.352	0.000	0.000	0.000	0.000
130	A	138	GLU	-1	-0.827	-0.893	21.898	-12.887	-12.887	0.000	0.000	0.000	0.000
131	A	139	LEU	0	-0.011	-0.007	24.980	0.131	0.131	0.000	0.000	0.000	0.000
132	A	140	ILE	0	0.008	-0.006	26.205	0.233	0.233	0.000	0.000	0.000	0.000
133	A	141	ARG	1	0.833	0.907	24.104	12.297	12.297	0.000	0.000	0.000	0.000
134	A	142	LEU	0	-0.041	-0.034	23.163	0.131	0.131	0.000	0.000	0.000	0.000
135	A	143	MET	0	-0.049	-0.028	27.802	0.180	0.180	0.000	0.000	0.000	0.000
136	A	144	GLU	-1	-0.953	-0.975	30.810	-8.673	-8.673	0.000	0.000	0.000	0.000
137	A	145	LEU	0	-0.081	-0.018	27.315	0.152	0.152	0.000	0.000	0.000	0.000
138	A	146	ALA	0	-0.065	-0.021	30.626	0.275	0.275	0.000	0.000	0.000	0.000

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