FMO DATABASE

FMODB ID: LN7M9

Calculation Name: 3PU2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PU2

Chain ID: A

ChEMBL ID:

UniProt ID: Q3J4M4

Base Structure: X-ray

Registration Date: 2023-09-21

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	154
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1449347.325624
FMO2-HF: Nuclear repulsion	1389681.943197
FMO2-HF: Total energy	-59665.382426
FMO2-MP2: Total energy	-59838.781733

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:16:GLU)

Summations of interaction energy for fragment #1(A:16:GLU)

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.
85.128	91.522	0.74	-2.845	-4.289	-0.001

Interaction energy analysis for fragmet #1(A:16:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.967 / q_NPA : -0.995

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	18	GLN	0	-0.033	-0.010	3.486	-1.332	0.374	-0.019	-0.545	-1.141	0.002
4	A	19	ILE	0	0.002	0.002	6.200	-2.004	-2.004	0.000	0.000	0.000	0.000
5	A	20	GLY	0	-0.008	0.000	9.342	-0.552	-0.552	0.000	0.000	0.000	0.000
6	A	21	PRO	0	-0.060	-0.035	12.347	-0.074	-0.074	0.000	0.000	0.000	0.000
7	A	22	GLY	0	0.025	0.019	15.775	-0.229	-0.229	0.000	0.000	0.000	0.000
8	A	23	SER	0	-0.028	-0.042	17.789	-0.796	-0.796	0.000	0.000	0.000	0.000
9	A	24	ALA	0	0.008	-0.009	20.413	0.463	0.463	0.000	0.000	0.000	0.000
10	A	25	THR	0	0.040	0.026	22.530	-0.051	-0.051	0.000	0.000	0.000	0.000
11	A	26	ARG	1	0.841	0.931	18.457	-14.652	-14.652	0.000	0.000	0.000	0.000
12	A	27	LEU	0	-0.014	0.001	14.151	0.306	0.306	0.000	0.000	0.000	0.000
13	A	28	GLU	-1	-0.871	-0.939	13.633	16.655	16.655	0.000	0.000	0.000	0.000
14	A	29	PHE	0	0.033	0.012	8.570	1.391	1.391	0.000	0.000	0.000	0.000
15	A	30	ARG	1	0.893	0.961	7.703	-25.089	-25.089	0.000	0.000	0.000	0.000
16	A	31	ARG	1	0.877	0.934	2.886	-44.228	-43.157	0.385	-0.520	-0.936	-0.003
17	A	32	HIS	0	-0.027	0.008	4.659	-4.015	-3.822	-0.001	-0.015	-0.177	0.000
18	A	33	PHE	0	0.064	0.017	5.768	2.773	2.773	0.000	0.000	0.000	0.000
19	A	34	ALA	0	0.038	0.025	8.442	-1.810	-1.810	0.000	0.000	0.000	0.000
20	A	35	ALA	0	0.023	0.004	10.978	-0.966	-0.966	0.000	0.000	0.000	0.000
21	A	36	THR	0	0.008	0.032	14.090	0.358	0.358	0.000	0.000	0.000	0.000
22	A	37	PRO	0	0.052	0.031	15.909	0.141	0.141	0.000	0.000	0.000	0.000
23	A	38	GLU	-1	-0.888	-0.963	16.876	13.471	13.471	0.000	0.000	0.000	0.000
24	A	39	GLN	0	-0.023	-0.013	16.751	0.192	0.192	0.000	0.000	0.000	0.000
25	A	40	LEU	0	0.035	0.025	11.393	0.014	0.014	0.000	0.000	0.000	0.000
26	A	41	TRP	0	0.043	0.012	15.336	0.143	0.143	0.000	0.000	0.000	0.000
27	A	42	ALA	0	-0.022	-0.014	18.177	-0.319	-0.319	0.000	0.000	0.000	0.000
28	A	43	ALA	0	-0.006	-0.008	15.293	-0.363	-0.363	0.000	0.000	0.000	0.000
29	A	44	LEU	0	-0.009	-0.019	13.089	0.069	0.069	0.000	0.000	0.000	0.000
30	A	45	THR	0	-0.040	-0.011	16.918	-0.564	-0.564	0.000	0.000	0.000	0.000
31	A	46	SER	0	0.013	0.015	20.534	-0.805	-0.805	0.000	0.000	0.000	0.000
32	A	47	PRO	0	0.027	-0.005	21.803	0.500	0.500	0.000	0.000	0.000	0.000
33	A	48	ALA	0	-0.032	-0.010	24.283	0.012	0.012	0.000	0.000	0.000	0.000
34	A	49	LEU	0	-0.021	-0.020	18.974	0.111	0.111	0.000	0.000	0.000	0.000
35	A	50	LEU	0	0.017	0.013	17.394	0.699	0.699	0.000	0.000	0.000	0.000
36	A	51	PRO	0	0.013	-0.010	18.056	0.813	0.813	0.000	0.000	0.000	0.000
37	A	52	ALA	0	-0.055	-0.017	18.483	0.253	0.253	0.000	0.000	0.000	0.000
38	A	53	TRP	0	-0.013	-0.022	11.981	1.155	1.155	0.000	0.000	0.000	0.000
39	A	54	LEU	0	0.006	0.022	13.830	1.406	1.406	0.000	0.000	0.000	0.000
40	A	55	PHE	0	-0.044	-0.011	14.790	-1.283	-1.283	0.000	0.000	0.000	0.000
41	A	56	ALA	0	0.112	0.070	14.557	1.358	1.358	0.000	0.000	0.000	0.000
42	A	57	ARG	1	0.966	0.960	14.668	-20.383	-20.383	0.000	0.000	0.000	0.000
43	A	58	GLY	0	-0.044	-0.023	16.654	-0.623	-0.623	0.000	0.000	0.000	0.000
44	A	59	TRP	0	-0.024	-0.013	19.410	-1.107	-1.107	0.000	0.000	0.000	0.000
45	A	60	PRO	0	0.039	0.034	19.994	0.602	0.602	0.000	0.000	0.000	0.000
46	A	61	MET	0	0.016	0.004	19.463	-0.519	-0.519	0.000	0.000	0.000	0.000
47	A	62	THR	0	-0.036	-0.019	22.208	-0.095	-0.095	0.000	0.000	0.000	0.000
48	A	63	GLU	-1	-0.955	-0.971	25.619	9.929	9.929	0.000	0.000	0.000	0.000
49	A	64	CYS	0	-0.033	-0.016	22.355	0.512	0.512	0.000	0.000	0.000	0.000
50	A	65	VAL	0	-0.008	0.017	25.606	-0.230	-0.230	0.000	0.000	0.000	0.000
51	A	66	PHE	0	0.065	0.012	20.941	0.238	0.238	0.000	0.000	0.000	0.000
52	A	67	GLU	-1	-0.855	-0.894	25.703	9.598	9.598	0.000	0.000	0.000	0.000
53	A	68	PRO	0	0.007	0.003	23.763	-0.057	-0.057	0.000	0.000	0.000	0.000
54	A	69	HIS	0	-0.016	-0.014	25.723	-0.091	-0.091	0.000	0.000	0.000	0.000
55	A	70	LYS	1	0.962	0.968	28.800	-9.208	-9.208	0.000	0.000	0.000	0.000
56	A	71	GLY	0	-0.014	-0.008	30.522	-0.264	-0.264	0.000	0.000	0.000	0.000
57	A	72	GLY	0	-0.024	0.013	29.213	-0.153	-0.153	0.000	0.000	0.000	0.000
58	A	73	LEU	0	-0.069	-0.056	29.419	0.091	0.091	0.000	0.000	0.000	0.000
59	A	74	ILE	0	0.017	0.020	22.947	0.116	0.116	0.000	0.000	0.000	0.000
60	A	75	ARG	1	0.920	0.954	26.452	-10.989	-10.989	0.000	0.000	0.000	0.000
61	A	76	GLN	0	0.032	0.014	19.826	0.210	0.210	0.000	0.000	0.000	0.000
62	A	77	VAL	0	0.013	0.011	24.470	-0.144	-0.144	0.000	0.000	0.000	0.000
63	A	78	TRP	0	-0.016	0.001	18.853	-0.111	-0.111	0.000	0.000	0.000	0.000
64	A	79	THR	0	-0.036	-0.038	23.513	-0.607	-0.607	0.000	0.000	0.000	0.000
65	A	80	GLY	0	0.030	0.022	23.796	0.457	0.457	0.000	0.000	0.000	0.000
66	A	81	PRO	0	-0.040	-0.031	23.371	-0.561	-0.561	0.000	0.000	0.000	0.000
67	A	82	GLU	-1	-0.977	-1.007	26.552	10.442	10.442	0.000	0.000	0.000	0.000
68	A	83	GLY	0	-0.021	0.002	28.929	-0.400	-0.400	0.000	0.000	0.000	0.000
69	A	84	ARG	1	0.931	0.984	25.202	-12.019	-12.019	0.000	0.000	0.000	0.000
70	A	85	THR	0	0.006	-0.008	26.899	0.358	0.358	0.000	0.000	0.000	0.000
71	A	86	ARG	1	0.881	0.942	19.562	-15.465	-15.465	0.000	0.000	0.000	0.000
72	A	87	GLY	0	0.003	-0.006	24.408	0.241	0.241	0.000	0.000	0.000	0.000
73	A	88	LEU	0	0.010	0.040	20.517	-0.152	-0.152	0.000	0.000	0.000	0.000
74	A	89	THR	0	-0.012	-0.022	24.966	-0.239	-0.239	0.000	0.000	0.000	0.000
75	A	90	GLY	0	0.056	0.030	25.595	0.265	0.265	0.000	0.000	0.000	0.000
76	A	91	ARG	1	0.877	0.935	26.652	-9.870	-9.870	0.000	0.000	0.000	0.000
77	A	92	VAL	0	0.042	0.029	25.286	0.324	0.324	0.000	0.000	0.000	0.000
78	A	93	ILE	0	-0.054	-0.037	26.353	-0.528	-0.528	0.000	0.000	0.000	0.000
79	A	94	LEU	0	-0.082	-0.056	24.751	-0.533	-0.533	0.000	0.000	0.000	0.000
80	A	95	ALA	0	0.010	0.000	24.555	0.470	0.470	0.000	0.000	0.000	0.000
81	A	96	GLU	-1	-0.894	-0.921	24.078	10.821	10.821	0.000	0.000	0.000	0.000
82	A	97	PRO	0	-0.018	0.033	22.694	0.430	0.430	0.000	0.000	0.000	0.000
83	A	98	PRO	0	0.002	-0.022	19.707	-0.450	-0.450	0.000	0.000	0.000	0.000
84	A	99	HIS	1	0.974	0.971	18.831	-11.787	-11.787	0.000	0.000	0.000	0.000
85	A	100	ARG	1	0.875	0.933	18.956	-11.412	-11.412	0.000	0.000	0.000	0.000
86	A	101	LEU	0	0.021	0.014	19.963	-0.641	-0.641	0.000	0.000	0.000	0.000
87	A	102	ILE	0	0.009	0.017	20.525	0.476	0.476	0.000	0.000	0.000	0.000
88	A	103	HIS	0	-0.028	-0.018	20.290	-0.274	-0.274	0.000	0.000	0.000	0.000
89	A	104	SER	0	0.024	0.027	23.145	0.422	0.422	0.000	0.000	0.000	0.000
90	A	105	GLU	-1	-0.913	-0.958	19.431	15.470	15.470	0.000	0.000	0.000	0.000
91	A	106	LEU	0	-0.012	-0.007	23.688	-0.092	-0.092	0.000	0.000	0.000	0.000
92	A	107	TYR	0	0.008	0.012	18.248	-0.103	-0.103	0.000	0.000	0.000	0.000
93	A	108	ASP	-1	-0.907	-0.959	25.045	10.485	10.485	0.000	0.000	0.000	0.000
94	A	109	GLU	-1	-0.910	-0.951	21.492	14.430	14.430	0.000	0.000	0.000	0.000
95	A	110	ASP	-1	-0.898	-0.958	23.864	11.882	11.882	0.000	0.000	0.000	0.000
96	A	111	TRP	0	0.010	-0.010	19.988	0.642	0.642	0.000	0.000	0.000	0.000
97	A	112	THR	0	-0.082	-0.027	24.624	-0.550	-0.550	0.000	0.000	0.000	0.000
98	A	113	GLY	0	0.026	0.005	23.379	0.627	0.627	0.000	0.000	0.000	0.000
99	A	114	GLY	0	-0.039	-0.016	25.133	-0.482	-0.482	0.000	0.000	0.000	0.000
100	A	115	GLU	-1	-0.980	-0.981	25.311	10.823	10.823	0.000	0.000	0.000	0.000
101	A	116	THR	0	-0.033	-0.009	21.324	0.269	0.269	0.000	0.000	0.000	0.000
102	A	117	LEU	0	-0.009	-0.013	22.823	-0.299	-0.299	0.000	0.000	0.000	0.000
103	A	118	VAL	0	0.055	0.033	17.260	0.515	0.515	0.000	0.000	0.000	0.000
104	A	119	THR	0	-0.089	-0.051	18.524	-0.843	-0.843	0.000	0.000	0.000	0.000
105	A	120	LEU	0	0.031	0.017	14.564	0.969	0.969	0.000	0.000	0.000	0.000
106	A	121	GLN	0	-0.023	-0.038	15.418	-1.770	-1.770	0.000	0.000	0.000	0.000
107	A	122	LEU	0	-0.036	-0.008	14.378	1.086	1.086	0.000	0.000	0.000	0.000
108	A	123	LEU	0	-0.018	-0.010	13.277	-1.348	-1.348	0.000	0.000	0.000	0.000
109	A	124	PRO	0	-0.012	-0.020	13.659	0.969	0.969	0.000	0.000	0.000	0.000
110	A	125	VAL	0	-0.001	0.014	10.059	-0.590	-0.590	0.000	0.000	0.000	0.000
111	A	126	GLU	-1	-0.978	-0.991	12.934	17.101	17.101	0.000	0.000	0.000	0.000
112	A	127	GLY	0	0.041	0.018	11.072	1.285	1.285	0.000	0.000	0.000	0.000
113	A	128	GLY	0	-0.039	-0.029	12.037	0.233	0.233	0.000	0.000	0.000	0.000
114	A	129	THR	0	-0.052	-0.044	11.263	-1.734	-1.734	0.000	0.000	0.000	0.000
115	A	130	GLU	-1	-0.912	-0.952	8.483	24.535	24.535	0.000	0.000	0.000	0.000
116	A	131	LEU	0	-0.033	-0.024	9.189	-2.043	-2.043	0.000	0.000	0.000	0.000
117	A	132	ALA	0	0.000	-0.002	9.888	1.662	1.662	0.000	0.000	0.000	0.000
118	A	133	MET	0	0.005	-0.006	12.048	-0.937	-0.937	0.000	0.000	0.000	0.000
119	A	134	ALA	0	-0.006	-0.010	13.730	0.547	0.547	0.000	0.000	0.000	0.000
120	A	135	VAL	0	0.005	0.016	15.604	-0.542	-0.542	0.000	0.000	0.000	0.000
121	A	136	ASP	-1	-0.841	-0.904	18.202	13.603	13.603	0.000	0.000	0.000	0.000
122	A	137	TYR	0	0.033	-0.024	16.721	-0.264	-0.264	0.000	0.000	0.000	0.000
123	A	138	ALA	0	0.018	0.009	23.098	-0.322	-0.322	0.000	0.000	0.000	0.000
124	A	139	THR	0	0.003	0.001	26.385	-0.152	-0.152	0.000	0.000	0.000	0.000
125	A	140	PRO	0	-0.026	-0.036	24.534	0.425	0.425	0.000	0.000	0.000	0.000
126	A	141	GLU	-1	-0.819	-0.920	24.040	11.159	11.159	0.000	0.000	0.000	0.000
127	A	142	ALA	0	-0.062	-0.023	24.279	0.275	0.275	0.000	0.000	0.000	0.000
128	A	143	ARG	1	0.877	0.958	18.217	-15.411	-15.411	0.000	0.000	0.000	0.000
129	A	144	ASP	-1	-0.918	-0.955	19.601	14.039	14.039	0.000	0.000	0.000	0.000
130	A	145	ALA	0	-0.022	-0.010	20.061	0.725	0.725	0.000	0.000	0.000	0.000
131	A	146	VAL	0	0.012	0.009	16.523	0.563	0.563	0.000	0.000	0.000	0.000
132	A	147	ALA	0	-0.031	-0.014	15.603	1.228	1.228	0.000	0.000	0.000	0.000
133	A	148	ALA	0	-0.077	-0.025	15.238	1.139	1.139	0.000	0.000	0.000	0.000
134	A	149	SER	0	0.063	0.040	16.013	-0.551	-0.551	0.000	0.000	0.000	0.000
135	A	150	ALA	0	-0.026	0.003	12.084	1.285	1.285	0.000	0.000	0.000	0.000
136	A	151	MET	0	0.065	0.016	12.096	1.612	1.612	0.000	0.000	0.000	0.000
137	A	152	ALA	0	0.039	0.003	8.609	1.139	1.139	0.000	0.000	0.000	0.000
138	A	153	THR	0	-0.044	-0.027	7.388	4.921	4.921	0.000	0.000	0.000	0.000
139	A	154	GLU	-1	-0.944	-0.976	8.235	23.294	23.294	0.000	0.000	0.000	0.000
140	A	155	MET	0	-0.024	0.006	9.048	-1.092	-1.092	0.000	0.000	0.000	0.000
141	A	156	GLU	-1	-0.848	-0.943	3.113	54.823	57.829	0.375	-1.635	-1.746	-0.001
142	A	157	GLU	-1	-0.966	-1.014	6.092	26.721	26.721	0.000	0.000	0.000	0.000
143	A	158	ALA	0	0.028	0.028	8.588	-1.415	-1.415	0.000	0.000	0.000	0.000
144	A	159	TYR	0	0.018	-0.006	6.223	-1.812	-1.812	0.000	0.000	0.000	0.000
145	A	160	ARG	1	0.955	1.002	3.910	-56.843	-56.425	0.000	-0.130	-0.289	0.001
146	A	161	HIS	0	-0.043	-0.018	7.304	-1.656	-1.656	0.000	0.000	0.000	0.000
147	A	162	LEU	0	-0.031	-0.014	9.954	-1.759	-1.759	0.000	0.000	0.000	0.000
148	A	163	ASP	-1	-0.843	-0.912	6.297	35.346	35.346	0.000	0.000	0.000	0.000
149	A	164	VAL	0	-0.060	-0.034	9.841	-1.872	-1.872	0.000	0.000	0.000	0.000
150	A	165	MET	0	-0.021	0.004	12.602	-1.746	-1.746	0.000	0.000	0.000	0.000
151	A	166	LEU	0	-0.019	-0.016	11.027	-1.303	-1.303	0.000	0.000	0.000	0.000
152	A	167	ALA	0	-0.001	0.001	13.154	-1.118	-1.118	0.000	0.000	0.000	0.000
153	A	168	ALA	0	-0.070	-0.021	14.956	-0.973	-0.973	0.000	0.000	0.000	0.000
154	A	169	LEU	0	-0.090	-0.034	17.481	-1.318	-1.318	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:16:GLU)