FMO DATABASE

FMODB ID: 76Z7K

Calculation Name: 2D3E-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D3E

Chain ID: A

ChEMBL ID:

UniProt ID: P03069

Base Structure: X-ray

Registration Date: 2023-09-23

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	130
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-680030.786151
FMO2-HF: Nuclear repulsion	627027.396474
FMO2-HF: Total energy	-53003.389677
FMO2-MP2: Total energy	-53159.04674

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:153:ASP)

Summations of interaction energy for fragment #1(A:153:ASP)

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.
28.255	35.07	0.33	-3.329	-3.816	0.027

Interaction energy analysis for fragmet #1(A:153:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.853 / q_NPA : -0.926

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

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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	155	VAL	0	0.003	-0.012	2.987	-19.609	-15.190	0.113	-2.268	-2.264	0.017
4	A	156	GLU	-1	-0.903	-0.943	3.057	28.259	30.452	0.218	-1.002	-1.408	0.010
5	A	157	GLU	-1	-0.770	-0.843	4.254	30.342	30.545	-0.001	-0.059	-0.144	0.000
6	A	158	LEU	0	-0.011	-0.016	6.033	-5.432	-5.432	0.000	0.000	0.000	0.000
7	A	159	LEU	0	0.010	0.015	7.325	-4.073	-4.073	0.000	0.000	0.000	0.000
8	A	160	SER	0	-0.015	-0.005	7.976	-3.631	-3.631	0.000	0.000	0.000	0.000
9	A	161	LYS	1	0.848	0.903	9.670	-30.574	-30.574	0.000	0.000	0.000	0.000
10	A	162	ASN	0	0.002	-0.001	12.130	-1.696	-1.696	0.000	0.000	0.000	0.000
11	A	163	TYR	0	0.063	0.045	13.490	-1.706	-1.706	0.000	0.000	0.000	0.000
12	A	164	HIS	0	-0.033	-0.014	14.499	-0.999	-0.999	0.000	0.000	0.000	0.000
13	A	165	LEU	0	0.022	0.000	15.882	-1.151	-1.151	0.000	0.000	0.000	0.000
14	A	166	GLU	-1	-0.960	-0.979	17.610	15.744	15.744	0.000	0.000	0.000	0.000
15	A	167	ASN	0	-0.086	-0.055	18.458	-1.650	-1.650	0.000	0.000	0.000	0.000
16	A	168	GLU	-1	-0.923	-0.952	20.488	13.635	13.635	0.000	0.000	0.000	0.000
17	A	169	VAL	0	0.015	0.000	22.169	-0.805	-0.805	0.000	0.000	0.000	0.000
18	A	170	ALA	0	-0.025	-0.007	23.833	-0.649	-0.649	0.000	0.000	0.000	0.000
19	A	171	ARG	1	0.962	0.959	24.084	-12.556	-12.556	0.000	0.000	0.000	0.000
20	A	172	LEU	0	0.005	0.005	25.106	-0.515	-0.515	0.000	0.000	0.000	0.000
21	A	173	LYS	1	0.954	0.977	26.874	-11.860	-11.860	0.000	0.000	0.000	0.000
22	A	174	LYS	1	0.780	0.879	29.880	-9.325	-9.325	0.000	0.000	0.000	0.000
23	A	175	LEU	0	-0.062	-0.034	29.766	-0.345	-0.345	0.000	0.000	0.000	0.000
24	A	176	LEU	0	0.020	0.001	32.386	-0.226	-0.226	0.000	0.000	0.000	0.000
25	A	177	GLU	-1	-0.728	-0.832	34.159	8.637	8.637	0.000	0.000	0.000	0.000
26	A	178	ARG	1	0.982	0.978	33.470	-8.973	-8.973	0.000	0.000	0.000	0.000
27	A	179	ALA	0	-0.100	-0.031	36.868	-0.227	-0.227	0.000	0.000	0.000	0.000
28	A	180	GLU	-1	-0.931	-0.972	38.027	8.177	8.177	0.000	0.000	0.000	0.000
29	A	181	GLU	-1	-0.901	-0.942	39.798	7.574	7.574	0.000	0.000	0.000	0.000
30	A	182	ARG	1	0.936	0.950	41.388	-7.756	-7.756	0.000	0.000	0.000	0.000
31	A	183	ALA	0	-0.059	-0.028	42.566	-0.188	-0.188	0.000	0.000	0.000	0.000
32	A	184	GLU	-1	-0.843	-0.929	43.736	7.054	7.054	0.000	0.000	0.000	0.000
33	A	185	LEU	0	-0.011	0.015	45.944	-0.183	-0.183	0.000	0.000	0.000	0.000
34	A	186	SER	0	-0.141	-0.073	47.288	-0.164	-0.164	0.000	0.000	0.000	0.000
35	A	187	GLU	-1	-0.919	-0.952	47.973	6.637	6.637	0.000	0.000	0.000	0.000
36	A	188	GLY	0	0.022	0.008	49.991	-0.125	-0.125	0.000	0.000	0.000	0.000
37	A	189	LYS	1	0.752	0.850	51.977	-5.806	-5.806	0.000	0.000	0.000	0.000
38	A	190	CYS	0	0.014	0.010	53.590	-0.119	-0.119	0.000	0.000	0.000	0.000
39	A	191	ALA	0	0.036	0.019	55.207	-0.121	-0.121	0.000	0.000	0.000	0.000
40	A	192	GLU	-1	-0.873	-0.903	56.985	5.492	5.492	0.000	0.000	0.000	0.000
41	A	193	LEU	0	0.029	0.005	56.526	-0.096	-0.096	0.000	0.000	0.000	0.000
42	A	194	GLU	-1	-0.952	-0.984	58.383	5.427	5.427	0.000	0.000	0.000	0.000
43	A	195	GLU	-1	-0.774	-0.864	60.871	4.939	4.939	0.000	0.000	0.000	0.000
44	A	196	GLU	-1	-0.908	-0.955	62.257	4.982	4.982	0.000	0.000	0.000	0.000
45	A	197	LEU	0	-0.030	-0.017	62.637	-0.115	-0.115	0.000	0.000	0.000	0.000
46	A	198	LYS	1	0.813	0.911	65.104	-5.024	-5.024	0.000	0.000	0.000	0.000
47	A	199	THR	0	-0.045	-0.025	67.202	-0.111	-0.111	0.000	0.000	0.000	0.000
48	A	200	VAL	0	-0.019	-0.012	68.079	-0.100	-0.100	0.000	0.000	0.000	0.000
49	A	201	THR	0	0.016	-0.007	68.127	-0.084	-0.084	0.000	0.000	0.000	0.000
50	A	202	ASN	0	-0.039	-0.017	70.920	-0.096	-0.096	0.000	0.000	0.000	0.000
51	A	203	ASN	0	-0.027	-0.045	73.047	-0.084	-0.084	0.000	0.000	0.000	0.000
52	A	204	LEU	0	0.050	0.050	73.385	-0.054	-0.054	0.000	0.000	0.000	0.000
53	A	205	LYS	1	0.889	0.940	74.110	-4.374	-4.374	0.000	0.000	0.000	0.000
54	A	206	SER	0	-0.072	-0.025	76.823	-0.080	-0.080	0.000	0.000	0.000	0.000
55	A	207	LEU	0	0.055	0.020	78.740	-0.051	-0.051	0.000	0.000	0.000	0.000
56	A	208	GLU	-1	-0.890	-0.930	78.729	4.046	4.046	0.000	0.000	0.000	0.000
57	A	209	ALA	0	0.007	-0.005	80.926	-0.058	-0.058	0.000	0.000	0.000	0.000
58	A	210	GLN	0	-0.090	-0.050	83.101	-0.085	-0.085	0.000	0.000	0.000	0.000
59	A	211	ALA	0	0.014	0.016	83.576	-0.060	-0.060	0.000	0.000	0.000	0.000
60	A	212	GLU	-1	-0.882	-0.931	84.986	3.732	3.732	0.000	0.000	0.000	0.000
61	A	213	LYS	1	0.911	0.945	86.709	-3.769	-3.769	0.000	0.000	0.000	0.000
62	A	214	TYR	0	-0.101	-0.085	87.839	-0.064	-0.064	0.000	0.000	0.000	0.000
63	A	215	SER	0	0.111	0.069	88.553	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	216	GLN	0	-0.056	-0.013	90.095	-0.059	-0.059	0.000	0.000	0.000	0.000
65	A	217	LYS	1	0.846	0.936	92.745	-3.450	-3.450	0.000	0.000	0.000	0.000
66	A	218	GLU	-1	-0.944	-0.986	91.897	3.482	3.482	0.000	0.000	0.000	0.000
67	A	219	ASP	-1	-0.851	-0.913	93.778	3.444	3.444	0.000	0.000	0.000	0.000
68	A	220	LYS	1	0.743	0.862	96.663	-3.235	-3.235	0.000	0.000	0.000	0.000
69	A	221	TYR	0	-0.034	-0.047	96.623	-0.023	-0.023	0.000	0.000	0.000	0.000
70	A	222	GLU	-1	-0.878	-0.927	98.201	3.258	3.258	0.000	0.000	0.000	0.000
71	A	223	GLU	-1	-0.929	-0.953	100.324	3.165	3.165	0.000	0.000	0.000	0.000
72	A	224	GLU	-1	-0.840	-0.903	102.913	3.113	3.113	0.000	0.000	0.000	0.000
73	A	225	ILE	0	0.041	0.010	101.634	-0.047	-0.047	0.000	0.000	0.000	0.000
74	A	226	LYS	1	0.824	0.906	104.687	-3.040	-3.040	0.000	0.000	0.000	0.000
75	A	227	VAL	0	-0.023	-0.019	106.632	-0.040	-0.040	0.000	0.000	0.000	0.000
76	A	228	LEU	0	-0.049	-0.023	107.546	-0.041	-0.041	0.000	0.000	0.000	0.000
77	A	229	SER	0	-0.017	-0.027	107.887	-0.036	-0.036	0.000	0.000	0.000	0.000
78	A	230	ASP	-1	-0.826	-0.891	110.300	2.943	2.943	0.000	0.000	0.000	0.000
79	A	231	LYS	1	0.967	0.980	112.476	-2.922	-2.922	0.000	0.000	0.000	0.000
80	A	232	LEU	0	-0.046	-0.001	112.905	-0.029	-0.029	0.000	0.000	0.000	0.000
81	A	233	LYS	1	0.872	0.924	112.682	-2.875	-2.875	0.000	0.000	0.000	0.000
82	A	234	GLU	-1	-0.924	-0.957	116.526	2.759	2.759	0.000	0.000	0.000	0.000
83	A	235	ALA	0	-0.059	-0.027	118.474	-0.035	-0.035	0.000	0.000	0.000	0.000
84	A	236	GLU	-1	-0.778	-0.896	116.859	2.775	2.775	0.000	0.000	0.000	0.000
85	A	237	THR	0	-0.025	-0.003	120.191	-0.024	-0.024	0.000	0.000	0.000	0.000
86	A	238	ARG	1	0.931	0.965	122.639	-2.658	-2.658	0.000	0.000	0.000	0.000
87	A	239	ALA	0	0.001	0.001	124.304	-0.027	-0.027	0.000	0.000	0.000	0.000
88	A	240	GLU	-1	-0.835	-0.918	122.625	2.628	2.628	0.000	0.000	0.000	0.000
89	A	241	PHE	0	-0.111	-0.050	126.395	-0.030	-0.030	0.000	0.000	0.000	0.000
90	A	242	ALA	0	-0.006	-0.021	128.650	-0.026	-0.026	0.000	0.000	0.000	0.000
91	A	243	GLU	-1	-0.885	-0.939	128.126	2.522	2.522	0.000	0.000	0.000	0.000
92	A	244	ARG	1	0.934	0.970	130.617	-2.505	-2.505	0.000	0.000	0.000	0.000
93	A	245	SER	0	-0.084	-0.050	132.405	-0.025	-0.025	0.000	0.000	0.000	0.000
94	A	246	VAL	0	0.013	0.016	134.173	-0.023	-0.023	0.000	0.000	0.000	0.000
95	A	247	THR	0	0.043	0.036	134.651	-0.018	-0.018	0.000	0.000	0.000	0.000
96	A	248	LYS	1	0.885	0.931	136.217	-2.404	-2.404	0.000	0.000	0.000	0.000
97	A	249	LEU	0	-0.016	-0.014	137.876	-0.019	-0.019	0.000	0.000	0.000	0.000
98	A	250	GLU	-1	-0.885	-0.944	138.309	2.346	2.346	0.000	0.000	0.000	0.000
99	A	251	LYS	1	0.785	0.885	141.452	-2.260	-2.260	0.000	0.000	0.000	0.000
100	A	252	SER	0	-0.047	-0.037	142.877	-0.018	-0.018	0.000	0.000	0.000	0.000
101	A	253	ILE	0	-0.011	-0.009	143.297	-0.018	-0.018	0.000	0.000	0.000	0.000
102	A	254	ASP	-1	-0.853	-0.918	145.152	2.233	2.233	0.000	0.000	0.000	0.000
103	A	255	ASP	-1	-0.811	-0.881	147.237	2.209	2.209	0.000	0.000	0.000	0.000
104	A	256	LEU	0	-0.043	-0.026	148.165	-0.020	-0.020	0.000	0.000	0.000	0.000
105	A	257	GLU	-1	-0.974	-0.989	149.478	2.166	2.166	0.000	0.000	0.000	0.000
106	A	258	ASP	-1	-0.910	-0.944	152.002	2.129	2.129	0.000	0.000	0.000	0.000
107	A	259	GLU	-1	-0.999	-0.996	153.809	2.100	2.100	0.000	0.000	0.000	0.000
108	A	260	LEU	0	-0.047	-0.031	154.922	-0.024	-0.024	0.000	0.000	0.000	0.000
109	A	261	TYR	0	0.012	0.004	156.344	-0.025	-0.025	0.000	0.000	0.000	0.000
110	A	262	ALA	0	0.049	0.023	158.120	-0.019	-0.019	0.000	0.000	0.000	0.000
111	A	263	GLN	0	-0.010	0.000	159.714	-0.035	-0.035	0.000	0.000	0.000	0.000
112	A	264	LYS	1	0.932	0.952	157.499	-2.089	-2.089	0.000	0.000	0.000	0.000
113	A	265	LEU	0	0.008	0.005	161.249	-0.018	-0.018	0.000	0.000	0.000	0.000
114	A	266	LYS	1	0.873	0.937	164.090	-2.009	-2.009	0.000	0.000	0.000	0.000
115	A	267	TYR	0	-0.026	-0.014	165.651	-0.015	-0.015	0.000	0.000	0.000	0.000
116	A	268	LYS	1	0.856	0.918	166.288	-1.956	-1.956	0.000	0.000	0.000	0.000
117	A	269	ALA	0	0.044	0.028	168.519	-0.012	-0.012	0.000	0.000	0.000	0.000
118	A	270	ILE	0	-0.013	0.000	170.493	-0.013	-0.013	0.000	0.000	0.000	0.000
119	A	271	SER	0	-0.005	-0.003	171.375	-0.011	-0.011	0.000	0.000	0.000	0.000
120	A	272	GLU	-1	-0.884	-0.934	171.198	1.909	1.909	0.000	0.000	0.000	0.000
121	A	273	GLU	-1	-0.927	-0.951	174.526	1.836	1.836	0.000	0.000	0.000	0.000
122	A	274	LEU	0	-0.044	-0.037	176.190	-0.013	-0.013	0.000	0.000	0.000	0.000
123	A	275	ASP	-1	-0.910	-0.968	177.119	1.824	1.824	0.000	0.000	0.000	0.000
124	A	276	HIS	0	-0.023	-0.019	178.517	-0.017	-0.017	0.000	0.000	0.000	0.000
125	A	277	ALA	0	-0.003	0.004	180.449	-0.011	-0.011	0.000	0.000	0.000	0.000
126	A	278	LEU	0	-0.013	-0.010	181.247	-0.014	-0.014	0.000	0.000	0.000	0.000
127	A	279	ASN	0	-0.128	-0.059	181.115	-0.020	-0.020	0.000	0.000	0.000	0.000
128	A	280	ASP	-1	-0.936	-0.955	184.877	1.752	1.752	0.000	0.000	0.000	0.000
129	A	281	MET	0	-0.080	-0.029	186.489	-0.012	-0.012	0.000	0.000	0.000	0.000
130	A	282	THR	0	-0.067	-0.025	188.611	-0.017	-0.017	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:153:ASP)