FMO DATABASE

FMODB ID: 8529Y

Calculation Name: 2Z5B-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2Z5B

Chain ID: A

ChEMBL ID:

UniProt ID: Q07951

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

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	137
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1246513.278701
FMO2-HF: Nuclear repulsion	1191672.311173
FMO2-HF: Total energy	-54840.967528
FMO2-MP2: Total energy	-54997.715295

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.
-6.173	0.56	3.822	-4.597	-5.956	-0.028

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 : 0.003 / q_NPA : 0.008

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	VAL	0	-0.012	0.001	2.373	-1.977	2.366	0.413	-2.094	-2.662	0.008
4	A	4	LYS	1	0.898	0.956	2.375	-3.477	-1.428	3.409	-2.464	-2.993	-0.036
5	A	5	THR	0	-0.026	-0.012	3.865	0.035	0.199	0.001	-0.001	-0.164	0.000
6	A	6	ILE	0	-0.002	0.016	6.470	0.293	0.293	0.000	0.000	0.000	0.000
7	A	7	SER	0	0.029	0.007	9.676	-0.049	-0.049	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.794	0.869	12.076	0.263	0.263	0.000	0.000	0.000	0.000
9	A	9	THR	0	-0.016	-0.012	16.035	-0.013	-0.013	0.000	0.000	0.000	0.000
10	A	10	ILE	0	-0.051	-0.030	19.656	-0.003	-0.003	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.819	-0.918	21.965	-0.098	-0.098	0.000	0.000	0.000	0.000
12	A	12	SER	0	-0.319	0.009	25.463	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.665	-0.882	29.013	-0.086	-0.086	0.000	0.000	0.000	0.000
14	A	14	SER	0	-0.044	-0.040	25.875	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.126	0.012	27.207	0.004	0.004	0.000	0.000	0.000	0.000
16	A	16	PHE	0	-0.072	-0.083	28.232	-0.017	-0.017	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.009	-0.018	31.045	0.008	0.008	0.000	0.000	0.000	0.000
18	A	18	GLN	0	0.033	0.042	30.432	0.002	0.002	0.000	0.000	0.000	0.000
19	A	19	PRO	0	0.008	0.016	28.026	0.004	0.004	0.000	0.000	0.000	0.000
20	A	20	THR	0	0.047	0.014	24.107	-0.011	-0.011	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.060	-0.039	21.899	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.864	-0.938	18.905	-0.155	-0.155	0.000	0.000	0.000	0.000
23	A	23	VAL	0	0.008	-0.004	14.576	-0.024	-0.024	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.028	0.023	10.854	0.011	0.011	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.016	0.010	11.284	-0.017	-0.017	0.000	0.000	0.000	0.000
26	A	26	THR	0	-0.037	-0.022	5.972	-0.096	-0.096	0.000	0.000	0.000	0.000
27	A	27	LEU	0	0.019	-0.004	7.082	0.157	0.157	0.000	0.000	0.000	0.000
28	A	28	PRO	0	0.008	0.008	6.679	-0.525	-0.525	0.000	0.000	0.000	0.000
29	A	29	ALA	0	-0.005	-0.016	4.330	0.415	0.592	-0.001	-0.038	-0.137	0.000
30	A	30	ASP	-1	-0.924	-0.951	6.398	-2.550	-2.550	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.887	-0.970	8.438	-1.027	-1.027	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.990	1.000	12.102	0.753	0.753	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.022	-0.012	15.120	-0.056	-0.056	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.943	0.941	14.318	0.638	0.638	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.967	0.987	13.466	0.649	0.649	0.000	0.000	0.000	0.000
36	A	36	ILE	0	0.027	0.040	7.444	0.141	0.141	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.021	0.008	11.157	0.024	0.024	0.000	0.000	0.000	0.000
38	A	38	ILE	0	0.016	0.028	10.799	-0.178	-0.178	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.009	-0.009	10.895	0.116	0.116	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.023	-0.007	12.038	-0.060	-0.060	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.022	0.013	13.923	0.037	0.037	0.000	0.000	0.000	0.000
42	A	42	VAL	0	-0.006	-0.013	16.169	0.000	0.000	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.083	0.052	19.203	0.008	0.008	0.000	0.000	0.000	0.000
44	A	44	PHE	0	-0.013	-0.007	22.379	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.818	0.921	20.328	0.131	0.131	0.000	0.000	0.000	0.000
46	A	46	GLN	0	-0.007	0.000	24.315	0.007	0.007	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.772	-0.864	24.684	-0.044	-0.044	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.006	0.005	25.548	0.003	0.003	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.025	-0.035	26.284	0.012	0.012	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.105	-0.046	26.098	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	51	ASN	0	-0.062	-0.049	21.319	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	52	SER	0	0.028	0.008	22.033	0.011	0.011	0.000	0.000	0.000	0.000
53	A	53	SER	0	0.013	0.012	21.354	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	54	SER	0	-0.053	-0.023	22.035	0.010	0.010	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.003	0.013	23.376	0.001	0.001	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.023	-0.007	19.527	-0.012	-0.012	0.000	0.000	0.000	0.000
57	A	57	SER	0	-0.024	-0.030	22.676	0.011	0.011	0.000	0.000	0.000	0.000
58	A	58	CYS	0	-0.063	-0.028	23.608	0.005	0.005	0.000	0.000	0.000	0.000
59	A	59	TYR	0	0.023	0.016	15.113	-0.016	-0.016	0.000	0.000	0.000	0.000
60	A	60	TYR	0	0.056	0.021	20.669	0.026	0.026	0.000	0.000	0.000	0.000
61	A	61	TYR	0	0.000	0.006	17.341	-0.027	-0.027	0.000	0.000	0.000	0.000
62	A	62	ALA	0	0.020	0.008	19.885	0.041	0.041	0.000	0.000	0.000	0.000
63	A	63	ILE	0	0.006	0.004	19.636	-0.066	-0.066	0.000	0.000	0.000	0.000
64	A	64	PRO	0	-0.023	-0.004	20.497	0.041	0.041	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.018	-0.011	23.539	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	66	MET	0	-0.015	-0.017	26.411	0.012	0.012	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.841	0.920	23.903	0.340	0.340	0.000	0.000	0.000	0.000
68	A	78	SER	0	0.058	0.039	26.722	-0.010	-0.010	0.000	0.000	0.000	0.000
69	A	79	ASN	0	0.001	-0.015	28.799	0.005	0.005	0.000	0.000	0.000	0.000
70	A	80	VAL	0	-0.004	0.021	23.642	-0.019	-0.019	0.000	0.000	0.000	0.000
71	A	81	VAL	0	0.016	0.018	25.389	0.023	0.023	0.000	0.000	0.000	0.000
72	A	82	GLY	0	0.044	-0.003	24.484	-0.031	-0.031	0.000	0.000	0.000	0.000
73	A	83	ILE	0	-0.061	-0.027	24.323	0.024	0.024	0.000	0.000	0.000	0.000
74	A	84	PRO	0	0.008	0.010	24.075	-0.025	-0.025	0.000	0.000	0.000	0.000
75	A	85	LEU	0	-0.034	-0.024	19.527	0.004	0.004	0.000	0.000	0.000	0.000
76	A	86	LEU	0	-0.009	0.001	23.302	0.015	0.015	0.000	0.000	0.000	0.000
77	A	87	ASP	-1	-0.826	-0.923	24.811	-0.185	-0.185	0.000	0.000	0.000	0.000
78	A	88	THR	0	0.006	0.006	27.902	0.011	0.011	0.000	0.000	0.000	0.000
79	A	89	LYS	1	0.970	0.973	29.799	0.114	0.114	0.000	0.000	0.000	0.000
80	A	90	ASP	-1	-0.789	-0.871	31.629	-0.122	-0.122	0.000	0.000	0.000	0.000
81	A	91	ASP	-1	-0.767	-0.880	31.538	-0.145	-0.145	0.000	0.000	0.000	0.000
82	A	92	ARG	1	0.823	0.906	32.012	0.106	0.106	0.000	0.000	0.000	0.000
83	A	93	ILE	0	-0.025	-0.007	26.692	-0.010	-0.010	0.000	0.000	0.000	0.000
84	A	94	ARG	1	0.812	0.876	27.393	0.143	0.143	0.000	0.000	0.000	0.000
85	A	95	ASP	-1	-0.848	-0.914	27.795	-0.189	-0.189	0.000	0.000	0.000	0.000
86	A	96	MET	0	-0.049	0.005	24.825	-0.020	-0.020	0.000	0.000	0.000	0.000
87	A	97	ALA	0	0.016	0.003	23.270	-0.021	-0.021	0.000	0.000	0.000	0.000
88	A	98	ARG	1	0.866	0.920	23.291	0.173	0.173	0.000	0.000	0.000	0.000
89	A	99	HIS	0	-0.027	-0.012	25.062	-0.016	-0.016	0.000	0.000	0.000	0.000
90	A	100	MET	0	0.004	0.017	20.238	-0.023	-0.023	0.000	0.000	0.000	0.000
91	A	101	ALA	0	0.016	0.000	20.104	-0.032	-0.032	0.000	0.000	0.000	0.000
92	A	102	THR	0	-0.038	-0.043	21.139	-0.029	-0.029	0.000	0.000	0.000	0.000
93	A	103	ILE	0	0.052	0.021	23.748	-0.013	-0.013	0.000	0.000	0.000	0.000
94	A	104	ILE	0	-0.002	0.002	16.965	-0.021	-0.021	0.000	0.000	0.000	0.000
95	A	105	SER	0	-0.059	-0.034	19.420	-0.025	-0.025	0.000	0.000	0.000	0.000
96	A	106	GLU	-1	-0.921	-0.976	20.414	-0.307	-0.307	0.000	0.000	0.000	0.000
97	A	107	ARG	1	0.851	0.941	21.117	0.392	0.392	0.000	0.000	0.000	0.000
98	A	108	PHE	0	-0.005	-0.018	16.931	-0.010	-0.010	0.000	0.000	0.000	0.000
99	A	109	ASN	0	-0.009	0.011	18.039	-0.032	-0.032	0.000	0.000	0.000	0.000
100	A	110	ARG	1	0.855	0.934	12.183	1.077	1.077	0.000	0.000	0.000	0.000
101	A	111	PRO	0	0.026	0.021	15.397	0.048	0.048	0.000	0.000	0.000	0.000
102	A	112	CYS	0	-0.063	-0.011	15.585	-0.078	-0.078	0.000	0.000	0.000	0.000
103	A	113	TYR	0	0.016	0.012	14.069	0.046	0.046	0.000	0.000	0.000	0.000
104	A	114	VAL	0	0.013	0.005	15.780	-0.043	-0.043	0.000	0.000	0.000	0.000
105	A	115	THR	0	-0.011	-0.006	17.234	0.036	0.036	0.000	0.000	0.000	0.000
106	A	116	TRP	0	-0.019	-0.016	19.122	-0.019	-0.019	0.000	0.000	0.000	0.000
107	A	117	SER	0	-0.009	-0.018	20.154	0.013	0.013	0.000	0.000	0.000	0.000
108	A	118	SER	0	-0.020	-0.035	22.143	0.001	0.001	0.000	0.000	0.000	0.000
109	A	119	LEU	0	0.002	0.007	24.831	0.007	0.007	0.000	0.000	0.000	0.000
110	A	120	PRO	0	0.021	0.003	26.490	0.001	0.001	0.000	0.000	0.000	0.000
111	A	121	SER	0	-0.008	-0.008	29.515	0.002	0.002	0.000	0.000	0.000	0.000
112	A	122	GLU	-1	-0.844	-0.885	27.272	-0.154	-0.154	0.000	0.000	0.000	0.000
113	A	123	ASP	-1	-0.714	-0.825	30.985	-0.095	-0.095	0.000	0.000	0.000	0.000
114	A	124	PRO	0	-0.018	-0.031	31.133	-0.004	-0.004	0.000	0.000	0.000	0.000
115	A	125	SER	0	-0.076	-0.065	32.370	-0.008	-0.008	0.000	0.000	0.000	0.000
116	A	126	MET	0	0.037	0.016	31.280	-0.004	-0.004	0.000	0.000	0.000	0.000
117	A	127	LEU	0	0.027	0.020	27.274	-0.004	-0.004	0.000	0.000	0.000	0.000
118	A	128	VAL	0	-0.052	-0.022	30.477	-0.007	-0.007	0.000	0.000	0.000	0.000
119	A	129	ALA	0	0.001	0.007	33.593	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	130	ASN	0	-0.024	-0.027	30.118	0.004	0.004	0.000	0.000	0.000	0.000
121	A	131	HIS	0	0.028	0.040	29.523	-0.023	-0.023	0.000	0.000	0.000	0.000
122	A	132	LEU	0	0.040	-0.003	28.450	-0.015	-0.015	0.000	0.000	0.000	0.000
123	A	133	TYR	0	0.013	0.006	27.378	-0.017	-0.017	0.000	0.000	0.000	0.000
124	A	134	ILE	0	0.049	0.018	24.017	-0.012	-0.012	0.000	0.000	0.000	0.000
125	A	135	LEU	0	0.035	0.015	23.824	-0.023	-0.023	0.000	0.000	0.000	0.000
126	A	136	LYS	1	0.852	0.909	23.450	0.179	0.179	0.000	0.000	0.000	0.000
127	A	137	LYS	1	0.903	0.968	23.304	0.159	0.159	0.000	0.000	0.000	0.000
128	A	138	CYS	0	-0.013	0.000	19.478	-0.016	-0.016	0.000	0.000	0.000	0.000
129	A	139	LEU	0	-0.006	-0.012	18.919	-0.047	-0.047	0.000	0.000	0.000	0.000
130	A	140	ASP	-1	-0.837	-0.902	19.996	-0.275	-0.275	0.000	0.000	0.000	0.000
131	A	141	LEU	0	-0.019	0.001	15.840	-0.017	-0.017	0.000	0.000	0.000	0.000
132	A	142	LEU	0	0.030	0.006	14.099	-0.042	-0.042	0.000	0.000	0.000	0.000
133	A	143	LYS	1	0.898	0.934	15.792	0.397	0.397	0.000	0.000	0.000	0.000
134	A	144	THR	0	-0.027	-0.021	16.907	-0.031	-0.031	0.000	0.000	0.000	0.000
135	A	145	GLU	-1	-0.852	-0.915	12.398	-0.424	-0.424	0.000	0.000	0.000	0.000
136	A	146	LEU	0	-0.077	-0.025	11.589	-0.152	-0.152	0.000	0.000	0.000	0.000
137	A	147	GLY	0	-0.057	0.003	13.457	0.049	0.049	0.000	0.000	0.000	0.000

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