FMO DATABASE

FMODB ID: YZYV2

Calculation Name: 2Z5B-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2Z5B

Chain ID: B

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1278940.198738
FMO2-HF: Nuclear repulsion	1222111.338378
FMO2-HF: Total energy	-56828.860361
FMO2-MP2: Total energy	-56993.019678

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(B:1:MET)

Summations of interaction energy for fragment #1(B: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.
0.708	2.455	-0.015	-0.744	-0.989	0

Interaction energy analysis for fragmet #1(B:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.023 / q_NPA : -0.022

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].
3	B	3	SER	0	-0.009	0.021	3.824	-0.148	1.482	-0.016	-0.715	-0.899
4	B	4	TYR	0	0.026	0.017	5.858	0.045	0.045	0.000	0.000	0.000
5	B	5	GLU	-1	-0.855	-0.918	9.499	-0.104	-0.104	0.000	0.000	0.000
6	B	6	PHE	0	0.018	0.005	12.333	0.021	0.021	0.000	0.000	0.000
7	B	7	GLN	0	0.039	0.014	16.153	-0.003	-0.003	0.000	0.000	0.000
8	B	8	THR	0	-0.014	0.002	18.767	0.006	0.006	0.000	0.000	0.000
9	B	9	HIS	0	0.060	0.037	22.405	-0.003	-0.003	0.000	0.000	0.000
10	B	10	LEU	0	-0.064	-0.030	25.437	0.005	0.005	0.000	0.000	0.000
11	B	11	PRO	0	-0.011	-0.010	27.213	-0.002	-0.002	0.000	0.000	0.000
12	B	12	LYS	1	0.922	0.972	30.330	-0.016	-0.016	0.000	0.000	0.000
13	B	23	GLU	-1	-0.922	-0.961	32.740	-0.004	-0.004	0.000	0.000	0.000
14	B	24	ASN	0	-0.068	-0.031	29.024	0.003	0.003	0.000	0.000	0.000
15	B	25	LYS	1	0.950	0.976	26.711	-0.007	-0.007	0.000	0.000	0.000
16	B	26	GLU	-1	-0.885	-0.936	22.340	-0.018	-0.018	0.000	0.000	0.000
17	B	27	LEU	0	-0.052	-0.041	20.440	-0.001	-0.001	0.000	0.000	0.000
18	B	28	TYR	0	-0.071	-0.074	12.353	-0.004	-0.004	0.000	0.000	0.000
19	B	29	VAL	0	-0.011	-0.009	14.386	0.001	0.001	0.000	0.000	0.000
20	B	30	GLN	0	0.049	-0.001	6.786	0.072	0.072	0.000	0.000	0.000
21	B	31	ALA	0	0.006	0.007	9.623	0.030	0.030	0.000	0.000	0.000
22	B	32	THR	0	0.017	0.018	3.705	-0.392	-0.275	0.001	-0.029	-0.090
23	B	33	HIS	0	-0.012	-0.007	5.982	-0.160	-0.160	0.000	0.000	0.000
24	B	34	PHE	0	-0.035	-0.022	5.545	1.028	1.028	0.000	0.000	0.000
25	B	35	ASN	0	0.010	-0.009	8.371	-0.070	-0.070	0.000	0.000	0.000
26	B	36	ASN	0	-0.015	0.002	11.261	-0.014	-0.014	0.000	0.000	0.000
27	B	37	THR	0	0.011	-0.001	11.324	-0.092	-0.092	0.000	0.000	0.000
28	B	38	ILE	0	0.075	0.049	10.243	0.173	0.173	0.000	0.000	0.000
29	B	39	LEU	0	-0.049	-0.018	8.999	-0.095	-0.095	0.000	0.000	0.000
30	B	40	LEU	0	0.014	0.004	10.114	-0.007	-0.007	0.000	0.000	0.000
31	B	41	GLN	0	0.007	-0.002	10.588	-0.020	-0.020	0.000	0.000	0.000
32	B	42	ILE	0	0.006	-0.012	14.202	0.005	0.005	0.000	0.000	0.000
33	B	43	ARG	1	0.846	0.904	14.185	0.089	0.089	0.000	0.000	0.000
34	B	44	LEU	0	-0.017	-0.002	19.112	0.005	0.005	0.000	0.000	0.000
35	B	45	ASN	0	0.048	0.017	22.719	-0.002	-0.002	0.000	0.000	0.000
36	B	46	GLY	0	0.034	0.025	19.350	-0.005	-0.005	0.000	0.000	0.000
37	B	47	GLU	-1	-0.958	-0.974	19.615	-0.036	-0.036	0.000	0.000	0.000
38	B	48	MET	0	-0.045	-0.039	14.576	0.011	0.011	0.000	0.000	0.000
39	B	49	ASP	-1	-0.834	-0.868	20.318	-0.010	-0.010	0.000	0.000	0.000
40	B	50	SER	0	0.005	-0.006	21.584	0.002	0.002	0.000	0.000	0.000
41	B	51	THR	0	-0.041	-0.025	17.484	-0.003	-0.003	0.000	0.000	0.000
42	B	52	TYR	0	-0.002	0.011	19.378	-0.006	-0.006	0.000	0.000	0.000
43	B	53	GLU	-1	-0.885	-0.932	18.460	0.119	0.119	0.000	0.000	0.000
44	B	54	VAL	0	-0.005	-0.002	19.196	-0.015	-0.015	0.000	0.000	0.000
45	B	55	SER	0	0.022	0.008	19.653	0.019	0.019	0.000	0.000	0.000
46	B	56	SER	0	0.022	0.012	21.840	-0.008	-0.008	0.000	0.000	0.000
47	B	57	LYS	1	0.913	0.949	24.258	-0.065	-0.065	0.000	0.000	0.000
48	B	58	GLY	0	-0.031	0.001	27.478	-0.002	-0.002	0.000	0.000	0.000
49	B	59	LEU	0	0.029	0.021	27.406	0.004	0.004	0.000	0.000	0.000
50	B	80	TYR	0	-0.075	-0.046	50.373	-0.001	-0.001	0.000	0.000	0.000
51	B	81	ASP	-1	-0.983	-0.995	47.569	0.032	0.032	0.000	0.000	0.000
52	B	82	ASP	-1	-0.916	-0.982	45.187	0.037	0.037	0.000	0.000	0.000
53	B	83	GLU	-1	-0.850	-0.911	41.394	0.040	0.040	0.000	0.000	0.000
54	B	84	GLU	-1	-0.944	-0.978	40.556	0.046	0.046	0.000	0.000	0.000
55	B	85	GLU	-1	-0.968	-0.977	40.300	0.042	0.042	0.000	0.000	0.000
56	B	86	GLU	-1	-0.917	-0.957	37.301	0.051	0.051	0.000	0.000	0.000
57	B	87	PHE	0	-0.023	0.011	35.510	0.006	0.006	0.000	0.000	0.000
58	B	88	VAL	0	-0.027	-0.036	35.495	0.004	0.004	0.000	0.000	0.000
59	B	89	ARG	1	0.925	0.956	34.388	-0.055	-0.055	0.000	0.000	0.000
60	B	90	ASP	-1	-0.918	-0.958	32.216	0.071	0.071	0.000	0.000	0.000
61	B	91	HIS	1	0.770	0.883	31.078	-0.063	-0.063	0.000	0.000	0.000
62	B	92	LEU	0	-0.029	0.016	31.867	-0.001	-0.001	0.000	0.000	0.000
63	B	93	SER	0	-0.043	-0.055	27.079	0.004	0.004	0.000	0.000	0.000
64	B	94	ASP	-1	-0.888	-0.895	28.526	0.061	0.061	0.000	0.000	0.000
65	B	95	TYR	0	-0.142	-0.183	22.218	0.012	0.012	0.000	0.000	0.000
66	B	96	GLN	0	-0.088	-0.045	24.773	-0.016	-0.016	0.000	0.000	0.000
67	B	97	VAL	0	0.013	0.008	23.763	0.009	0.009	0.000	0.000	0.000
68	B	98	VAL	0	-0.012	-0.005	23.393	-0.008	-0.008	0.000	0.000	0.000
69	B	99	THR	0	0.033	0.006	22.962	0.007	0.007	0.000	0.000	0.000
70	B	100	LYS	1	0.804	0.899	19.678	-0.066	-0.066	0.000	0.000	0.000
71	B	101	LEU	0	0.007	0.005	20.956	-0.008	-0.008	0.000	0.000	0.000
72	B	102	GLY	0	0.077	0.046	23.572	0.004	0.004	0.000	0.000	0.000
73	B	103	ASP	-1	-0.861	-0.931	26.217	0.014	0.014	0.000	0.000	0.000
74	B	104	SER	0	-0.011	-0.022	28.139	0.003	0.003	0.000	0.000	0.000
75	B	105	ALA	0	-0.045	-0.013	29.564	0.003	0.003	0.000	0.000	0.000
76	B	106	ASP	-1	-0.795	-0.893	29.329	0.023	0.023	0.000	0.000	0.000
77	B	107	PRO	0	0.018	0.010	30.486	0.004	0.004	0.000	0.000	0.000
78	B	108	LYS	1	0.779	0.890	29.930	-0.017	-0.017	0.000	0.000	0.000
79	B	109	VAL	0	0.020	0.016	24.741	0.004	0.004	0.000	0.000	0.000
80	B	110	PRO	0	-0.002	0.000	25.889	0.007	0.007	0.000	0.000	0.000
81	B	111	VAL	0	0.012	0.007	27.059	0.006	0.006	0.000	0.000	0.000
82	B	112	VAL	0	-0.013	-0.002	23.017	0.006	0.006	0.000	0.000	0.000
83	B	113	CYS	0	-0.033	-0.019	22.009	0.008	0.008	0.000	0.000	0.000
84	B	114	VAL	0	0.046	0.033	22.128	0.014	0.014	0.000	0.000	0.000
85	B	115	GLN	0	-0.011	0.002	24.043	0.011	0.011	0.000	0.000	0.000
86	B	116	ILE	0	-0.012	-0.007	18.304	0.007	0.007	0.000	0.000	0.000
87	B	117	ALA	0	0.007	-0.007	19.522	0.016	0.016	0.000	0.000	0.000
88	B	118	GLU	-1	-0.715	-0.773	20.543	0.122	0.122	0.000	0.000	0.000
89	B	119	LEU	0	-0.056	-0.010	19.635	0.003	0.003	0.000	0.000	0.000
90	B	120	TYR	0	0.031	-0.022	12.924	-0.006	-0.006	0.000	0.000	0.000
91	B	121	ARG	1	0.904	0.961	18.298	-0.135	-0.135	0.000	0.000	0.000
92	B	122	ARG	1	0.891	0.935	20.571	-0.095	-0.095	0.000	0.000	0.000
93	B	123	VAL	0	-0.064	-0.026	20.814	-0.010	-0.010	0.000	0.000	0.000
94	B	124	ILE	0	-0.008	0.013	14.888	0.004	0.004	0.000	0.000	0.000
95	B	125	LEU	0	-0.060	-0.019	13.517	0.030	0.030	0.000	0.000	0.000
96	B	126	PRO	0	-0.050	-0.022	16.602	-0.012	-0.012	0.000	0.000	0.000
97	B	127	GLU	-1	-0.925	-0.966	15.761	0.124	0.124	0.000	0.000	0.000
98	B	138	GLN	0	-0.023	-0.019	16.201	0.021	0.021	0.000	0.000	0.000
99	B	139	PHE	0	0.000	-0.024	17.131	0.002	0.002	0.000	0.000	0.000
100	B	140	SER	0	0.020	0.016	16.033	-0.043	-0.043	0.000	0.000	0.000
101	B	141	LEU	0	-0.009	0.012	14.370	0.045	0.045	0.000	0.000	0.000
102	B	142	LEU	0	-0.011	0.003	13.504	-0.038	-0.038	0.000	0.000	0.000
103	B	143	ILE	0	0.032	0.009	14.383	0.012	0.012	0.000	0.000	0.000
104	B	144	SER	0	-0.012	-0.018	15.326	-0.012	-0.012	0.000	0.000	0.000
105	B	145	MET	0	0.006	-0.004	16.950	0.001	0.001	0.000	0.000	0.000
106	B	146	SER	0	0.019	0.029	19.634	-0.004	-0.004	0.000	0.000	0.000
107	B	147	SER	0	-0.029	-0.049	22.729	0.006	0.006	0.000	0.000	0.000
108	B	148	LYS	1	0.928	0.954	25.889	0.005	0.005	0.000	0.000	0.000
109	B	149	ILE	0	0.003	0.018	21.895	0.000	0.000	0.000	0.000	0.000
110	B	150	TRP	0	0.037	-0.009	23.245	0.002	0.002	0.000	0.000	0.000
111	B	151	ARG	1	0.784	0.916	28.733	-0.035	-0.035	0.000	0.000	0.000
112	B	152	ALA	0	0.031	0.010	30.919	0.000	0.000	0.000	0.000	0.000
113	B	153	THR	0	-0.016	0.000	32.566	-0.001	-0.001	0.000	0.000	0.000
114	B	154	LYS	1	0.829	0.888	32.548	-0.009	-0.009	0.000	0.000	0.000
115	B	155	GLU	-1	-0.839	-0.897	35.001	0.020	0.020	0.000	0.000	0.000
116	B	156	GLN	0	0.035	0.001	35.610	0.001	0.001	0.000	0.000	0.000
117	B	157	SER	0	-0.103	-0.062	38.923	-0.002	-0.002	0.000	0.000	0.000
118	B	158	ALA	0	-0.012	0.005	36.872	-0.001	-0.001	0.000	0.000	0.000
119	B	159	ASP	-1	-0.755	-0.890	33.809	0.024	0.024	0.000	0.000	0.000
120	B	160	ASP	-1	-0.949	-0.962	33.820	0.013	0.013	0.000	0.000	0.000
121	B	161	ASN	0	0.018	-0.018	33.592	0.001	0.001	0.000	0.000	0.000
122	B	162	ASP	-1	-0.857	-0.947	31.691	0.029	0.029	0.000	0.000	0.000
123	B	163	PHE	0	0.039	0.028	30.673	0.003	0.003	0.000	0.000	0.000
124	B	164	GLY	0	0.041	0.017	30.594	0.003	0.003	0.000	0.000	0.000
125	B	165	LYS	1	0.890	0.947	27.623	-0.018	-0.018	0.000	0.000	0.000
126	B	166	LEU	0	0.011	0.007	25.471	0.002	0.002	0.000	0.000	0.000
127	B	167	VAL	0	0.002	0.000	25.692	0.006	0.006	0.000	0.000	0.000
128	B	168	PHE	0	-0.004	0.000	24.305	0.005	0.005	0.000	0.000	0.000
129	B	169	VAL	0	0.037	0.016	20.998	0.002	0.002	0.000	0.000	0.000
130	B	170	LEU	0	0.005	0.002	21.156	0.007	0.007	0.000	0.000	0.000
131	B	171	LYS	1	0.886	0.946	21.336	-0.051	-0.051	0.000	0.000	0.000
132	B	172	CYS	0	-0.026	-0.004	19.676	0.002	0.002	0.000	0.000	0.000
133	B	173	ILE	0	0.009	0.009	16.082	0.003	0.003	0.000	0.000	0.000
134	B	174	LYS	1	0.988	0.979	16.676	-0.080	-0.080	0.000	0.000	0.000
135	B	175	ASP	-1	-0.903	-0.955	18.490	0.080	0.080	0.000	0.000	0.000
136	B	176	MET	0	-0.121	-0.028	12.603	-0.012	-0.012	0.000	0.000	0.000
137	B	177	TYR	0	-0.071	-0.022	13.686	-0.002	-0.002	0.000	0.000	0.000
138	B	178	ALA	0	0.017	0.036	10.888	0.053	0.053	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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