FMO DATABASE

FMODB ID: V5RQ1

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	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	138
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1278347.145558
FMO2-HF: Nuclear repulsion	1221517.313028
FMO2-HF: Total energy	-56829.832531
FMO2-MP2: Total energy	-56993.944571

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.
0.75	2.489	-0.016	-0.748	-0.977	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 : -0.023

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].
3	B	3	SER	0	-0.014	0.015	3.824	0.136	1.759	-0.017	-0.719	-0.888
4	B	4	TYR	0	0.000	0.001	5.866	-0.007	-0.007	0.000	0.000	0.000
5	B	5	GLU	-1	-0.852	-0.935	9.508	-0.107	-0.107	0.000	0.000	0.000
6	B	6	PHE	0	0.009	-0.003	12.340	0.017	0.017	0.000	0.000	0.000
7	B	7	GLN	0	0.039	0.022	16.160	-0.004	-0.004	0.000	0.000	0.000
8	B	8	THR	0	-0.026	-0.015	18.772	0.005	0.005	0.000	0.000	0.000
9	B	9	HIS	0	-0.008	-0.005	22.410	-0.002	-0.002	0.000	0.000	0.000
10	B	10	LEU	0	-0.048	-0.016	25.197	0.003	0.003	0.000	0.000	0.000
11	B	11	PRO	0	-0.017	-0.013	27.219	-0.001	-0.001	0.000	0.000	0.000
12	B	12	LYS	1	0.936	0.977	30.337	-0.012	-0.012	0.000	0.000	0.000
13	B	23	GLU	-1	-0.904	-0.955	32.754	-0.001	-0.001	0.000	0.000	0.000
14	B	24	ASN	0	-0.068	-0.034	29.265	0.002	0.002	0.000	0.000	0.000
15	B	25	LYS	1	0.956	0.982	26.801	-0.005	-0.005	0.000	0.000	0.000
16	B	26	GLU	-1	-0.812	-0.901	22.425	-0.011	-0.011	0.000	0.000	0.000
17	B	27	LEU	0	-0.058	-0.038	20.430	-0.001	-0.001	0.000	0.000	0.000
18	B	28	TYR	0	-0.048	-0.040	12.402	-0.003	-0.003	0.000	0.000	0.000
19	B	29	VAL	0	-0.021	-0.014	14.479	0.005	0.005	0.000	0.000	0.000
20	B	30	GLN	0	0.061	0.016	6.847	0.065	0.065	0.000	0.000	0.000
21	B	31	ALA	0	-0.004	0.001	9.631	0.038	0.038	0.000	0.000	0.000
22	B	32	THR	0	0.015	0.017	3.719	-0.387	-0.271	0.001	-0.029	-0.089
23	B	33	HIS	0	0.012	0.010	6.002	-0.154	-0.154	0.000	0.000	0.000
24	B	34	PHE	0	-0.016	-0.017	5.081	0.989	0.989	0.000	0.000	0.000
25	B	35	ASN	0	-0.005	-0.012	8.371	-0.058	-0.058	0.000	0.000	0.000
26	B	36	ASN	0	-0.006	0.002	11.227	-0.019	-0.019	0.000	0.000	0.000
27	B	37	THR	0	0.013	0.008	11.463	-0.094	-0.094	0.000	0.000	0.000
28	B	38	ILE	0	0.066	0.050	10.253	0.177	0.177	0.000	0.000	0.000
29	B	39	LEU	0	-0.044	-0.018	8.959	-0.095	-0.095	0.000	0.000	0.000
30	B	40	LEU	0	0.011	0.006	10.121	-0.009	-0.009	0.000	0.000	0.000
31	B	41	GLN	0	-0.004	-0.017	10.352	-0.012	-0.012	0.000	0.000	0.000
32	B	42	ILE	0	0.001	-0.013	14.207	0.000	0.000	0.000	0.000	0.000
33	B	43	ARG	1	0.870	0.913	14.259	0.065	0.065	0.000	0.000	0.000
34	B	44	LEU	0	-0.004	0.000	19.115	0.003	0.003	0.000	0.000	0.000
35	B	45	ASN	0	0.024	0.002	22.723	-0.001	-0.001	0.000	0.000	0.000
36	B	46	GLY	0	0.046	0.031	19.350	-0.003	-0.003	0.000	0.000	0.000
37	B	47	GLU	-1	-0.964	-0.971	19.615	-0.021	-0.021	0.000	0.000	0.000
38	B	48	MET	0	-0.054	-0.043	14.798	0.007	0.007	0.000	0.000	0.000
39	B	49	ASP	-1	-0.828	-0.879	20.320	-0.002	-0.002	0.000	0.000	0.000
40	B	50	SER	0	0.001	0.000	21.524	0.001	0.001	0.000	0.000	0.000
41	B	51	THR	0	-0.022	-0.025	17.406	-0.003	-0.003	0.000	0.000	0.000
42	B	52	TYR	0	0.006	0.001	19.385	-0.005	-0.005	0.000	0.000	0.000
43	B	53	GLU	-1	-0.842	-0.909	18.325	0.107	0.107	0.000	0.000	0.000
44	B	54	VAL	0	0.006	0.004	19.203	-0.014	-0.014	0.000	0.000	0.000
45	B	55	SER	0	0.026	0.007	19.660	0.017	0.017	0.000	0.000	0.000
46	B	56	SER	0	0.023	0.016	21.847	-0.008	-0.008	0.000	0.000	0.000
47	B	57	LYS	1	0.875	0.923	24.265	-0.057	-0.057	0.000	0.000	0.000
48	B	58	GLY	0	-0.029	0.001	27.499	-0.002	-0.002	0.000	0.000	0.000
49	B	59	LEU	0	0.044	0.038	27.454	0.001	0.001	0.000	0.000	0.000
50	B	80	TYR	0	-0.086	-0.046	49.860	-0.001	-0.001	0.000	0.000	0.000
51	B	81	ASP	-1	-0.982	-0.996	47.402	0.025	0.025	0.000	0.000	0.000
52	B	82	ASP	-1	-0.886	-0.958	44.560	0.028	0.028	0.000	0.000	0.000
53	B	83	GLU	-1	-0.850	-0.918	41.191	0.030	0.030	0.000	0.000	0.000
54	B	84	GLU	-1	-0.956	-0.988	40.447	0.036	0.036	0.000	0.000	0.000
55	B	85	GLU	-1	-0.992	-0.992	40.269	0.035	0.035	0.000	0.000	0.000
56	B	86	GLU	-1	-0.916	-0.956	37.268	0.040	0.040	0.000	0.000	0.000
57	B	87	PHE	0	0.020	0.017	36.026	0.005	0.005	0.000	0.000	0.000
58	B	88	VAL	0	-0.034	-0.034	35.495	0.003	0.003	0.000	0.000	0.000
59	B	89	ARG	1	0.910	0.943	33.720	-0.046	-0.046	0.000	0.000	0.000
60	B	90	ASP	-1	-0.920	-0.954	32.109	0.059	0.059	0.000	0.000	0.000
61	B	91	HIS	1	0.720	0.856	30.931	-0.051	-0.051	0.000	0.000	0.000
62	B	92	LEU	0	-0.014	0.032	31.877	0.000	0.000	0.000	0.000	0.000
63	B	93	SER	0	-0.050	-0.024	27.084	0.004	0.004	0.000	0.000	0.000
64	B	94	ASP	-1	-0.866	-0.922	28.536	0.052	0.052	0.000	0.000	0.000
65	B	95	TYR	0	-0.065	-0.085	22.472	0.012	0.012	0.000	0.000	0.000
66	B	96	GLN	0	-0.051	-0.014	25.293	-0.012	-0.012	0.000	0.000	0.000
67	B	97	VAL	0	0.012	0.003	23.715	0.008	0.008	0.000	0.000	0.000
68	B	98	VAL	0	-0.017	-0.009	23.326	-0.008	-0.008	0.000	0.000	0.000
69	B	99	THR	0	0.028	0.006	22.966	0.007	0.007	0.000	0.000	0.000
70	B	100	LYS	1	0.758	0.873	19.702	-0.070	-0.070	0.000	0.000	0.000
71	B	101	LEU	0	0.014	0.009	20.995	-0.007	-0.007	0.000	0.000	0.000
72	B	102	GLY	0	0.069	0.042	23.573	0.003	0.003	0.000	0.000	0.000
73	B	103	ASP	-1	-0.860	-0.921	26.219	0.015	0.015	0.000	0.000	0.000
74	B	104	SER	0	-0.010	-0.020	28.142	0.003	0.003	0.000	0.000	0.000
75	B	105	ALA	0	-0.039	-0.014	29.567	0.002	0.002	0.000	0.000	0.000
76	B	106	ASP	-1	-0.816	-0.883	29.377	0.020	0.020	0.000	0.000	0.000
77	B	107	PRO	0	0.034	0.006	30.492	0.004	0.004	0.000	0.000	0.000
78	B	108	LYS	1	0.766	0.856	30.068	-0.017	-0.017	0.000	0.000	0.000
79	B	109	VAL	0	0.004	0.009	24.812	0.003	0.003	0.000	0.000	0.000
80	B	110	PRO	0	0.014	0.009	25.895	0.006	0.006	0.000	0.000	0.000
81	B	111	VAL	0	0.025	0.016	27.067	0.005	0.005	0.000	0.000	0.000
82	B	112	VAL	0	-0.001	0.001	23.032	0.004	0.004	0.000	0.000	0.000
83	B	113	CYS	0	-0.042	-0.024	22.003	0.007	0.007	0.000	0.000	0.000
84	B	114	VAL	0	0.040	0.029	22.136	0.012	0.012	0.000	0.000	0.000
85	B	115	GLN	0	-0.004	0.005	24.052	0.008	0.008	0.000	0.000	0.000
86	B	116	ILE	0	-0.008	-0.008	18.357	0.005	0.005	0.000	0.000	0.000
87	B	117	ALA	0	-0.010	-0.011	19.530	0.014	0.014	0.000	0.000	0.000
88	B	118	GLU	-1	-0.762	-0.860	20.553	0.102	0.102	0.000	0.000	0.000
89	B	119	LEU	0	-0.051	-0.007	19.739	0.002	0.002	0.000	0.000	0.000
90	B	120	TYR	0	0.009	-0.034	12.830	0.000	0.000	0.000	0.000	0.000
91	B	121	ARG	1	0.881	0.948	18.309	-0.118	-0.118	0.000	0.000	0.000
92	B	122	ARG	1	0.891	0.941	20.582	-0.077	-0.077	0.000	0.000	0.000
93	B	123	VAL	0	-0.058	-0.026	21.153	-0.009	-0.009	0.000	0.000	0.000
94	B	124	ILE	0	-0.015	0.007	14.948	0.003	0.003	0.000	0.000	0.000
95	B	125	LEU	0	-0.067	-0.019	13.483	0.022	0.022	0.000	0.000	0.000
96	B	126	PRO	0	-0.041	-0.018	16.530	-0.009	-0.009	0.000	0.000	0.000
97	B	127	GLU	-1	-0.778	-0.877	15.981	0.078	0.078	0.000	0.000	0.000
98	B	138	GLN	0	-0.016	-0.016	16.374	0.015	0.015	0.000	0.000	0.000
99	B	139	PHE	0	0.006	-0.021	17.191	0.003	0.003	0.000	0.000	0.000
100	B	140	SER	0	0.005	0.000	15.834	-0.040	-0.040	0.000	0.000	0.000
101	B	141	LEU	0	-0.014	0.009	14.296	0.043	0.043	0.000	0.000	0.000
102	B	142	LEU	0	-0.015	0.006	13.435	-0.035	-0.035	0.000	0.000	0.000
103	B	143	ILE	0	0.037	0.010	14.389	0.012	0.012	0.000	0.000	0.000
104	B	144	SER	0	-0.005	0.005	15.330	-0.018	-0.018	0.000	0.000	0.000
105	B	145	MET	0	0.015	0.000	16.954	0.000	0.000	0.000	0.000	0.000
106	B	146	SER	0	0.026	0.031	19.638	-0.003	-0.003	0.000	0.000	0.000
107	B	147	SER	0	-0.040	-0.057	22.732	0.004	0.004	0.000	0.000	0.000
108	B	148	LYS	1	0.872	0.939	25.893	0.001	0.001	0.000	0.000	0.000
109	B	149	ILE	0	-0.005	0.015	21.913	-0.001	-0.001	0.000	0.000	0.000
110	B	150	TRP	0	0.008	-0.022	23.514	0.001	0.001	0.000	0.000	0.000
111	B	151	ARG	1	0.840	0.923	28.785	-0.029	-0.029	0.000	0.000	0.000
112	B	152	ALA	0	0.043	0.014	30.864	0.000	0.000	0.000	0.000	0.000
113	B	153	THR	0	-0.041	-0.020	32.416	-0.001	-0.001	0.000	0.000	0.000
114	B	154	LYS	1	0.859	0.912	32.409	-0.010	-0.010	0.000	0.000	0.000
115	B	155	GLU	-1	-0.826	-0.886	35.369	0.018	0.018	0.000	0.000	0.000
116	B	156	GLN	0	0.026	-0.009	35.749	0.000	0.000	0.000	0.000	0.000
117	B	157	SER	0	-0.104	-0.061	39.084	-0.002	-0.002	0.000	0.000	0.000
118	B	158	ALA	0	0.005	0.011	36.909	-0.001	-0.001	0.000	0.000	0.000
119	B	159	ASP	-1	-0.792	-0.893	33.972	0.021	0.021	0.000	0.000	0.000
120	B	160	ASP	-1	-0.881	-0.928	33.528	0.013	0.013	0.000	0.000	0.000
121	B	161	ASN	0	-0.002	-0.019	33.678	0.001	0.001	0.000	0.000	0.000
122	B	162	ASP	-1	-0.904	-0.954	31.704	0.025	0.025	0.000	0.000	0.000
123	B	163	PHE	0	0.068	0.037	30.681	0.002	0.002	0.000	0.000	0.000
124	B	164	GLY	0	0.037	0.015	30.603	0.002	0.002	0.000	0.000	0.000
125	B	165	LYS	1	0.852	0.926	27.771	-0.015	-0.015	0.000	0.000	0.000
126	B	166	LEU	0	0.008	0.005	25.512	0.001	0.001	0.000	0.000	0.000
127	B	167	VAL	0	0.004	-0.001	25.701	0.004	0.004	0.000	0.000	0.000
128	B	168	PHE	0	-0.001	0.003	24.368	0.003	0.003	0.000	0.000	0.000
129	B	169	VAL	0	0.037	0.019	21.055	0.001	0.001	0.000	0.000	0.000
130	B	170	LEU	0	0.000	-0.001	21.165	0.005	0.005	0.000	0.000	0.000
131	B	171	LYS	1	0.845	0.896	21.346	-0.033	-0.033	0.000	0.000	0.000
132	B	172	CYS	0	-0.033	-0.008	19.706	0.000	0.000	0.000	0.000	0.000
133	B	173	ILE	0	-0.009	-0.002	16.250	0.000	0.000	0.000	0.000	0.000
134	B	174	LYS	1	0.853	0.894	16.686	-0.072	-0.072	0.000	0.000	0.000
135	B	175	ASP	-1	-0.870	-0.914	18.500	0.046	0.046	0.000	0.000	0.000
136	B	176	MET	0	-0.113	-0.015	12.717	-0.013	-0.013	0.000	0.000	0.000
137	B	177	TYR	0	-0.083	-0.025	13.781	-0.011	-0.011	0.000	0.000	0.000
138	B	178	ALA	0	0.038	0.043	10.994	0.036	0.036	0.000	0.000	0.000

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