FMO DATABASE

FMODB ID: G6N51

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1244417.862941
FMO2-HF: Nuclear repulsion	1189578.417341
FMO2-HF: Total energy	-54839.4456
FMO2-MP2: Total energy	-54996.297604

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.
-4.144	-2.146	9.246	-4.525	-6.719	-0.037

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 : -0.030 / q_NPA : -0.025

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	-0.005	0.012	2.303	-1.213	2.185	0.584	-1.525	-2.457	0.003
4	A	4	LYS	1	0.998	0.986	2.173	-2.988	-4.259	8.651	-3.543	-3.837	-0.040
5	A	5	THR	0	-0.023	-0.006	3.201	1.234	0.910	0.012	0.583	-0.271	0.000
6	A	6	ILE	0	-0.010	0.005	5.872	0.155	0.155	0.000	0.000	0.000	0.000
7	A	7	SER	0	0.044	0.017	8.812	0.042	0.042	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.792	0.885	11.148	0.670	0.670	0.000	0.000	0.000	0.000
9	A	9	THR	0	0.049	0.023	15.244	0.013	0.013	0.000	0.000	0.000	0.000
10	A	10	ILE	0	-0.060	-0.032	18.670	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.902	-0.887	21.127	-0.196	-0.196	0.000	0.000	0.000	0.000
12	A	12	SER	0	0.005	0.554	24.580	0.010	0.010	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-1.121	-1.373	28.119	-0.152	-0.152	0.000	0.000	0.000	0.000
14	A	14	SER	0	0.139	-0.066	24.251	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.032	-0.106	25.329	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	16	PHE	0	-0.046	-0.115	26.271	-0.014	-0.014	0.000	0.000	0.000	0.000
17	A	17	LEU	0	0.110	0.055	29.996	0.008	0.008	0.000	0.000	0.000	0.000
18	A	18	GLN	0	0.012	0.023	29.496	0.005	0.005	0.000	0.000	0.000	0.000
19	A	19	PRO	0	-0.004	0.007	27.437	0.001	0.001	0.000	0.000	0.000	0.000
20	A	20	THR	0	0.071	0.031	23.353	-0.010	-0.010	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.057	-0.034	21.411	0.000	0.000	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.889	-0.968	18.174	-0.346	-0.346	0.000	0.000	0.000	0.000
23	A	23	VAL	0	0.003	0.003	13.953	-0.008	-0.008	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.037	0.030	10.419	-0.022	-0.022	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.017	0.007	10.746	0.036	0.036	0.000	0.000	0.000	0.000
26	A	26	THR	0	-0.039	-0.029	6.036	-0.216	-0.216	0.000	0.000	0.000	0.000
27	A	27	LEU	0	0.010	-0.007	6.818	0.297	0.297	0.000	0.000	0.000	0.000
28	A	28	PRO	0	-0.005	-0.008	6.492	-0.738	-0.738	0.000	0.000	0.000	0.000
29	A	29	ALA	0	-0.049	-0.024	4.350	0.053	0.248	-0.001	-0.040	-0.154	0.000
30	A	30	ASP	-1	-0.921	-0.950	6.409	-0.984	-0.984	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.887	-0.953	8.158	-0.864	-0.864	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.988	0.998	11.825	0.469	0.469	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.024	-0.009	14.939	-0.075	-0.075	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.960	0.952	14.307	0.310	0.310	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.951	0.977	13.312	0.257	0.257	0.000	0.000	0.000	0.000
36	A	36	ILE	0	0.031	0.042	7.350	0.117	0.117	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.030	0.015	10.942	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	38	ILE	0	0.019	0.026	10.924	-0.203	-0.203	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.023	-0.008	11.009	0.162	0.162	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.020	-0.012	11.951	-0.113	-0.113	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.013	0.011	13.902	0.066	0.066	0.000	0.000	0.000	0.000
42	A	42	VAL	0	-0.009	-0.017	16.013	-0.021	-0.021	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.092	0.057	18.883	0.021	0.021	0.000	0.000	0.000	0.000
44	A	44	PHE	0	-0.010	-0.006	22.022	-0.010	-0.010	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.833	0.932	20.074	0.272	0.272	0.000	0.000	0.000	0.000
46	A	46	GLN	0	-0.020	-0.017	23.988	0.013	0.013	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.959	-0.947	24.819	-0.150	-0.150	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.063	0.034	26.887	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	49	SER	0	0.069	-0.002	28.026	0.005	0.005	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.050	-0.025	25.838	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	51	ASN	0	-0.106	-0.041	21.753	0.001	0.001	0.000	0.000	0.000	0.000
52	A	52	SER	0	0.060	0.011	22.535	0.007	0.007	0.000	0.000	0.000	0.000
53	A	53	SER	0	0.011	0.005	21.626	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	54	SER	0	-0.025	0.000	21.968	0.017	0.017	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.004	0.012	23.314	0.003	0.003	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.028	-0.008	19.347	-0.016	-0.016	0.000	0.000	0.000	0.000
57	A	57	SER	0	-0.043	-0.054	22.651	0.019	0.019	0.000	0.000	0.000	0.000
58	A	58	CYS	0	-0.048	-0.017	23.732	0.013	0.013	0.000	0.000	0.000	0.000
59	A	59	TYR	0	0.022	0.016	14.983	-0.021	-0.021	0.000	0.000	0.000	0.000
60	A	60	TYR	0	0.068	0.023	20.795	0.036	0.036	0.000	0.000	0.000	0.000
61	A	61	TYR	0	0.007	0.013	17.445	-0.054	-0.054	0.000	0.000	0.000	0.000
62	A	62	ALA	0	0.022	0.006	19.970	0.040	0.040	0.000	0.000	0.000	0.000
63	A	63	ILE	0	-0.012	-0.002	19.391	-0.055	-0.055	0.000	0.000	0.000	0.000
64	A	64	PRO	0	-0.011	0.003	20.370	0.035	0.035	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.023	-0.012	23.437	0.005	0.005	0.000	0.000	0.000	0.000
66	A	66	MET	0	-0.012	-0.013	26.332	0.015	0.015	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.877	0.951	23.203	0.229	0.229	0.000	0.000	0.000	0.000
68	A	78	SER	0	0.002	-0.010	26.594	0.001	0.001	0.000	0.000	0.000	0.000
69	A	79	ASN	0	0.053	0.028	28.735	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	80	VAL	0	0.005	0.024	23.575	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	81	VAL	0	0.005	0.015	25.232	0.016	0.016	0.000	0.000	0.000	0.000
72	A	82	GLY	0	0.041	-0.006	24.542	-0.027	-0.027	0.000	0.000	0.000	0.000
73	A	83	ILE	0	-0.057	-0.024	24.369	0.023	0.023	0.000	0.000	0.000	0.000
74	A	84	PRO	0	0.008	0.009	24.110	-0.027	-0.027	0.000	0.000	0.000	0.000
75	A	85	LEU	0	-0.039	-0.027	19.468	0.010	0.010	0.000	0.000	0.000	0.000
76	A	86	LEU	0	-0.009	0.002	23.306	0.016	0.016	0.000	0.000	0.000	0.000
77	A	87	ASP	-1	-0.832	-0.936	24.807	-0.187	-0.187	0.000	0.000	0.000	0.000
78	A	88	THR	0	0.009	0.015	27.944	0.008	0.008	0.000	0.000	0.000	0.000
79	A	89	LYS	1	0.963	0.964	29.892	0.117	0.117	0.000	0.000	0.000	0.000
80	A	90	ASP	-1	-0.793	-0.890	31.576	-0.144	-0.144	0.000	0.000	0.000	0.000
81	A	91	ASP	-1	-0.783	-0.904	31.604	-0.148	-0.148	0.000	0.000	0.000	0.000
82	A	92	ARG	1	0.851	0.934	32.009	0.131	0.131	0.000	0.000	0.000	0.000
83	A	93	ILE	0	-0.022	-0.003	26.589	-0.012	-0.012	0.000	0.000	0.000	0.000
84	A	94	ARG	1	0.830	0.903	27.375	0.142	0.142	0.000	0.000	0.000	0.000
85	A	95	ASP	-1	-0.894	-0.948	27.861	-0.186	-0.186	0.000	0.000	0.000	0.000
86	A	96	MET	0	-0.037	0.003	24.578	-0.017	-0.017	0.000	0.000	0.000	0.000
87	A	97	ALA	0	0.015	0.003	23.265	-0.023	-0.023	0.000	0.000	0.000	0.000
88	A	98	ARG	1	0.907	0.962	23.336	0.171	0.171	0.000	0.000	0.000	0.000
89	A	99	HIS	0	-0.042	-0.046	25.116	-0.006	-0.006	0.000	0.000	0.000	0.000
90	A	100	MET	0	0.000	0.018	20.035	-0.018	-0.018	0.000	0.000	0.000	0.000
91	A	101	ALA	0	0.014	-0.002	20.141	-0.029	-0.029	0.000	0.000	0.000	0.000
92	A	102	THR	0	-0.045	-0.036	21.197	-0.017	-0.017	0.000	0.000	0.000	0.000
93	A	103	ILE	0	0.063	0.030	23.430	-0.005	-0.005	0.000	0.000	0.000	0.000
94	A	104	ILE	0	-0.012	-0.007	16.831	-0.015	-0.015	0.000	0.000	0.000	0.000
95	A	105	SER	0	-0.060	-0.029	19.468	-0.011	-0.011	0.000	0.000	0.000	0.000
96	A	106	GLU	-1	-0.907	-0.975	20.473	-0.251	-0.251	0.000	0.000	0.000	0.000
97	A	107	ARG	1	0.852	0.953	20.802	0.376	0.376	0.000	0.000	0.000	0.000
98	A	108	PHE	0	-0.018	-0.032	16.760	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	109	ASN	0	-0.037	-0.017	17.875	-0.023	-0.023	0.000	0.000	0.000	0.000
100	A	110	ARG	1	0.858	0.924	11.984	0.887	0.887	0.000	0.000	0.000	0.000
101	A	111	PRO	0	0.023	0.014	15.268	0.024	0.024	0.000	0.000	0.000	0.000
102	A	112	CYS	0	-0.056	-0.004	15.716	-0.089	-0.089	0.000	0.000	0.000	0.000
103	A	113	TYR	0	0.011	0.009	14.476	0.060	0.060	0.000	0.000	0.000	0.000
104	A	114	VAL	0	0.011	-0.002	15.916	-0.066	-0.066	0.000	0.000	0.000	0.000
105	A	115	THR	0	-0.013	-0.006	17.212	0.047	0.047	0.000	0.000	0.000	0.000
106	A	116	TRP	0	-0.042	-0.031	19.195	-0.031	-0.031	0.000	0.000	0.000	0.000
107	A	117	SER	0	-0.028	-0.025	19.974	0.025	0.025	0.000	0.000	0.000	0.000
108	A	118	SER	0	0.021	0.004	22.021	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	119	LEU	0	0.014	0.007	24.659	0.006	0.006	0.000	0.000	0.000	0.000
110	A	120	PRO	0	0.012	0.000	26.397	0.006	0.006	0.000	0.000	0.000	0.000
111	A	121	SER	0	-0.003	-0.008	29.434	0.004	0.004	0.000	0.000	0.000	0.000
112	A	122	GLU	-1	-0.831	-0.877	27.245	-0.201	-0.201	0.000	0.000	0.000	0.000
113	A	123	ASP	-1	-0.764	-0.869	30.757	-0.123	-0.123	0.000	0.000	0.000	0.000
114	A	124	PRO	0	0.005	-0.023	31.146	-0.005	-0.005	0.000	0.000	0.000	0.000
115	A	125	SER	0	-0.069	-0.034	32.146	-0.006	-0.006	0.000	0.000	0.000	0.000
116	A	126	MET	0	0.050	0.018	30.672	-0.005	-0.005	0.000	0.000	0.000	0.000
117	A	127	LEU	0	0.000	0.006	27.077	-0.006	-0.006	0.000	0.000	0.000	0.000
118	A	128	VAL	0	-0.038	-0.013	30.154	-0.005	-0.005	0.000	0.000	0.000	0.000
119	A	129	ALA	0	-0.004	0.003	33.287	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	130	ASN	0	-0.016	-0.016	29.612	0.002	0.002	0.000	0.000	0.000	0.000
121	A	131	HIS	0	0.033	0.057	29.083	-0.023	-0.023	0.000	0.000	0.000	0.000
122	A	132	LEU	0	0.044	-0.001	28.051	-0.016	-0.016	0.000	0.000	0.000	0.000
123	A	133	TYR	0	0.007	0.000	26.399	-0.014	-0.014	0.000	0.000	0.000	0.000
124	A	134	ILE	0	0.059	0.016	23.488	-0.018	-0.018	0.000	0.000	0.000	0.000
125	A	135	LEU	0	0.025	0.009	23.321	-0.030	-0.030	0.000	0.000	0.000	0.000
126	A	136	LYS	1	0.869	0.952	22.978	0.206	0.206	0.000	0.000	0.000	0.000
127	A	137	LYS	1	0.874	0.964	22.462	0.244	0.244	0.000	0.000	0.000	0.000
128	A	138	CYS	0	-0.010	0.008	19.021	-0.033	-0.033	0.000	0.000	0.000	0.000
129	A	139	LEU	0	-0.010	-0.012	18.356	-0.053	-0.053	0.000	0.000	0.000	0.000
130	A	140	ASP	-1	-0.932	-0.968	19.396	-0.351	-0.351	0.000	0.000	0.000	0.000
131	A	141	LEU	0	-0.029	-0.005	15.123	-0.022	-0.022	0.000	0.000	0.000	0.000
132	A	142	LEU	0	0.021	-0.003	13.712	-0.063	-0.063	0.000	0.000	0.000	0.000
133	A	143	LYS	1	0.940	0.966	15.161	0.367	0.367	0.000	0.000	0.000	0.000
134	A	144	THR	0	-0.018	-0.010	16.246	-0.012	-0.012	0.000	0.000	0.000	0.000
135	A	145	GLU	-1	-0.865	-0.935	11.534	-0.783	-0.783	0.000	0.000	0.000	0.000
136	A	146	LEU	0	-0.101	-0.032	11.360	-0.183	-0.183	0.000	0.000	0.000	0.000
137	A	147	GLY	0	-0.069	-0.016	13.434	0.125	0.125	0.000	0.000	0.000	0.000

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