FMO DATABASE

FMODB ID: Q1ZVY

Calculation Name: 2XZZ-A-Xray372

Preferred Name: Protein-glutamine gamma-glutamyltransferase K

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2XZZ

Chain ID: A

ChEMBL ID: CHEMBL2810

UniProt ID: P22735

Base Structure: X-ray

Registration Date: 2023-06-19

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	97
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-593914.392019
FMO2-HF: Nuclear repulsion	558103.206449
FMO2-HF: Total energy	-35811.18557
FMO2-MP2: Total energy	-35916.658196

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:SER)

Summations of interaction energy for fragment #1(A:-1:SER)

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.
-4.648	-7.585	21.384	-8.287	-10.161	-0.01

Interaction energy analysis for fragmet #1(A:-1:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : 0.018

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	693	LEU	0	-0.005	0.013	3.791	-1.040	1.253	-0.018	-1.059	-1.216	0.005
4	A	694	SER	0	-0.045	-0.019	5.519	-0.023	-0.023	0.000	0.000	0.000	0.000
5	A	695	LEU	0	0.029	-0.002	9.299	0.056	0.056	0.000	0.000	0.000	0.000
6	A	696	THR	0	-0.041	-0.020	12.448	0.045	0.045	0.000	0.000	0.000	0.000
7	A	697	LEU	0	-0.004	0.003	15.969	0.004	0.004	0.000	0.000	0.000	0.000
8	A	698	LEU	0	-0.034	-0.024	18.141	0.016	0.016	0.000	0.000	0.000	0.000
9	A	699	GLY	0	0.055	0.026	21.320	0.023	0.023	0.000	0.000	0.000	0.000
10	A	700	ALA	0	0.007	0.006	23.826	-0.018	-0.018	0.000	0.000	0.000	0.000
11	A	701	ALA	0	0.031	0.014	23.633	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	702	VAL	0	-0.001	-0.006	25.731	0.006	0.006	0.000	0.000	0.000	0.000
13	A	703	VAL	0	-0.039	-0.025	29.127	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	704	GLY	0	-0.004	0.006	30.029	0.010	0.010	0.000	0.000	0.000	0.000
15	A	705	GLN	0	-0.063	-0.043	27.789	0.007	0.007	0.000	0.000	0.000	0.000
16	A	706	GLU	-1	-0.912	-0.952	26.027	-0.168	-0.168	0.000	0.000	0.000	0.000
17	A	707	CYS	0	-0.069	-0.017	23.191	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	708	GLU	-1	-0.834	-0.935	20.137	-0.205	-0.205	0.000	0.000	0.000	0.000
19	A	709	VAL	0	-0.025	-0.001	15.067	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	710	GLN	0	-0.028	-0.022	13.632	0.044	0.044	0.000	0.000	0.000	0.000
21	A	711	ILE	0	-0.020	-0.015	8.950	-0.052	-0.052	0.000	0.000	0.000	0.000
22	A	712	VAL	0	0.036	0.014	8.393	0.084	0.084	0.000	0.000	0.000	0.000
23	A	713	PHE	0	0.012	-0.004	1.850	-1.818	-8.814	17.781	-5.201	-5.584	-0.018
24	A	714	LYS	1	0.922	0.973	4.209	-1.157	-1.053	-0.001	-0.020	-0.084	0.000
25	A	715	ASN	0	-0.015	-0.019	3.033	0.332	1.404	0.114	-0.571	-0.615	-0.005
26	A	716	PRO	0	-0.058	-0.026	2.138	-1.183	-0.915	3.498	-1.363	-2.402	0.008
27	A	717	LEU	0	-0.002	0.011	4.996	-0.713	-0.658	-0.001	-0.006	-0.049	0.000
28	A	718	PRO	0	0.005	0.005	7.882	-0.233	-0.233	0.000	0.000	0.000	0.000
29	A	719	VAL	0	0.011	-0.002	10.154	-0.148	-0.148	0.000	0.000	0.000	0.000
30	A	720	THR	0	0.026	-0.001	9.790	0.037	0.037	0.000	0.000	0.000	0.000
31	A	721	LEU	0	-0.052	-0.008	4.848	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	722	THR	0	0.027	-0.011	9.540	-0.094	-0.094	0.000	0.000	0.000	0.000
33	A	723	ASN	0	-0.020	-0.012	11.840	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	724	VAL	0	0.041	0.033	8.384	-0.007	-0.007	0.000	0.000	0.000	0.000
35	A	725	VAL	0	-0.029	-0.002	11.057	0.003	0.003	0.000	0.000	0.000	0.000
36	A	726	PHE	0	0.046	0.011	9.691	-0.057	-0.057	0.000	0.000	0.000	0.000
37	A	727	ARG	1	0.937	0.967	11.279	0.356	0.356	0.000	0.000	0.000	0.000
38	A	728	LEU	0	0.007	0.006	12.253	-0.104	-0.104	0.000	0.000	0.000	0.000
39	A	729	GLU	-1	-0.905	-0.955	14.827	-0.256	-0.256	0.000	0.000	0.000	0.000
40	A	730	GLY	0	0.087	0.048	16.473	-0.055	-0.055	0.000	0.000	0.000	0.000
41	A	731	SER	0	-0.040	-0.025	18.843	0.042	0.042	0.000	0.000	0.000	0.000
42	A	732	GLY	0	-0.035	-0.038	22.138	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	733	LEU	0	0.003	0.005	19.658	0.012	0.012	0.000	0.000	0.000	0.000
44	A	734	GLN	0	0.049	0.016	19.113	0.030	0.030	0.000	0.000	0.000	0.000
45	A	735	ARG	1	0.873	0.943	20.906	0.194	0.194	0.000	0.000	0.000	0.000
46	A	736	PRO	0	0.070	0.023	18.832	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	737	LYS	1	0.911	0.988	17.677	0.260	0.260	0.000	0.000	0.000	0.000
48	A	738	ILE	0	0.001	0.001	15.770	-0.042	-0.042	0.000	0.000	0.000	0.000
49	A	739	LEU	0	-0.052	-0.032	14.827	0.038	0.038	0.000	0.000	0.000	0.000
50	A	740	ASN	0	0.042	0.024	14.407	-0.032	-0.032	0.000	0.000	0.000	0.000
51	A	741	VAL	0	-0.043	-0.019	10.300	-0.012	-0.012	0.000	0.000	0.000	0.000
52	A	742	GLY	0	-0.010	0.000	13.308	0.034	0.034	0.000	0.000	0.000	0.000
53	A	743	ASP	-1	-0.841	-0.942	12.012	-0.064	-0.064	0.000	0.000	0.000	0.000
54	A	744	ILE	0	-0.044	-0.005	6.783	-0.064	-0.064	0.000	0.000	0.000	0.000
55	A	745	GLY	0	0.079	0.044	9.804	0.080	0.080	0.000	0.000	0.000	0.000
56	A	746	GLY	0	0.029	0.023	9.521	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	747	ASN	0	-0.055	-0.043	8.447	0.067	0.067	0.000	0.000	0.000	0.000
58	A	748	GLU	-1	-0.907	-0.938	9.030	0.052	0.052	0.000	0.000	0.000	0.000
59	A	749	THR	0	-0.045	-0.037	7.288	-0.051	-0.051	0.000	0.000	0.000	0.000
60	A	750	VAL	0	0.023	0.025	7.603	0.038	0.038	0.000	0.000	0.000	0.000
61	A	751	THR	0	-0.029	-0.027	9.183	-0.090	-0.090	0.000	0.000	0.000	0.000
62	A	752	LEU	0	0.023	0.012	10.569	0.025	0.025	0.000	0.000	0.000	0.000
63	A	753	ARG	1	0.933	0.987	13.920	0.150	0.150	0.000	0.000	0.000	0.000
64	A	754	GLN	0	-0.001	-0.005	16.740	0.005	0.005	0.000	0.000	0.000	0.000
65	A	755	SER	0	0.068	0.033	18.538	-0.017	-0.017	0.000	0.000	0.000	0.000
66	A	756	PHE	0	-0.081	-0.056	19.598	-0.007	-0.007	0.000	0.000	0.000	0.000
67	A	757	VAL	0	0.067	0.041	23.132	0.004	0.004	0.000	0.000	0.000	0.000
68	A	758	PRO	0	-0.034	0.001	24.575	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	759	VAL	0	0.010	0.013	26.280	0.014	0.014	0.000	0.000	0.000	0.000
70	A	760	ARG	1	0.909	0.941	26.763	0.178	0.178	0.000	0.000	0.000	0.000
71	A	761	PRO	0	0.066	0.042	27.036	-0.014	-0.014	0.000	0.000	0.000	0.000
72	A	762	GLY	0	0.002	-0.002	27.271	0.001	0.001	0.000	0.000	0.000	0.000
73	A	763	PRO	0	0.020	-0.002	23.229	-0.012	-0.012	0.000	0.000	0.000	0.000
74	A	764	ARG	1	0.866	0.957	21.559	0.219	0.219	0.000	0.000	0.000	0.000
75	A	765	GLN	0	0.019	0.014	16.170	-0.040	-0.040	0.000	0.000	0.000	0.000
76	A	766	LEU	0	-0.003	-0.008	15.664	0.046	0.046	0.000	0.000	0.000	0.000
77	A	767	ILE	0	-0.021	-0.013	11.296	-0.067	-0.067	0.000	0.000	0.000	0.000
78	A	768	ALA	0	0.040	0.022	9.808	0.104	0.104	0.000	0.000	0.000	0.000
79	A	769	SER	0	-0.039	-0.030	8.109	-0.129	-0.129	0.000	0.000	0.000	0.000
80	A	770	LEU	0	0.010	-0.008	5.307	0.025	0.025	0.000	0.000	0.000	0.000
81	A	771	ASP	-1	-0.931	-0.954	7.150	0.237	0.237	0.000	0.000	0.000	0.000
82	A	772	SER	0	0.050	-0.012	8.010	-0.078	-0.078	0.000	0.000	0.000	0.000
83	A	773	PRO	0	0.031	0.016	9.253	0.191	0.191	0.000	0.000	0.000	0.000
84	A	774	GLN	0	0.057	0.052	9.016	0.036	0.036	0.000	0.000	0.000	0.000
85	A	775	LEU	0	-0.029	-0.012	3.430	-0.088	0.179	0.011	-0.067	-0.211	0.000
86	A	776	SER	0	-0.034	-0.007	6.868	0.320	0.320	0.000	0.000	0.000	0.000
87	A	777	GLN	0	-0.056	-0.017	9.387	-0.150	-0.150	0.000	0.000	0.000	0.000
88	A	778	VAL	0	0.003	0.003	9.508	0.239	0.239	0.000	0.000	0.000	0.000
89	A	779	HIS	0	-0.001	-0.009	8.580	-0.174	-0.174	0.000	0.000	0.000	0.000
90	A	780	GLY	0	-0.002	0.001	11.774	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	781	VAL	0	-0.031	-0.021	11.788	-0.008	-0.008	0.000	0.000	0.000	0.000
92	A	782	ILE	0	-0.001	0.003	15.004	-0.022	-0.022	0.000	0.000	0.000	0.000
93	A	783	GLN	0	-0.045	-0.026	18.355	0.036	0.036	0.000	0.000	0.000	0.000
94	A	784	VAL	0	-0.007	-0.008	19.797	-0.026	-0.026	0.000	0.000	0.000	0.000
95	A	785	ASP	-1	-0.871	-0.924	23.216	0.241	0.241	0.000	0.000	0.000	0.000
96	A	786	VAL	0	-0.052	-0.029	25.396	-0.014	-0.014	0.000	0.000	0.000	0.000
97	A	787	ALA	0	0.001	0.009	27.947	-0.008	-0.008	0.000	0.000	0.000	0.000

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