FMO DATABASE

FMODB ID: GQKK1

Calculation Name: 2XZZ-A-Xray311

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	98
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-598143.24524
FMO2-HF: Nuclear repulsion	562180.943555
FMO2-HF: Total energy	-35962.301685
FMO2-MP2: Total energy	-36068.194639

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:-2:ACE )

Summations of interaction energy for fragment #1(A:-2:ACE )

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.
1.006	1.817	-0.006	-0.403	-0.402	0

Interaction energy analysis for fragmet #1(A:-2:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : 0.000

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	A	0	MET	0	0.015	0.003	3.847	1.000	1.811	-0.006	-0.403	-0.402
4	A	693	LEU	0	-0.003	0.016	6.822	0.106	0.106	0.000	0.000	0.000
5	A	694	SER	0	-0.046	-0.019	8.407	0.148	0.148	0.000	0.000	0.000
6	A	695	LEU	0	0.030	-0.002	11.558	0.002	0.002	0.000	0.000	0.000
7	A	696	THR	0	-0.043	-0.022	14.620	0.005	0.005	0.000	0.000	0.000
8	A	697	LEU	0	-0.005	0.003	18.286	-0.001	-0.001	0.000	0.000	0.000
9	A	698	LEU	0	-0.034	-0.023	21.398	-0.006	-0.006	0.000	0.000	0.000
10	A	699	GLY	0	0.056	0.026	24.136	0.000	0.000	0.000	0.000	0.000
11	A	700	ALA	0	0.005	0.005	25.749	0.003	0.003	0.000	0.000	0.000
12	A	701	ALA	0	0.032	0.016	25.051	-0.001	-0.001	0.000	0.000	0.000
13	A	702	VAL	0	-0.002	-0.007	27.162	0.004	0.004	0.000	0.000	0.000
14	A	703	VAL	0	-0.038	-0.024	30.342	0.000	0.000	0.000	0.000	0.000
15	A	704	GLY	0	-0.002	0.007	30.995	-0.002	-0.002	0.000	0.000	0.000
16	A	705	GLN	0	-0.067	-0.045	29.581	-0.002	-0.002	0.000	0.000	0.000
17	A	706	GLU	-1	-0.912	-0.952	28.135	-0.010	-0.010	0.000	0.000	0.000
18	A	707	CYS	0	-0.068	-0.017	24.978	-0.002	-0.002	0.000	0.000	0.000
19	A	708	GLU	-1	-0.834	-0.936	23.178	-0.048	-0.048	0.000	0.000	0.000
20	A	709	VAL	0	-0.026	-0.001	17.316	0.003	0.003	0.000	0.000	0.000
21	A	710	GLN	0	-0.029	-0.023	17.741	-0.010	-0.010	0.000	0.000	0.000
22	A	711	ILE	0	-0.021	-0.015	12.307	0.010	0.010	0.000	0.000	0.000
23	A	712	VAL	0	0.035	0.014	13.255	-0.007	-0.007	0.000	0.000	0.000
24	A	713	PHE	0	0.013	-0.004	5.948	-0.082	-0.082	0.000	0.000	0.000
25	A	714	LYS	1	0.919	0.972	10.086	0.596	0.596	0.000	0.000	0.000
26	A	715	ASN	0	-0.016	-0.020	9.210	-0.419	-0.419	0.000	0.000	0.000
27	A	716	PRO	0	-0.054	-0.023	6.005	0.172	0.172	0.000	0.000	0.000
28	A	717	LEU	0	-0.004	0.009	8.131	0.148	0.148	0.000	0.000	0.000
29	A	718	PRO	0	0.009	0.008	10.956	0.052	0.052	0.000	0.000	0.000
30	A	719	VAL	0	0.014	0.000	12.595	0.068	0.068	0.000	0.000	0.000
31	A	720	THR	0	0.022	-0.003	13.716	-0.063	-0.063	0.000	0.000	0.000
32	A	721	LEU	0	-0.050	-0.007	9.151	-0.013	-0.013	0.000	0.000	0.000
33	A	722	THR	0	0.026	-0.012	13.002	0.048	0.048	0.000	0.000	0.000
34	A	723	ASN	0	-0.021	-0.013	13.804	-0.020	-0.020	0.000	0.000	0.000
35	A	724	VAL	0	0.043	0.035	11.212	0.015	0.015	0.000	0.000	0.000
36	A	725	VAL	0	-0.028	-0.002	12.550	0.031	0.031	0.000	0.000	0.000
37	A	726	PHE	0	0.042	0.010	11.809	-0.001	-0.001	0.000	0.000	0.000
38	A	727	ARG	1	0.937	0.967	12.430	-0.066	-0.066	0.000	0.000	0.000
39	A	728	LEU	0	0.010	0.007	13.214	0.001	0.001	0.000	0.000	0.000
40	A	729	GLU	-1	-0.908	-0.956	15.299	0.148	0.148	0.000	0.000	0.000
41	A	730	GLY	0	0.088	0.047	16.835	0.009	0.009	0.000	0.000	0.000
42	A	731	SER	0	-0.039	-0.025	19.091	-0.018	-0.018	0.000	0.000	0.000
43	A	732	GLY	0	-0.036	-0.038	22.232	-0.004	-0.004	0.000	0.000	0.000
44	A	733	LEU	0	0.001	0.005	20.396	-0.007	-0.007	0.000	0.000	0.000
45	A	734	GLN	0	0.053	0.017	20.185	-0.006	-0.006	0.000	0.000	0.000
46	A	735	ARG	1	0.871	0.942	21.138	-0.049	-0.049	0.000	0.000	0.000
47	A	736	PRO	0	0.069	0.023	18.660	-0.007	-0.007	0.000	0.000	0.000
48	A	737	LYS	1	0.908	0.987	18.920	0.008	0.008	0.000	0.000	0.000
49	A	738	ILE	0	0.006	0.003	16.594	0.005	0.005	0.000	0.000	0.000
50	A	739	LEU	0	-0.054	-0.033	16.701	0.000	0.000	0.000	0.000	0.000
51	A	740	ASN	0	0.042	0.024	16.424	-0.001	-0.001	0.000	0.000	0.000
52	A	741	VAL	0	-0.041	-0.018	14.419	0.003	0.003	0.000	0.000	0.000
53	A	742	GLY	0	-0.013	-0.002	16.925	0.005	0.005	0.000	0.000	0.000
54	A	743	ASP	-1	-0.841	-0.941	16.151	-0.209	-0.209	0.000	0.000	0.000
55	A	744	ILE	0	-0.046	-0.006	11.557	-0.003	-0.003	0.000	0.000	0.000
56	A	745	GLY	0	0.082	0.045	14.842	-0.030	-0.030	0.000	0.000	0.000
57	A	746	GLY	0	0.031	0.025	14.391	-0.057	-0.057	0.000	0.000	0.000
58	A	747	ASN	0	-0.052	-0.041	13.681	0.007	0.007	0.000	0.000	0.000
59	A	748	GLU	-1	-0.909	-0.938	14.736	-0.255	-0.255	0.000	0.000	0.000
60	A	749	THR	0	-0.043	-0.038	13.671	-0.094	-0.094	0.000	0.000	0.000
61	A	750	VAL	0	0.020	0.024	13.318	0.054	0.054	0.000	0.000	0.000
62	A	751	THR	0	-0.028	-0.027	14.682	-0.024	-0.024	0.000	0.000	0.000
63	A	752	LEU	0	0.023	0.011	14.295	0.013	0.013	0.000	0.000	0.000
64	A	753	ARG	1	0.932	0.987	17.952	0.072	0.072	0.000	0.000	0.000
65	A	754	GLN	0	-0.002	-0.005	19.160	-0.003	-0.003	0.000	0.000	0.000
66	A	755	SER	0	0.065	0.032	21.026	0.004	0.004	0.000	0.000	0.000
67	A	756	PHE	0	-0.077	-0.055	21.319	0.008	0.008	0.000	0.000	0.000
68	A	757	VAL	0	0.064	0.040	24.708	-0.002	-0.002	0.000	0.000	0.000
69	A	758	PRO	0	-0.034	0.001	25.647	0.007	0.007	0.000	0.000	0.000
70	A	759	VAL	0	0.013	0.015	26.926	-0.001	-0.001	0.000	0.000	0.000
71	A	760	ARG	1	0.908	0.940	26.749	-0.059	-0.059	0.000	0.000	0.000
72	A	761	PRO	0	0.065	0.041	27.701	0.002	0.002	0.000	0.000	0.000
73	A	762	GLY	0	0.003	-0.001	28.043	0.005	0.005	0.000	0.000	0.000
74	A	763	PRO	0	0.019	-0.002	24.048	-0.001	-0.001	0.000	0.000	0.000
75	A	764	ARG	1	0.865	0.957	22.198	-0.063	-0.063	0.000	0.000	0.000
76	A	765	GLN	0	0.019	0.013	16.408	-0.012	-0.012	0.000	0.000	0.000
77	A	766	LEU	0	-0.001	-0.008	16.757	-0.008	-0.008	0.000	0.000	0.000
78	A	767	ILE	0	-0.022	-0.014	11.382	0.010	0.010	0.000	0.000	0.000
79	A	768	ALA	0	0.040	0.022	11.254	-0.028	-0.028	0.000	0.000	0.000
80	A	769	SER	0	-0.044	-0.031	8.491	0.062	0.062	0.000	0.000	0.000
81	A	770	LEU	0	0.015	-0.006	6.919	-0.065	-0.065	0.000	0.000	0.000
82	A	771	ASP	-1	-0.935	-0.956	7.337	0.158	0.158	0.000	0.000	0.000
83	A	772	SER	0	0.053	-0.011	9.277	-0.086	-0.086	0.000	0.000	0.000
84	A	773	PRO	0	0.029	0.015	9.590	-0.001	-0.001	0.000	0.000	0.000
85	A	774	GLN	0	0.057	0.053	10.500	0.014	0.014	0.000	0.000	0.000
86	A	775	LEU	0	-0.024	-0.009	5.183	-0.165	-0.165	0.000	0.000	0.000
87	A	776	SER	0	-0.038	-0.010	5.517	0.200	0.200	0.000	0.000	0.000
88	A	777	GLN	0	-0.056	-0.017	8.146	0.039	0.039	0.000	0.000	0.000
89	A	778	VAL	0	0.000	0.002	8.163	-0.097	-0.097	0.000	0.000	0.000
90	A	779	HIS	0	-0.001	-0.009	8.219	0.044	0.044	0.000	0.000	0.000
91	A	780	GLY	0	-0.003	0.000	11.389	0.016	0.016	0.000	0.000	0.000
92	A	781	VAL	0	-0.033	-0.022	13.147	-0.007	-0.007	0.000	0.000	0.000
93	A	782	ILE	0	-0.005	0.000	15.918	0.014	0.014	0.000	0.000	0.000
94	A	783	GLN	0	-0.051	-0.029	19.515	-0.022	-0.022	0.000	0.000	0.000
95	A	784	VAL	0	-0.014	-0.013	21.715	0.015	0.015	0.000	0.000	0.000
96	A	785	ASP	-1	-0.891	-0.937	24.974	-0.124	-0.124	0.000	0.000	0.000
97	A	786	VAL	0	-0.103	-0.049	27.847	0.007	0.007	0.000	0.000	0.000
98	A	787	ALA	-1	-0.909	-0.947	30.367	-0.074	-0.074	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:-2:ACE )