FMO DATABASE

FMODB ID: 435JN

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	OptAll
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	-593898.258058
FMO2-HF: Nuclear repulsion	558086.312578
FMO2-HF: Total energy	-35811.94548
FMO2-MP2: Total energy	-35917.372811

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.
-10.451	-3.619	5.531	-5	-7.359	-0.009

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 : 0.047 / q_NPA : 0.026

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	-0.007	0.003	3.741	-1.856	0.677	0.002	-1.252	-1.283	0.005
4	A	694	SER	0	-0.054	-0.026	4.971	0.330	0.350	-0.001	-0.007	-0.012	0.000
5	A	695	LEU	0	0.045	0.008	8.766	0.028	0.028	0.000	0.000	0.000	0.000
6	A	696	THR	0	-0.039	-0.024	12.161	0.097	0.097	0.000	0.000	0.000	0.000
7	A	697	LEU	0	-0.009	0.000	15.747	-0.002	-0.002	0.000	0.000	0.000	0.000
8	A	698	LEU	0	-0.023	-0.011	18.481	0.021	0.021	0.000	0.000	0.000	0.000
9	A	699	GLY	0	0.021	0.012	21.396	0.032	0.032	0.000	0.000	0.000	0.000
10	A	700	ALA	0	0.011	0.013	23.764	-0.020	-0.020	0.000	0.000	0.000	0.000
11	A	701	ALA	0	0.042	0.023	23.660	-0.008	-0.008	0.000	0.000	0.000	0.000
12	A	702	VAL	0	0.014	0.004	25.815	0.008	0.008	0.000	0.000	0.000	0.000
13	A	703	VAL	0	-0.032	-0.027	29.061	-0.006	-0.006	0.000	0.000	0.000	0.000
14	A	704	GLY	0	-0.010	0.000	30.088	0.013	0.013	0.000	0.000	0.000	0.000
15	A	705	GLN	0	-0.092	-0.059	27.335	0.012	0.012	0.000	0.000	0.000	0.000
16	A	706	GLU	-1	-0.878	-0.921	25.962	-0.265	-0.265	0.000	0.000	0.000	0.000
17	A	707	CYS	0	-0.078	-0.019	23.170	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	708	GLU	-1	-0.772	-0.896	19.810	-0.344	-0.344	0.000	0.000	0.000	0.000
19	A	709	VAL	0	-0.034	-0.010	14.828	0.002	0.002	0.000	0.000	0.000	0.000
20	A	710	GLN	0	0.003	0.003	13.994	0.036	0.036	0.000	0.000	0.000	0.000
21	A	711	ILE	0	-0.020	-0.015	9.180	-0.053	-0.053	0.000	0.000	0.000	0.000
22	A	712	VAL	0	0.017	-0.003	8.537	0.135	0.135	0.000	0.000	0.000	0.000
23	A	713	PHE	0	0.027	0.008	2.276	-4.242	-2.893	2.510	-1.555	-2.304	-0.015
24	A	714	LYS	1	0.825	0.915	4.169	-1.140	-1.006	-0.001	-0.030	-0.102	0.000
25	A	715	ASN	0	0.017	-0.015	2.540	-2.256	-0.979	0.705	-0.868	-1.114	-0.010
26	A	716	PRO	0	-0.048	-0.019	2.243	-1.404	-0.206	2.313	-1.235	-2.276	0.011
27	A	717	LEU	0	0.017	0.023	4.978	-0.659	-0.603	-0.001	-0.005	-0.049	0.000
28	A	718	PRO	0	-0.024	-0.011	8.044	-0.315	-0.315	0.000	0.000	0.000	0.000
29	A	719	VAL	0	0.007	-0.007	10.303	-0.169	-0.169	0.000	0.000	0.000	0.000
30	A	720	THR	0	0.015	-0.004	9.726	0.068	0.068	0.000	0.000	0.000	0.000
31	A	721	LEU	0	-0.035	-0.003	4.788	-0.046	0.001	-0.001	-0.001	-0.044	0.000
32	A	722	THR	0	-0.009	-0.027	9.515	-0.086	-0.086	0.000	0.000	0.000	0.000
33	A	723	ASN	0	-0.017	-0.011	12.286	-0.035	-0.035	0.000	0.000	0.000	0.000
34	A	724	VAL	0	-0.005	0.015	8.798	-0.034	-0.034	0.000	0.000	0.000	0.000
35	A	725	VAL	0	-0.003	0.006	11.102	0.036	0.036	0.000	0.000	0.000	0.000
36	A	726	PHE	0	0.055	0.011	9.437	-0.156	-0.156	0.000	0.000	0.000	0.000
37	A	727	ARG	1	0.815	0.889	11.320	0.737	0.737	0.000	0.000	0.000	0.000
38	A	728	LEU	0	0.030	0.021	12.248	-0.141	-0.141	0.000	0.000	0.000	0.000
39	A	729	GLU	-1	-0.919	-0.961	14.875	-0.460	-0.460	0.000	0.000	0.000	0.000
40	A	730	GLY	0	0.101	0.041	16.844	-0.051	-0.051	0.000	0.000	0.000	0.000
41	A	731	SER	0	-0.040	-0.013	19.414	0.051	0.051	0.000	0.000	0.000	0.000
42	A	732	GLY	0	0.011	-0.002	22.504	0.007	0.007	0.000	0.000	0.000	0.000
43	A	733	LEU	0	-0.016	0.002	19.853	0.016	0.016	0.000	0.000	0.000	0.000
44	A	734	GLN	0	0.075	0.040	19.448	0.036	0.036	0.000	0.000	0.000	0.000
45	A	735	ARG	1	0.861	0.921	21.095	0.304	0.304	0.000	0.000	0.000	0.000
46	A	736	PRO	0	0.029	0.000	18.572	-0.010	-0.010	0.000	0.000	0.000	0.000
47	A	737	LYS	1	0.901	0.984	17.852	0.440	0.440	0.000	0.000	0.000	0.000
48	A	738	ILE	0	0.005	0.007	15.688	-0.068	-0.068	0.000	0.000	0.000	0.000
49	A	739	LEU	0	-0.049	-0.037	14.760	0.057	0.057	0.000	0.000	0.000	0.000
50	A	740	ASN	0	0.007	0.011	14.545	-0.023	-0.023	0.000	0.000	0.000	0.000
51	A	741	VAL	0	-0.042	-0.021	10.298	-0.014	-0.014	0.000	0.000	0.000	0.000
52	A	742	GLY	0	0.022	0.012	13.374	0.071	0.071	0.000	0.000	0.000	0.000
53	A	743	ASP	-1	-0.826	-0.936	11.765	-0.292	-0.292	0.000	0.000	0.000	0.000
54	A	744	ILE	0	-0.018	0.012	6.639	-0.016	-0.016	0.000	0.000	0.000	0.000
55	A	745	GLY	0	0.085	0.038	9.586	0.114	0.114	0.000	0.000	0.000	0.000
56	A	746	GLY	0	-0.008	0.009	9.435	-0.012	-0.012	0.000	0.000	0.000	0.000
57	A	747	ASN	0	-0.021	-0.029	8.371	0.120	0.120	0.000	0.000	0.000	0.000
58	A	748	GLU	-1	-0.849	-0.888	9.111	-0.204	-0.204	0.000	0.000	0.000	0.000
59	A	749	THR	0	-0.026	-0.024	7.189	-0.044	-0.044	0.000	0.000	0.000	0.000
60	A	750	VAL	0	0.021	0.022	7.566	0.094	0.094	0.000	0.000	0.000	0.000
61	A	751	THR	0	-0.029	-0.026	8.978	-0.150	-0.150	0.000	0.000	0.000	0.000
62	A	752	LEU	0	0.010	0.016	10.840	0.053	0.053	0.000	0.000	0.000	0.000
63	A	753	ARG	1	0.869	0.920	13.992	0.294	0.294	0.000	0.000	0.000	0.000
64	A	754	GLN	0	-0.016	-0.018	16.816	0.004	0.004	0.000	0.000	0.000	0.000
65	A	755	SER	0	0.007	0.002	18.535	-0.022	-0.022	0.000	0.000	0.000	0.000
66	A	756	PHE	0	-0.032	-0.031	19.765	-0.020	-0.020	0.000	0.000	0.000	0.000
67	A	757	VAL	0	0.081	0.045	23.026	0.014	0.014	0.000	0.000	0.000	0.000
68	A	758	PRO	0	-0.028	0.005	24.625	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	759	VAL	0	0.013	0.004	26.359	0.021	0.021	0.000	0.000	0.000	0.000
70	A	760	ARG	1	0.927	0.948	27.796	0.230	0.230	0.000	0.000	0.000	0.000
71	A	761	PRO	0	0.065	0.049	27.480	-0.018	-0.018	0.000	0.000	0.000	0.000
72	A	762	GLY	0	0.012	0.012	27.859	0.000	0.000	0.000	0.000	0.000	0.000
73	A	763	PRO	0	0.034	0.007	23.718	-0.015	-0.015	0.000	0.000	0.000	0.000
74	A	764	ARG	1	0.801	0.897	21.927	0.280	0.280	0.000	0.000	0.000	0.000
75	A	765	GLN	0	0.033	0.020	16.464	-0.056	-0.056	0.000	0.000	0.000	0.000
76	A	766	LEU	0	-0.023	-0.018	15.682	0.047	0.047	0.000	0.000	0.000	0.000
77	A	767	ILE	0	0.006	0.011	11.735	-0.083	-0.083	0.000	0.000	0.000	0.000
78	A	768	ALA	0	0.034	0.010	10.130	0.108	0.108	0.000	0.000	0.000	0.000
79	A	769	SER	0	-0.043	-0.019	8.071	-0.143	-0.143	0.000	0.000	0.000	0.000
80	A	770	LEU	0	-0.013	-0.014	5.136	0.109	0.109	0.000	0.000	0.000	0.000
81	A	771	ASP	-1	-0.826	-0.888	6.790	-0.330	-0.330	0.000	0.000	0.000	0.000
82	A	772	SER	0	0.058	-0.002	8.195	-0.033	-0.033	0.000	0.000	0.000	0.000
83	A	773	PRO	0	0.021	0.015	9.393	0.168	0.168	0.000	0.000	0.000	0.000
84	A	774	GLN	0	0.065	0.054	8.829	0.032	0.032	0.000	0.000	0.000	0.000
85	A	775	LEU	0	-0.023	-0.005	3.613	0.132	0.350	0.005	-0.047	-0.175	0.000
86	A	776	SER	0	-0.045	-0.012	6.834	0.309	0.309	0.000	0.000	0.000	0.000
87	A	777	GLN	0	-0.035	-0.017	9.364	-0.141	-0.141	0.000	0.000	0.000	0.000
88	A	778	VAL	0	-0.001	0.004	9.636	0.313	0.313	0.000	0.000	0.000	0.000
89	A	779	HIS	0	-0.019	-0.015	8.418	-0.235	-0.235	0.000	0.000	0.000	0.000
90	A	780	GLY	0	0.001	-0.006	11.784	0.033	0.033	0.000	0.000	0.000	0.000
91	A	781	VAL	0	-0.036	-0.023	12.001	-0.028	-0.028	0.000	0.000	0.000	0.000
92	A	782	ILE	0	-0.013	-0.004	15.044	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	783	GLN	0	-0.015	-0.014	18.290	0.032	0.032	0.000	0.000	0.000	0.000
94	A	784	VAL	0	-0.012	-0.015	20.035	-0.024	-0.024	0.000	0.000	0.000	0.000
95	A	785	ASP	-1	-0.850	-0.908	23.334	0.291	0.291	0.000	0.000	0.000	0.000
96	A	786	VAL	0	-0.036	-0.017	25.337	-0.020	-0.020	0.000	0.000	0.000	0.000
97	A	787	ALA	0	-0.046	-0.013	27.812	-0.023	-0.023	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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