FMO DATABASE

FMODB ID: K3JG3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-594284.346422
FMO2-HF: Nuclear repulsion	558472.719988
FMO2-HF: Total energy	-35811.626434
FMO2-MP2: Total energy	-35917.055437

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.
-7.448	-2.493	7.971	-5.24	-7.684	-0.011

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 : 0.034 / q_NPA : 0.022

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	-0.014	0.004	3.791	-1.110	1.273	-0.018	-1.126	-1.240	0.005
4	A	694	SER	0	-0.028	-0.015	5.363	0.079	0.104	-0.001	-0.004	-0.019	0.000
5	A	695	LEU	0	0.025	-0.001	9.145	0.039	0.039	0.000	0.000	0.000	0.000
6	A	696	THR	0	-0.048	-0.023	12.296	0.073	0.073	0.000	0.000	0.000	0.000
7	A	697	LEU	0	0.009	0.004	15.813	-0.002	-0.002	0.000	0.000	0.000	0.000
8	A	698	LEU	0	-0.035	-0.021	18.239	0.021	0.021	0.000	0.000	0.000	0.000
9	A	699	GLY	0	0.046	0.021	21.298	0.028	0.028	0.000	0.000	0.000	0.000
10	A	700	ALA	0	0.003	0.006	23.675	-0.021	-0.021	0.000	0.000	0.000	0.000
11	A	701	ALA	0	0.039	0.018	23.645	-0.004	-0.004	0.000	0.000	0.000	0.000
12	A	702	VAL	0	-0.006	-0.008	25.727	0.009	0.009	0.000	0.000	0.000	0.000
13	A	703	VAL	0	-0.029	-0.022	29.068	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	704	GLY	0	-0.006	0.007	29.914	0.013	0.013	0.000	0.000	0.000	0.000
15	A	705	GLN	0	-0.073	-0.048	27.578	0.009	0.009	0.000	0.000	0.000	0.000
16	A	706	GLU	-1	-0.864	-0.916	25.766	-0.228	-0.228	0.000	0.000	0.000	0.000
17	A	707	CYS	0	-0.078	-0.025	23.194	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	708	GLU	-1	-0.775	-0.896	19.920	-0.276	-0.276	0.000	0.000	0.000	0.000
19	A	709	VAL	0	-0.026	0.003	14.905	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	710	GLN	0	-0.032	-0.022	13.618	0.043	0.043	0.000	0.000	0.000	0.000
21	A	711	ILE	0	-0.022	-0.019	8.968	-0.060	-0.060	0.000	0.000	0.000	0.000
22	A	712	VAL	0	0.036	0.014	8.631	0.112	0.112	0.000	0.000	0.000	0.000
23	A	713	PHE	0	0.019	0.002	2.148	-4.721	-4.215	5.109	-2.349	-3.265	-0.022
24	A	714	LYS	1	0.874	0.953	4.251	-1.481	-1.384	-0.001	-0.021	-0.075	0.000
25	A	715	ASN	0	0.006	-0.012	3.104	1.085	2.012	0.102	-0.479	-0.550	-0.003
26	A	716	PRO	0	-0.058	-0.031	2.229	-1.538	-0.802	2.777	-1.207	-2.305	0.009
27	A	717	LEU	0	0.013	0.022	5.030	-0.754	-0.697	-0.001	-0.005	-0.051	0.000
28	A	718	PRO	0	-0.010	-0.003	7.929	-0.269	-0.269	0.000	0.000	0.000	0.000
29	A	719	VAL	0	0.016	-0.001	10.196	-0.169	-0.169	0.000	0.000	0.000	0.000
30	A	720	THR	0	0.015	-0.005	9.791	0.049	0.049	0.000	0.000	0.000	0.000
31	A	721	LEU	0	-0.051	-0.011	4.819	-0.024	-0.024	0.000	0.000	0.000	0.000
32	A	722	THR	0	0.021	-0.003	9.487	-0.099	-0.099	0.000	0.000	0.000	0.000
33	A	723	ASN	0	-0.022	-0.015	11.755	-0.034	-0.034	0.000	0.000	0.000	0.000
34	A	724	VAL	0	0.038	0.031	8.415	-0.030	-0.030	0.000	0.000	0.000	0.000
35	A	725	VAL	0	-0.016	0.006	11.051	0.033	0.033	0.000	0.000	0.000	0.000
36	A	726	PHE	0	0.052	0.013	9.557	-0.116	-0.116	0.000	0.000	0.000	0.000
37	A	727	ARG	1	0.829	0.895	11.212	0.608	0.608	0.000	0.000	0.000	0.000
38	A	728	LEU	0	0.011	0.011	12.171	-0.137	-0.137	0.000	0.000	0.000	0.000
39	A	729	GLU	-1	-0.918	-0.959	14.738	-0.395	-0.395	0.000	0.000	0.000	0.000
40	A	730	GLY	0	0.108	0.051	16.426	-0.063	-0.063	0.000	0.000	0.000	0.000
41	A	731	SER	0	-0.051	-0.030	18.812	0.049	0.049	0.000	0.000	0.000	0.000
42	A	732	GLY	0	-0.024	-0.028	22.124	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	733	LEU	0	0.017	0.006	19.792	0.015	0.015	0.000	0.000	0.000	0.000
44	A	734	GLN	0	0.049	0.021	19.194	0.035	0.035	0.000	0.000	0.000	0.000
45	A	735	ARG	1	0.875	0.947	20.822	0.261	0.261	0.000	0.000	0.000	0.000
46	A	736	PRO	0	0.055	0.016	18.658	-0.010	-0.010	0.000	0.000	0.000	0.000
47	A	737	LYS	1	0.891	0.977	17.678	0.376	0.376	0.000	0.000	0.000	0.000
48	A	738	ILE	0	0.018	0.013	15.670	-0.060	-0.060	0.000	0.000	0.000	0.000
49	A	739	LEU	0	-0.055	-0.036	14.731	0.059	0.059	0.000	0.000	0.000	0.000
50	A	740	ASN	0	0.037	0.021	14.347	-0.043	-0.043	0.000	0.000	0.000	0.000
51	A	741	VAL	0	-0.041	-0.020	10.240	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	742	GLY	0	-0.012	-0.002	13.222	0.039	0.039	0.000	0.000	0.000	0.000
53	A	743	ASP	-1	-0.838	-0.944	11.947	-0.151	-0.151	0.000	0.000	0.000	0.000
54	A	744	ILE	0	-0.045	-0.001	6.891	-0.066	-0.066	0.000	0.000	0.000	0.000
55	A	745	GLY	0	0.066	0.032	9.778	0.099	0.099	0.000	0.000	0.000	0.000
56	A	746	GLY	0	0.020	0.015	9.545	0.003	0.003	0.000	0.000	0.000	0.000
57	A	747	ASN	0	-0.062	-0.054	8.468	0.093	0.093	0.000	0.000	0.000	0.000
58	A	748	GLU	-1	-0.848	-0.898	9.037	0.008	0.008	0.000	0.000	0.000	0.000
59	A	749	THR	0	-0.032	-0.030	7.306	-0.020	-0.020	0.000	0.000	0.000	0.000
60	A	750	VAL	0	0.025	0.026	7.641	0.031	0.031	0.000	0.000	0.000	0.000
61	A	751	THR	0	-0.012	-0.018	9.161	-0.115	-0.115	0.000	0.000	0.000	0.000
62	A	752	LEU	0	-0.002	0.004	10.495	0.033	0.033	0.000	0.000	0.000	0.000
63	A	753	ARG	1	0.913	0.962	13.866	0.210	0.210	0.000	0.000	0.000	0.000
64	A	754	GLN	0	-0.026	-0.029	16.790	0.004	0.004	0.000	0.000	0.000	0.000
65	A	755	SER	0	-0.010	-0.012	18.417	-0.018	-0.018	0.000	0.000	0.000	0.000
66	A	756	PHE	0	-0.042	-0.030	19.605	-0.012	-0.012	0.000	0.000	0.000	0.000
67	A	757	VAL	0	0.085	0.049	23.006	0.008	0.008	0.000	0.000	0.000	0.000
68	A	758	PRO	0	-0.030	0.002	24.609	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	759	VAL	0	0.004	0.006	26.222	0.019	0.019	0.000	0.000	0.000	0.000
70	A	760	ARG	1	0.915	0.944	27.408	0.221	0.221	0.000	0.000	0.000	0.000
71	A	761	PRO	0	0.075	0.048	27.069	-0.018	-0.018	0.000	0.000	0.000	0.000
72	A	762	GLY	0	0.007	0.004	27.367	0.001	0.001	0.000	0.000	0.000	0.000
73	A	763	PRO	0	0.023	0.000	23.326	-0.015	-0.015	0.000	0.000	0.000	0.000
74	A	764	ARG	1	0.835	0.934	21.634	0.266	0.266	0.000	0.000	0.000	0.000
75	A	765	GLN	0	0.020	0.019	16.273	-0.039	-0.039	0.000	0.000	0.000	0.000
76	A	766	LEU	0	-0.019	-0.016	15.596	0.048	0.048	0.000	0.000	0.000	0.000
77	A	767	ILE	0	-0.017	-0.014	11.295	-0.069	-0.069	0.000	0.000	0.000	0.000
78	A	768	ALA	0	0.036	0.026	9.704	0.117	0.117	0.000	0.000	0.000	0.000
79	A	769	SER	0	-0.041	-0.030	8.054	-0.174	-0.174	0.000	0.000	0.000	0.000
80	A	770	LEU	0	0.005	-0.006	5.235	0.080	0.080	0.000	0.000	0.000	0.000
81	A	771	ASP	-1	-0.865	-0.907	7.169	-0.129	-0.129	0.000	0.000	0.000	0.000
82	A	772	SER	0	0.077	0.004	7.944	-0.037	-0.037	0.000	0.000	0.000	0.000
83	A	773	PRO	0	0.031	0.015	9.188	0.185	0.185	0.000	0.000	0.000	0.000
84	A	774	GLN	0	0.057	0.045	9.064	0.037	0.037	0.000	0.000	0.000	0.000
85	A	775	LEU	0	-0.031	-0.013	3.581	0.020	0.244	0.004	-0.049	-0.179	0.000
86	A	776	SER	0	-0.036	-0.007	6.843	0.370	0.370	0.000	0.000	0.000	0.000
87	A	777	GLN	0	-0.045	-0.014	9.408	-0.133	-0.133	0.000	0.000	0.000	0.000
88	A	778	VAL	0	0.002	0.003	9.551	0.289	0.289	0.000	0.000	0.000	0.000
89	A	779	HIS	0	-0.013	-0.015	8.456	-0.222	-0.222	0.000	0.000	0.000	0.000
90	A	780	GLY	0	0.005	0.004	11.867	0.020	0.020	0.000	0.000	0.000	0.000
91	A	781	VAL	0	-0.033	-0.022	12.037	-0.020	-0.020	0.000	0.000	0.000	0.000
92	A	782	ILE	0	-0.007	-0.001	15.059	-0.019	-0.019	0.000	0.000	0.000	0.000
93	A	783	GLN	0	-0.046	-0.023	18.345	0.041	0.041	0.000	0.000	0.000	0.000
94	A	784	VAL	0	-0.011	-0.014	19.790	-0.029	-0.029	0.000	0.000	0.000	0.000
95	A	785	ASP	-1	-0.865	-0.921	23.229	0.294	0.294	0.000	0.000	0.000	0.000
96	A	786	VAL	0	-0.060	-0.031	25.341	-0.016	-0.016	0.000	0.000	0.000	0.000
97	A	787	ALA	0	0.014	0.016	27.976	-0.011	-0.011	0.000	0.000	0.000	0.000

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