FMO DATABASE

FMODB ID: N9QKQ

Calculation Name: 5MZ7-A-Xray372

Preferred Name: Disks large homolog 4

Target Type: SINGLE PROTEIN

Ligand Name: azidohomoalanine

ligand 3-letter code: AZH

PDB ID: 5MZ7

Chain ID: A

ChEMBL ID: CHEMBL3797015

UniProt ID: P31016

Base Structure: X-ray

Registration Date: 2023-09-19

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	100
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-697738.457285
FMO2-HF: Nuclear repulsion	660746.337247
FMO2-HF: Total energy	-36992.120038
FMO2-MP2: Total energy	-37102.8088

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:303:GLY)

Summations of interaction energy for fragment #1(A:303:GLY)

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.
-17.753	-19.346	14.511	-6.946	-5.972	-0.07

Interaction energy analysis for fragmet #1(A:303:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.036 / q_NPA : -0.014

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	305	GLU	-1	-0.925	-0.957	1.948	-9.847	-9.856	6.919	-3.669	-3.242	-0.029
4	A	306	ASP	-1	-0.921	-0.956	1.906	-12.144	-13.876	7.593	-3.240	-2.621	-0.041
5	A	307	ILE	0	-0.024	0.006	4.716	1.552	1.700	-0.001	-0.037	-0.109	0.000
6	A	308	PRO	0	-0.017	-0.012	6.687	0.347	0.347	0.000	0.000	0.000	0.000
7	A	309	ARG	1	0.829	0.910	7.215	2.719	2.719	0.000	0.000	0.000	0.000
8	A	310	GLU	-1	-0.891	-0.936	12.275	-0.854	-0.854	0.000	0.000	0.000	0.000
9	A	311	PRO	0	-0.054	-0.047	15.188	-0.044	-0.044	0.000	0.000	0.000	0.000
10	A	312	ARG	1	0.842	0.922	14.039	0.912	0.912	0.000	0.000	0.000	0.000
11	A	313	ARG	1	0.903	0.938	18.375	0.296	0.296	0.000	0.000	0.000	0.000
12	A	314	ILE	0	0.073	0.064	17.343	0.035	0.035	0.000	0.000	0.000	0.000
13	A	315	VAL	0	-0.049	-0.033	20.814	0.028	0.028	0.000	0.000	0.000	0.000
14	A	316	ILE	0	0.013	0.025	21.210	0.007	0.007	0.000	0.000	0.000	0.000
15	A	317	HIS	0	0.040	0.017	24.315	0.013	0.013	0.000	0.000	0.000	0.000
16	A	318	ARG	1	0.807	0.890	26.595	0.157	0.157	0.000	0.000	0.000	0.000
17	A	319	GLY	0	0.016	0.008	28.825	0.007	0.007	0.000	0.000	0.000	0.000
18	A	320	SER	0	-0.021	-0.019	30.579	0.000	0.000	0.000	0.000	0.000	0.000
19	A	321	THR	0	0.002	0.001	26.978	0.010	0.010	0.000	0.000	0.000	0.000
20	A	322	GLY	0	-0.001	0.014	27.799	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	323	LEU	0	0.025	-0.006	24.207	0.004	0.004	0.000	0.000	0.000	0.000
22	A	324	GLY	0	0.042	0.025	22.271	-0.015	-0.015	0.000	0.000	0.000	0.000
23	A	325	PHE	0	-0.034	-0.014	19.645	-0.013	-0.013	0.000	0.000	0.000	0.000
24	A	326	ASN	0	-0.013	0.009	20.989	0.031	0.031	0.000	0.000	0.000	0.000
25	A	327	ILE	0	0.002	-0.002	21.045	-0.038	-0.038	0.000	0.000	0.000	0.000
26	A	328	ILE	0	0.006	0.008	20.651	0.027	0.027	0.000	0.000	0.000	0.000
27	A	329	GLY	0	0.047	0.021	23.173	-0.032	-0.032	0.000	0.000	0.000	0.000
28	A	330	GLY	0	0.026	0.019	25.295	0.016	0.016	0.000	0.000	0.000	0.000
29	A	331	GLU	-1	-0.938	-0.982	28.662	-0.160	-0.160	0.000	0.000	0.000	0.000
30	A	332	ASP	-1	-0.846	-0.922	30.033	-0.197	-0.197	0.000	0.000	0.000	0.000
31	A	333	GLY	0	-0.049	-0.021	29.384	0.007	0.007	0.000	0.000	0.000	0.000
32	A	334	GLU	-1	-0.909	-0.949	26.351	-0.244	-0.244	0.000	0.000	0.000	0.000
33	A	335	GLY	0	-0.005	0.010	24.060	-0.032	-0.032	0.000	0.000	0.000	0.000
34	A	336	ILE	0	-0.027	-0.014	23.197	0.015	0.015	0.000	0.000	0.000	0.000
35	A	337	PHE	0	-0.006	-0.008	17.857	-0.053	-0.053	0.000	0.000	0.000	0.000
36	A	338	ILE	0	-0.035	-0.009	16.748	0.062	0.062	0.000	0.000	0.000	0.000
37	A	339	SER	0	0.015	-0.010	17.377	-0.048	-0.048	0.000	0.000	0.000	0.000
38	A	340	PHE	0	-0.033	-0.021	18.138	0.018	0.018	0.000	0.000	0.000	0.000
39	A	341	AZH	0	0.014	-0.001	15.764	-0.044	-0.044	0.000	0.000	0.000	0.000
40	A	342	LEU	0	-0.043	-0.013	18.127	0.025	0.025	0.000	0.000	0.000	0.000
41	A	343	ALA	0	0.034	0.016	18.130	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	344	GLY	0	-0.010	-0.008	19.000	0.022	0.022	0.000	0.000	0.000	0.000
43	A	345	GLY	0	-0.016	-0.008	20.673	0.009	0.009	0.000	0.000	0.000	0.000
44	A	346	PRO	0	-0.049	-0.036	20.636	-0.018	-0.018	0.000	0.000	0.000	0.000
45	A	347	ALA	0	0.008	0.006	18.899	-0.011	-0.011	0.000	0.000	0.000	0.000
46	A	348	ASP	-1	-0.832	-0.891	15.786	-0.250	-0.250	0.000	0.000	0.000	0.000
47	A	349	LEU	0	-0.033	-0.023	16.081	-0.016	-0.016	0.000	0.000	0.000	0.000
48	A	350	SER	0	-0.053	-0.027	17.234	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	351	GLY	0	0.003	0.010	13.430	0.002	0.002	0.000	0.000	0.000	0.000
50	A	352	GLU	-1	-0.915	-0.978	12.404	-0.585	-0.585	0.000	0.000	0.000	0.000
51	A	353	LEU	0	-0.064	-0.025	14.111	-0.106	-0.106	0.000	0.000	0.000	0.000
52	A	354	ARG	1	0.878	0.948	9.054	1.258	1.258	0.000	0.000	0.000	0.000
53	A	355	LYS	1	0.816	0.878	13.056	0.447	0.447	0.000	0.000	0.000	0.000
54	A	356	GLY	0	0.064	0.020	12.589	-0.150	-0.150	0.000	0.000	0.000	0.000
55	A	357	ASP	-1	-0.782	-0.878	14.102	-1.047	-1.047	0.000	0.000	0.000	0.000
56	A	358	GLN	0	-0.006	0.001	15.465	0.064	0.064	0.000	0.000	0.000	0.000
57	A	359	ILE	0	-0.027	-0.028	18.727	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	360	LEU	0	-0.018	-0.005	20.333	0.035	0.035	0.000	0.000	0.000	0.000
59	A	361	SER	0	0.015	-0.010	23.431	0.032	0.032	0.000	0.000	0.000	0.000
60	A	362	VAL	0	0.004	0.004	25.149	-0.018	-0.018	0.000	0.000	0.000	0.000
61	A	363	ASN	0	-0.011	-0.016	27.433	0.004	0.004	0.000	0.000	0.000	0.000
62	A	364	GLY	0	-0.003	0.010	29.045	0.014	0.014	0.000	0.000	0.000	0.000
63	A	365	VAL	0	-0.022	-0.003	30.633	0.001	0.001	0.000	0.000	0.000	0.000
64	A	366	ASP	-1	-0.810	-0.905	28.106	-0.294	-0.294	0.000	0.000	0.000	0.000
65	A	367	LEU	0	-0.012	-0.020	26.121	0.017	0.017	0.000	0.000	0.000	0.000
66	A	368	ARG	1	0.866	0.925	24.560	0.322	0.322	0.000	0.000	0.000	0.000
67	A	369	ASN	0	-0.045	-0.035	26.302	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	370	ALA	0	0.006	0.027	28.909	0.013	0.013	0.000	0.000	0.000	0.000
69	A	371	SER	0	0.083	0.053	28.870	-0.015	-0.015	0.000	0.000	0.000	0.000
70	A	372	HIS	0	-0.009	-0.027	26.905	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	373	GLU	-1	-0.951	-0.970	29.058	-0.137	-0.137	0.000	0.000	0.000	0.000
72	A	374	GLN	0	-0.017	-0.023	31.991	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	375	ALA	0	0.050	0.026	27.116	0.002	0.002	0.000	0.000	0.000	0.000
74	A	376	ALA	0	-0.006	0.007	28.793	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	377	ILE	0	-0.022	-0.016	29.741	0.008	0.008	0.000	0.000	0.000	0.000
76	A	378	ALA	0	-0.003	0.001	29.963	0.007	0.007	0.000	0.000	0.000	0.000
77	A	379	LEU	0	0.025	0.007	24.752	0.005	0.005	0.000	0.000	0.000	0.000
78	A	380	LYS	1	0.901	0.967	28.857	0.127	0.127	0.000	0.000	0.000	0.000
79	A	381	ASN	0	0.002	-0.016	31.734	0.011	0.011	0.000	0.000	0.000	0.000
80	A	382	ALA	0	-0.020	0.012	30.019	0.007	0.007	0.000	0.000	0.000	0.000
81	A	383	GLY	0	0.024	0.016	31.928	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	384	GLN	0	-0.013	-0.024	31.636	-0.012	-0.012	0.000	0.000	0.000	0.000
83	A	385	THR	0	-0.014	-0.010	28.814	0.003	0.003	0.000	0.000	0.000	0.000
84	A	386	VAL	0	-0.037	-0.012	26.281	0.003	0.003	0.000	0.000	0.000	0.000
85	A	387	THR	0	-0.010	-0.002	25.463	-0.011	-0.011	0.000	0.000	0.000	0.000
86	A	388	ILE	0	0.007	-0.008	21.351	0.014	0.014	0.000	0.000	0.000	0.000
87	A	389	ILE	0	-0.048	-0.015	21.642	-0.022	-0.022	0.000	0.000	0.000	0.000
88	A	390	ALA	0	0.007	0.003	18.012	0.021	0.021	0.000	0.000	0.000	0.000
89	A	391	GLN	0	-0.022	-0.023	15.920	0.056	0.056	0.000	0.000	0.000	0.000
90	A	392	TYR	0	-0.070	-0.050	7.890	0.418	0.418	0.000	0.000	0.000	0.000
91	A	393	LYS	1	0.830	0.909	13.317	0.685	0.685	0.000	0.000	0.000	0.000
92	A	394	PRO	0	0.070	0.050	9.818	0.214	0.214	0.000	0.000	0.000	0.000
93	A	395	GLU	-1	-0.807	-0.911	11.452	-1.179	-1.179	0.000	0.000	0.000	0.000
94	A	396	GLU	-1	-0.832	-0.907	15.001	-0.528	-0.528	0.000	0.000	0.000	0.000
95	A	397	TYR	0	-0.016	-0.021	14.242	0.067	0.067	0.000	0.000	0.000	0.000
96	A	398	SER	0	-0.011	-0.025	14.564	0.093	0.093	0.000	0.000	0.000	0.000
97	A	399	ARG	1	0.787	0.897	16.517	0.537	0.537	0.000	0.000	0.000	0.000
98	A	400	PHE	0	-0.045	-0.012	19.491	0.040	0.040	0.000	0.000	0.000	0.000
99	A	401	GLU	-1	-0.841	-0.865	14.825	-0.388	-0.388	0.000	0.000	0.000	0.000
100	A	402	ALA	0	-0.010	0.000	17.840	0.002	0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:303:GLY)