FMO DATABASE

FMODB ID: GQM81

Calculation Name: 3U4Z-A-Xray313

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3U4Z

Chain ID: A

ChEMBL ID:

UniProt ID: D2CVN6

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	109
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-905018.196101
FMO2-HF: Nuclear repulsion	859599.939647
FMO2-HF: Total energy	-45418.256454
FMO2-MP2: Total energy	-45551.449966

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:375:THR )

Summations of interaction energy for fragment #1(A:375:THR )

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.
-11.312	-2.696	2.237	-4.365	-6.486	-0.018

Interaction energy analysis for fragmet #1(A:375:THR )

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 : -0.031

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	377	LEU	0	0.040	0.020	3.104	-1.790	0.530	0.118	-1.137	-1.301	-0.004
4	A	378	ILE	0	0.042	0.010	4.944	0.785	0.826	0.000	-0.002	-0.038	0.000
5	A	379	SER	0	0.004	-0.005	7.821	0.194	0.194	0.000	0.000	0.000	0.000
6	A	380	GLU	-1	-0.880	-0.957	6.699	-0.604	-0.604	0.000	0.000	0.000	0.000
7	A	381	VAL	0	0.005	0.019	6.774	0.349	0.349	0.000	0.000	0.000	0.000
8	A	382	LEU	0	0.028	0.014	9.329	0.140	0.140	0.000	0.000	0.000	0.000
9	A	383	LYS	1	0.909	0.939	12.110	0.115	0.115	0.000	0.000	0.000	0.000
10	A	384	THR	0	-0.072	-0.025	9.320	0.096	0.096	0.000	0.000	0.000	0.000
11	A	385	SER	0	0.013	0.001	12.039	0.024	0.024	0.000	0.000	0.000	0.000
12	A	386	LYS	1	0.936	0.982	6.608	-2.263	-2.263	0.000	0.000	0.000	0.000
13	A	387	GLN	0	0.034	0.021	11.600	-0.030	-0.030	0.000	0.000	0.000	0.000
14	A	388	TYR	0	0.038	0.013	9.242	-0.094	-0.094	0.000	0.000	0.000	0.000
15	A	389	LEU	0	-0.030	-0.024	5.704	0.089	0.089	0.000	0.000	0.000	0.000
16	A	390	SER	0	0.035	0.027	2.647	-2.224	-1.442	0.262	-0.341	-0.703	0.001
17	A	391	VAL	0	-0.004	0.012	2.638	-1.086	1.536	1.396	-1.990	-2.028	-0.012
18	A	392	LEU	0	-0.028	0.004	2.780	-3.295	-1.652	0.402	-0.523	-1.522	-0.004
19	A	393	ALA	0	0.019	0.001	3.842	0.013	0.123	0.002	-0.022	-0.090	0.000
20	A	394	GLN	0	-0.020	-0.022	7.564	0.136	0.136	0.000	0.000	0.000	0.000
21	A	395	VAL	0	-0.008	0.008	11.166	0.108	0.108	0.000	0.000	0.000	0.000
22	A	396	VAL	0	0.016	0.009	13.672	-0.022	-0.022	0.000	0.000	0.000	0.000
23	A	397	ASP	-1	-0.901	-0.954	16.740	0.001	0.001	0.000	0.000	0.000	0.000
24	A	398	ILE	0	0.003	0.005	17.782	0.040	0.040	0.000	0.000	0.000	0.000
25	A	399	GLN	0	0.010	0.017	19.832	0.008	0.008	0.000	0.000	0.000	0.000
26	A	400	SER	0	-0.021	-0.029	21.994	0.032	0.032	0.000	0.000	0.000	0.000
27	A	401	SER	0	-0.005	-0.005	23.547	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	402	ASP	-1	-0.904	-0.953	26.054	0.133	0.133	0.000	0.000	0.000	0.000
29	A	403	LYS	1	0.899	0.947	25.620	-0.147	-0.147	0.000	0.000	0.000	0.000
30	A	404	ASN	0	0.040	0.004	21.890	0.054	0.054	0.000	0.000	0.000	0.000
31	A	405	ILE	0	0.000	0.030	17.828	-0.030	-0.030	0.000	0.000	0.000	0.000
32	A	406	ARG	1	0.888	0.936	18.463	-0.135	-0.135	0.000	0.000	0.000	0.000
33	A	407	LEU	0	0.023	0.011	13.599	-0.034	-0.034	0.000	0.000	0.000	0.000
34	A	408	LYS	1	0.942	0.985	15.667	-0.018	-0.018	0.000	0.000	0.000	0.000
35	A	409	ILE	0	-0.035	-0.022	8.813	-0.017	-0.017	0.000	0.000	0.000	0.000
36	A	410	CYS	0	0.076	0.028	11.608	0.041	0.041	0.000	0.000	0.000	0.000
37	A	411	ASP	-1	-0.755	-0.846	6.712	-1.924	-1.924	0.000	0.000	0.000	0.000
38	A	412	ASN	0	0.027	0.004	8.899	0.212	0.212	0.000	0.000	0.000	0.000
39	A	413	SER	0	-0.101	-0.073	7.745	0.165	0.165	0.000	0.000	0.000	0.000
40	A	414	CYS	0	-0.049	-0.025	10.090	0.158	0.158	0.000	0.000	0.000	0.000
41	A	415	ASN	0	0.014	0.014	12.551	-0.039	-0.039	0.000	0.000	0.000	0.000
42	A	416	GLN	0	-0.015	-0.007	14.249	0.064	0.064	0.000	0.000	0.000	0.000
43	A	417	GLU	-1	-0.886	-0.944	13.475	-0.213	-0.213	0.000	0.000	0.000	0.000
44	A	418	LEU	0	-0.021	0.000	9.918	0.063	0.063	0.000	0.000	0.000	0.000
45	A	419	LYN	0	0.027	0.027	13.593	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	420	VAL	0	0.009	0.013	11.359	0.097	0.097	0.000	0.000	0.000	0.000
47	A	421	VAL	0	-0.020	-0.014	14.552	-0.083	-0.083	0.000	0.000	0.000	0.000
48	A	422	ILE	0	0.011	0.006	13.842	0.101	0.101	0.000	0.000	0.000	0.000
49	A	423	PHE	0	0.004	-0.025	17.031	-0.051	-0.051	0.000	0.000	0.000	0.000
50	A	424	PRO	0	0.013	-0.033	19.692	0.024	0.024	0.000	0.000	0.000	0.000
51	A	425	ASP	-1	-0.869	-0.921	20.184	0.430	0.430	0.000	0.000	0.000	0.000
52	A	426	LEU	0	0.030	0.012	13.372	-0.038	-0.038	0.000	0.000	0.000	0.000
53	A	427	CYS	0	-0.089	-0.029	18.015	-0.047	-0.047	0.000	0.000	0.000	0.000
54	A	428	TYR	0	-0.017	-0.010	19.561	-0.043	-0.043	0.000	0.000	0.000	0.000
55	A	429	GLU	-1	-0.945	-0.961	17.476	0.338	0.338	0.000	0.000	0.000	0.000
56	A	430	TRP	0	0.007	-0.019	13.188	-0.067	-0.067	0.000	0.000	0.000	0.000
57	A	431	ARG	1	0.881	0.954	18.339	-0.166	-0.166	0.000	0.000	0.000	0.000
58	A	432	ASP	-1	-0.920	-0.965	21.512	0.072	0.072	0.000	0.000	0.000	0.000
59	A	433	LYS	1	0.917	0.983	15.905	-0.140	-0.140	0.000	0.000	0.000	0.000
60	A	434	PHE	0	-0.013	-0.013	12.314	-0.028	-0.028	0.000	0.000	0.000	0.000
61	A	435	SER	0	-0.021	-0.016	16.052	-0.016	-0.016	0.000	0.000	0.000	0.000
62	A	436	ILE	0	0.029	0.011	16.013	-0.029	-0.029	0.000	0.000	0.000	0.000
63	A	437	ASN	0	-0.028	-0.029	15.487	-0.024	-0.024	0.000	0.000	0.000	0.000
64	A	438	LYS	1	0.831	0.932	13.534	0.131	0.131	0.000	0.000	0.000	0.000
65	A	439	TRP	0	-0.027	-0.010	7.431	-0.023	-0.023	0.000	0.000	0.000	0.000
66	A	440	TYR	0	0.002	-0.014	8.311	0.075	0.075	0.000	0.000	0.000	0.000
67	A	441	TYR	0	0.016	0.002	2.940	-1.910	-0.930	0.057	-0.348	-0.690	0.001
68	A	442	PHE	0	-0.017	-0.004	5.247	0.101	0.101	0.000	0.000	0.000	0.000
69	A	443	ASN	0	-0.022	-0.034	5.399	2.609	2.727	0.000	-0.002	-0.114	0.000
70	A	444	GLU	-1	-0.898	-0.966	6.456	1.284	1.284	0.000	0.000	0.000	0.000
71	A	445	PHE	0	0.001	0.018	8.032	-0.729	-0.729	0.000	0.000	0.000	0.000
72	A	446	VAL	0	-0.032	-0.024	9.766	0.138	0.138	0.000	0.000	0.000	0.000
73	A	447	ARG	1	0.880	0.942	11.005	-0.630	-0.630	0.000	0.000	0.000	0.000
74	A	448	GLN	0	-0.007	-0.015	12.768	-0.073	-0.073	0.000	0.000	0.000	0.000
75	A	449	ILE	0	0.024	0.007	16.437	-0.016	-0.016	0.000	0.000	0.000	0.000
76	A	450	TYR	0	-0.072	-0.033	18.982	-0.010	-0.010	0.000	0.000	0.000	0.000
77	A	451	ASN	0	-0.017	-0.022	22.001	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	452	ASP	-1	-0.920	-0.940	22.694	0.089	0.089	0.000	0.000	0.000	0.000
79	A	453	GLU	-1	-0.944	-0.959	19.233	0.040	0.040	0.000	0.000	0.000	0.000
80	A	454	VAL	0	-0.057	-0.031	13.442	0.055	0.055	0.000	0.000	0.000	0.000
81	A	455	GLN	0	-0.016	-0.023	14.675	-0.083	-0.083	0.000	0.000	0.000	0.000
82	A	456	LEU	0	-0.020	-0.005	8.959	0.111	0.111	0.000	0.000	0.000	0.000
83	A	457	LYS	1	0.848	0.943	13.039	-0.729	-0.729	0.000	0.000	0.000	0.000
84	A	458	ASN	0	0.072	0.027	13.448	0.267	0.267	0.000	0.000	0.000	0.000
85	A	459	ASN	0	-0.024	-0.028	14.316	0.027	0.027	0.000	0.000	0.000	0.000
86	A	460	ILE	0	0.029	0.019	15.508	0.046	0.046	0.000	0.000	0.000	0.000
87	A	461	HIS	0	0.006	0.002	13.237	-0.051	-0.051	0.000	0.000	0.000	0.000
88	A	462	SER	0	-0.046	-0.009	11.495	0.090	0.090	0.000	0.000	0.000	0.000
89	A	463	SER	0	0.007	0.000	10.557	-0.245	-0.245	0.000	0.000	0.000	0.000
90	A	464	ILE	0	0.016	0.007	9.250	0.299	0.299	0.000	0.000	0.000	0.000
91	A	465	LYS	1	0.928	0.964	8.633	-0.722	-0.722	0.000	0.000	0.000	0.000
92	A	466	GLU	-1	-0.829	-0.893	8.656	-0.341	-0.341	0.000	0.000	0.000	0.000
93	A	467	SER	0	-0.040	-0.016	7.712	-0.017	-0.017	0.000	0.000	0.000	0.000
94	A	468	ASP	-1	-0.842	-0.928	9.415	-0.260	-0.260	0.000	0.000	0.000	0.000
95	A	469	ASP	-1	-0.984	-0.975	10.732	-0.731	-0.731	0.000	0.000	0.000	0.000
96	A	470	GLN	0	-0.001	0.006	11.303	-0.147	-0.147	0.000	0.000	0.000	0.000
97	A	471	ARG	1	0.927	0.956	13.417	0.616	0.616	0.000	0.000	0.000	0.000
98	A	472	LYS	1	0.991	0.993	16.794	0.204	0.204	0.000	0.000	0.000	0.000
99	A	473	VAL	0	0.021	0.013	18.881	0.026	0.026	0.000	0.000	0.000	0.000
100	A	474	ILE	0	-0.029	-0.018	21.196	0.009	0.009	0.000	0.000	0.000	0.000
101	A	475	THR	0	0.003	0.007	24.396	0.001	0.001	0.000	0.000	0.000	0.000
102	A	476	TYR	0	-0.010	-0.007	26.394	0.013	0.013	0.000	0.000	0.000	0.000
103	A	477	ASN	0	-0.012	-0.008	27.031	-0.010	-0.010	0.000	0.000	0.000	0.000
104	A	478	GLN	0	-0.007	0.004	30.940	0.006	0.006	0.000	0.000	0.000	0.000
105	A	479	GLU	-1	-0.916	-0.957	34.722	-0.100	-0.100	0.000	0.000	0.000	0.000
106	A	480	GLN	0	0.016	-0.021	32.791	0.001	0.001	0.000	0.000	0.000	0.000
107	A	481	GLY	0	0.012	0.022	37.622	0.001	0.001	0.000	0.000	0.000	0.000
108	A	482	VAL	0	-0.100	-0.046	40.407	0.005	0.005	0.000	0.000	0.000	0.000
109	A	483	PHE	-1	-0.968	-0.973	36.836	-0.096	-0.096	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:375:THR )