FMO DATABASE

FMODB ID: MVVZZ

Calculation Name: 4U3Q-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4U3Q

Chain ID: B

ChEMBL ID:

UniProt ID: P29722

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	103
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-743061.835113
FMO2-HF: Nuclear repulsion	703381.111136
FMO2-HF: Total energy	-39680.723977
FMO2-MP2: Total energy	-39794.536591

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(B:10:LYS)

Summations of interaction energy for fragment #1(B:10:LYS)

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.
-81.043	-73.255	6.972	-6.245	-8.516	-0.049

Interaction energy analysis for fragmet #1(B:10:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.974 / q_NPA : 0.981

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	B	12	LYS	1	0.922	0.978	2.997	21.621	24.155	0.040	-1.190	-1.384	0.005
4	B	13	ALA	0	0.040	0.005	2.892	2.426	3.264	0.111	-0.257	-0.692	0.000
5	B	14	GLU	-1	-0.857	-0.917	3.883	-34.795	-34.190	0.003	-0.193	-0.416	-0.001
6	B	15	LYS	1	0.955	0.983	6.095	20.917	20.917	0.000	0.000	0.000	0.000
7	B	16	VAL	0	-0.031	-0.024	7.842	2.002	2.002	0.000	0.000	0.000	0.000
8	B	17	GLU	-1	-0.819	-0.909	7.736	-24.755	-24.755	0.000	0.000	0.000	0.000
9	B	18	CYS	0	-0.084	-0.045	9.799	1.829	1.829	0.000	0.000	0.000	0.000
10	B	19	ALA	0	-0.029	-0.009	12.113	1.222	1.222	0.000	0.000	0.000	0.000
11	B	20	LEU	0	-0.006	0.015	11.928	1.196	1.196	0.000	0.000	0.000	0.000
12	B	21	LYS	1	0.887	0.938	11.396	21.685	21.685	0.000	0.000	0.000	0.000
13	B	22	GLY	0	-0.052	-0.021	15.802	0.222	0.222	0.000	0.000	0.000	0.000
14	B	23	GLY	0	-0.036	-0.014	18.498	0.671	0.671	0.000	0.000	0.000	0.000
15	B	24	ILE	0	-0.025	-0.018	20.012	-0.205	-0.205	0.000	0.000	0.000	0.000
16	B	25	PHE	0	-0.036	-0.030	17.451	0.175	0.175	0.000	0.000	0.000	0.000
17	B	26	ARG	1	0.864	0.888	22.734	9.039	9.039	0.000	0.000	0.000	0.000
18	B	27	GLY	0	0.010	0.005	25.675	-0.120	-0.120	0.000	0.000	0.000	0.000
19	B	28	THR	0	-0.030	-0.008	27.040	0.057	0.057	0.000	0.000	0.000	0.000
20	B	29	LEU	0	-0.003	0.023	24.388	-0.055	-0.055	0.000	0.000	0.000	0.000
21	B	30	PRO	0	0.031	0.011	27.782	0.293	0.293	0.000	0.000	0.000	0.000
22	B	31	ALA	0	0.013	0.016	30.519	-0.193	-0.193	0.000	0.000	0.000	0.000
23	B	32	ALA	0	-0.011	-0.012	32.616	0.234	0.234	0.000	0.000	0.000	0.000
24	B	33	ASP	-1	-0.905	-0.965	31.380	-8.753	-8.753	0.000	0.000	0.000	0.000
25	B	34	CYS	0	-0.021	-0.002	33.890	0.220	0.220	0.000	0.000	0.000	0.000
26	B	35	PRO	0	-0.053	-0.023	36.140	-0.047	-0.047	0.000	0.000	0.000	0.000
27	B	36	GLY	0	-0.006	-0.007	33.118	-0.091	-0.091	0.000	0.000	0.000	0.000
28	B	37	ILE	0	0.014	0.007	30.470	0.168	0.168	0.000	0.000	0.000	0.000
29	B	38	ASP	-1	-0.825	-0.874	30.213	-9.173	-9.173	0.000	0.000	0.000	0.000
30	B	39	THR	0	-0.003	-0.011	25.533	-0.038	-0.038	0.000	0.000	0.000	0.000
31	B	40	THR	0	-0.027	-0.026	25.888	-0.033	-0.033	0.000	0.000	0.000	0.000
32	B	41	VAL	0	0.023	0.011	19.975	-0.017	-0.017	0.000	0.000	0.000	0.000
33	B	42	THR	0	-0.015	-0.007	21.629	0.050	0.050	0.000	0.000	0.000	0.000
34	B	43	PHE	0	0.047	0.024	16.004	-0.142	-0.142	0.000	0.000	0.000	0.000
35	B	44	ASN	0	-0.010	-0.005	18.145	0.259	0.259	0.000	0.000	0.000	0.000
36	B	45	ALA	0	0.042	0.001	16.206	-0.756	-0.756	0.000	0.000	0.000	0.000
37	B	46	ASP	-1	-0.851	-0.894	16.044	-14.891	-14.891	0.000	0.000	0.000	0.000
38	B	47	GLY	0	0.034	0.025	15.072	-0.462	-0.462	0.000	0.000	0.000	0.000
39	B	48	THR	0	-0.064	-0.061	15.977	0.233	0.233	0.000	0.000	0.000	0.000
40	B	49	ALA	0	0.003	-0.015	18.556	-0.258	-0.258	0.000	0.000	0.000	0.000
41	B	50	GLN	0	-0.065	-0.025	20.534	0.421	0.421	0.000	0.000	0.000	0.000
42	B	51	LYS	1	0.832	0.908	23.347	10.975	10.975	0.000	0.000	0.000	0.000
43	B	52	VAL	0	0.004	0.004	25.381	0.252	0.252	0.000	0.000	0.000	0.000
44	B	53	GLU	-1	-0.800	-0.870	27.772	-10.199	-10.199	0.000	0.000	0.000	0.000
45	B	54	LEU	0	0.020	0.012	30.827	0.253	0.253	0.000	0.000	0.000	0.000
46	B	64	PRO	0	0.014	-0.022	34.365	0.044	0.044	0.000	0.000	0.000	0.000
47	B	65	LEU	0	-0.026	0.020	32.253	0.021	0.021	0.000	0.000	0.000	0.000
48	B	66	THR	0	0.002	0.000	29.156	-0.245	-0.245	0.000	0.000	0.000	0.000
49	B	67	TYR	0	-0.053	-0.050	25.948	-0.062	-0.062	0.000	0.000	0.000	0.000
50	B	68	ARG	1	0.896	0.931	23.430	12.025	12.025	0.000	0.000	0.000	0.000
51	B	69	GLY	0	0.022	0.010	21.811	0.089	0.089	0.000	0.000	0.000	0.000
52	B	70	THR	0	-0.019	-0.004	16.910	0.145	0.145	0.000	0.000	0.000	0.000
53	B	71	TRP	0	-0.049	-0.025	11.300	-0.134	-0.134	0.000	0.000	0.000	0.000
54	B	72	MET	0	0.002	0.015	9.640	0.192	0.192	0.000	0.000	0.000	0.000
55	B	73	VAL	0	0.003	0.003	6.719	1.229	1.229	0.000	0.000	0.000	0.000
56	B	74	ARG	1	0.789	0.890	6.822	19.000	19.000	0.000	0.000	0.000	0.000
57	B	75	GLU	-1	-0.880	-0.969	2.331	-91.961	-88.715	6.806	-4.292	-5.760	-0.051
58	B	76	ASP	-1	-0.825	-0.900	3.478	-24.306	-23.741	0.012	-0.313	-0.264	-0.002
59	B	77	GLY	0	-0.040	-0.038	5.822	2.158	2.158	0.000	0.000	0.000	0.000
60	B	78	ILE	0	-0.051	-0.023	6.700	1.807	1.807	0.000	0.000	0.000	0.000
61	B	79	VAL	0	-0.001	-0.002	9.574	-1.585	-1.585	0.000	0.000	0.000	0.000
62	B	80	GLU	-1	-0.837	-0.916	11.991	-18.540	-18.540	0.000	0.000	0.000	0.000
63	B	81	LEU	0	-0.002	0.003	14.223	-0.266	-0.266	0.000	0.000	0.000	0.000
64	B	82	SER	0	0.001	-0.004	17.531	0.367	0.367	0.000	0.000	0.000	0.000
65	B	83	LEU	0	0.003	0.018	20.063	0.091	0.091	0.000	0.000	0.000	0.000
66	B	84	VAL	0	0.011	0.005	23.530	0.031	0.031	0.000	0.000	0.000	0.000
67	B	85	SER	0	-0.022	-0.003	26.650	0.543	0.543	0.000	0.000	0.000	0.000
68	B	95	LYS	1	0.909	0.949	16.491	16.772	16.772	0.000	0.000	0.000	0.000
69	B	96	GLU	-1	-0.858	-0.901	19.046	-11.851	-11.851	0.000	0.000	0.000	0.000
70	B	97	LEU	0	-0.021	-0.015	14.124	-0.803	-0.803	0.000	0.000	0.000	0.000
71	B	98	TYR	0	-0.019	-0.043	14.566	1.044	1.044	0.000	0.000	0.000	0.000
72	B	99	GLU	-1	-0.805	-0.894	12.853	-16.351	-16.351	0.000	0.000	0.000	0.000
73	B	100	LEU	0	-0.025	-0.008	11.737	0.661	0.661	0.000	0.000	0.000	0.000
74	B	101	ILE	0	-0.037	-0.008	13.530	-0.254	-0.254	0.000	0.000	0.000	0.000
75	B	102	ASP	-1	-0.809	-0.901	15.729	-12.671	-12.671	0.000	0.000	0.000	0.000
76	B	103	SER	0	-0.037	-0.034	15.788	-0.588	-0.588	0.000	0.000	0.000	0.000
77	B	104	ASN	0	-0.029	-0.013	16.816	-0.355	-0.355	0.000	0.000	0.000	0.000
78	B	105	SER	0	0.000	0.000	18.322	0.768	0.768	0.000	0.000	0.000	0.000
79	B	106	VAL	0	0.021	0.020	15.475	-0.718	-0.718	0.000	0.000	0.000	0.000
80	B	107	ARG	1	0.850	0.919	17.112	14.044	14.044	0.000	0.000	0.000	0.000
81	B	108	TYR	0	0.022	0.016	17.720	-0.503	-0.503	0.000	0.000	0.000	0.000
82	B	109	MET	0	-0.046	-0.018	14.215	0.126	0.126	0.000	0.000	0.000	0.000
83	B	110	GLY	0	0.035	0.015	19.046	0.395	0.395	0.000	0.000	0.000	0.000
84	B	111	ALA	0	0.041	0.030	19.690	-0.449	-0.449	0.000	0.000	0.000	0.000
85	B	112	PRO	0	0.012	-0.016	17.210	-0.131	-0.131	0.000	0.000	0.000	0.000
86	B	113	GLY	0	-0.006	0.008	18.536	0.422	0.422	0.000	0.000	0.000	0.000
87	B	114	ALA	0	-0.030	-0.010	20.481	0.582	0.582	0.000	0.000	0.000	0.000
88	B	115	GLY	0	0.015	0.016	19.699	0.071	0.071	0.000	0.000	0.000	0.000
89	B	116	LYS	1	0.933	0.964	20.457	11.300	11.300	0.000	0.000	0.000	0.000
90	B	117	PRO	0	-0.013	-0.023	20.861	-0.069	-0.069	0.000	0.000	0.000	0.000
91	B	118	SER	0	0.009	0.019	21.997	0.134	0.134	0.000	0.000	0.000	0.000
92	B	119	LYS	1	1.037	1.005	23.997	9.731	9.731	0.000	0.000	0.000	0.000
93	B	120	GLU	-1	-0.961	-0.982	25.007	-8.876	-8.876	0.000	0.000	0.000	0.000
94	B	121	MET	0	0.022	0.013	26.846	0.181	0.181	0.000	0.000	0.000	0.000
95	B	122	ALA	0	-0.004	-0.002	22.165	-0.134	-0.134	0.000	0.000	0.000	0.000
96	B	123	PRO	0	-0.019	-0.022	23.727	-0.261	-0.261	0.000	0.000	0.000	0.000
97	B	124	PHE	0	0.010	0.011	25.433	-0.014	-0.014	0.000	0.000	0.000	0.000
98	B	125	TYR	0	0.040	0.018	22.722	0.015	0.015	0.000	0.000	0.000	0.000
99	B	126	VAL	0	-0.053	-0.019	21.325	-0.557	-0.557	0.000	0.000	0.000	0.000
100	B	127	LEU	0	-0.019	0.001	20.919	0.363	0.363	0.000	0.000	0.000	0.000
101	B	128	LYS	1	0.908	0.933	21.311	10.508	10.508	0.000	0.000	0.000	0.000
102	B	129	LYS	1	0.877	0.953	17.750	14.011	14.011	0.000	0.000	0.000	0.000
103	B	130	THR	0	-0.019	-0.003	22.748	0.334	0.334	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(B:10:LYS)