FMO DATABASE

FMODB ID: VQKY1

Calculation Name: 3KZ3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KZ3

Chain ID: A

ChEMBL ID:

UniProt ID: P03034

Base Structure: X-ray

Registration Date: 2023-09-22

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	80
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-514490.602585
FMO2-HF: Nuclear repulsion	483763.25144
FMO2-HF: Total energy	-30727.351145
FMO2-MP2: Total energy	-30817.573788

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:5:SER)

Summations of interaction energy for fragment #1(A:5: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.
0.671	2.189	-0.013	-0.68	-0.826	0.002

Interaction energy analysis for fragmet #1(A:5:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.024

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

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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	7	THR	0	0.011	0.001	3.813	-0.766	0.752	-0.013	-0.680	-0.826	0.002
4	A	8	GLN	0	0.060	0.015	6.138	0.391	0.391	0.000	0.000	0.000	0.000
5	A	9	GLU	-1	-0.829	-0.919	8.734	-0.315	-0.315	0.000	0.000	0.000	0.000
6	A	10	GLN	0	0.035	0.025	6.446	-0.610	-0.610	0.000	0.000	0.000	0.000
7	A	11	LEU	0	-0.002	-0.002	5.905	0.307	0.307	0.000	0.000	0.000	0.000
8	A	12	GLU	-1	-0.799	-0.862	9.256	0.043	0.043	0.000	0.000	0.000	0.000
9	A	13	ASP	-1	-0.793	-0.859	12.043	-0.341	-0.341	0.000	0.000	0.000	0.000
10	A	14	ALA	0	-0.012	0.006	10.488	0.085	0.085	0.000	0.000	0.000	0.000
11	A	15	ARG	1	0.816	0.878	12.486	0.142	0.142	0.000	0.000	0.000	0.000
12	A	16	ARG	1	0.762	0.858	14.520	0.330	0.330	0.000	0.000	0.000	0.000
13	A	17	LEU	0	0.019	0.008	14.726	0.022	0.022	0.000	0.000	0.000	0.000
14	A	18	LYS	1	0.850	0.916	15.128	-0.205	-0.205	0.000	0.000	0.000	0.000
15	A	19	ALA	0	-0.001	-0.002	17.490	0.008	0.008	0.000	0.000	0.000	0.000
16	A	20	ILE	0	-0.029	-0.021	20.262	0.003	0.003	0.000	0.000	0.000	0.000
17	A	21	TRP	0	0.028	0.012	19.864	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	22	GLU	-1	-0.840	-0.905	20.308	0.163	0.163	0.000	0.000	0.000	0.000
19	A	23	LYS	1	0.878	0.951	23.311	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	24	LYS	1	0.918	0.970	25.300	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	25	LYS	1	0.876	0.939	23.310	-0.135	-0.135	0.000	0.000	0.000	0.000
22	A	26	ASN	0	-0.008	-0.019	26.522	0.006	0.006	0.000	0.000	0.000	0.000
23	A	27	GLU	-1	-0.930	-0.959	29.894	0.024	0.024	0.000	0.000	0.000	0.000
24	A	28	LEU	0	-0.064	-0.029	27.268	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	29	GLY	0	-0.017	0.013	30.661	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	30	LEU	0	-0.109	-0.051	24.817	0.004	0.004	0.000	0.000	0.000	0.000
27	A	31	SER	0	0.023	0.005	25.811	0.006	0.006	0.000	0.000	0.000	0.000
28	A	32	TYR	0	0.042	0.000	18.120	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	33	GLU	-1	-0.840	-0.928	22.656	0.172	0.172	0.000	0.000	0.000	0.000
30	A	34	SER	0	0.028	0.030	25.078	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	35	VAL	0	-0.044	-0.034	20.816	-0.011	-0.011	0.000	0.000	0.000	0.000
32	A	36	ALA	0	-0.004	-0.011	21.150	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	37	ASP	-1	-0.877	-0.929	22.106	0.110	0.110	0.000	0.000	0.000	0.000
34	A	38	LYS	1	0.868	0.927	24.957	-0.058	-0.058	0.000	0.000	0.000	0.000
35	A	39	MET	0	-0.087	-0.049	17.426	-0.013	-0.013	0.000	0.000	0.000	0.000
36	A	40	GLY	0	0.002	0.030	20.779	0.003	0.003	0.000	0.000	0.000	0.000
37	A	41	MET	0	-0.057	-0.019	16.248	0.031	0.031	0.000	0.000	0.000	0.000
38	A	42	GLY	0	0.073	0.037	18.896	-0.014	-0.014	0.000	0.000	0.000	0.000
39	A	43	GLN	0	0.077	0.021	18.574	0.050	0.050	0.000	0.000	0.000	0.000
40	A	44	SER	0	0.020	-0.006	15.786	0.007	0.007	0.000	0.000	0.000	0.000
41	A	45	ALA	0	-0.013	0.006	13.848	0.077	0.077	0.000	0.000	0.000	0.000
42	A	46	VAL	0	0.041	0.018	14.024	0.015	0.015	0.000	0.000	0.000	0.000
43	A	47	ALA	0	-0.017	-0.006	15.105	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	48	ALA	0	-0.021	-0.009	10.219	0.013	0.013	0.000	0.000	0.000	0.000
45	A	49	LEU	0	0.002	0.012	10.215	0.048	0.048	0.000	0.000	0.000	0.000
46	A	50	PHE	0	-0.013	-0.020	11.906	-0.072	-0.072	0.000	0.000	0.000	0.000
47	A	51	ASN	0	-0.034	-0.029	11.639	-0.123	-0.123	0.000	0.000	0.000	0.000
48	A	52	GLY	0	0.020	0.016	8.639	0.052	0.052	0.000	0.000	0.000	0.000
49	A	53	ILE	0	-0.048	-0.019	6.196	0.053	0.053	0.000	0.000	0.000	0.000
50	A	54	ASN	0	-0.017	-0.011	5.442	1.251	1.251	0.000	0.000	0.000	0.000
51	A	55	ALA	0	0.009	0.005	6.862	-0.336	-0.336	0.000	0.000	0.000	0.000
52	A	56	LEU	0	0.013	0.009	8.483	0.108	0.108	0.000	0.000	0.000	0.000
53	A	57	ASN	0	0.056	0.027	11.563	-0.082	-0.082	0.000	0.000	0.000	0.000
54	A	58	ALA	0	0.111	0.047	13.982	0.031	0.031	0.000	0.000	0.000	0.000
55	A	59	TYR	0	0.001	0.001	17.599	0.011	0.011	0.000	0.000	0.000	0.000
56	A	60	ASN	0	0.024	-0.017	15.340	0.032	0.032	0.000	0.000	0.000	0.000
57	A	61	ALA	0	0.030	0.035	16.613	0.017	0.017	0.000	0.000	0.000	0.000
58	A	62	ALA	0	0.041	0.007	18.243	0.011	0.011	0.000	0.000	0.000	0.000
59	A	63	LEU	0	-0.060	-0.015	21.288	0.006	0.006	0.000	0.000	0.000	0.000
60	A	64	LEU	0	0.067	0.013	17.088	0.010	0.010	0.000	0.000	0.000	0.000
61	A	65	ALA	0	0.011	0.021	21.188	0.004	0.004	0.000	0.000	0.000	0.000
62	A	66	LYS	1	0.942	0.973	23.074	0.051	0.051	0.000	0.000	0.000	0.000
63	A	67	ILE	0	-0.071	-0.033	22.956	0.003	0.003	0.000	0.000	0.000	0.000
64	A	68	LEU	0	0.053	0.022	21.044	0.007	0.007	0.000	0.000	0.000	0.000
65	A	69	LYS	1	0.816	0.919	25.301	-0.012	-0.012	0.000	0.000	0.000	0.000
66	A	70	VAL	0	-0.009	0.007	22.959	0.002	0.002	0.000	0.000	0.000	0.000
67	A	71	SER	0	-0.046	-0.043	25.432	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	72	VAL	0	0.030	0.000	19.480	0.004	0.004	0.000	0.000	0.000	0.000
69	A	73	GLU	-1	-0.889	-0.946	20.391	-0.152	-0.152	0.000	0.000	0.000	0.000
70	A	74	GLU	-1	-0.879	-0.905	21.382	-0.065	-0.065	0.000	0.000	0.000	0.000
71	A	75	PHE	0	-0.045	-0.043	16.417	0.011	0.011	0.000	0.000	0.000	0.000
72	A	76	SER	0	0.008	-0.019	14.752	-0.031	-0.031	0.000	0.000	0.000	0.000
73	A	77	PRO	0	0.049	0.019	17.232	0.004	0.004	0.000	0.000	0.000	0.000
74	A	78	SER	0	-0.055	-0.031	14.786	0.008	0.008	0.000	0.000	0.000	0.000
75	A	79	ILE	0	0.056	0.026	13.290	0.025	0.025	0.000	0.000	0.000	0.000
76	A	80	ALA	0	-0.002	0.006	17.382	0.027	0.027	0.000	0.000	0.000	0.000
77	A	81	ARG	1	0.928	0.957	18.033	0.384	0.384	0.000	0.000	0.000	0.000
78	A	82	GLU	-1	-0.922	-0.954	15.854	-0.359	-0.359	0.000	0.000	0.000	0.000
79	A	83	ILE	0	-0.048	-0.010	20.005	0.021	0.021	0.000	0.000	0.000	0.000
80	A	84	ARG	1	0.874	0.945	22.377	0.225	0.225	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:SER)