FMO DATABASE

FMODB ID: 1N69Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-515640.220182
FMO2-HF: Nuclear repulsion	484912.689035
FMO2-HF: Total energy	-30727.531146
FMO2-MP2: Total energy	-30817.703881

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.
0.787	2.02	-0.008	-0.527	-0.697	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 : -0.014 / 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

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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	0.016	-0.011	3.859	-0.920	0.313	-0.008	-0.527	-0.697	0.002
4	A	8	GLN	0	0.038	0.006	6.168	0.470	0.470	0.000	0.000	0.000	0.000
5	A	9	GLU	-1	-0.806	-0.899	8.843	-0.226	-0.226	0.000	0.000	0.000	0.000
6	A	10	GLN	0	0.043	0.044	6.969	-0.484	-0.484	0.000	0.000	0.000	0.000
7	A	11	LEU	0	0.010	0.007	5.481	0.323	0.323	0.000	0.000	0.000	0.000
8	A	12	GLU	-1	-0.810	-0.873	8.865	0.084	0.084	0.000	0.000	0.000	0.000
9	A	13	ASP	-1	-0.760	-0.847	12.067	-0.254	-0.254	0.000	0.000	0.000	0.000
10	A	14	ALA	0	-0.007	0.010	10.441	0.065	0.065	0.000	0.000	0.000	0.000
11	A	15	ARG	1	0.850	0.899	12.361	0.052	0.052	0.000	0.000	0.000	0.000
12	A	16	ARG	1	0.746	0.841	14.279	0.247	0.247	0.000	0.000	0.000	0.000
13	A	17	LEU	0	0.031	0.013	14.738	0.013	0.013	0.000	0.000	0.000	0.000
14	A	18	LYS	1	0.854	0.926	14.971	-0.273	-0.273	0.000	0.000	0.000	0.000
15	A	19	ALA	0	-0.005	-0.005	17.488	0.000	0.000	0.000	0.000	0.000	0.000
16	A	20	ILE	0	-0.040	-0.023	20.183	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	21	TRP	0	0.018	0.012	19.786	-0.009	-0.009	0.000	0.000	0.000	0.000
18	A	22	GLU	-1	-0.840	-0.910	20.011	0.194	0.194	0.000	0.000	0.000	0.000
19	A	23	LYS	1	0.893	0.958	23.195	-0.039	-0.039	0.000	0.000	0.000	0.000
20	A	24	LYS	1	0.906	0.958	25.287	-0.023	-0.023	0.000	0.000	0.000	0.000
21	A	25	LYS	1	0.858	0.930	23.511	-0.153	-0.153	0.000	0.000	0.000	0.000
22	A	26	ASN	0	-0.027	-0.017	26.405	0.005	0.005	0.000	0.000	0.000	0.000
23	A	27	GLU	-1	-0.911	-0.962	29.838	0.038	0.038	0.000	0.000	0.000	0.000
24	A	28	LEU	0	-0.067	-0.021	27.351	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	29	GLY	0	-0.011	0.007	30.780	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	30	LEU	0	-0.092	-0.037	25.125	0.003	0.003	0.000	0.000	0.000	0.000
27	A	31	SER	0	0.011	-0.002	25.928	0.006	0.006	0.000	0.000	0.000	0.000
28	A	32	TYR	0	0.035	-0.001	18.234	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	33	GLU	-1	-0.848	-0.933	22.501	0.185	0.185	0.000	0.000	0.000	0.000
30	A	34	SER	0	0.029	0.028	24.856	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	35	VAL	0	-0.055	-0.024	21.074	-0.015	-0.015	0.000	0.000	0.000	0.000
32	A	36	ALA	0	0.000	-0.014	21.075	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	37	ASP	-1	-0.871	-0.931	22.006	0.104	0.104	0.000	0.000	0.000	0.000
34	A	38	LYS	1	0.889	0.939	24.891	-0.073	-0.073	0.000	0.000	0.000	0.000
35	A	39	MET	0	-0.071	-0.035	17.179	-0.011	-0.011	0.000	0.000	0.000	0.000
36	A	40	GLY	0	-0.001	0.024	20.357	0.002	0.002	0.000	0.000	0.000	0.000
37	A	41	MET	0	-0.050	-0.021	15.990	0.029	0.029	0.000	0.000	0.000	0.000
38	A	42	GLY	0	0.071	0.038	18.682	-0.014	-0.014	0.000	0.000	0.000	0.000
39	A	43	GLN	0	0.059	0.012	18.423	0.063	0.063	0.000	0.000	0.000	0.000
40	A	44	SER	0	0.028	0.000	16.362	0.009	0.009	0.000	0.000	0.000	0.000
41	A	45	ALA	0	-0.025	0.003	13.885	0.093	0.093	0.000	0.000	0.000	0.000
42	A	46	VAL	0	0.045	0.017	13.968	0.050	0.050	0.000	0.000	0.000	0.000
43	A	47	ALA	0	-0.009	-0.003	15.316	0.007	0.007	0.000	0.000	0.000	0.000
44	A	48	ALA	0	-0.019	-0.012	10.550	0.035	0.035	0.000	0.000	0.000	0.000
45	A	49	LEU	0	-0.009	0.001	10.308	0.124	0.124	0.000	0.000	0.000	0.000
46	A	50	PHE	0	-0.004	-0.017	11.815	-0.060	-0.060	0.000	0.000	0.000	0.000
47	A	51	ASN	0	-0.037	-0.031	11.598	-0.129	-0.129	0.000	0.000	0.000	0.000
48	A	52	GLY	0	0.019	0.015	8.479	0.026	0.026	0.000	0.000	0.000	0.000
49	A	53	ILE	0	-0.045	-0.016	6.233	0.206	0.206	0.000	0.000	0.000	0.000
50	A	54	ASN	0	-0.011	-0.016	6.164	1.223	1.223	0.000	0.000	0.000	0.000
51	A	55	ALA	0	0.008	0.010	6.660	-0.364	-0.364	0.000	0.000	0.000	0.000
52	A	56	LEU	0	0.009	0.007	8.407	0.010	0.010	0.000	0.000	0.000	0.000
53	A	57	ASN	0	0.058	0.026	11.437	-0.080	-0.080	0.000	0.000	0.000	0.000
54	A	58	ALA	0	0.081	0.028	14.067	0.053	0.053	0.000	0.000	0.000	0.000
55	A	59	TYR	0	-0.008	0.005	17.784	0.014	0.014	0.000	0.000	0.000	0.000
56	A	60	ASN	0	0.014	-0.020	15.370	0.043	0.043	0.000	0.000	0.000	0.000
57	A	61	ALA	0	0.031	0.025	16.683	0.020	0.020	0.000	0.000	0.000	0.000
58	A	62	ALA	0	0.052	0.016	18.369	0.010	0.010	0.000	0.000	0.000	0.000
59	A	63	LEU	0	-0.060	-0.012	21.002	0.004	0.004	0.000	0.000	0.000	0.000
60	A	64	LEU	0	0.048	0.004	17.217	0.008	0.008	0.000	0.000	0.000	0.000
61	A	65	ALA	0	0.018	0.021	21.375	0.006	0.006	0.000	0.000	0.000	0.000
62	A	66	LYS	1	0.916	0.958	23.437	0.038	0.038	0.000	0.000	0.000	0.000
63	A	67	ILE	0	-0.051	-0.014	22.793	0.002	0.002	0.000	0.000	0.000	0.000
64	A	68	LEU	0	0.051	0.009	20.880	0.003	0.003	0.000	0.000	0.000	0.000
65	A	69	LYS	1	0.835	0.924	25.363	-0.025	-0.025	0.000	0.000	0.000	0.000
66	A	70	VAL	0	-0.025	0.000	23.175	0.002	0.002	0.000	0.000	0.000	0.000
67	A	71	SER	0	-0.035	-0.046	25.454	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	72	VAL	0	-0.002	-0.014	19.523	0.010	0.010	0.000	0.000	0.000	0.000
69	A	73	GLU	-1	-0.850	-0.938	20.339	-0.118	-0.118	0.000	0.000	0.000	0.000
70	A	74	GLU	-1	-0.861	-0.896	21.481	-0.035	-0.035	0.000	0.000	0.000	0.000
71	A	75	PHE	0	-0.064	-0.037	16.535	0.015	0.015	0.000	0.000	0.000	0.000
72	A	76	SER	0	-0.020	-0.033	14.930	-0.025	-0.025	0.000	0.000	0.000	0.000
73	A	77	PRO	0	0.055	0.020	17.290	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	78	SER	0	-0.065	-0.024	14.237	-0.009	-0.009	0.000	0.000	0.000	0.000
75	A	79	ILE	0	0.052	0.031	13.162	0.022	0.022	0.000	0.000	0.000	0.000
76	A	80	ALA	0	0.009	0.009	17.253	0.021	0.021	0.000	0.000	0.000	0.000
77	A	81	ARG	1	0.886	0.931	17.699	0.350	0.350	0.000	0.000	0.000	0.000
78	A	82	GLU	-1	-0.870	-0.931	15.586	-0.345	-0.345	0.000	0.000	0.000	0.000
79	A	83	ILE	0	-0.050	-0.010	19.845	0.017	0.017	0.000	0.000	0.000	0.000
80	A	84	ARG	1	0.871	0.943	22.145	0.205	0.205	0.000	0.000	0.000	0.000

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