FMO DATABASE

FMODB ID: YY432

Calculation Name: 3KU7-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3KU7

Chain ID: A

ChEMBL ID:
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UniProt ID: O25099

Base Structure: X-ray

Registration Date: 2023-06-19

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	OptH
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	64
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-352173.543862
FMO2-HF: Nuclear repulsion	326450.410494
FMO2-HF: Total energy	-25723.133368
FMO2-MP2: Total energy	-25798.220055

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:13:ALA)

Summations of interaction energy for fragment #1(A:13:ALA)

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.
-0.0090000000000004	4.351	0.013	-2.174	-2.198	0.005

Interaction energy analysis for fragmet #1(A:13:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.070 / q_NPA : 0.033

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	15	THR	0	-0.018	-0.038	3.505	-1.691	2.152	0.011	-2.076	-1.778	0.005
4	A	16	ALA	0	0.016	0.033	3.468	0.490	0.903	0.004	-0.074	-0.342	0.000
5	A	17	THR	0	-0.024	-0.008	4.608	-0.753	-0.738	-0.001	-0.010	-0.004	0.000
6	A	18	ASP	-1	-0.875	-0.926	7.343	-1.515	-1.515	0.000	0.000	0.000	0.000
7	A	19	ARG	1	0.908	0.953	4.264	3.671	3.760	-0.001	-0.014	-0.074	0.000
8	A	20	LEU	0	0.003	0.010	11.689	0.023	0.023	0.000	0.000	0.000	0.000
9	A	21	LYS	1	0.867	0.936	14.588	0.455	0.455	0.000	0.000	0.000	0.000
10	A	22	LEU	0	0.003	0.008	16.713	0.021	0.021	0.000	0.000	0.000	0.000
11	A	23	ILE	0	0.014	0.006	19.637	0.007	0.007	0.000	0.000	0.000	0.000
12	A	24	LEU	0	-0.015	-0.008	22.491	0.009	0.009	0.000	0.000	0.000	0.000
13	A	25	ALA	0	-0.021	0.002	26.105	0.007	0.007	0.000	0.000	0.000	0.000
14	A	26	LYS	1	0.843	0.931	28.006	0.097	0.097	0.000	0.000	0.000	0.000
15	A	27	GLU	-1	-0.894	-0.936	31.564	-0.087	-0.087	0.000	0.000	0.000	0.000
16	A	28	ARG	1	0.974	0.988	32.316	0.070	0.070	0.000	0.000	0.000	0.000
17	A	29	THR	0	-0.032	-0.022	33.815	0.003	0.003	0.000	0.000	0.000	0.000
18	A	30	LEU	0	0.005	-0.003	35.934	0.003	0.003	0.000	0.000	0.000	0.000
19	A	31	ASN	0	0.005	0.007	37.211	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	32	LEU	0	-0.015	-0.011	34.685	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	33	PRO	0	0.053	0.015	36.405	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	34	TYR	0	0.048	0.027	34.824	0.003	0.003	0.000	0.000	0.000	0.000
23	A	35	MET	0	0.045	0.036	29.514	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	36	GLU	-1	-0.856	-0.935	29.806	-0.118	-0.118	0.000	0.000	0.000	0.000
25	A	37	GLU	-1	-0.924	-0.971	30.891	-0.101	-0.101	0.000	0.000	0.000	0.000
26	A	38	MET	0	0.017	0.005	31.479	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	39	ARG	1	0.853	0.951	25.709	0.119	0.119	0.000	0.000	0.000	0.000
28	A	40	LYS	1	0.928	0.949	27.335	0.086	0.086	0.000	0.000	0.000	0.000
29	A	41	GLU	-1	-0.870	-0.930	28.264	-0.128	-0.128	0.000	0.000	0.000	0.000
30	A	42	ILE	0	-0.021	-0.003	25.216	-0.010	-0.010	0.000	0.000	0.000	0.000
31	A	43	ILE	0	-0.022	-0.019	22.556	-0.018	-0.018	0.000	0.000	0.000	0.000
32	A	44	ALA	0	0.013	0.011	24.673	-0.013	-0.013	0.000	0.000	0.000	0.000
33	A	45	VAL	0	-0.016	-0.015	26.805	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	46	ILE	0	0.036	0.019	20.632	-0.009	-0.009	0.000	0.000	0.000	0.000
35	A	47	GLN	0	-0.017	-0.015	21.838	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	48	LYS	1	0.895	0.989	23.269	0.161	0.161	0.000	0.000	0.000	0.000
37	A	49	TYR	0	-0.049	-0.053	24.304	0.011	0.011	0.000	0.000	0.000	0.000
38	A	50	THR	0	-0.024	-0.025	18.965	-0.011	-0.011	0.000	0.000	0.000	0.000
39	A	51	LYS	1	0.868	0.938	19.706	0.205	0.205	0.000	0.000	0.000	0.000
40	A	52	SER	0	-0.006	-0.006	16.490	0.026	0.026	0.000	0.000	0.000	0.000
41	A	53	SER	0	-0.020	-0.019	17.832	0.040	0.040	0.000	0.000	0.000	0.000
42	A	54	ASP	-1	-0.930	-0.933	13.478	-0.358	-0.358	0.000	0.000	0.000	0.000
43	A	55	ILE	0	-0.001	-0.026	16.237	-0.048	-0.048	0.000	0.000	0.000	0.000
44	A	56	HIS	0	-0.002	0.002	14.714	0.049	0.049	0.000	0.000	0.000	0.000
45	A	57	PHE	0	-0.002	-0.007	17.791	-0.020	-0.020	0.000	0.000	0.000	0.000
46	A	58	LYS	1	0.949	1.005	15.558	0.275	0.275	0.000	0.000	0.000	0.000
47	A	59	THR	0	0.002	-0.020	21.740	-0.011	-0.011	0.000	0.000	0.000	0.000
48	A	60	LEU	0	0.026	0.023	24.183	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	61	ASP	-1	-0.929	-0.953	19.433	-0.146	-0.146	0.000	0.000	0.000	0.000
50	A	62	SER	0	-0.030	-0.025	21.492	0.001	0.001	0.000	0.000	0.000	0.000
51	A	63	ASN	0	-0.011	-0.024	22.456	0.029	0.029	0.000	0.000	0.000	0.000
52	A	64	GLN	0	0.009	0.011	25.609	0.002	0.002	0.000	0.000	0.000	0.000
53	A	65	SER	0	-0.007	-0.005	29.413	0.004	0.004	0.000	0.000	0.000	0.000
54	A	66	VAL	0	-0.009	0.002	28.591	0.003	0.003	0.000	0.000	0.000	0.000
55	A	67	GLU	-1	-0.927	-0.975	28.045	-0.098	-0.098	0.000	0.000	0.000	0.000
56	A	68	THR	0	-0.026	-0.045	22.460	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	69	ILE	0	0.012	0.024	23.803	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	70	GLU	-1	-0.910	-0.954	18.101	-0.309	-0.309	0.000	0.000	0.000	0.000
59	A	71	VAL	0	0.020	-0.010	19.176	0.017	0.017	0.000	0.000	0.000	0.000
60	A	72	GLU	-1	-0.899	-0.959	13.626	-0.404	-0.404	0.000	0.000	0.000	0.000
61	A	73	ILE	0	-0.003	-0.008	15.227	0.044	0.044	0.000	0.000	0.000	0.000
62	A	74	ILE	0	0.038	0.028	10.834	-0.125	-0.125	0.000	0.000	0.000	0.000
63	A	75	LEU	0	-0.043	-0.023	12.922	0.130	0.130	0.000	0.000	0.000	0.000
64	A	76	PRO	0	-0.011	0.007	13.103	-0.053	-0.053	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:13:ALA)