FMO DATABASE

FMODB ID: 52J5Z

Calculation Name: 1KW4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KW4

Chain ID: A

ChEMBL ID:

UniProt ID: P39769

Base Structure: X-ray

Registration Date: 2023-06-22

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

DOI:

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	70
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-429126.58432
FMO2-HF: Nuclear repulsion	401371.957558
FMO2-HF: Total energy	-27754.626763
FMO2-MP2: Total energy	-27834.886981

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:10:ASP)

Summations of interaction energy for fragment #1(A:10:ASP)

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.
52.937	54.935	-0.016	-1.043	-0.939	0.003

Interaction energy analysis for fragmet #1(A:10:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.902 / q_NPA : -0.962

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	12	PRO	0	0.028	0.030	3.892	-3.810	-1.812	-0.016	-1.043	-0.939	0.003
4	A	13	PRO	0	0.033	0.007	7.173	2.371	2.371	0.000	0.000	0.000	0.000
5	A	14	ILE	0	0.064	0.039	8.393	-1.622	-1.622	0.000	0.000	0.000	0.000
6	A	15	SER	0	-0.032	-0.014	10.223	-0.619	-0.619	0.000	0.000	0.000	0.000
7	A	16	SER	0	-0.105	-0.065	11.215	-1.410	-1.410	0.000	0.000	0.000	0.000
8	A	17	TRP	0	-0.044	-0.017	5.998	0.009	0.009	0.000	0.000	0.000	0.000
9	A	18	SER	0	0.042	-0.011	12.132	-2.129	-2.129	0.000	0.000	0.000	0.000
10	A	19	VAL	0	0.041	0.011	14.426	1.229	1.229	0.000	0.000	0.000	0.000
11	A	20	ASP	-1	-0.869	-0.919	15.435	18.482	18.482	0.000	0.000	0.000	0.000
12	A	21	ASP	-1	-0.837	-0.870	10.382	27.843	27.843	0.000	0.000	0.000	0.000
13	A	22	VAL	0	-0.045	-0.019	10.967	2.553	2.553	0.000	0.000	0.000	0.000
14	A	23	SER	0	-0.044	-0.032	12.995	0.226	0.226	0.000	0.000	0.000	0.000
15	A	24	ASN	0	-0.022	-0.034	10.271	-0.393	-0.393	0.000	0.000	0.000	0.000
16	A	25	PHE	0	0.040	0.016	7.689	0.647	0.647	0.000	0.000	0.000	0.000
17	A	26	ILE	0	-0.041	-0.030	9.999	-0.154	-0.154	0.000	0.000	0.000	0.000
18	A	27	ARG	1	0.859	0.934	12.871	-20.492	-20.492	0.000	0.000	0.000	0.000
19	A	28	GLU	-1	-0.812	-0.865	6.369	47.611	47.611	0.000	0.000	0.000	0.000
20	A	29	LEU	0	-0.026	-0.001	10.845	-0.695	-0.695	0.000	0.000	0.000	0.000
21	A	30	PRO	0	0.028	0.025	12.445	-2.118	-2.118	0.000	0.000	0.000	0.000
22	A	31	GLY	0	0.021	0.006	15.252	-0.752	-0.752	0.000	0.000	0.000	0.000
23	A	32	CYS	0	-0.077	-0.046	15.613	-0.930	-0.930	0.000	0.000	0.000	0.000
24	A	33	GLN	0	0.039	0.012	16.626	0.432	0.432	0.000	0.000	0.000	0.000
25	A	34	ASP	-1	-0.906	-0.945	17.616	14.865	14.865	0.000	0.000	0.000	0.000
26	A	35	TYR	0	0.023	0.019	19.821	-0.678	-0.678	0.000	0.000	0.000	0.000
27	A	36	VAL	0	-0.021	-0.004	15.902	0.181	0.181	0.000	0.000	0.000	0.000
28	A	37	ASP	-1	-0.863	-0.933	18.528	14.765	14.765	0.000	0.000	0.000	0.000
29	A	38	ASP	-1	-0.892	-0.951	21.661	13.060	13.060	0.000	0.000	0.000	0.000
30	A	39	PHE	0	-0.032	-0.041	16.935	0.008	0.008	0.000	0.000	0.000	0.000
31	A	40	ILE	0	0.022	0.014	18.552	0.068	0.068	0.000	0.000	0.000	0.000
32	A	41	GLN	0	-0.053	-0.013	20.899	-0.700	-0.700	0.000	0.000	0.000	0.000
33	A	42	GLN	0	-0.079	-0.042	22.907	-0.604	-0.604	0.000	0.000	0.000	0.000
34	A	43	GLU	-1	-0.960	-0.974	21.680	13.055	13.055	0.000	0.000	0.000	0.000
35	A	44	ILE	0	-0.050	-0.029	16.995	0.286	0.286	0.000	0.000	0.000	0.000
36	A	45	ASP	-1	-0.739	-0.871	16.513	18.973	18.973	0.000	0.000	0.000	0.000
37	A	46	GLY	0	0.042	0.012	13.493	0.368	0.368	0.000	0.000	0.000	0.000
38	A	47	GLN	0	-0.045	-0.034	14.193	0.792	0.792	0.000	0.000	0.000	0.000
39	A	48	ALA	0	-0.028	-0.012	17.179	-0.560	-0.560	0.000	0.000	0.000	0.000
40	A	49	LEU	0	-0.010	-0.006	11.611	-0.425	-0.425	0.000	0.000	0.000	0.000
41	A	50	LEU	0	-0.038	-0.017	12.854	0.019	0.019	0.000	0.000	0.000	0.000
42	A	51	ARG	1	0.839	0.919	15.840	-15.233	-15.233	0.000	0.000	0.000	0.000
43	A	52	LEU	0	-0.003	0.020	17.864	-1.058	-1.058	0.000	0.000	0.000	0.000
44	A	53	LYS	1	0.936	0.958	19.116	-13.228	-13.228	0.000	0.000	0.000	0.000
45	A	54	GLU	-1	-0.825	-0.936	21.339	12.384	12.384	0.000	0.000	0.000	0.000
46	A	55	LYS	1	0.970	0.996	22.737	-11.197	-11.197	0.000	0.000	0.000	0.000
47	A	56	HIS	0	-0.001	0.005	22.738	-0.049	-0.049	0.000	0.000	0.000	0.000
48	A	57	LEU	0	0.057	0.027	18.479	-0.216	-0.216	0.000	0.000	0.000	0.000
49	A	58	VAL	0	-0.020	-0.013	22.993	-0.338	-0.338	0.000	0.000	0.000	0.000
50	A	59	ASN	0	-0.105	-0.067	26.024	-0.449	-0.449	0.000	0.000	0.000	0.000
51	A	60	ALA	0	-0.023	-0.008	26.665	-0.381	-0.381	0.000	0.000	0.000	0.000
52	A	61	MET	0	0.008	0.023	20.893	0.137	0.137	0.000	0.000	0.000	0.000
53	A	62	GLY	0	0.016	0.028	25.718	0.113	0.113	0.000	0.000	0.000	0.000
54	A	63	MET	0	-0.058	-0.002	19.638	0.191	0.191	0.000	0.000	0.000	0.000
55	A	64	LYS	1	0.965	0.969	24.384	-12.424	-12.424	0.000	0.000	0.000	0.000
56	A	65	LEU	0	0.068	0.023	23.262	0.636	0.636	0.000	0.000	0.000	0.000
57	A	66	GLY	0	0.010	0.012	22.383	0.461	0.461	0.000	0.000	0.000	0.000
58	A	67	PRO	0	0.014	-0.022	19.047	0.692	0.692	0.000	0.000	0.000	0.000
59	A	68	ALA	0	0.068	0.039	18.220	1.010	1.010	0.000	0.000	0.000	0.000
60	A	69	LEU	0	-0.014	-0.016	18.572	0.740	0.740	0.000	0.000	0.000	0.000
61	A	70	LYS	1	0.809	0.898	15.744	-17.451	-17.451	0.000	0.000	0.000	0.000
62	A	71	ILE	0	0.046	0.025	13.954	1.717	1.717	0.000	0.000	0.000	0.000
63	A	72	VAL	0	0.003	0.005	13.625	1.451	1.451	0.000	0.000	0.000	0.000
64	A	73	ALA	0	0.019	0.006	14.531	0.883	0.883	0.000	0.000	0.000	0.000
65	A	74	LYS	1	0.904	0.960	6.849	-38.975	-38.975	0.000	0.000	0.000	0.000
66	A	75	VAL	0	0.065	0.036	9.766	3.168	3.168	0.000	0.000	0.000	0.000
67	A	76	GLU	-1	-0.903	-0.943	11.161	19.637	19.637	0.000	0.000	0.000	0.000
68	A	77	SER	0	-0.094	-0.051	9.571	1.510	1.510	0.000	0.000	0.000	0.000
69	A	78	ILE	0	-0.016	0.003	5.489	1.888	1.888	0.000	0.000	0.000	0.000
70	A	79	LYS	1	0.810	0.903	7.990	-22.434	-22.434	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:10:ASP)