FMO DATABASE

FMODB ID: 538RZ

Calculation Name: 1KA8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KA8

Chain ID: A

ChEMBL ID:

UniProt ID: P10277

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:

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	100
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-803320.54334
FMO2-HF: Nuclear repulsion	762209.206577
FMO2-HF: Total energy	-41111.336762
FMO2-MP2: Total energy	-41230.1209

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:1:ASP)

Summations of interaction energy for fragment #1(A:1: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.
-66.141	-57.895	10.305	-8.912	-9.638	0.105

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.875 / q_NPA : -0.952

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	3	ASP	-1	-0.869	-0.925	1.955	27.522	29.895	7.491	-4.914	-4.951	0.047
4	A	4	PRO	0	0.057	0.019	2.884	-18.359	-16.262	0.533	-0.919	-1.710	0.014
5	A	5	THR	0	-0.032	-0.030	5.750	-9.925	-9.898	-0.001	0.001	-0.027	0.000
6	A	6	PHE	0	0.064	0.023	7.054	-5.745	-5.745	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.818	-0.894	7.926	33.810	33.810	0.000	0.000	0.000	0.000
8	A	8	PHE	0	-0.052	-0.013	9.689	-4.397	-4.397	0.000	0.000	0.000	0.000
9	A	9	ILE	0	-0.078	-0.047	11.580	-2.951	-2.951	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.091	0.049	12.885	-1.778	-1.778	0.000	0.000	0.000	0.000
11	A	11	TYR	0	-0.126	-0.089	13.149	-1.380	-1.380	0.000	0.000	0.000	0.000
12	A	12	LEU	0	-0.060	-0.027	16.255	-1.265	-1.265	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.829	-0.910	18.766	13.194	13.194	0.000	0.000	0.000	0.000
14	A	14	THR	0	-0.006	-0.012	22.207	0.061	0.061	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.046	-0.015	24.498	-0.401	-0.401	0.000	0.000	0.000	0.000
16	A	16	PRO	0	-0.012	-0.014	28.036	0.059	0.059	0.000	0.000	0.000	0.000
17	A	17	GLN	0	0.044	0.012	30.728	-0.340	-0.340	0.000	0.000	0.000	0.000
18	A	18	THR	0	0.021	0.017	28.296	0.169	0.169	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.020	-0.020	29.477	-0.313	-0.313	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.018	0.021	26.418	-0.157	-0.157	0.000	0.000	0.000	0.000
21	A	21	MET	0	-0.005	0.006	20.517	-0.229	-0.229	0.000	0.000	0.000	0.000
22	A	22	TYR	0	-0.005	0.001	24.883	-0.282	-0.282	0.000	0.000	0.000	0.000
23	A	23	MET	0	-0.018	0.015	18.547	0.787	0.787	0.000	0.000	0.000	0.000
24	A	24	GLY	0	-0.028	-0.029	22.420	-0.260	-0.260	0.000	0.000	0.000	0.000
25	A	25	ASN	0	0.031	0.006	21.141	0.234	0.234	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.060	0.019	19.828	-0.184	-0.184	0.000	0.000	0.000	0.000
27	A	27	SER	0	0.002	0.016	21.511	-0.035	-0.035	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.040	-0.019	25.123	-0.395	-0.395	0.000	0.000	0.000	0.000
29	A	29	ILE	0	0.018	0.003	25.087	0.438	0.438	0.000	0.000	0.000	0.000
30	A	30	PRO	0	0.059	0.042	25.718	0.407	0.407	0.000	0.000	0.000	0.000
31	A	31	ARG	1	0.864	0.949	20.783	-14.998	-14.998	0.000	0.000	0.000	0.000
32	A	32	ASN	0	0.012	-0.016	23.904	-0.183	-0.183	0.000	0.000	0.000	0.000
33	A	33	TYR	0	0.055	0.009	20.137	0.190	0.190	0.000	0.000	0.000	0.000
34	A	34	ARG	1	0.968	1.002	21.733	-11.706	-11.706	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.910	0.972	24.309	-11.238	-11.238	0.000	0.000	0.000	0.000
36	A	36	TYR	0	-0.033	-0.031	22.445	-0.404	-0.404	0.000	0.000	0.000	0.000
37	A	37	LEU	0	0.098	0.042	17.780	0.414	0.414	0.000	0.000	0.000	0.000
38	A	38	TYR	0	0.004	-0.024	14.851	0.026	0.026	0.000	0.000	0.000	0.000
39	A	39	HIS	0	-0.034	-0.020	16.931	0.643	0.643	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.028	0.019	18.075	0.449	0.449	0.000	0.000	0.000	0.000
41	A	41	TYR	0	0.008	-0.006	8.964	-0.193	-0.193	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.054	-0.024	13.289	1.254	1.254	0.000	0.000	0.000	0.000
43	A	43	ALA	0	0.003	-0.003	14.439	0.793	0.793	0.000	0.000	0.000	0.000
44	A	44	TYR	0	0.057	0.041	8.843	0.597	0.597	0.000	0.000	0.000	0.000
45	A	45	MET	0	0.014	0.006	6.559	1.801	1.801	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-1.014	-0.997	10.499	20.976	20.976	0.000	0.000	0.000	0.000
47	A	47	ALA	0	0.037	0.021	13.062	0.053	0.053	0.000	0.000	0.000	0.000
48	A	48	ASN	0	-0.093	-0.058	8.665	0.107	0.107	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.008	0.024	8.602	3.427	3.427	0.000	0.000	0.000	0.000
50	A	50	TYR	0	-0.069	-0.038	2.119	-20.801	-17.052	2.282	-3.080	-2.950	0.044
51	A	51	ARG	1	0.916	0.943	6.891	-40.248	-40.248	0.000	0.000	0.000	0.000
52	A	52	ASN	0	-0.035	-0.006	6.082	-4.161	-4.161	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.055	0.029	8.540	3.631	3.631	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.033	0.028	8.654	-2.602	-2.602	0.000	0.000	0.000	0.000
55	A	55	SER	0	0.049	0.024	11.341	-1.813	-1.813	0.000	0.000	0.000	0.000
56	A	56	LEU	0	0.035	0.021	14.938	0.362	0.362	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.942	0.965	17.342	-14.597	-14.597	0.000	0.000	0.000	0.000
58	A	58	MET	0	0.014	0.005	12.851	-1.069	-1.069	0.000	0.000	0.000	0.000
59	A	59	PHE	0	0.046	0.022	12.330	-0.309	-0.309	0.000	0.000	0.000	0.000
60	A	60	GLY	0	-0.019	-0.019	14.112	-0.273	-0.273	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.057	-0.042	15.845	-0.588	-0.588	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.040	0.031	13.012	-0.381	-0.381	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.001	0.008	14.015	-0.401	-0.401	0.000	0.000	0.000	0.000
64	A	64	PRO	0	-0.039	-0.033	15.763	-0.260	-0.260	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.007	0.004	14.706	-0.694	-0.694	0.000	0.000	0.000	0.000
66	A	66	MET	0	0.052	0.037	8.291	-0.874	-0.874	0.000	0.000	0.000	0.000
67	A	67	LEU	0	-0.002	-0.002	13.974	-0.450	-0.450	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.899	0.951	17.169	-13.932	-13.932	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.926	-0.951	12.644	22.938	22.938	0.000	0.000	0.000	0.000
70	A	70	TYR	0	-0.055	-0.021	11.739	-1.096	-1.096	0.000	0.000	0.000	0.000
71	A	71	GLY	0	-0.049	-0.018	17.434	-0.834	-0.834	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.051	-0.024	19.070	-0.886	-0.886	0.000	0.000	0.000	0.000
73	A	73	ASN	0	-0.033	-0.040	21.540	0.463	0.463	0.000	0.000	0.000	0.000
74	A	74	TYR	0	0.018	0.010	20.711	-0.292	-0.292	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.852	-0.918	22.752	11.046	11.046	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.905	0.963	24.272	-12.418	-12.418	0.000	0.000	0.000	0.000
77	A	77	ARG	1	0.896	0.924	26.389	-10.457	-10.457	0.000	0.000	0.000	0.000
78	A	78	HIS	0	0.007	0.006	28.255	0.172	0.172	0.000	0.000	0.000	0.000
79	A	79	THR	0	-0.032	-0.005	30.978	-0.408	-0.408	0.000	0.000	0.000	0.000
80	A	80	LYS	1	1.000	1.008	33.084	-8.169	-8.169	0.000	0.000	0.000	0.000
81	A	81	GLN	0	-0.012	-0.021	31.719	-0.184	-0.184	0.000	0.000	0.000	0.000
82	A	82	GLY	0	0.034	0.027	28.863	0.349	0.349	0.000	0.000	0.000	0.000
83	A	83	ILE	0	-0.030	-0.020	25.121	-0.264	-0.264	0.000	0.000	0.000	0.000
84	A	84	GLN	0	-0.024	-0.005	26.126	0.078	0.078	0.000	0.000	0.000	0.000
85	A	85	THR	0	-0.012	-0.031	21.968	0.038	0.038	0.000	0.000	0.000	0.000
86	A	86	ASN	0	0.031	0.018	24.519	-0.027	-0.027	0.000	0.000	0.000	0.000
87	A	87	LEU	0	0.032	0.024	19.575	0.019	0.019	0.000	0.000	0.000	0.000
88	A	88	THR	0	-0.022	-0.018	23.015	-0.436	-0.436	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.030	-0.017	18.795	0.365	0.365	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.904	0.962	18.329	-17.280	-17.280	0.000	0.000	0.000	0.000
91	A	91	GLU	-1	-0.903	-0.955	22.042	12.414	12.414	0.000	0.000	0.000	0.000
92	A	92	GLU	-1	-0.817	-0.914	19.037	15.248	15.248	0.000	0.000	0.000	0.000
93	A	93	SER	0	-0.045	-0.033	18.611	0.406	0.406	0.000	0.000	0.000	0.000
94	A	94	TYR	0	-0.044	-0.028	19.637	-0.093	-0.093	0.000	0.000	0.000	0.000
95	A	95	GLY	0	-0.022	-0.011	22.062	-0.281	-0.281	0.000	0.000	0.000	0.000
96	A	96	ASP	-1	-0.826	-0.880	16.426	18.252	18.252	0.000	0.000	0.000	0.000
97	A	97	TRP	0	-0.024	-0.016	15.268	0.327	0.327	0.000	0.000	0.000	0.000
98	A	98	LEU	0	-0.057	-0.016	17.382	-0.183	-0.183	0.000	0.000	0.000	0.000
99	A	99	PRO	0	-0.042	-0.019	19.357	-0.636	-0.636	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.879	0.958	21.876	-15.145	-15.145	0.000	0.000	0.000	0.000

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