FMO DATABASE

FMODB ID: 438QN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-803878.11178
FMO2-HF: Nuclear repulsion	762768.11986
FMO2-HF: Total energy	-41109.99192
FMO2-MP2: Total energy	-41228.995262

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.
-43.617	-34.766	5.622	-6.534	-7.939	0.064

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 : -0.893 / q_NPA : -0.947

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	-0.857	-0.924	2.225	27.247	31.363	4.998	-4.115	-4.999	0.039
4	A	4	PRO	0	0.052	0.030	2.892	-18.598	-15.657	0.581	-1.480	-2.042	0.018
5	A	5	THR	0	-0.032	-0.060	5.892	-8.382	-8.382	0.000	0.000	0.000	0.000
6	A	6	PHE	0	0.086	0.042	7.151	-6.180	-6.180	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.804	-0.876	7.009	36.787	36.787	0.000	0.000	0.000	0.000
8	A	8	PHE	0	-0.046	-0.006	9.837	-4.443	-4.443	0.000	0.000	0.000	0.000
9	A	9	ILE	0	-0.103	-0.050	11.609	-3.016	-3.016	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.095	0.049	13.054	-1.827	-1.827	0.000	0.000	0.000	0.000
11	A	11	TYR	0	-0.114	-0.083	12.980	-1.278	-1.278	0.000	0.000	0.000	0.000
12	A	12	LEU	0	-0.061	-0.031	16.328	-1.294	-1.294	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.873	-0.928	18.906	13.364	13.364	0.000	0.000	0.000	0.000
14	A	14	THR	0	0.010	-0.003	22.353	0.079	0.079	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.087	-0.016	24.615	-0.370	-0.370	0.000	0.000	0.000	0.000
16	A	16	PRO	0	-0.015	-0.010	28.143	0.079	0.079	0.000	0.000	0.000	0.000
17	A	17	GLN	0	0.088	0.041	30.857	-0.178	-0.178	0.000	0.000	0.000	0.000
18	A	18	THR	0	0.016	0.001	28.521	0.188	0.188	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.078	-0.056	29.486	-0.337	-0.337	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.055	0.007	26.472	-0.139	-0.139	0.000	0.000	0.000	0.000
21	A	21	MET	0	-0.014	0.012	20.434	-0.214	-0.214	0.000	0.000	0.000	0.000
22	A	22	TYR	0	0.031	0.015	24.912	-0.280	-0.280	0.000	0.000	0.000	0.000
23	A	23	MET	0	-0.014	0.023	19.247	0.826	0.826	0.000	0.000	0.000	0.000
24	A	24	GLY	0	-0.038	-0.039	22.367	-0.257	-0.257	0.000	0.000	0.000	0.000
25	A	25	ASN	0	0.042	0.015	21.010	0.413	0.413	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.086	0.030	19.684	-0.171	-0.171	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.010	0.003	21.364	-0.039	-0.039	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.035	-0.014	24.822	-0.404	-0.404	0.000	0.000	0.000	0.000
29	A	29	ILE	0	0.064	0.017	24.987	0.422	0.422	0.000	0.000	0.000	0.000
30	A	30	PRO	0	0.023	0.031	25.635	0.391	0.391	0.000	0.000	0.000	0.000
31	A	31	ARG	1	0.880	0.951	20.480	-15.025	-15.025	0.000	0.000	0.000	0.000
32	A	32	ASN	0	0.000	-0.010	23.870	-0.239	-0.239	0.000	0.000	0.000	0.000
33	A	33	TYR	0	0.042	0.002	19.784	0.239	0.239	0.000	0.000	0.000	0.000
34	A	34	ARG	1	0.973	1.002	21.775	-11.819	-11.819	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.902	0.968	24.361	-11.196	-11.196	0.000	0.000	0.000	0.000
36	A	36	TYR	0	-0.023	-0.025	22.500	-0.406	-0.406	0.000	0.000	0.000	0.000
37	A	37	LEU	0	0.091	0.042	17.936	0.418	0.418	0.000	0.000	0.000	0.000
38	A	38	TYR	0	0.000	-0.033	14.531	0.064	0.064	0.000	0.000	0.000	0.000
39	A	39	HIS	0	-0.076	-0.039	16.879	0.614	0.614	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.035	0.023	18.062	0.419	0.419	0.000	0.000	0.000	0.000
41	A	41	TYR	0	-0.017	-0.021	8.610	-0.191	-0.191	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.046	-0.026	13.289	1.189	1.189	0.000	0.000	0.000	0.000
43	A	43	ALA	0	-0.001	-0.004	14.392	0.744	0.744	0.000	0.000	0.000	0.000
44	A	44	TYR	0	0.044	0.034	8.943	0.447	0.447	0.000	0.000	0.000	0.000
45	A	45	MET	0	0.022	0.015	7.016	1.220	1.220	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-1.008	-0.997	10.514	21.395	21.395	0.000	0.000	0.000	0.000
47	A	47	ALA	0	0.049	0.029	13.116	0.056	0.056	0.000	0.000	0.000	0.000
48	A	48	ASN	0	-0.095	-0.051	8.655	0.363	0.363	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.012	0.019	8.666	3.365	3.365	0.000	0.000	0.000	0.000
50	A	50	TYR	0	-0.049	-0.016	3.308	-6.927	-5.133	0.043	-0.939	-0.898	0.007
51	A	51	ARG	1	0.915	0.933	7.620	-38.272	-38.272	0.000	0.000	0.000	0.000
52	A	52	ASN	0	-0.024	-0.002	5.694	-3.461	-3.461	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.068	0.045	8.358	3.592	3.592	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.026	0.024	8.684	-2.488	-2.488	0.000	0.000	0.000	0.000
55	A	55	SER	0	0.060	0.048	11.147	-1.776	-1.776	0.000	0.000	0.000	0.000
56	A	56	LEU	0	0.039	0.021	14.767	0.362	0.362	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.938	0.959	17.194	-14.635	-14.635	0.000	0.000	0.000	0.000
58	A	58	MET	0	0.016	0.003	12.424	-1.119	-1.119	0.000	0.000	0.000	0.000
59	A	59	PHE	0	0.041	0.024	12.425	-0.168	-0.168	0.000	0.000	0.000	0.000
60	A	60	GLY	0	-0.025	-0.022	13.992	-0.279	-0.279	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.055	-0.039	15.560	-0.575	-0.575	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.046	0.032	12.935	-0.393	-0.393	0.000	0.000	0.000	0.000
63	A	63	LEU	0	0.028	0.006	13.942	-0.315	-0.315	0.000	0.000	0.000	0.000
64	A	64	PRO	0	-0.061	-0.036	15.745	-0.242	-0.242	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.012	0.011	14.604	-0.689	-0.689	0.000	0.000	0.000	0.000
66	A	66	MET	0	0.063	0.035	8.561	-0.427	-0.427	0.000	0.000	0.000	0.000
67	A	67	LEU	0	0.010	0.008	14.037	-0.422	-0.422	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.949	0.978	17.257	-14.157	-14.157	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.952	-0.963	12.439	23.148	23.148	0.000	0.000	0.000	0.000
70	A	70	TYR	0	-0.069	-0.045	11.908	-1.039	-1.039	0.000	0.000	0.000	0.000
71	A	71	GLY	0	-0.056	-0.022	17.600	-0.842	-0.842	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.052	-0.028	19.141	-0.861	-0.861	0.000	0.000	0.000	0.000
73	A	73	ASN	0	0.003	-0.012	21.633	0.677	0.677	0.000	0.000	0.000	0.000
74	A	74	TYR	0	-0.013	-0.012	20.773	-0.234	-0.234	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.905	-0.942	22.792	10.911	10.911	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.899	0.955	24.352	-12.388	-12.388	0.000	0.000	0.000	0.000
77	A	77	ARG	1	0.952	0.972	26.370	-10.264	-10.264	0.000	0.000	0.000	0.000
78	A	78	HIS	0	-0.022	-0.009	28.313	0.092	0.092	0.000	0.000	0.000	0.000
79	A	79	THR	0	-0.015	0.011	31.072	-0.436	-0.436	0.000	0.000	0.000	0.000
80	A	80	LYS	1	0.978	0.988	33.008	-8.122	-8.122	0.000	0.000	0.000	0.000
81	A	81	GLN	0	0.049	0.007	31.462	0.111	0.111	0.000	0.000	0.000	0.000
82	A	82	GLY	0	-0.026	0.002	28.781	0.351	0.351	0.000	0.000	0.000	0.000
83	A	83	ILE	0	-0.025	-0.022	25.108	-0.277	-0.277	0.000	0.000	0.000	0.000
84	A	84	GLN	0	-0.055	-0.022	26.079	0.086	0.086	0.000	0.000	0.000	0.000
85	A	85	THR	0	-0.010	-0.018	22.046	0.015	0.015	0.000	0.000	0.000	0.000
86	A	86	ASN	0	0.047	0.027	24.798	-0.098	-0.098	0.000	0.000	0.000	0.000
87	A	87	LEU	0	0.022	0.017	19.743	0.033	0.033	0.000	0.000	0.000	0.000
88	A	88	THR	0	0.006	-0.004	23.103	-0.459	-0.459	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.021	-0.014	19.300	0.378	0.378	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.899	0.943	18.266	-17.444	-17.444	0.000	0.000	0.000	0.000
91	A	91	GLU	-1	-0.918	-0.940	21.816	12.575	12.575	0.000	0.000	0.000	0.000
92	A	92	GLU	-1	-0.820	-0.914	19.082	14.697	14.697	0.000	0.000	0.000	0.000
93	A	93	SER	0	-0.069	-0.066	18.227	0.366	0.366	0.000	0.000	0.000	0.000
94	A	94	TYR	0	-0.069	-0.037	19.253	-0.065	-0.065	0.000	0.000	0.000	0.000
95	A	95	GLY	0	-0.053	-0.017	21.684	-0.306	-0.306	0.000	0.000	0.000	0.000
96	A	96	ASP	-1	-0.831	-0.875	16.113	18.136	18.136	0.000	0.000	0.000	0.000
97	A	97	TRP	0	-0.033	-0.028	15.067	0.358	0.358	0.000	0.000	0.000	0.000
98	A	98	LEU	0	-0.063	-0.017	17.155	-0.201	-0.201	0.000	0.000	0.000	0.000
99	A	99	PRO	0	-0.043	-0.016	19.341	-0.607	-0.607	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.975	0.992	21.799	-13.563	-13.563	0.000	0.000	0.000	0.000

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