FMO DATABASE

FMODB ID: 63J5Z

Calculation Name: 1KA8-A-Xray314

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	100
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-803711.929229
FMO2-HF: Nuclear repulsion	762602.524426
FMO2-HF: Total energy	-41109.404804
FMO2-MP2: Total energy	-41228.400175

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.
-30.416	-21.749	5.652	-6.451	-7.868	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 : -0.945

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	-0.861	-0.926	2.226	27.466	31.487	5.023	-4.086	-4.958	0.039
4	A	4	PRO	0	0.055	0.031	2.892	-18.703	-15.816	0.584	-1.446	-2.025	0.018
5	A	5	THR	0	-0.034	-0.060	5.892	-8.612	-8.612	0.000	0.000	0.000	0.000
6	A	6	PHE	0	0.088	0.041	7.151	-6.283	-6.283	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.808	-0.877	7.009	36.745	36.745	0.000	0.000	0.000	0.000
8	A	8	PHE	0	-0.035	-0.001	9.837	-4.489	-4.489	0.000	0.000	0.000	0.000
9	A	9	ILE	0	-0.112	-0.053	11.609	-3.088	-3.088	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.094	0.047	13.053	-1.869	-1.869	0.000	0.000	0.000	0.000
11	A	11	TYR	0	-0.110	-0.080	12.980	-1.298	-1.298	0.000	0.000	0.000	0.000
12	A	12	LEU	0	-0.062	-0.030	16.328	-1.330	-1.330	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.876	-0.929	18.906	13.327	13.327	0.000	0.000	0.000	0.000
14	A	14	THR	0	0.012	-0.003	22.353	0.059	0.059	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.088	-0.016	24.615	-0.399	-0.399	0.000	0.000	0.000	0.000
16	A	16	PRO	0	-0.019	-0.011	28.143	0.061	0.061	0.000	0.000	0.000	0.000
17	A	17	GLN	0	0.088	0.040	30.858	-0.182	-0.182	0.000	0.000	0.000	0.000
18	A	18	THR	0	0.012	0.000	28.520	0.195	0.195	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.077	-0.055	29.486	-0.343	-0.343	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.055	0.005	26.472	-0.127	-0.127	0.000	0.000	0.000	0.000
21	A	21	MET	0	-0.010	0.016	20.434	-0.211	-0.211	0.000	0.000	0.000	0.000
22	A	22	TYR	0	0.029	0.014	24.912	-0.286	-0.286	0.000	0.000	0.000	0.000
23	A	23	MET	0	-0.012	0.024	19.247	0.847	0.847	0.000	0.000	0.000	0.000
24	A	24	GLY	0	-0.038	-0.040	22.367	-0.261	-0.261	0.000	0.000	0.000	0.000
25	A	25	ASN	0	0.041	0.014	21.010	0.423	0.423	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.083	0.029	19.683	-0.169	-0.169	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.013	0.002	21.364	-0.066	-0.066	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.036	-0.015	24.822	-0.418	-0.418	0.000	0.000	0.000	0.000
29	A	29	ILE	0	0.062	0.016	24.987	0.417	0.417	0.000	0.000	0.000	0.000
30	A	30	PRO	0	0.021	0.031	25.635	0.387	0.387	0.000	0.000	0.000	0.000
31	A	31	ARG	1	0.882	0.952	20.480	-15.018	-15.018	0.000	0.000	0.000	0.000
32	A	32	ASN	0	0.004	-0.009	23.870	-0.244	-0.244	0.000	0.000	0.000	0.000
33	A	33	TYR	0	0.051	0.008	19.784	0.300	0.300	0.000	0.000	0.000	0.000
34	A	34	ARG	1	0.980	1.006	21.775	-11.832	-11.832	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.895	0.964	24.361	-11.215	-11.215	0.000	0.000	0.000	0.000
36	A	36	TYR	0	-0.028	-0.028	22.500	-0.386	-0.386	0.000	0.000	0.000	0.000
37	A	37	LEU	0	0.094	0.042	17.936	0.447	0.447	0.000	0.000	0.000	0.000
38	A	38	TYR	0	-0.006	-0.037	14.531	0.097	0.097	0.000	0.000	0.000	0.000
39	A	39	HIS	0	-0.077	-0.039	16.879	0.625	0.625	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.043	0.028	18.062	0.441	0.441	0.000	0.000	0.000	0.000
41	A	41	TYR	0	-0.019	-0.022	8.610	-0.055	-0.055	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.059	-0.031	13.289	1.225	1.225	0.000	0.000	0.000	0.000
43	A	43	ALA	0	0.018	0.005	14.392	0.774	0.774	0.000	0.000	0.000	0.000
44	A	44	TYR	0	0.042	0.033	8.942	0.631	0.631	0.000	0.000	0.000	0.000
45	A	45	MET	0	0.012	0.010	7.017	1.401	1.401	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-1.006	-0.995	10.514	21.378	21.378	0.000	0.000	0.000	0.000
47	A	47	ALA	0	0.060	0.036	13.116	0.070	0.070	0.000	0.000	0.000	0.000
48	A	48	ASN	0	-0.101	-0.054	8.655	0.517	0.517	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.015	0.019	8.666	3.454	3.454	0.000	0.000	0.000	0.000
50	A	50	TYR	0	-0.051	-0.019	3.308	-6.383	-4.624	0.045	-0.919	-0.885	0.007
51	A	51	ARG	1	0.913	0.933	7.620	-38.366	-38.366	0.000	0.000	0.000	0.000
52	A	52	ASN	0	-0.027	-0.003	5.694	-3.446	-3.446	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.072	0.047	8.358	3.645	3.645	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.022	0.021	8.684	-2.542	-2.542	0.000	0.000	0.000	0.000
55	A	55	SER	0	0.059	0.047	11.147	-1.878	-1.878	0.000	0.000	0.000	0.000
56	A	56	LEU	0	0.045	0.024	14.767	0.337	0.337	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.933	0.957	17.194	-14.658	-14.658	0.000	0.000	0.000	0.000
58	A	58	MET	0	0.016	0.003	12.424	-1.090	-1.090	0.000	0.000	0.000	0.000
59	A	59	PHE	0	0.040	0.024	12.425	-0.150	-0.150	0.000	0.000	0.000	0.000
60	A	60	GLY	0	-0.022	-0.021	13.992	-0.336	-0.336	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.057	-0.040	15.560	-0.579	-0.579	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.047	0.032	12.935	-0.363	-0.363	0.000	0.000	0.000	0.000
63	A	63	LEU	0	0.029	0.008	13.942	-0.336	-0.336	0.000	0.000	0.000	0.000
64	A	64	PRO	0	-0.061	-0.036	15.745	-0.286	-0.286	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.010	0.010	14.604	-0.677	-0.677	0.000	0.000	0.000	0.000
66	A	66	MET	0	0.064	0.035	8.561	-0.408	-0.408	0.000	0.000	0.000	0.000
67	A	67	LEU	0	0.012	0.009	14.037	-0.466	-0.466	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.951	0.979	17.257	-14.197	-14.197	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.954	-0.964	12.440	23.191	23.191	0.000	0.000	0.000	0.000
70	A	70	TYR	0	-0.073	-0.046	11.908	-1.081	-1.081	0.000	0.000	0.000	0.000
71	A	71	GLY	0	-0.056	-0.022	17.600	-0.892	-0.892	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.050	-0.027	19.141	-0.886	-0.886	0.000	0.000	0.000	0.000
73	A	73	ASN	0	0.000	-0.014	21.633	0.666	0.666	0.000	0.000	0.000	0.000
74	A	74	TYR	0	-0.012	-0.012	20.773	-0.232	-0.232	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.908	-0.943	22.792	10.892	10.892	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.902	0.956	24.352	-12.398	-12.398	0.000	0.000	0.000	0.000
77	A	77	ARG	1	0.949	0.971	26.370	-10.290	-10.290	0.000	0.000	0.000	0.000
78	A	78	HIS	0	-0.026	-0.010	28.312	0.085	0.085	0.000	0.000	0.000	0.000
79	A	79	THR	0	-0.015	0.011	31.072	-0.450	-0.450	0.000	0.000	0.000	0.000
80	A	80	LYS	1	0.976	0.987	33.008	-8.125	-8.125	0.000	0.000	0.000	0.000
81	A	81	GLN	0	0.050	0.008	31.461	0.118	0.118	0.000	0.000	0.000	0.000
82	A	82	GLY	0	-0.025	0.002	28.781	0.365	0.365	0.000	0.000	0.000	0.000
83	A	83	ILE	0	-0.027	-0.023	25.108	-0.272	-0.272	0.000	0.000	0.000	0.000
84	A	84	GLN	0	-0.055	-0.022	26.079	0.087	0.087	0.000	0.000	0.000	0.000
85	A	85	THR	0	-0.007	-0.018	22.046	0.022	0.022	0.000	0.000	0.000	0.000
86	A	86	ASN	0	0.037	0.024	24.798	-0.106	-0.106	0.000	0.000	0.000	0.000
87	A	87	LEU	0	0.024	0.018	19.742	0.044	0.044	0.000	0.000	0.000	0.000
88	A	88	THR	0	0.008	-0.005	23.103	-0.465	-0.465	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.012	-0.011	19.300	0.396	0.396	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.895	0.940	18.267	-17.465	-17.465	0.000	0.000	0.000	0.000
91	A	91	GLU	-1	-0.922	-0.942	21.816	12.559	12.559	0.000	0.000	0.000	0.000
92	A	92	GLU	-1	-0.825	-0.916	19.082	14.718	14.718	0.000	0.000	0.000	0.000
93	A	93	SER	0	-0.073	-0.069	18.227	0.385	0.385	0.000	0.000	0.000	0.000
94	A	94	TYR	0	-0.061	-0.033	19.253	-0.079	-0.079	0.000	0.000	0.000	0.000
95	A	95	GLY	0	-0.046	-0.011	21.684	-0.297	-0.297	0.000	0.000	0.000	0.000
96	A	96	ASP	-1	-0.838	-0.880	16.113	18.183	18.183	0.000	0.000	0.000	0.000
97	A	97	TRP	0	-0.042	-0.035	15.067	0.431	0.431	0.000	0.000	0.000	0.000
98	A	98	LEU	0	-0.077	-0.028	17.155	-0.176	-0.176	0.000	0.000	0.000	0.000
99	A	99	PRO	0	-0.066	-0.033	19.342	-0.507	-0.507	0.000	0.000	0.000	0.000
100	A	100	LYS	0	0.038	0.031	21.799	-1.061	-1.061	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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