FMO DATABASE

FMODB ID: YYJN2

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-801359.853987
FMO2-HF: Nuclear repulsion	760247.950859
FMO2-HF: Total energy	-41111.903128
FMO2-MP2: Total energy	-41230.578856

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.
-79.837	-86.169	32.791	-15.189	-11.269	0.15

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 : -0.805 / q_NPA : -0.887

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	3	ASP	-1	-0.825	-0.907	1.825	25.520	25.467	10.973	-6.109	-4.811	0.058
4	A	4	PRO	0	0.042	0.020	2.857	-17.721	-16.190	0.842	-0.643	-1.730	0.013
5	A	5	THR	0	-0.052	-0.031	5.577	-10.638	-10.606	-0.001	0.001	-0.032	0.000
6	A	6	PHE	0	0.050	0.018	7.048	-5.410	-5.410	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.856	-0.917	7.635	32.306	32.306	0.000	0.000	0.000	0.000
8	A	8	PHE	0	-0.083	-0.038	9.326	-4.253	-4.253	0.000	0.000	0.000	0.000
9	A	9	ILE	0	-0.052	-0.044	11.359	-2.935	-2.935	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.081	0.059	12.395	-1.960	-1.960	0.000	0.000	0.000	0.000
11	A	11	TYR	0	-0.053	-0.051	12.687	-1.366	-1.366	0.000	0.000	0.000	0.000
12	A	12	LEU	0	-0.076	-0.024	15.895	-1.468	-1.468	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.831	-0.883	18.349	13.113	13.113	0.000	0.000	0.000	0.000
14	A	14	THR	0	-0.036	-0.036	21.837	0.231	0.231	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.014	0.000	24.482	-0.437	-0.437	0.000	0.000	0.000	0.000
16	A	16	PRO	0	0.014	-0.002	28.021	0.142	0.142	0.000	0.000	0.000	0.000
17	A	17	GLN	0	0.022	0.002	30.461	-0.316	-0.316	0.000	0.000	0.000	0.000
18	A	18	THR	0	-0.021	-0.027	27.952	0.197	0.197	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.028	-0.017	29.481	-0.333	-0.333	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.043	0.037	26.573	-0.205	-0.205	0.000	0.000	0.000	0.000
21	A	21	MET	0	-0.004	0.009	20.553	-0.174	-0.174	0.000	0.000	0.000	0.000
22	A	22	TYR	0	-0.041	-0.028	24.798	-0.287	-0.287	0.000	0.000	0.000	0.000
23	A	23	MET	0	0.008	0.013	18.851	0.834	0.834	0.000	0.000	0.000	0.000
24	A	24	GLY	0	-0.019	-0.015	22.420	-0.438	-0.438	0.000	0.000	0.000	0.000
25	A	25	ASN	0	0.012	-0.010	21.209	0.611	0.611	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.086	0.036	19.980	-0.203	-0.203	0.000	0.000	0.000	0.000
27	A	27	SER	0	0.020	0.013	21.709	0.018	0.018	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.050	-0.008	24.967	-0.556	-0.556	0.000	0.000	0.000	0.000
29	A	29	ILE	0	0.019	0.021	24.930	0.517	0.517	0.000	0.000	0.000	0.000
30	A	30	PRO	0	0.017	-0.005	25.631	0.393	0.393	0.000	0.000	0.000	0.000
31	A	31	ARG	1	0.866	0.943	21.019	-15.034	-15.034	0.000	0.000	0.000	0.000
32	A	32	ASN	0	0.010	-0.007	23.990	-0.078	-0.078	0.000	0.000	0.000	0.000
33	A	33	TYR	0	0.072	0.015	19.648	0.080	0.080	0.000	0.000	0.000	0.000
34	A	34	ARG	1	0.967	1.004	21.657	-11.821	-11.821	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.889	0.965	24.452	-11.336	-11.336	0.000	0.000	0.000	0.000
36	A	36	TYR	0	-0.024	-0.026	22.312	-0.420	-0.420	0.000	0.000	0.000	0.000
37	A	37	LEU	0	0.085	0.043	17.562	0.437	0.437	0.000	0.000	0.000	0.000
38	A	38	TYR	0	0.000	-0.026	14.792	0.113	0.113	0.000	0.000	0.000	0.000
39	A	39	HIS	0	-0.028	-0.023	16.737	0.598	0.598	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.024	0.016	17.662	0.470	0.470	0.000	0.000	0.000	0.000
41	A	41	TYR	0	0.023	0.015	8.693	-0.648	-0.648	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.036	-0.024	12.806	1.432	1.432	0.000	0.000	0.000	0.000
43	A	43	ALA	0	0.009	0.006	14.009	0.852	0.852	0.000	0.000	0.000	0.000
44	A	44	TYR	0	0.054	0.029	8.408	0.913	0.913	0.000	0.000	0.000	0.000
45	A	45	MET	0	-0.016	0.000	6.568	1.924	1.924	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-1.015	-0.998	10.074	21.435	21.435	0.000	0.000	0.000	0.000
47	A	47	ALA	0	0.018	0.008	12.518	0.486	0.486	0.000	0.000	0.000	0.000
48	A	48	ASN	0	-0.055	-0.028	8.407	-0.330	-0.330	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.014	0.013	8.251	3.888	3.888	0.000	0.000	0.000	0.000
50	A	50	TYR	0	-0.086	-0.074	1.596	-30.747	-38.589	20.977	-8.438	-4.696	0.079
51	A	51	ARG	1	0.880	0.942	6.300	-42.588	-42.588	0.000	0.000	0.000	0.000
52	A	52	ASN	0	-0.031	-0.024	5.714	-2.572	-2.572	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.046	0.030	8.439	3.435	3.435	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.041	0.032	9.276	-2.490	-2.490	0.000	0.000	0.000	0.000
55	A	55	SER	0	0.051	0.026	11.625	-1.564	-1.564	0.000	0.000	0.000	0.000
56	A	56	LEU	0	0.012	0.006	15.344	0.221	0.221	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.943	0.966	17.688	-14.795	-14.795	0.000	0.000	0.000	0.000
58	A	58	MET	0	0.027	0.011	13.323	-1.065	-1.065	0.000	0.000	0.000	0.000
59	A	59	PHE	0	0.046	0.024	12.455	-0.049	-0.049	0.000	0.000	0.000	0.000
60	A	60	GLY	0	-0.002	-0.008	14.240	-0.165	-0.165	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.069	-0.039	16.217	-0.927	-0.927	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.042	0.031	13.010	-0.359	-0.359	0.000	0.000	0.000	0.000
63	A	63	LEU	0	0.005	0.011	14.017	-0.286	-0.286	0.000	0.000	0.000	0.000
64	A	64	PRO	0	-0.046	-0.038	15.543	-0.434	-0.434	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.010	0.007	15.063	-0.719	-0.719	0.000	0.000	0.000	0.000
66	A	66	MET	0	0.048	0.036	8.565	-0.821	-0.821	0.000	0.000	0.000	0.000
67	A	67	LEU	0	-0.031	-0.022	14.181	-0.483	-0.483	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.800	0.882	17.320	-14.261	-14.261	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.910	-0.951	13.008	22.588	22.588	0.000	0.000	0.000	0.000
70	A	70	TYR	0	-0.038	-0.010	11.458	-1.282	-1.282	0.000	0.000	0.000	0.000
71	A	71	GLY	0	-0.006	0.002	17.373	-0.831	-0.831	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.013	-0.001	18.784	-0.914	-0.914	0.000	0.000	0.000	0.000
73	A	73	ASN	0	-0.031	-0.018	21.739	0.282	0.282	0.000	0.000	0.000	0.000
74	A	74	TYR	0	0.029	0.021	21.012	0.003	0.003	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.827	-0.905	23.135	11.373	11.373	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.932	0.975	24.140	-12.701	-12.701	0.000	0.000	0.000	0.000
77	A	77	ARG	1	0.865	0.901	26.539	-10.487	-10.487	0.000	0.000	0.000	0.000
78	A	78	HIS	0	0.029	0.015	28.876	0.210	0.210	0.000	0.000	0.000	0.000
79	A	79	THR	0	0.022	0.019	30.733	-0.369	-0.369	0.000	0.000	0.000	0.000
80	A	80	LYS	1	0.968	0.996	32.845	-8.192	-8.192	0.000	0.000	0.000	0.000
81	A	81	GLN	0	-0.013	-0.011	32.081	-0.251	-0.251	0.000	0.000	0.000	0.000
82	A	82	GLY	0	0.042	0.023	28.793	0.363	0.363	0.000	0.000	0.000	0.000
83	A	83	ILE	0	-0.025	-0.017	25.209	-0.271	-0.271	0.000	0.000	0.000	0.000
84	A	84	GLN	0	-0.022	0.008	26.274	0.083	0.083	0.000	0.000	0.000	0.000
85	A	85	THR	0	0.015	-0.015	22.305	0.147	0.147	0.000	0.000	0.000	0.000
86	A	86	ASN	0	0.031	0.023	24.561	-0.053	-0.053	0.000	0.000	0.000	0.000
87	A	87	LEU	0	0.021	0.029	19.522	-0.044	-0.044	0.000	0.000	0.000	0.000
88	A	88	THR	0	-0.060	-0.063	22.659	-0.548	-0.548	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.023	-0.014	18.469	0.613	0.613	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.928	0.964	18.034	-17.424	-17.424	0.000	0.000	0.000	0.000
91	A	91	GLU	-1	-0.931	-0.962	21.560	12.493	12.493	0.000	0.000	0.000	0.000
92	A	92	GLU	-1	-0.810	-0.917	18.495	15.581	15.581	0.000	0.000	0.000	0.000
93	A	93	SER	0	-0.045	-0.032	18.283	0.372	0.372	0.000	0.000	0.000	0.000
94	A	94	TYR	0	-0.048	-0.024	19.256	-0.079	-0.079	0.000	0.000	0.000	0.000
95	A	95	GLY	0	0.002	0.007	21.913	-0.420	-0.420	0.000	0.000	0.000	0.000
96	A	96	ASP	-1	-0.844	-0.892	16.501	18.452	18.452	0.000	0.000	0.000	0.000
97	A	97	TRP	0	-0.037	-0.022	15.281	0.243	0.243	0.000	0.000	0.000	0.000
98	A	98	LEU	0	-0.040	-0.007	17.238	0.019	0.019	0.000	0.000	0.000	0.000
99	A	99	PRO	0	-0.013	-0.012	19.366	-0.500	-0.500	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.822	0.920	21.251	-15.767	-15.767	0.000	0.000	0.000	0.000

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