FMO DATABASE

FMODB ID: YY2V2

Calculation Name: 1KAF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KAF

Chain ID: A

ChEMBL ID:

UniProt ID: P22915

Base Structure: X-ray

Registration Date: 2023-06-21

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	108
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-911106.660147
FMO2-HF: Nuclear repulsion	865982.361126
FMO2-HF: Total energy	-45124.29902
FMO2-MP2: Total energy	-45251.487605

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:104:MET)

Summations of interaction energy for fragment #1(A:104:MET)

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.
-18.085	-15.523	15.946	-5.839	-12.668	-0.014

Interaction energy analysis for fragmet #1(A:104:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.051 / q_NPA : -0.007

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	106	ILE	0	-0.008	-0.017	2.895	0.830	2.940	0.079	-0.858	-1.331	0.001
4	A	107	THR	0	0.003	-0.017	5.473	-0.301	-0.301	0.000	0.000	0.000	0.000
5	A	108	SER	0	0.033	0.009	9.297	0.083	0.083	0.000	0.000	0.000	0.000
6	A	109	ASP	-1	-0.712	-0.816	12.262	-0.297	-0.297	0.000	0.000	0.000	0.000
7	A	110	MET	0	-0.062	-0.024	7.218	0.075	0.075	0.000	0.000	0.000	0.000
8	A	111	GLU	-1	-0.810	-0.876	8.536	-0.936	-0.936	0.000	0.000	0.000	0.000
9	A	112	GLU	-1	-0.929	-0.973	11.199	-0.300	-0.300	0.000	0.000	0.000	0.000
10	A	113	ASP	-1	-0.773	-0.881	13.416	0.092	0.092	0.000	0.000	0.000	0.000
11	A	114	LYS	1	0.747	0.863	10.588	0.559	0.559	0.000	0.000	0.000	0.000
12	A	115	ASP	-1	-0.843	-0.907	13.195	-0.311	-0.311	0.000	0.000	0.000	0.000
13	A	116	LEU	0	-0.066	-0.019	15.687	0.022	0.022	0.000	0.000	0.000	0.000
14	A	117	MET	0	-0.015	-0.012	15.337	0.046	0.046	0.000	0.000	0.000	0.000
15	A	118	LEU	0	-0.016	-0.016	13.866	0.030	0.030	0.000	0.000	0.000	0.000
16	A	119	LYS	1	0.992	1.011	17.757	0.074	0.074	0.000	0.000	0.000	0.000
17	A	120	LEU	0	-0.035	-0.023	20.591	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	121	LEU	0	-0.023	-0.006	17.741	0.020	0.020	0.000	0.000	0.000	0.000
19	A	122	ASP	-1	-0.910	-0.955	20.412	0.033	0.033	0.000	0.000	0.000	0.000
20	A	123	LYS	1	0.742	0.878	23.048	-0.049	-0.049	0.000	0.000	0.000	0.000
21	A	124	ASN	0	-0.048	-0.030	25.222	-0.011	-0.011	0.000	0.000	0.000	0.000
22	A	125	GLY	0	0.005	0.015	25.873	0.011	0.011	0.000	0.000	0.000	0.000
23	A	126	PHE	0	-0.029	-0.023	21.218	0.021	0.021	0.000	0.000	0.000	0.000
24	A	127	VAL	0	-0.013	-0.010	21.024	0.002	0.002	0.000	0.000	0.000	0.000
25	A	128	LEU	0	0.059	0.024	15.795	0.045	0.045	0.000	0.000	0.000	0.000
26	A	129	LYS	1	0.795	0.894	15.746	-0.246	-0.246	0.000	0.000	0.000	0.000
27	A	130	LYS	1	0.802	0.882	9.730	-0.636	-0.636	0.000	0.000	0.000	0.000
28	A	131	VAL	0	0.036	0.020	10.211	0.087	0.087	0.000	0.000	0.000	0.000
29	A	132	GLU	-1	-0.847	-0.912	6.266	0.616	0.616	0.000	0.000	0.000	0.000
30	A	133	ILE	0	0.080	0.040	2.463	-1.111	-0.740	2.554	-0.604	-2.322	-0.002
31	A	134	TYR	0	0.013	-0.005	2.365	-3.311	-1.632	2.770	-1.696	-2.753	-0.016
32	A	135	ARG	1	0.874	0.920	2.143	-3.988	-3.843	2.015	0.042	-2.201	-0.004
33	A	136	SER	0	0.079	0.032	2.338	-4.964	-6.420	8.514	-3.326	-3.732	0.007
34	A	137	ASN	0	0.040	0.048	3.906	-3.262	-3.651	0.015	0.605	-0.231	0.000
35	A	138	TYR	0	0.037	-0.009	5.985	0.975	1.077	-0.001	-0.002	-0.098	0.000
36	A	139	LEU	0	-0.064	-0.029	7.656	-0.163	-0.163	0.000	0.000	0.000	0.000
37	A	140	ALA	0	0.073	0.033	10.304	-0.139	-0.139	0.000	0.000	0.000	0.000
38	A	141	ILE	0	-0.047	-0.022	10.611	-0.016	-0.016	0.000	0.000	0.000	0.000
39	A	142	LEU	0	0.025	0.015	14.429	-0.076	-0.076	0.000	0.000	0.000	0.000
40	A	143	GLU	-1	-0.861	-0.917	18.189	0.192	0.192	0.000	0.000	0.000	0.000
41	A	144	LYS	1	0.862	0.924	19.921	-0.134	-0.134	0.000	0.000	0.000	0.000
42	A	145	ARG	1	0.929	0.974	17.349	-0.411	-0.411	0.000	0.000	0.000	0.000
43	A	146	THR	0	0.063	0.032	22.910	-0.026	-0.026	0.000	0.000	0.000	0.000
44	A	147	ASN	0	0.023	0.012	25.084	0.016	0.016	0.000	0.000	0.000	0.000
45	A	148	GLY	0	0.038	0.021	25.081	0.003	0.003	0.000	0.000	0.000	0.000
46	A	149	ILE	0	0.005	0.007	20.229	0.042	0.042	0.000	0.000	0.000	0.000
47	A	150	ARG	1	0.835	0.907	17.569	-0.489	-0.489	0.000	0.000	0.000	0.000
48	A	151	ASN	0	-0.085	-0.064	12.730	-0.074	-0.074	0.000	0.000	0.000	0.000
49	A	152	PHE	0	0.102	0.057	15.551	-0.047	-0.047	0.000	0.000	0.000	0.000
50	A	153	GLU	-1	-0.845	-0.910	12.095	1.307	1.307	0.000	0.000	0.000	0.000
51	A	154	ILE	0	0.043	0.016	10.417	-0.142	-0.142	0.000	0.000	0.000	0.000
52	A	155	ASN	0	-0.046	-0.043	9.646	0.571	0.571	0.000	0.000	0.000	0.000
53	A	156	ASN	0	0.035	-0.005	6.762	-0.620	-0.620	0.000	0.000	0.000	0.000
54	A	157	ASN	0	-0.025	-0.004	9.755	-0.233	-0.233	0.000	0.000	0.000	0.000
55	A	158	GLY	0	0.050	0.018	12.857	-0.112	-0.112	0.000	0.000	0.000	0.000
56	A	159	ASN	0	-0.064	-0.036	14.294	-0.126	-0.126	0.000	0.000	0.000	0.000
57	A	160	MET	0	0.033	0.041	14.147	0.083	0.083	0.000	0.000	0.000	0.000
58	A	161	ARG	1	0.780	0.866	14.247	-0.868	-0.868	0.000	0.000	0.000	0.000
59	A	162	ILE	0	0.030	0.033	17.052	0.002	0.002	0.000	0.000	0.000	0.000
60	A	163	PHE	0	-0.043	-0.004	14.962	-0.010	-0.010	0.000	0.000	0.000	0.000
61	A	164	GLY	0	0.076	0.015	17.729	-0.035	-0.035	0.000	0.000	0.000	0.000
62	A	165	TYR	0	-0.098	-0.058	20.865	0.015	0.015	0.000	0.000	0.000	0.000
63	A	166	LYS	1	0.893	0.951	23.356	-0.306	-0.306	0.000	0.000	0.000	0.000
64	A	167	MET	0	0.021	0.038	23.847	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	168	MET	0	-0.003	0.008	27.346	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	169	GLU	-1	-0.823	-0.908	30.447	0.200	0.200	0.000	0.000	0.000	0.000
67	A	170	HIS	0	0.035	0.025	32.225	0.004	0.004	0.000	0.000	0.000	0.000
68	A	171	HIS	0	-0.025	-0.018	29.147	-0.008	-0.008	0.000	0.000	0.000	0.000
69	A	172	ILE	0	-0.009	-0.023	26.844	0.010	0.010	0.000	0.000	0.000	0.000
70	A	173	GLN	0	-0.014	-0.024	28.910	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	174	LYS	1	0.864	0.925	30.398	-0.134	-0.134	0.000	0.000	0.000	0.000
72	A	175	PHE	0	0.006	-0.008	24.736	0.001	0.001	0.000	0.000	0.000	0.000
73	A	176	THR	0	-0.076	-0.047	27.515	0.002	0.002	0.000	0.000	0.000	0.000
74	A	177	ASP	-1	-0.967	-0.962	29.214	0.112	0.112	0.000	0.000	0.000	0.000
75	A	178	ILE	0	-0.026	-0.004	25.980	-0.008	-0.008	0.000	0.000	0.000	0.000
76	A	179	GLY	0	0.018	0.012	27.289	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	180	MET	0	-0.108	-0.035	20.861	0.016	0.016	0.000	0.000	0.000	0.000
78	A	181	SER	0	0.008	0.004	23.110	-0.014	-0.014	0.000	0.000	0.000	0.000
79	A	182	CYS	0	0.000	-0.004	23.777	0.033	0.033	0.000	0.000	0.000	0.000
80	A	183	LYS	1	0.937	0.975	21.381	-0.484	-0.484	0.000	0.000	0.000	0.000
81	A	184	ILE	0	0.070	0.036	23.304	0.028	0.028	0.000	0.000	0.000	0.000
82	A	185	ALA	0	-0.033	-0.012	21.986	-0.016	-0.016	0.000	0.000	0.000	0.000
83	A	186	LYS	1	0.936	0.949	24.127	-0.330	-0.330	0.000	0.000	0.000	0.000
84	A	187	ASN	0	0.049	0.033	20.983	-0.030	-0.030	0.000	0.000	0.000	0.000
85	A	188	GLY	0	0.014	-0.007	25.543	-0.016	-0.016	0.000	0.000	0.000	0.000
86	A	189	ASN	0	-0.050	-0.027	18.802	-0.047	-0.047	0.000	0.000	0.000	0.000
87	A	190	VAL	0	-0.017	-0.009	21.654	-0.014	-0.014	0.000	0.000	0.000	0.000
88	A	191	TYR	0	-0.010	-0.008	16.074	0.017	0.017	0.000	0.000	0.000	0.000
89	A	192	LEU	0	0.069	0.035	20.139	-0.037	-0.037	0.000	0.000	0.000	0.000
90	A	193	ASP	-1	-0.788	-0.876	17.587	0.704	0.704	0.000	0.000	0.000	0.000
91	A	194	ILE	0	0.058	0.039	19.475	-0.039	-0.039	0.000	0.000	0.000	0.000
92	A	195	LYS	1	0.845	0.922	17.305	-0.308	-0.308	0.000	0.000	0.000	0.000
93	A	196	ARG	1	0.729	0.841	12.192	-0.069	-0.069	0.000	0.000	0.000	0.000
94	A	197	SER	0	0.024	-0.008	17.752	-0.026	-0.026	0.000	0.000	0.000	0.000
95	A	198	ALA	0	0.067	0.031	20.151	0.026	0.026	0.000	0.000	0.000	0.000
96	A	199	GLU	-1	-0.831	-0.908	21.369	0.029	0.029	0.000	0.000	0.000	0.000
97	A	200	ASN	0	-0.013	-0.007	21.513	0.001	0.001	0.000	0.000	0.000	0.000
98	A	201	ILE	0	-0.013	-0.013	16.803	0.031	0.031	0.000	0.000	0.000	0.000
99	A	202	GLU	-1	-0.770	-0.894	20.931	0.062	0.062	0.000	0.000	0.000	0.000
100	A	203	ALA	0	0.004	0.020	24.162	0.006	0.006	0.000	0.000	0.000	0.000
101	A	204	VAL	0	0.017	-0.012	21.306	0.009	0.009	0.000	0.000	0.000	0.000
102	A	205	ILE	0	-0.017	-0.012	19.649	0.017	0.017	0.000	0.000	0.000	0.000
103	A	206	THR	0	-0.007	0.002	23.710	-0.008	-0.008	0.000	0.000	0.000	0.000
104	A	207	VAL	0	0.013	0.004	27.147	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	208	ALA	0	-0.039	-0.036	24.420	0.005	0.005	0.000	0.000	0.000	0.000
106	A	209	SER	0	-0.025	-0.023	26.391	0.001	0.001	0.000	0.000	0.000	0.000
107	A	210	GLU	-1	-0.880	-0.914	28.500	0.105	0.105	0.000	0.000	0.000	0.000
108	A	211	LEU	0	-0.112	-0.037	26.971	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:104:MET)