FMO DATABASE

FMODB ID: 43MLN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-909169.798658
FMO2-HF: Nuclear repulsion	864046.539112
FMO2-HF: Total energy	-45123.259547
FMO2-MP2: Total energy	-45250.435485

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.
-16.16	-12.821	14.875	-5.177	-13.036	-0.024

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 : -0.098 / q_NPA : -0.050

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	-0.034	-0.013	2.529	0.448	2.632	0.444	-0.875	-1.753	-0.003
4	A	107	THR	0	0.037	0.010	4.949	-0.096	-0.070	-0.001	-0.005	-0.019	0.000
5	A	108	SER	0	0.099	0.025	8.737	-0.011	-0.011	0.000	0.000	0.000	0.000
6	A	109	ASP	-1	-0.838	-0.905	11.565	-0.362	-0.362	0.000	0.000	0.000	0.000
7	A	110	MET	0	-0.147	-0.054	6.159	0.048	0.048	0.000	0.000	0.000	0.000
8	A	111	GLU	-1	-0.955	-0.981	8.724	-1.620	-1.620	0.000	0.000	0.000	0.000
9	A	112	GLU	-1	-0.886	-0.934	10.814	-0.415	-0.415	0.000	0.000	0.000	0.000
10	A	113	ASP	-1	-0.814	-0.914	13.097	-0.160	-0.160	0.000	0.000	0.000	0.000
11	A	114	LYS	1	0.880	0.946	10.538	0.888	0.888	0.000	0.000	0.000	0.000
12	A	115	ASP	-1	-0.908	-0.955	13.112	-0.646	-0.646	0.000	0.000	0.000	0.000
13	A	116	LEU	0	-0.057	-0.013	15.586	0.048	0.048	0.000	0.000	0.000	0.000
14	A	117	MET	0	-0.002	-0.003	15.109	0.040	0.040	0.000	0.000	0.000	0.000
15	A	118	LEU	0	-0.029	-0.036	13.633	0.022	0.022	0.000	0.000	0.000	0.000
16	A	119	LYS	1	0.989	1.022	17.556	0.250	0.250	0.000	0.000	0.000	0.000
17	A	120	LEU	0	-0.031	-0.017	20.745	0.022	0.022	0.000	0.000	0.000	0.000
18	A	121	LEU	0	-0.034	-0.014	17.067	0.027	0.027	0.000	0.000	0.000	0.000
19	A	122	ASP	-1	-0.899	-0.943	20.430	-0.230	-0.230	0.000	0.000	0.000	0.000
20	A	123	LYS	1	0.880	0.943	22.518	0.123	0.123	0.000	0.000	0.000	0.000
21	A	124	ASN	0	-0.078	-0.054	24.770	0.015	0.015	0.000	0.000	0.000	0.000
22	A	125	GLY	0	0.002	0.020	25.498	0.015	0.015	0.000	0.000	0.000	0.000
23	A	126	PHE	0	-0.055	-0.026	20.894	0.020	0.020	0.000	0.000	0.000	0.000
24	A	127	VAL	0	0.000	-0.003	20.908	-0.020	-0.020	0.000	0.000	0.000	0.000
25	A	128	LEU	0	0.028	0.008	15.243	0.034	0.034	0.000	0.000	0.000	0.000
26	A	129	LYS	1	0.944	0.987	14.630	0.042	0.042	0.000	0.000	0.000	0.000
27	A	130	LYS	1	0.874	0.928	10.338	0.059	0.059	0.000	0.000	0.000	0.000
28	A	131	VAL	0	0.041	0.023	9.012	0.094	0.094	0.000	0.000	0.000	0.000
29	A	132	GLU	-1	-0.932	-0.979	6.157	0.052	0.052	0.000	0.000	0.000	0.000
30	A	133	ILE	0	0.083	0.048	2.403	-1.202	-0.319	2.115	-0.575	-2.423	-0.002
31	A	134	TYR	0	0.000	-0.019	2.379	-2.408	-1.928	3.392	-1.530	-2.342	-0.018
32	A	135	ARG	1	0.892	0.935	2.116	-2.561	-2.320	1.377	0.011	-1.628	-0.003
33	A	136	SER	0	0.081	0.027	2.519	-5.284	-4.921	7.482	-3.229	-4.616	0.000
34	A	137	ASN	0	0.053	0.053	3.672	-2.046	-2.884	0.066	1.026	-0.255	0.002
35	A	138	TYR	0	0.082	0.037	5.828	0.116	0.116	0.000	0.000	0.000	0.000
36	A	139	LEU	0	-0.060	-0.032	7.765	0.103	0.103	0.000	0.000	0.000	0.000
37	A	140	ALA	0	0.059	0.039	9.906	-0.156	-0.156	0.000	0.000	0.000	0.000
38	A	141	ILE	0	-0.066	-0.042	10.625	0.069	0.069	0.000	0.000	0.000	0.000
39	A	142	LEU	0	0.018	0.011	14.202	-0.051	-0.051	0.000	0.000	0.000	0.000
40	A	143	GLU	-1	-0.997	-1.001	17.959	-0.071	-0.071	0.000	0.000	0.000	0.000
41	A	144	LYS	1	0.933	0.967	19.703	0.077	0.077	0.000	0.000	0.000	0.000
42	A	145	ARG	1	0.945	0.972	17.841	-0.132	-0.132	0.000	0.000	0.000	0.000
43	A	146	THR	0	0.074	0.035	22.805	-0.008	-0.008	0.000	0.000	0.000	0.000
44	A	147	ASN	0	0.010	0.012	24.838	0.012	0.012	0.000	0.000	0.000	0.000
45	A	148	GLY	0	0.021	0.011	24.801	0.009	0.009	0.000	0.000	0.000	0.000
46	A	149	ILE	0	0.016	0.016	19.905	0.031	0.031	0.000	0.000	0.000	0.000
47	A	150	ARG	1	0.847	0.907	17.440	-0.232	-0.232	0.000	0.000	0.000	0.000
48	A	151	ASN	0	-0.026	-0.020	13.157	-0.039	-0.039	0.000	0.000	0.000	0.000
49	A	152	PHE	0	0.097	0.061	15.144	0.023	0.023	0.000	0.000	0.000	0.000
50	A	153	GLU	-1	-0.904	-0.976	11.784	0.612	0.612	0.000	0.000	0.000	0.000
51	A	154	ILE	0	0.066	0.040	10.278	-0.020	-0.020	0.000	0.000	0.000	0.000
52	A	155	ASN	0	-0.019	-0.025	9.543	0.222	0.222	0.000	0.000	0.000	0.000
53	A	156	ASN	0	0.035	0.012	6.879	-0.498	-0.498	0.000	0.000	0.000	0.000
54	A	157	ASN	0	-0.043	-0.011	9.221	-0.178	-0.178	0.000	0.000	0.000	0.000
55	A	158	GLY	0	0.037	0.013	12.344	-0.068	-0.068	0.000	0.000	0.000	0.000
56	A	159	ASN	0	-0.014	0.007	14.155	-0.115	-0.115	0.000	0.000	0.000	0.000
57	A	160	MET	0	0.044	0.040	14.006	0.031	0.031	0.000	0.000	0.000	0.000
58	A	161	ARG	1	0.762	0.849	14.624	-0.501	-0.501	0.000	0.000	0.000	0.000
59	A	162	ILE	0	0.017	0.036	16.522	-0.022	-0.022	0.000	0.000	0.000	0.000
60	A	163	PHE	0	-0.051	-0.011	15.696	0.031	0.031	0.000	0.000	0.000	0.000
61	A	164	GLY	0	0.064	0.014	17.768	-0.039	-0.039	0.000	0.000	0.000	0.000
62	A	165	TYR	0	-0.104	-0.053	20.892	0.027	0.027	0.000	0.000	0.000	0.000
63	A	166	LYS	1	0.903	0.952	23.297	-0.174	-0.174	0.000	0.000	0.000	0.000
64	A	167	MET	0	0.007	0.027	24.050	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	168	MET	0	0.001	0.002	27.400	0.002	0.002	0.000	0.000	0.000	0.000
66	A	169	GLU	-1	-0.864	-0.947	30.357	0.103	0.103	0.000	0.000	0.000	0.000
67	A	170	HIS	0	0.058	0.034	32.166	0.005	0.005	0.000	0.000	0.000	0.000
68	A	171	HIS	0	-0.030	-0.012	28.920	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	172	ILE	0	0.009	-0.013	26.865	0.002	0.002	0.000	0.000	0.000	0.000
70	A	173	GLN	0	0.018	0.001	28.844	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	174	LYS	1	0.992	1.001	30.482	-0.034	-0.034	0.000	0.000	0.000	0.000
72	A	175	PHE	0	0.011	0.000	24.768	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	176	THR	0	-0.038	-0.033	27.556	0.003	0.003	0.000	0.000	0.000	0.000
74	A	177	ASP	-1	-1.016	-0.990	29.121	0.040	0.040	0.000	0.000	0.000	0.000
75	A	178	ILE	0	0.006	0.021	25.766	-0.006	-0.006	0.000	0.000	0.000	0.000
76	A	179	GLY	0	-0.003	0.000	27.125	-0.006	-0.006	0.000	0.000	0.000	0.000
77	A	180	MET	0	-0.095	-0.022	21.160	0.011	0.011	0.000	0.000	0.000	0.000
78	A	181	SER	0	-0.004	-0.004	23.308	0.000	0.000	0.000	0.000	0.000	0.000
79	A	182	CYS	0	-0.002	-0.012	23.729	0.013	0.013	0.000	0.000	0.000	0.000
80	A	183	LYS	1	0.945	0.988	21.475	-0.374	-0.374	0.000	0.000	0.000	0.000
81	A	184	ILE	0	0.062	0.031	23.345	0.015	0.015	0.000	0.000	0.000	0.000
82	A	185	ALA	0	-0.061	-0.030	22.380	0.003	0.003	0.000	0.000	0.000	0.000
83	A	186	LYS	1	0.978	0.971	24.511	-0.241	-0.241	0.000	0.000	0.000	0.000
84	A	187	ASN	0	0.021	0.010	21.230	-0.025	-0.025	0.000	0.000	0.000	0.000
85	A	188	GLY	0	0.016	-0.001	25.489	-0.012	-0.012	0.000	0.000	0.000	0.000
86	A	189	ASN	0	-0.017	-0.002	19.597	-0.049	-0.049	0.000	0.000	0.000	0.000
87	A	190	VAL	0	-0.012	-0.009	21.714	0.003	0.003	0.000	0.000	0.000	0.000
88	A	191	TYR	0	-0.048	-0.029	16.234	0.009	0.009	0.000	0.000	0.000	0.000
89	A	192	LEU	0	0.063	0.030	20.053	-0.009	-0.009	0.000	0.000	0.000	0.000
90	A	193	ASP	-1	-0.793	-0.877	17.785	0.420	0.420	0.000	0.000	0.000	0.000
91	A	194	ILE	0	0.071	0.041	19.263	-0.017	-0.017	0.000	0.000	0.000	0.000
92	A	195	LYS	1	0.873	0.930	18.297	-0.211	-0.211	0.000	0.000	0.000	0.000
93	A	196	ARG	1	0.831	0.912	11.281	0.091	0.091	0.000	0.000	0.000	0.000
94	A	197	SER	0	0.077	0.038	17.529	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	198	ALA	0	0.077	0.042	19.927	0.006	0.006	0.000	0.000	0.000	0.000
96	A	199	GLU	-1	-0.885	-0.955	21.323	-0.083	-0.083	0.000	0.000	0.000	0.000
97	A	200	ASN	0	-0.013	-0.020	21.341	0.007	0.007	0.000	0.000	0.000	0.000
98	A	201	ILE	0	-0.039	-0.021	16.668	0.021	0.021	0.000	0.000	0.000	0.000
99	A	202	GLU	-1	-0.898	-0.960	20.656	-0.112	-0.112	0.000	0.000	0.000	0.000
100	A	203	ALA	0	0.007	0.010	23.866	0.008	0.008	0.000	0.000	0.000	0.000
101	A	204	VAL	0	0.002	-0.015	21.187	0.012	0.012	0.000	0.000	0.000	0.000
102	A	205	ILE	0	-0.011	-0.013	19.743	0.013	0.013	0.000	0.000	0.000	0.000
103	A	206	THR	0	-0.019	-0.001	23.736	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	207	VAL	0	0.047	0.021	26.966	0.003	0.003	0.000	0.000	0.000	0.000
105	A	208	ALA	0	-0.061	-0.049	23.943	0.006	0.006	0.000	0.000	0.000	0.000
106	A	209	SER	0	-0.035	-0.033	25.923	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	210	GLU	-1	-0.974	-0.951	27.725	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	211	LEU	0	-0.136	-0.060	26.860	0.009	0.009	0.000	0.000	0.000	0.000

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