FMO DATABASE

FMODB ID: 53LNZ

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	OptHSide
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	-910066.18864
FMO2-HF: Nuclear repulsion	864942.140744
FMO2-HF: Total energy	-45124.047896
FMO2-MP2: Total energy	-45251.218386

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.
-17.015	-15.929	18.572	-6.187	-13.474	-0.012

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 : -0.050 / 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	-0.023	-0.010	2.498	0.539	3.154	0.411	-1.141	-1.886	0.000
4	A	107	THR	0	0.012	-0.003	4.945	-0.286	-0.274	-0.001	-0.005	-0.007	0.000
5	A	108	SER	0	0.058	0.010	8.734	0.081	0.081	0.000	0.000	0.000	0.000
6	A	109	ASP	-1	-0.749	-0.853	11.555	-0.357	-0.357	0.000	0.000	0.000	0.000
7	A	110	MET	0	-0.054	-0.006	6.898	0.073	0.073	0.000	0.000	0.000	0.000
8	A	111	GLU	-1	-0.823	-0.888	8.638	-0.854	-0.854	0.000	0.000	0.000	0.000
9	A	112	GLU	-1	-0.928	-0.960	10.799	-0.316	-0.316	0.000	0.000	0.000	0.000
10	A	113	ASP	-1	-0.807	-0.899	13.100	0.073	0.073	0.000	0.000	0.000	0.000
11	A	114	LYS	1	0.761	0.868	10.491	0.473	0.473	0.000	0.000	0.000	0.000
12	A	115	ASP	-1	-0.846	-0.906	13.101	-0.261	-0.261	0.000	0.000	0.000	0.000
13	A	116	LEU	0	-0.059	-0.013	15.569	0.024	0.024	0.000	0.000	0.000	0.000
14	A	117	MET	0	-0.012	-0.010	15.279	0.046	0.046	0.000	0.000	0.000	0.000
15	A	118	LEU	0	-0.009	-0.020	13.692	0.031	0.031	0.000	0.000	0.000	0.000
16	A	119	LYS	1	0.986	1.016	17.717	0.050	0.050	0.000	0.000	0.000	0.000
17	A	120	LEU	0	-0.055	-0.026	20.730	0.001	0.001	0.000	0.000	0.000	0.000
18	A	121	LEU	0	-0.031	-0.010	17.484	0.016	0.016	0.000	0.000	0.000	0.000
19	A	122	ASP	-1	-0.905	-0.945	20.644	0.065	0.065	0.000	0.000	0.000	0.000
20	A	123	LYS	1	0.813	0.919	22.798	-0.053	-0.053	0.000	0.000	0.000	0.000
21	A	124	ASN	0	-0.071	-0.050	25.090	-0.013	-0.013	0.000	0.000	0.000	0.000
22	A	125	GLY	0	0.003	0.019	25.783	0.010	0.010	0.000	0.000	0.000	0.000
23	A	126	PHE	0	-0.046	-0.024	21.171	0.024	0.024	0.000	0.000	0.000	0.000
24	A	127	VAL	0	-0.002	0.000	21.098	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	128	LEU	0	0.039	0.012	15.627	0.049	0.049	0.000	0.000	0.000	0.000
26	A	129	LYS	1	0.926	0.968	15.494	-0.347	-0.347	0.000	0.000	0.000	0.000
27	A	130	LYS	1	0.809	0.893	9.797	-0.721	-0.721	0.000	0.000	0.000	0.000
28	A	131	VAL	0	0.043	0.021	9.550	0.077	0.077	0.000	0.000	0.000	0.000
29	A	132	GLU	-1	-0.867	-0.932	6.369	0.815	0.815	0.000	0.000	0.000	0.000
30	A	133	ILE	0	0.092	0.050	2.602	-0.789	-0.870	3.106	-0.645	-2.380	-0.002
31	A	134	TYR	0	-0.003	-0.018	2.425	-2.719	-1.316	1.929	-1.272	-2.060	-0.012
32	A	135	ARG	1	0.888	0.930	2.312	-4.122	-3.125	1.009	-0.290	-1.717	-0.003
33	A	136	SER	0	0.071	0.017	2.295	-5.145	-7.475	12.072	-4.708	-5.034	0.004
34	A	137	ASN	0	0.052	0.059	3.698	-2.419	-4.041	0.047	1.877	-0.302	0.001
35	A	138	TYR	0	0.025	-0.017	6.171	0.914	1.006	-0.001	-0.003	-0.088	0.000
36	A	139	LEU	0	-0.075	-0.038	7.805	-0.183	-0.183	0.000	0.000	0.000	0.000
37	A	140	ALA	0	0.069	0.043	10.292	-0.117	-0.117	0.000	0.000	0.000	0.000
38	A	141	ILE	0	-0.063	-0.036	10.753	-0.013	-0.013	0.000	0.000	0.000	0.000
39	A	142	LEU	0	0.017	0.016	14.433	-0.070	-0.070	0.000	0.000	0.000	0.000
40	A	143	GLU	-1	-0.981	-1.004	18.182	0.216	0.216	0.000	0.000	0.000	0.000
41	A	144	LYS	1	0.910	0.961	19.832	-0.154	-0.154	0.000	0.000	0.000	0.000
42	A	145	ARG	1	0.944	0.973	17.661	-0.428	-0.428	0.000	0.000	0.000	0.000
43	A	146	THR	0	0.059	0.035	22.938	-0.029	-0.029	0.000	0.000	0.000	0.000
44	A	147	ASN	0	0.034	0.018	24.989	0.013	0.013	0.000	0.000	0.000	0.000
45	A	148	GLY	0	0.024	0.015	24.864	0.006	0.006	0.000	0.000	0.000	0.000
46	A	149	ILE	0	0.013	0.013	20.148	0.043	0.043	0.000	0.000	0.000	0.000
47	A	150	ARG	1	0.841	0.909	17.552	-0.495	-0.495	0.000	0.000	0.000	0.000
48	A	151	ASN	0	-0.065	-0.048	12.441	-0.067	-0.067	0.000	0.000	0.000	0.000
49	A	152	PHE	0	0.092	0.056	15.538	-0.025	-0.025	0.000	0.000	0.000	0.000
50	A	153	GLU	-1	-0.845	-0.925	12.027	1.312	1.312	0.000	0.000	0.000	0.000
51	A	154	ILE	0	0.051	0.029	10.203	-0.130	-0.130	0.000	0.000	0.000	0.000
52	A	155	ASN	0	-0.034	-0.039	9.550	0.591	0.591	0.000	0.000	0.000	0.000
53	A	156	ASN	0	0.034	-0.006	6.498	-0.748	-0.748	0.000	0.000	0.000	0.000
54	A	157	ASN	0	-0.034	-0.011	9.241	-0.249	-0.249	0.000	0.000	0.000	0.000
55	A	158	GLY	0	0.016	0.001	12.361	-0.120	-0.120	0.000	0.000	0.000	0.000
56	A	159	ASN	0	-0.065	-0.032	14.161	-0.136	-0.136	0.000	0.000	0.000	0.000
57	A	160	MET	0	0.026	0.036	14.019	0.090	0.090	0.000	0.000	0.000	0.000
58	A	161	ARG	1	0.783	0.859	14.760	-0.833	-0.833	0.000	0.000	0.000	0.000
59	A	162	ILE	0	0.029	0.039	16.731	0.022	0.022	0.000	0.000	0.000	0.000
60	A	163	PHE	0	-0.043	-0.008	15.080	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	164	GLY	0	0.068	0.017	17.918	-0.027	-0.027	0.000	0.000	0.000	0.000
62	A	165	TYR	0	-0.101	-0.055	21.007	0.010	0.010	0.000	0.000	0.000	0.000
63	A	166	LYS	1	0.896	0.949	23.383	-0.304	-0.304	0.000	0.000	0.000	0.000
64	A	167	MET	0	0.014	0.031	24.097	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	168	MET	0	0.003	0.003	27.522	-0.009	-0.009	0.000	0.000	0.000	0.000
66	A	169	GLU	-1	-0.818	-0.913	30.511	0.195	0.195	0.000	0.000	0.000	0.000
67	A	170	HIS	0	0.053	0.030	32.347	0.005	0.005	0.000	0.000	0.000	0.000
68	A	171	HIS	0	-0.015	-0.010	29.119	-0.007	-0.007	0.000	0.000	0.000	0.000
69	A	172	ILE	0	-0.003	-0.021	26.989	0.009	0.009	0.000	0.000	0.000	0.000
70	A	173	GLN	0	-0.026	-0.029	29.033	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	174	LYS	1	0.877	0.931	30.601	-0.139	-0.139	0.000	0.000	0.000	0.000
72	A	175	PHE	0	-0.003	-0.012	24.940	0.001	0.001	0.000	0.000	0.000	0.000
73	A	176	THR	0	-0.041	-0.031	27.567	0.003	0.003	0.000	0.000	0.000	0.000
74	A	177	ASP	-1	-0.994	-0.979	29.145	0.108	0.108	0.000	0.000	0.000	0.000
75	A	178	ILE	0	-0.018	0.005	25.914	-0.010	-0.010	0.000	0.000	0.000	0.000
76	A	179	GLY	0	0.001	0.004	27.137	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	180	MET	0	-0.096	-0.023	21.194	0.013	0.013	0.000	0.000	0.000	0.000
78	A	181	SER	0	-0.008	-0.006	23.281	-0.017	-0.017	0.000	0.000	0.000	0.000
79	A	182	CYS	0	-0.005	-0.010	23.894	0.035	0.035	0.000	0.000	0.000	0.000
80	A	183	LYS	1	0.943	0.982	21.822	-0.469	-0.469	0.000	0.000	0.000	0.000
81	A	184	ILE	0	0.066	0.034	23.538	0.032	0.032	0.000	0.000	0.000	0.000
82	A	185	ALA	0	-0.049	-0.022	22.523	-0.012	-0.012	0.000	0.000	0.000	0.000
83	A	186	LYS	1	0.959	0.959	24.660	-0.317	-0.317	0.000	0.000	0.000	0.000
84	A	187	ASN	0	0.030	0.014	21.053	-0.031	-0.031	0.000	0.000	0.000	0.000
85	A	188	GLY	0	0.012	-0.004	25.570	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	189	ASN	0	-0.044	-0.015	19.203	-0.044	-0.044	0.000	0.000	0.000	0.000
87	A	190	VAL	0	-0.004	-0.004	21.855	-0.015	-0.015	0.000	0.000	0.000	0.000
88	A	191	TYR	0	-0.018	-0.012	16.376	0.018	0.018	0.000	0.000	0.000	0.000
89	A	192	LEU	0	0.075	0.035	20.265	-0.036	-0.036	0.000	0.000	0.000	0.000
90	A	193	ASP	-1	-0.785	-0.869	17.671	0.676	0.676	0.000	0.000	0.000	0.000
91	A	194	ILE	0	0.071	0.045	19.274	-0.041	-0.041	0.000	0.000	0.000	0.000
92	A	195	LYS	1	0.887	0.945	17.462	-0.245	-0.245	0.000	0.000	0.000	0.000
93	A	196	ARG	1	0.758	0.862	11.486	-0.065	-0.065	0.000	0.000	0.000	0.000
94	A	197	SER	0	0.029	-0.009	17.537	-0.027	-0.027	0.000	0.000	0.000	0.000
95	A	198	ALA	0	0.058	0.034	19.930	0.027	0.027	0.000	0.000	0.000	0.000
96	A	199	GLU	-1	-0.838	-0.917	21.320	0.018	0.018	0.000	0.000	0.000	0.000
97	A	200	ASN	0	-0.012	-0.014	21.298	0.006	0.006	0.000	0.000	0.000	0.000
98	A	201	ILE	0	-0.024	-0.016	16.580	0.034	0.034	0.000	0.000	0.000	0.000
99	A	202	GLU	-1	-0.834	-0.939	20.656	0.056	0.056	0.000	0.000	0.000	0.000
100	A	203	ALA	0	0.009	0.020	23.863	0.008	0.008	0.000	0.000	0.000	0.000
101	A	204	VAL	0	0.014	-0.016	21.132	0.011	0.011	0.000	0.000	0.000	0.000
102	A	205	ILE	0	-0.008	-0.008	19.776	0.017	0.017	0.000	0.000	0.000	0.000
103	A	206	THR	0	-0.015	0.003	23.798	-0.007	-0.007	0.000	0.000	0.000	0.000
104	A	207	VAL	0	0.037	0.017	27.116	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	208	ALA	0	-0.049	-0.040	24.385	0.004	0.004	0.000	0.000	0.000	0.000
106	A	209	SER	0	-0.031	-0.044	26.340	0.002	0.002	0.000	0.000	0.000	0.000
107	A	210	GLU	-1	-0.887	-0.895	28.112	0.104	0.104	0.000	0.000	0.000	0.000
108	A	211	LEU	0	-0.125	-0.052	27.239	-0.007	-0.007	0.000	0.000	0.000	0.000

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