FMO DATABASE

FMODB ID: 2NKVR

Calculation Name: 4ID3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ID3

Chain ID: A

ChEMBL ID:

UniProt ID: P12689

Base Structure: X-ray

Registration Date: 2023-09-20

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	87
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-640892.221361
FMO2-HF: Nuclear repulsion	606182.818491
FMO2-HF: Total energy	-34709.40287
FMO2-MP2: Total energy	-34812.617834

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:164:LYS)

Summations of interaction energy for fragment #1(A:164:LYS)

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.
111.391	111.567	11.54	-3.674	-8.041	-0.029

Interaction energy analysis for fragmet #1(A:164:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.955 / q_NPA : 0.966

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	166	PHE	0	-0.006	0.008	3.337	1.933	4.236	-0.005	-1.056	-1.241	0.000
4	A	167	LYS	1	0.972	0.993	2.901	35.584	36.507	0.094	-0.216	-0.800	0.000
5	A	168	ASN	0	-0.038	-0.031	4.480	2.567	2.679	0.000	-0.019	-0.093	0.000
6	A	169	CYS	0	-0.024	0.018	7.493	3.938	3.938	0.000	0.000	0.000	0.000
7	A	170	VAL	0	-0.016	-0.020	9.237	-2.385	-2.385	0.000	0.000	0.000	0.000
8	A	171	ILE	0	0.026	0.014	9.949	2.063	2.063	0.000	0.000	0.000	0.000
9	A	172	TYR	0	0.008	0.010	13.696	-0.147	-0.147	0.000	0.000	0.000	0.000
10	A	173	ILE	0	0.013	0.011	14.672	0.400	0.400	0.000	0.000	0.000	0.000
11	A	174	ASN	0	0.023	0.011	18.380	0.612	0.612	0.000	0.000	0.000	0.000
12	A	175	GLY	0	0.008	0.004	22.061	0.163	0.163	0.000	0.000	0.000	0.000
13	A	176	TYR	0	0.036	0.013	22.847	-0.503	-0.503	0.000	0.000	0.000	0.000
14	A	177	THR	0	-0.007	0.000	19.308	0.051	0.051	0.000	0.000	0.000	0.000
15	A	178	LYS	1	0.905	0.975	21.129	11.758	11.758	0.000	0.000	0.000	0.000
16	A	179	PRO	0	0.115	0.048	16.198	0.128	0.128	0.000	0.000	0.000	0.000
17	A	180	GLY	0	0.062	0.043	18.844	0.056	0.056	0.000	0.000	0.000	0.000
18	A	181	ARG	1	0.897	0.923	17.476	14.334	14.334	0.000	0.000	0.000	0.000
19	A	182	LEU	0	0.018	0.016	15.508	-1.041	-1.041	0.000	0.000	0.000	0.000
20	A	183	GLN	0	0.118	0.055	14.828	-0.550	-0.550	0.000	0.000	0.000	0.000
21	A	184	LEU	0	0.014	0.002	13.009	-1.591	-1.591	0.000	0.000	0.000	0.000
22	A	185	HIS	1	0.850	0.923	11.396	19.059	19.059	0.000	0.000	0.000	0.000
23	A	186	GLU	-1	-0.868	-0.924	10.269	-24.425	-24.425	0.000	0.000	0.000	0.000
24	A	187	MET	0	-0.013	0.002	8.797	-3.081	-3.081	0.000	0.000	0.000	0.000
25	A	188	ILE	0	-0.001	0.005	6.949	-2.988	-2.988	0.000	0.000	0.000	0.000
26	A	189	VAL	0	-0.025	-0.014	5.855	-4.879	-4.879	0.000	0.000	0.000	0.000
27	A	190	LEU	0	-0.016	0.006	4.299	-13.290	-13.111	-0.001	-0.031	-0.147	0.000
28	A	191	HIS	0	-0.020	-0.017	2.742	-8.889	-7.675	0.311	-0.323	-1.201	-0.002
29	A	192	GLY	0	-0.076	-0.051	2.104	-3.859	-5.667	11.108	-5.406	-3.895	-0.022
30	A	193	GLY	0	0.042	0.042	2.809	7.195	4.448	0.033	3.377	-0.664	-0.005
31	A	194	LYS	1	0.930	0.955	6.174	34.170	34.170	0.000	0.000	0.000	0.000
32	A	195	PHE	0	0.020	0.004	8.979	1.687	1.687	0.000	0.000	0.000	0.000
33	A	196	LEU	0	-0.012	-0.002	12.382	0.061	0.061	0.000	0.000	0.000	0.000
34	A	197	HIS	0	0.022	-0.007	15.770	0.373	0.373	0.000	0.000	0.000	0.000
35	A	198	TYR	0	0.025	0.010	18.574	0.702	0.702	0.000	0.000	0.000	0.000
36	A	199	LEU	0	-0.025	-0.006	19.991	-0.725	-0.725	0.000	0.000	0.000	0.000
37	A	200	SER	0	0.029	0.020	19.470	0.540	0.540	0.000	0.000	0.000	0.000
38	A	201	SER	0	0.034	0.007	20.989	0.690	0.690	0.000	0.000	0.000	0.000
39	A	202	LYS	1	0.910	0.947	20.294	11.799	11.799	0.000	0.000	0.000	0.000
40	A	203	LYS	1	0.963	1.002	19.585	13.641	13.641	0.000	0.000	0.000	0.000
41	A	204	THR	0	-0.003	-0.006	15.979	-0.307	-0.307	0.000	0.000	0.000	0.000
42	A	205	VAL	0	-0.039	-0.010	15.255	-1.198	-1.198	0.000	0.000	0.000	0.000
43	A	206	THR	0	0.004	-0.006	12.449	0.095	0.095	0.000	0.000	0.000	0.000
44	A	207	HIS	0	-0.019	0.006	12.730	0.355	0.355	0.000	0.000	0.000	0.000
45	A	208	ILE	0	0.000	0.011	15.832	-0.589	-0.589	0.000	0.000	0.000	0.000
46	A	209	VAL	0	-0.017	0.005	14.509	0.109	0.109	0.000	0.000	0.000	0.000
47	A	210	ALA	0	-0.002	-0.011	17.801	0.307	0.307	0.000	0.000	0.000	0.000
48	A	211	SER	0	0.039	-0.007	21.218	-0.246	-0.246	0.000	0.000	0.000	0.000
49	A	212	ASN	0	-0.009	-0.010	23.298	0.089	0.089	0.000	0.000	0.000	0.000
50	A	213	LEU	0	-0.006	-0.006	24.316	-0.211	-0.211	0.000	0.000	0.000	0.000
51	A	214	PRO	0	0.061	0.039	28.035	0.299	0.299	0.000	0.000	0.000	0.000
52	A	215	LEU	0	0.093	0.036	30.913	-0.278	-0.278	0.000	0.000	0.000	0.000
53	A	216	LYS	1	0.961	0.975	31.598	9.659	9.659	0.000	0.000	0.000	0.000
54	A	217	LYS	1	0.809	0.895	27.083	11.135	11.135	0.000	0.000	0.000	0.000
55	A	218	ARG	1	0.936	0.978	27.947	9.505	9.505	0.000	0.000	0.000	0.000
56	A	219	ILE	0	0.014	0.011	29.307	-0.120	-0.120	0.000	0.000	0.000	0.000
57	A	220	GLU	-1	-0.818	-0.899	27.877	-11.103	-11.103	0.000	0.000	0.000	0.000
58	A	221	PHE	0	-0.035	-0.031	24.067	-0.384	-0.384	0.000	0.000	0.000	0.000
59	A	222	ALA	0	0.068	0.046	25.117	-0.349	-0.349	0.000	0.000	0.000	0.000
60	A	223	ASN	0	-0.028	-0.034	25.281	-0.298	-0.298	0.000	0.000	0.000	0.000
61	A	224	TYR	0	0.053	0.035	20.342	-0.573	-0.573	0.000	0.000	0.000	0.000
62	A	225	LYS	1	0.916	0.976	16.611	16.605	16.605	0.000	0.000	0.000	0.000
63	A	226	VAL	0	-0.006	-0.009	18.846	-0.638	-0.638	0.000	0.000	0.000	0.000
64	A	227	VAL	0	0.005	0.007	15.262	0.438	0.438	0.000	0.000	0.000	0.000
65	A	228	SER	0	0.026	-0.021	18.665	-0.299	-0.299	0.000	0.000	0.000	0.000
66	A	229	PRO	0	-0.030	-0.045	16.184	-0.780	-0.780	0.000	0.000	0.000	0.000
67	A	230	ASP	-1	-0.810	-0.877	15.145	-14.942	-14.942	0.000	0.000	0.000	0.000
68	A	231	TRP	0	-0.004	0.014	11.040	-1.007	-1.007	0.000	0.000	0.000	0.000
69	A	232	ILE	0	-0.038	-0.015	9.835	-0.995	-0.995	0.000	0.000	0.000	0.000
70	A	233	VAL	0	0.003	-0.018	10.647	-1.188	-1.188	0.000	0.000	0.000	0.000
71	A	234	ASP	-1	-0.783	-0.870	12.610	-15.797	-15.797	0.000	0.000	0.000	0.000
72	A	235	SER	0	-0.047	-0.031	9.003	-0.162	-0.162	0.000	0.000	0.000	0.000
73	A	236	VAL	0	-0.036	-0.030	7.169	-0.906	-0.906	0.000	0.000	0.000	0.000
74	A	237	LYS	1	0.894	0.951	9.050	16.253	16.253	0.000	0.000	0.000	0.000
75	A	238	GLU	-1	-0.852	-0.909	11.545	-16.132	-16.132	0.000	0.000	0.000	0.000
76	A	239	ALA	0	-0.035	-0.002	7.063	-0.164	-0.164	0.000	0.000	0.000	0.000
77	A	240	ARG	1	0.862	0.909	7.115	17.131	17.131	0.000	0.000	0.000	0.000
78	A	241	LEU	0	-0.059	-0.027	7.675	0.484	0.484	0.000	0.000	0.000	0.000
79	A	242	LEU	0	0.056	0.041	9.212	1.021	1.021	0.000	0.000	0.000	0.000
80	A	243	PRO	0	0.020	0.008	12.894	-0.602	-0.602	0.000	0.000	0.000	0.000
81	A	244	TRP	0	0.036	0.005	14.773	0.574	0.574	0.000	0.000	0.000	0.000
82	A	245	GLN	0	0.031	-0.001	16.142	-0.084	-0.084	0.000	0.000	0.000	0.000
83	A	246	ASN	0	0.023	0.012	18.255	0.755	0.755	0.000	0.000	0.000	0.000
84	A	247	TYR	0	-0.025	-0.044	16.119	0.090	0.090	0.000	0.000	0.000	0.000
85	A	248	SER	0	-0.045	-0.014	19.352	-0.164	-0.164	0.000	0.000	0.000	0.000
86	A	249	LEU	0	-0.012	0.003	21.296	0.441	0.441	0.000	0.000	0.000	0.000
87	A	250	THR	0	-0.047	-0.015	24.049	0.411	0.411	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:164:LYS)