FMO DATABASE

FMODB ID: LJKK9

Calculation Name: 3ZIG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3ZIG

Chain ID: A

ChEMBL ID:

UniProt ID: I6V3Q6

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	82
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-523652.892144
FMO2-HF: Nuclear repulsion	492683.001769
FMO2-HF: Total energy	-30969.890376
FMO2-MP2: Total energy	-31061.400367

3D Structure Molmil

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:49:LYS)

Summations of interaction energy for fragment #1(A:49: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.
-5.097	-1.035	0.797	-2.04	-2.817	-0.011

Interaction energy analysis for fragmet #1(A:49:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.005 / q_NPA : 1.001

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	51	VAL	0	0.051	0.034	2.589	-10.428	-6.533	0.799	-2.035	-2.659	-0.011
4	A	52	TYR	0	-0.023	-0.011	4.993	5.616	5.700	-0.001	-0.003	-0.079	0.000
5	A	53	ILE	0	0.010	0.008	8.220	0.302	0.302	0.000	0.000	0.000	0.000
6	A	54	LYS	1	0.888	0.958	9.865	27.227	27.227	0.000	0.000	0.000	0.000
7	A	55	LYS	1	0.955	0.977	13.695	16.622	16.622	0.000	0.000	0.000	0.000
8	A	56	ILE	0	-0.016	-0.011	15.629	-0.107	-0.107	0.000	0.000	0.000	0.000
9	A	57	VAL	0	0.023	0.018	19.320	0.232	0.232	0.000	0.000	0.000	0.000
10	A	58	ILE	0	-0.023	-0.005	21.549	-0.090	-0.090	0.000	0.000	0.000	0.000
11	A	59	SER	0	-0.025	-0.014	24.465	0.553	0.553	0.000	0.000	0.000	0.000
12	A	60	THR	0	-0.008	-0.004	25.710	0.360	0.360	0.000	0.000	0.000	0.000
13	A	61	HIS	0	0.043	0.000	26.072	-0.328	-0.328	0.000	0.000	0.000	0.000
14	A	62	ALA	0	0.041	0.018	23.422	-0.394	-0.394	0.000	0.000	0.000	0.000
15	A	63	ASP	-1	-0.811	-0.908	21.361	-14.096	-14.096	0.000	0.000	0.000	0.000
16	A	64	LEU	0	0.042	0.011	20.213	-0.717	-0.717	0.000	0.000	0.000	0.000
17	A	65	LYS	1	0.933	0.972	17.072	17.110	17.110	0.000	0.000	0.000	0.000
18	A	66	ARG	1	0.926	0.977	16.559	14.577	14.577	0.000	0.000	0.000	0.000
19	A	67	VAL	0	0.032	0.014	15.063	-1.321	-1.321	0.000	0.000	0.000	0.000
20	A	68	SER	0	-0.021	-0.004	14.455	-1.528	-1.528	0.000	0.000	0.000	0.000
21	A	69	ASP	-1	-0.881	-0.960	12.763	-22.262	-22.262	0.000	0.000	0.000	0.000
22	A	70	GLU	-1	-0.873	-0.942	10.448	-29.474	-29.474	0.000	0.000	0.000	0.000
23	A	71	LEU	0	-0.014	-0.005	9.380	-3.039	-3.039	0.000	0.000	0.000	0.000
24	A	72	LYS	1	0.935	0.964	9.533	21.115	21.115	0.000	0.000	0.000	0.000
25	A	73	SER	0	-0.081	-0.024	6.372	-3.161	-3.161	0.000	0.000	0.000	0.000
26	A	74	GLY	0	0.024	0.015	5.035	-9.457	-9.374	-0.001	-0.002	-0.079	0.000
27	A	75	ASN	0	-0.059	-0.037	6.249	-2.170	-2.170	0.000	0.000	0.000	0.000
28	A	76	ILE	0	0.027	0.012	8.440	1.948	1.948	0.000	0.000	0.000	0.000
29	A	77	VAL	0	-0.022	-0.013	11.594	0.135	0.135	0.000	0.000	0.000	0.000
30	A	78	ILE	0	-0.032	-0.013	14.803	1.021	1.021	0.000	0.000	0.000	0.000
31	A	79	VAL	0	0.018	-0.006	17.895	0.005	0.005	0.000	0.000	0.000	0.000
32	A	80	GLU	-1	-0.905	-0.934	20.607	-11.588	-11.588	0.000	0.000	0.000	0.000
33	A	81	LEU	0	-0.004	-0.025	23.875	-0.026	-0.026	0.000	0.000	0.000	0.000
34	A	82	THR	0	0.032	-0.018	26.808	0.324	0.324	0.000	0.000	0.000	0.000
35	A	83	PRO	0	-0.029	-0.002	27.844	0.420	0.420	0.000	0.000	0.000	0.000
36	A	84	LEU	0	-0.039	-0.036	28.000	0.355	0.355	0.000	0.000	0.000	0.000
37	A	85	GLU	-1	-0.859	-0.923	30.999	-9.833	-9.833	0.000	0.000	0.000	0.000
38	A	86	GLN	0	-0.042	-0.014	33.235	0.073	0.073	0.000	0.000	0.000	0.000
39	A	87	LYS	1	0.934	0.965	34.204	9.371	9.371	0.000	0.000	0.000	0.000
40	A	88	PRO	0	0.084	0.042	34.937	-0.276	-0.276	0.000	0.000	0.000	0.000
41	A	89	GLU	-1	-0.861	-0.935	34.760	-8.406	-8.406	0.000	0.000	0.000	0.000
42	A	90	LEU	0	-0.044	-0.013	31.294	-0.214	-0.214	0.000	0.000	0.000	0.000
43	A	91	LEU	0	-0.010	-0.005	29.326	-0.421	-0.421	0.000	0.000	0.000	0.000
44	A	92	LYS	1	0.944	0.971	29.881	9.141	9.141	0.000	0.000	0.000	0.000
45	A	93	LYS	1	0.981	0.999	30.061	10.093	10.093	0.000	0.000	0.000	0.000
46	A	94	ILE	0	0.009	-0.002	25.544	-0.376	-0.376	0.000	0.000	0.000	0.000
47	A	95	ALA	0	0.010	0.004	25.589	-0.590	-0.590	0.000	0.000	0.000	0.000
48	A	96	GLU	-1	-0.903	-0.958	25.453	-10.666	-10.666	0.000	0.000	0.000	0.000
49	A	97	GLN	0	-0.013	-0.016	24.504	-0.212	-0.212	0.000	0.000	0.000	0.000
50	A	98	LEU	0	-0.027	-0.004	20.449	-0.748	-0.748	0.000	0.000	0.000	0.000
51	A	99	MET	0	0.013	0.011	20.675	-0.690	-0.690	0.000	0.000	0.000	0.000
52	A	100	THR	0	-0.006	0.002	21.775	-0.288	-0.288	0.000	0.000	0.000	0.000
53	A	101	THR	0	-0.062	-0.036	17.237	-0.600	-0.600	0.000	0.000	0.000	0.000
54	A	102	ALA	0	0.013	-0.001	16.829	-0.944	-0.944	0.000	0.000	0.000	0.000
55	A	103	SER	0	0.023	0.015	17.157	-0.602	-0.602	0.000	0.000	0.000	0.000
56	A	104	ILE	0	-0.056	-0.021	17.366	-0.253	-0.253	0.000	0.000	0.000	0.000
57	A	105	ILE	0	-0.099	-0.040	12.403	-0.489	-0.489	0.000	0.000	0.000	0.000
58	A	106	GLY	0	0.011	0.003	13.727	-1.529	-1.529	0.000	0.000	0.000	0.000
59	A	107	GLY	0	-0.018	0.003	14.493	-0.428	-0.428	0.000	0.000	0.000	0.000
60	A	108	ASP	-1	-0.846	-0.935	15.145	-15.230	-15.230	0.000	0.000	0.000	0.000
61	A	109	TYR	0	-0.005	-0.022	17.467	-0.335	-0.335	0.000	0.000	0.000	0.000
62	A	110	ALA	0	-0.005	-0.004	20.145	0.608	0.608	0.000	0.000	0.000	0.000
63	A	111	LYS	1	0.964	1.003	22.125	10.091	10.091	0.000	0.000	0.000	0.000
64	A	112	ILE	0	-0.034	-0.022	20.159	0.030	0.030	0.000	0.000	0.000	0.000
65	A	113	CYS	0	-0.030	-0.004	24.008	0.326	0.326	0.000	0.000	0.000	0.000
66	A	114	GLY	0	-0.033	-0.033	26.805	-0.046	-0.046	0.000	0.000	0.000	0.000
67	A	115	SER	0	0.034	0.037	29.975	0.209	0.209	0.000	0.000	0.000	0.000
68	A	116	PRO	0	0.037	-0.013	26.774	0.022	0.022	0.000	0.000	0.000	0.000
69	A	117	LEU	0	0.014	0.029	27.557	-0.266	-0.266	0.000	0.000	0.000	0.000
70	A	118	LYS	1	0.919	0.960	22.634	12.528	12.528	0.000	0.000	0.000	0.000
71	A	119	VAL	0	0.015	0.012	21.198	0.359	0.359	0.000	0.000	0.000	0.000
72	A	120	ILE	0	-0.046	-0.022	15.719	-0.431	-0.431	0.000	0.000	0.000	0.000
73	A	121	LEU	0	0.000	-0.005	16.119	0.548	0.548	0.000	0.000	0.000	0.000
74	A	122	THR	0	-0.022	-0.015	12.902	-0.597	-0.597	0.000	0.000	0.000	0.000
75	A	123	PRO	0	0.011	0.021	8.593	1.655	1.655	0.000	0.000	0.000	0.000
76	A	124	PRO	0	0.052	0.017	9.968	0.815	0.815	0.000	0.000	0.000	0.000
77	A	125	GLU	-1	-0.950	-0.972	6.618	-36.187	-36.187	0.000	0.000	0.000	0.000
78	A	126	ILE	0	-0.046	-0.019	8.198	1.025	1.025	0.000	0.000	0.000	0.000
79	A	127	LYS	1	0.983	0.994	11.456	17.515	17.515	0.000	0.000	0.000	0.000
80	A	128	ILE	0	-0.036	-0.009	15.027	0.190	0.190	0.000	0.000	0.000	0.000
81	A	129	ALA	0	-0.033	-0.009	17.931	0.537	0.537	0.000	0.000	0.000	0.000
82	A	130	LYS	1	0.972	0.984	19.374	12.688	12.688	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:49:LYS)