FMO DATABASE

FMODB ID: VQKZ1

Calculation Name: 3ZKC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZKC

Chain ID: A

ChEMBL ID:

UniProt ID: P06533

Base Structure: X-ray

Registration Date: 2023-09-22

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	61
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-344312.491463
FMO2-HF: Nuclear repulsion	320931.085689
FMO2-HF: Total energy	-23381.405774
FMO2-MP2: Total energy	-23451.600627

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:2:ILE)

Summations of interaction energy for fragment #1(A:2:ILE)

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.
-17.352	-6.427	2.799	-4.365	-9.357	-0.019

Interaction energy analysis for fragmet #1(A:2:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.049 / q_NPA : 0.025

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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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	4	GLN	0	0.012	-0.011	3.364	-3.844	-1.423	0.034	-1.070	-1.385	0.006
4	A	5	ARG	1	0.915	0.957	3.320	-2.365	-1.408	0.033	-0.222	-0.768	0.001
5	A	6	ILE	0	0.004	0.009	2.908	-1.049	-0.260	0.157	-0.182	-0.764	0.000
6	A	7	LYS	1	0.820	0.900	6.056	-1.212	-1.212	0.000	0.000	0.000	0.000
7	A	8	GLN	0	-0.077	-0.031	7.884	0.107	0.107	0.000	0.000	0.000	0.000
8	A	9	TYR	0	0.067	0.017	6.751	-0.102	-0.102	0.000	0.000	0.000	0.000
9	A	10	ARG	1	0.756	0.837	10.254	-0.218	-0.218	0.000	0.000	0.000	0.000
10	A	11	LYS	1	0.907	0.949	12.010	-0.538	-0.538	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.871	-0.923	12.731	0.252	0.252	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.788	0.879	14.700	0.037	0.037	0.000	0.000	0.000	0.000
13	A	14	GLY	0	0.005	0.019	16.475	-0.016	-0.016	0.000	0.000	0.000	0.000
14	A	15	TYR	0	-0.052	-0.008	14.265	0.014	0.014	0.000	0.000	0.000	0.000
15	A	16	SER	0	0.017	-0.017	15.547	0.031	0.031	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.044	-0.033	11.727	-0.023	-0.023	0.000	0.000	0.000	0.000
17	A	18	SER	0	-0.020	-0.034	14.575	-0.036	-0.036	0.000	0.000	0.000	0.000
18	A	19	GLU	-1	-0.734	-0.834	17.413	0.014	0.014	0.000	0.000	0.000	0.000
19	A	20	LEU	0	0.033	0.018	10.196	-0.014	-0.014	0.000	0.000	0.000	0.000
20	A	21	ALA	0	-0.055	-0.033	13.812	-0.036	-0.036	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.944	-0.965	14.658	-0.055	-0.055	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.958	0.980	16.799	0.055	0.055	0.000	0.000	0.000	0.000
23	A	24	ALA	0	0.021	0.014	13.155	-0.011	-0.011	0.000	0.000	0.000	0.000
24	A	25	GLY	0	0.024	0.026	15.230	-0.024	-0.024	0.000	0.000	0.000	0.000
25	A	26	VAL	0	-0.071	-0.041	11.680	-0.026	-0.026	0.000	0.000	0.000	0.000
26	A	27	ALA	0	0.064	0.027	14.725	0.031	0.031	0.000	0.000	0.000	0.000
27	A	28	LYS	1	0.999	0.982	13.602	-0.023	-0.023	0.000	0.000	0.000	0.000
28	A	29	SER	0	0.001	-0.008	13.691	0.022	0.022	0.000	0.000	0.000	0.000
29	A	30	TYR	0	0.021	0.025	8.183	0.013	0.013	0.000	0.000	0.000	0.000
30	A	31	LEU	0	0.057	0.032	8.044	-0.010	-0.010	0.000	0.000	0.000	0.000
31	A	32	SER	0	0.004	0.008	9.062	0.056	0.056	0.000	0.000	0.000	0.000
32	A	33	SER	0	-0.040	-0.027	9.715	0.109	0.109	0.000	0.000	0.000	0.000
33	A	34	ILE	0	0.015	0.008	4.109	-0.128	0.083	0.000	-0.022	-0.188	0.000
34	A	35	GLU	-1	-0.777	-0.862	4.919	0.416	0.472	-0.001	-0.009	-0.046	0.000
35	A	36	ARG	1	0.835	0.904	7.063	0.161	0.161	0.000	0.000	0.000	0.000
36	A	37	ASN	0	-0.037	-0.018	4.080	0.391	0.527	0.002	-0.072	-0.065	0.000
37	A	38	LEU	0	0.001	0.012	5.861	-0.106	-0.106	0.000	0.000	0.000	0.000
38	A	39	GLN	0	0.019	0.027	7.255	-0.066	-0.066	0.000	0.000	0.000	0.000
39	A	40	THR	0	0.012	-0.007	3.524	-0.282	0.137	0.018	-0.098	-0.339	0.000
40	A	41	ASN	0	-0.001	0.009	3.533	-1.821	-0.928	0.026	-0.405	-0.514	-0.003
41	A	42	PRO	0	0.004	0.013	3.311	-0.281	0.196	0.047	-0.096	-0.428	0.000
42	A	43	SER	0	0.033	0.016	6.085	-0.087	-0.087	0.000	0.000	0.000	0.000
43	A	44	ILE	0	0.056	0.012	7.343	-0.074	-0.074	0.000	0.000	0.000	0.000
44	A	45	GLN	0	0.050	0.031	8.526	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	46	PHE	0	-0.034	-0.015	6.169	0.078	0.078	0.000	0.000	0.000	0.000
46	A	47	LEU	0	0.024	-0.004	2.906	-0.607	-0.047	0.176	-0.135	-0.600	0.000
47	A	48	GLU	-1	-0.877	-0.924	6.726	-0.438	-0.438	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.869	0.946	10.208	0.300	0.300	0.000	0.000	0.000	0.000
49	A	50	VAL	0	-0.009	-0.004	7.898	0.061	0.061	0.000	0.000	0.000	0.000
50	A	51	SER	0	-0.050	-0.051	8.115	0.069	0.069	0.000	0.000	0.000	0.000
51	A	52	ALA	0	0.039	0.020	9.954	0.069	0.069	0.000	0.000	0.000	0.000
52	A	53	VAL	0	-0.023	-0.009	13.376	0.045	0.045	0.000	0.000	0.000	0.000
53	A	54	LEU	0	-0.047	-0.022	8.586	0.039	0.039	0.000	0.000	0.000	0.000
54	A	55	ASP	-1	-0.863	-0.899	12.744	-0.062	-0.062	0.000	0.000	0.000	0.000
55	A	56	VAL	0	0.008	0.012	8.851	0.025	0.025	0.000	0.000	0.000	0.000
56	A	57	SER	0	0.010	0.005	10.592	-0.079	-0.079	0.000	0.000	0.000	0.000
57	A	58	VAL	0	0.077	0.032	6.261	-0.081	-0.081	0.000	0.000	0.000	0.000
58	A	59	HIS	0	0.056	0.022	6.218	-0.432	-0.432	0.000	0.000	0.000	0.000
59	A	60	THR	0	0.008	0.015	7.199	-0.068	-0.068	0.000	0.000	0.000	0.000
60	A	61	LEU	0	-0.013	0.002	2.753	-0.320	0.332	0.147	-0.144	-0.656	0.000
61	A	62	LEU	0	-0.065	-0.040	2.613	-5.207	-1.853	2.160	-1.910	-3.604	-0.023

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ILE)