FMO DATABASE

FMODB ID: 5JNQZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-341190.152574
FMO2-HF: Nuclear repulsion	317809.25373
FMO2-HF: Total energy	-23380.898844
FMO2-MP2: Total energy	-23451.09315

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.
-17.431	-8.124	2.549	-3.492	-8.363	-0.004

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 : 0.053 / 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

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	4	GLN	0	-0.026	-0.030	3.111	-5.826	-2.734	0.108	-1.333	-1.866	0.012
4	A	5	ARG	1	0.844	0.909	3.019	-2.364	-1.307	0.113	-0.222	-0.949	0.001
5	A	6	ILE	0	0.026	0.030	2.935	-1.233	-0.596	0.068	-0.127	-0.578	0.000
6	A	7	LYS	1	0.923	0.959	6.348	-1.310	-1.310	0.000	0.000	0.000	0.000
7	A	8	GLN	0	-0.010	0.012	8.432	0.065	0.065	0.000	0.000	0.000	0.000
8	A	9	TYR	0	0.089	0.032	7.860	-0.085	-0.085	0.000	0.000	0.000	0.000
9	A	10	ARG	1	0.807	0.906	10.597	-0.234	-0.234	0.000	0.000	0.000	0.000
10	A	11	LYS	1	0.901	0.930	12.245	-0.617	-0.617	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.911	-0.946	13.067	0.184	0.184	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.938	0.972	15.340	0.051	0.051	0.000	0.000	0.000	0.000
13	A	14	GLY	0	-0.002	0.021	16.939	-0.013	-0.013	0.000	0.000	0.000	0.000
14	A	15	TYR	0	-0.016	0.003	15.043	0.006	0.006	0.000	0.000	0.000	0.000
15	A	16	SER	0	0.042	0.015	15.929	0.037	0.037	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.046	-0.036	12.531	-0.027	-0.027	0.000	0.000	0.000	0.000
17	A	18	SER	0	-0.020	-0.041	14.582	-0.044	-0.044	0.000	0.000	0.000	0.000
18	A	19	GLU	-1	-0.819	-0.900	17.460	-0.015	-0.015	0.000	0.000	0.000	0.000
19	A	20	LEU	0	0.008	0.002	10.642	-0.015	-0.015	0.000	0.000	0.000	0.000
20	A	21	ALA	0	-0.058	-0.038	14.452	-0.042	-0.042	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.943	-0.958	15.269	-0.075	-0.075	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.942	0.980	16.976	0.098	0.098	0.000	0.000	0.000	0.000
23	A	24	ALA	0	0.007	-0.007	13.211	-0.011	-0.011	0.000	0.000	0.000	0.000
24	A	25	GLY	0	0.017	0.031	15.308	-0.020	-0.020	0.000	0.000	0.000	0.000
25	A	26	VAL	0	-0.075	-0.050	11.768	-0.033	-0.033	0.000	0.000	0.000	0.000
26	A	27	ALA	0	0.050	0.027	14.836	0.038	0.038	0.000	0.000	0.000	0.000
27	A	28	LYS	1	1.046	1.008	13.888	-0.026	-0.026	0.000	0.000	0.000	0.000
28	A	29	SER	0	-0.003	-0.007	13.791	0.021	0.021	0.000	0.000	0.000	0.000
29	A	30	TYR	0	0.023	0.025	8.158	0.006	0.006	0.000	0.000	0.000	0.000
30	A	31	LEU	0	0.057	0.023	8.523	-0.016	-0.016	0.000	0.000	0.000	0.000
31	A	32	SER	0	-0.042	-0.022	9.493	0.057	0.057	0.000	0.000	0.000	0.000
32	A	33	SER	0	-0.039	-0.038	10.218	0.130	0.130	0.000	0.000	0.000	0.000
33	A	34	ILE	0	0.015	0.017	4.619	-0.039	0.088	-0.001	-0.007	-0.119	0.000
34	A	35	GLU	-1	-0.796	-0.888	5.405	0.489	0.489	0.000	0.000	0.000	0.000
35	A	36	ARG	1	0.832	0.920	7.145	0.220	0.220	0.000	0.000	0.000	0.000
36	A	37	ASN	0	-0.035	-0.024	4.113	0.384	0.551	0.001	-0.049	-0.118	0.000
37	A	38	LEU	0	-0.010	0.016	6.103	-0.096	-0.096	0.000	0.000	0.000	0.000
38	A	39	GLN	0	0.010	0.005	7.792	-0.071	-0.071	0.000	0.000	0.000	0.000
39	A	40	THR	0	0.002	-0.012	3.674	-0.302	-0.013	0.005	-0.056	-0.238	0.000
40	A	41	ASN	0	-0.002	0.003	3.981	-1.060	-0.687	0.002	-0.108	-0.267	-0.001
41	A	42	PRO	0	0.014	0.022	3.489	-0.227	0.192	0.031	-0.079	-0.371	0.000
42	A	43	SER	0	0.038	0.015	6.220	-0.021	-0.021	0.000	0.000	0.000	0.000
43	A	44	ILE	0	0.081	0.016	7.557	-0.093	-0.093	0.000	0.000	0.000	0.000
44	A	45	GLN	0	0.054	0.023	9.011	0.001	0.001	0.000	0.000	0.000	0.000
45	A	46	PHE	0	-0.031	-0.023	6.815	0.079	0.079	0.000	0.000	0.000	0.000
46	A	47	LEU	0	0.028	-0.002	3.341	-0.327	-0.025	0.019	-0.066	-0.255	0.000
47	A	48	GLU	-1	-0.915	-0.917	7.312	-0.505	-0.505	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.957	0.989	10.620	0.395	0.395	0.000	0.000	0.000	0.000
49	A	50	VAL	0	-0.011	-0.007	8.398	0.068	0.068	0.000	0.000	0.000	0.000
50	A	51	SER	0	-0.070	-0.063	8.270	0.099	0.099	0.000	0.000	0.000	0.000
51	A	52	ALA	0	0.026	0.025	10.164	0.067	0.067	0.000	0.000	0.000	0.000
52	A	53	VAL	0	-0.052	-0.011	13.466	0.057	0.057	0.000	0.000	0.000	0.000
53	A	54	LEU	0	-0.086	-0.055	9.084	0.049	0.049	0.000	0.000	0.000	0.000
54	A	55	ASP	-1	-0.983	-0.970	13.017	-0.152	-0.152	0.000	0.000	0.000	0.000
55	A	56	VAL	0	0.014	0.009	9.164	0.016	0.016	0.000	0.000	0.000	0.000
56	A	57	SER	0	0.005	0.000	10.792	-0.072	-0.072	0.000	0.000	0.000	0.000
57	A	58	VAL	0	0.079	0.024	6.450	-0.078	-0.078	0.000	0.000	0.000	0.000
58	A	59	HIS	0	0.026	0.000	6.523	-0.421	-0.421	0.000	0.000	0.000	0.000
59	A	60	THR	0	0.028	0.024	7.464	-0.043	-0.043	0.000	0.000	0.000	0.000
60	A	61	LEU	0	-0.024	0.002	3.283	-0.149	0.249	0.015	-0.064	-0.349	0.000
61	A	62	LEU	0	-0.012	0.008	2.521	-4.386	-1.940	2.188	-1.381	-3.253	-0.016

Top

Graph

Manual

About

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