FMO DATABASE

FMODB ID: YVN72

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

Total energy (hartree)

FMO2-HF: Electronic energy	-341776.761591
FMO2-HF: Nuclear repulsion	318395.536278
FMO2-HF: Total energy	-23381.225313
FMO2-MP2: Total energy	-23451.421988

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.
-17.211	-8.391	3.435	-3.673	-8.58	-0.009

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 : 0.040 / q_NPA : 0.019

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	4	GLN	0	0.006	-0.017	3.103	-5.671	-2.536	0.099	-1.424	-1.810	0.011
4	A	5	ARG	1	0.891	0.941	3.041	-2.364	-1.383	0.099	-0.200	-0.880	0.000
5	A	6	ILE	0	0.022	0.023	3.110	-1.092	-0.545	0.042	-0.093	-0.495	0.000
6	A	7	LYS	1	0.830	0.910	6.440	-1.541	-1.541	0.000	0.000	0.000	0.000
7	A	8	GLN	0	-0.071	-0.029	8.443	0.044	0.044	0.000	0.000	0.000	0.000
8	A	9	TYR	0	0.088	0.029	7.317	-0.091	-0.091	0.000	0.000	0.000	0.000
9	A	10	ARG	1	0.776	0.866	10.679	-0.208	-0.208	0.000	0.000	0.000	0.000
10	A	11	LYS	1	0.921	0.942	12.331	-0.561	-0.561	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.870	-0.917	12.988	0.203	0.203	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.799	0.884	15.284	0.079	0.079	0.000	0.000	0.000	0.000
13	A	14	GLY	0	-0.001	0.020	17.009	-0.012	-0.012	0.000	0.000	0.000	0.000
14	A	15	TYR	0	-0.037	-0.006	14.896	0.006	0.006	0.000	0.000	0.000	0.000
15	A	16	SER	0	0.034	0.009	16.054	0.036	0.036	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.039	-0.033	12.070	-0.028	-0.028	0.000	0.000	0.000	0.000
17	A	18	SER	0	-0.001	-0.029	14.743	-0.043	-0.043	0.000	0.000	0.000	0.000
18	A	19	GLU	-1	-0.779	-0.882	17.613	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	20	LEU	0	0.016	0.007	10.803	-0.015	-0.015	0.000	0.000	0.000	0.000
20	A	21	ALA	0	-0.070	-0.041	14.549	-0.039	-0.039	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.944	-0.961	15.382	-0.070	-0.070	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.947	0.981	17.087	0.086	0.086	0.000	0.000	0.000	0.000
23	A	24	ALA	0	0.018	0.006	13.404	-0.010	-0.010	0.000	0.000	0.000	0.000
24	A	25	GLY	0	0.027	0.033	15.530	-0.020	-0.020	0.000	0.000	0.000	0.000
25	A	26	VAL	0	-0.064	-0.047	11.857	-0.031	-0.031	0.000	0.000	0.000	0.000
26	A	27	ALA	0	0.059	0.033	15.028	0.035	0.035	0.000	0.000	0.000	0.000
27	A	28	LYS	1	1.025	0.993	14.025	-0.024	-0.024	0.000	0.000	0.000	0.000
28	A	29	SER	0	0.001	-0.003	13.964	0.017	0.017	0.000	0.000	0.000	0.000
29	A	30	TYR	0	0.025	0.022	8.497	0.007	0.007	0.000	0.000	0.000	0.000
30	A	31	LEU	0	0.061	0.025	8.619	-0.016	-0.016	0.000	0.000	0.000	0.000
31	A	32	SER	0	-0.029	-0.012	9.680	0.056	0.056	0.000	0.000	0.000	0.000
32	A	33	SER	0	-0.034	-0.046	10.334	0.121	0.121	0.000	0.000	0.000	0.000
33	A	34	ILE	0	0.006	0.014	4.716	-0.039	0.079	-0.001	-0.007	-0.110	0.000
34	A	35	GLU	-1	-0.771	-0.851	5.518	0.466	0.466	0.000	0.000	0.000	0.000
35	A	36	ARG	1	0.833	0.918	7.299	0.256	0.256	0.000	0.000	0.000	0.000
36	A	37	ASN	0	-0.030	-0.024	4.092	0.391	0.506	0.000	-0.056	-0.059	0.000
37	A	38	LEU	0	0.001	0.022	6.175	-0.076	-0.076	0.000	0.000	0.000	0.000
38	A	39	GLN	0	0.014	0.021	7.776	-0.057	-0.057	0.000	0.000	0.000	0.000
39	A	40	THR	0	0.008	-0.012	3.772	-0.312	-0.005	0.005	-0.062	-0.250	0.000
40	A	41	ASN	0	-0.005	0.004	3.945	-1.114	-0.700	0.003	-0.121	-0.295	-0.001
41	A	42	PRO	0	0.004	0.018	3.481	-0.230	0.189	0.029	-0.079	-0.369	0.000
42	A	43	SER	0	0.037	0.013	6.207	-0.031	-0.031	0.000	0.000	0.000	0.000
43	A	44	ILE	0	0.069	0.012	7.546	-0.089	-0.089	0.000	0.000	0.000	0.000
44	A	45	GLN	0	0.051	0.030	8.953	0.003	0.003	0.000	0.000	0.000	0.000
45	A	46	PHE	0	-0.036	-0.023	6.559	0.075	0.075	0.000	0.000	0.000	0.000
46	A	47	LEU	0	0.027	-0.002	3.174	-0.365	-0.020	0.031	-0.077	-0.299	0.000
47	A	48	GLU	-1	-0.890	-0.915	7.426	-0.504	-0.504	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.912	0.962	10.714	0.356	0.356	0.000	0.000	0.000	0.000
49	A	50	VAL	0	-0.010	-0.007	8.505	0.065	0.065	0.000	0.000	0.000	0.000
50	A	51	SER	0	-0.060	-0.049	8.421	0.090	0.090	0.000	0.000	0.000	0.000
51	A	52	ALA	0	0.022	0.023	10.357	0.062	0.062	0.000	0.000	0.000	0.000
52	A	53	VAL	0	-0.047	-0.015	13.687	0.052	0.052	0.000	0.000	0.000	0.000
53	A	54	LEU	0	-0.052	-0.033	9.107	0.043	0.043	0.000	0.000	0.000	0.000
54	A	55	ASP	-1	-0.876	-0.909	13.192	-0.108	-0.108	0.000	0.000	0.000	0.000
55	A	56	VAL	0	0.015	0.016	9.102	0.022	0.022	0.000	0.000	0.000	0.000
56	A	57	SER	0	0.010	0.007	10.863	-0.094	-0.094	0.000	0.000	0.000	0.000
57	A	58	VAL	0	0.085	0.030	6.479	-0.070	-0.070	0.000	0.000	0.000	0.000
58	A	59	HIS	0	0.042	0.014	6.426	-0.436	-0.436	0.000	0.000	0.000	0.000
59	A	60	THR	0	0.018	0.025	7.317	-0.053	-0.053	0.000	0.000	0.000	0.000
60	A	61	LEU	0	-0.024	0.000	3.306	-0.128	0.266	0.015	-0.068	-0.341	0.000
61	A	62	LEU	0	-0.064	-0.036	2.545	-4.234	-2.189	3.113	-1.486	-3.672	-0.019

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