FMO DATABASE

FMODB ID: VQKK1

Calculation Name: 1ZVB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ZVB

Chain ID: A

ChEMBL ID:

UniProt ID: P59594

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	34
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-104860.835354
FMO2-HF: Nuclear repulsion	92335.171857
FMO2-HF: Total energy	-12525.663497
FMO2-MP2: Total energy	-12563.100429

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:1:ALA)

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

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.
-0.489	4.777	0.503	-2.506	-3.264	-0.001

Interaction energy analysis for fragmet #1(A:1:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.070 / q_NPA : 0.036

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	3	ASN	0	0.090	0.037	3.391	-2.003	0.551	-0.002	-1.246	-1.306	0.006
4	A	4	THR	0	-0.008	-0.007	2.543	-2.005	0.338	0.506	-1.147	-1.702	-0.007
5	A	5	LEU	0	0.078	0.054	3.959	0.854	1.223	-0.001	-0.113	-0.256	0.000
6	A	6	VAL	0	0.028	0.013	5.681	0.887	0.887	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.897	0.941	7.327	1.097	1.097	0.000	0.000	0.000	0.000
8	A	8	GLN	0	0.010	0.003	6.151	-0.210	-0.210	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.005	-0.003	9.471	0.252	0.252	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.003	-0.007	11.639	0.194	0.194	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.009	0.002	12.769	0.123	0.123	0.000	0.000	0.000	0.000
12	A	12	ASN	0	-0.022	-0.017	12.247	0.133	0.133	0.000	0.000	0.000	0.000
13	A	13	PHE	0	0.018	0.002	14.707	0.063	0.063	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.024	0.029	17.247	0.054	0.054	0.000	0.000	0.000	0.000
15	A	15	ALA	0	-0.009	-0.001	18.362	0.047	0.047	0.000	0.000	0.000	0.000
16	A	16	ILE	0	-0.001	-0.011	18.437	0.035	0.035	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.015	0.002	21.477	0.033	0.033	0.000	0.000	0.000	0.000
18	A	18	SER	0	0.019	0.004	23.013	0.026	0.026	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.022	-0.013	23.852	0.020	0.020	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.004	-0.004	24.868	0.016	0.016	0.000	0.000	0.000	0.000
21	A	21	ASN	0	0.020	0.012	27.217	0.017	0.017	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.856	-0.901	28.870	-0.123	-0.123	0.000	0.000	0.000	0.000
23	A	23	ILE	0	-0.009	-0.021	28.539	0.011	0.011	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.003	-0.001	30.609	0.009	0.009	0.000	0.000	0.000	0.000
25	A	25	SER	0	0.015	0.012	33.173	0.009	0.009	0.000	0.000	0.000	0.000
26	A	26	ARG	1	0.795	0.878	32.049	0.130	0.130	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.028	-0.003	35.896	0.006	0.006	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.865	-0.933	37.524	-0.103	-0.103	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.801	0.885	39.426	0.087	0.087	0.000	0.000	0.000	0.000
30	A	30	VAL	0	-0.021	-0.008	40.285	0.004	0.004	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.932	-0.969	40.361	-0.090	-0.090	0.000	0.000	0.000	0.000
32	A	32	ALA	0	-0.066	-0.025	43.540	0.004	0.004	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.945	-0.969	44.292	-0.071	-0.071	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.081	-0.020	45.991	0.005	0.005	0.000	0.000	0.000	0.000

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