FMO DATABASE

FMODB ID: YVNN2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-104944.641172
FMO2-HF: Nuclear repulsion	92419.235605
FMO2-HF: Total energy	-12525.405568
FMO2-MP2: Total energy	-12562.862503

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.
1.897	5.98	0.335	-1.726	-2.691	0

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 : 0.051 / q_NPA : 0.009

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	3	ASN	0	0.073	0.021	3.374	-0.755	0.853	0.003	-0.670	-0.941	0.001
4	A	4	THR	0	-0.035	-0.018	2.497	-1.001	0.993	0.334	-0.929	-1.399	-0.001
5	A	5	LEU	0	0.066	0.051	3.745	0.805	1.182	-0.001	-0.121	-0.255	0.000
6	A	6	VAL	0	0.050	0.021	5.387	0.613	0.717	-0.001	-0.006	-0.096	0.000
7	A	7	LYS	1	0.919	0.958	7.333	1.376	1.376	0.000	0.000	0.000	0.000
8	A	8	GLN	0	0.004	0.001	6.116	0.177	0.177	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.004	0.001	9.320	0.210	0.210	0.000	0.000	0.000	0.000
10	A	10	SER	0	0.000	-0.004	11.374	0.140	0.140	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.047	-0.012	12.642	0.104	0.104	0.000	0.000	0.000	0.000
12	A	12	ASN	0	0.030	0.005	12.301	0.049	0.049	0.000	0.000	0.000	0.000
13	A	13	PHE	0	0.008	-0.004	14.448	0.053	0.053	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.013	0.023	17.068	0.035	0.035	0.000	0.000	0.000	0.000
15	A	15	ALA	0	-0.010	-0.001	18.191	0.031	0.031	0.000	0.000	0.000	0.000
16	A	16	ILE	0	-0.002	-0.012	18.122	0.026	0.026	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.009	-0.001	21.258	0.025	0.025	0.000	0.000	0.000	0.000
18	A	18	SER	0	-0.014	-0.002	22.838	0.020	0.020	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.015	0.002	23.592	0.013	0.013	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.005	-0.004	24.628	0.012	0.012	0.000	0.000	0.000	0.000
21	A	21	ASN	0	0.032	0.016	27.194	0.016	0.016	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.921	-0.956	28.680	-0.079	-0.079	0.000	0.000	0.000	0.000
23	A	23	ILE	0	-0.022	-0.029	28.271	0.008	0.008	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.007	0.003	30.309	0.006	0.006	0.000	0.000	0.000	0.000
25	A	25	SER	0	0.037	0.032	33.188	0.005	0.005	0.000	0.000	0.000	0.000
26	A	26	ARG	1	0.803	0.898	32.265	0.074	0.074	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.011	0.005	35.211	0.004	0.004	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.847	-0.920	37.281	-0.057	-0.057	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.844	0.909	38.001	0.062	0.062	0.000	0.000	0.000	0.000
30	A	30	VAL	0	0.020	0.017	40.136	0.002	0.002	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.967	-0.986	40.209	-0.041	-0.041	0.000	0.000	0.000	0.000
32	A	32	ALA	0	-0.071	-0.029	43.276	0.002	0.002	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.989	-0.996	44.171	-0.041	-0.041	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.098	-0.031	46.040	0.003	0.003	0.000	0.000	0.000	0.000

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