FMO DATABASE

FMODB ID: R8N88

Calculation Name: 1ZMM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ZMM

Chain ID: A

ChEMBL ID:

UniProt ID: P12838

Base Structure: X-ray

Registration Date: 2023-09-20

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	28
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-114406.221341
FMO2-HF: Nuclear repulsion	100889.356345
FMO2-HF: Total energy	-13516.864996
FMO2-MP2: Total energy	-13551.097338

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:VAL)

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

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.
-6.121	-2.137	4.617	-3.479	-5.122	-0.02

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.002

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	SER	0	-0.029	-0.015	3.582	-2.099	0.538	-0.020	-1.268	-1.349	0.002
4	A	4	CYS	0	0.024	0.038	5.513	0.153	0.153	0.000	0.000	0.000	0.000
5	A	5	ARG	1	0.786	0.861	6.192	0.796	0.796	0.000	0.000	0.000	0.000
6	A	6	LEU	0	0.058	0.021	11.113	0.040	0.040	0.000	0.000	0.000	0.000
7	A	7	VAL	0	0.011	0.019	14.345	0.020	0.020	0.000	0.000	0.000	0.000
8	A	8	PHE	0	-0.006	0.001	14.541	0.024	0.024	0.000	0.000	0.000	0.000
9	A	9	CYS	0	-0.058	-0.009	7.472	0.158	0.158	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.970	0.967	7.464	0.897	0.897	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.998	0.992	10.961	0.317	0.317	0.000	0.000	0.000	0.000
12	A	12	THR	0	-0.015	-0.018	7.534	0.152	0.152	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.782	-0.854	5.910	-1.615	-1.615	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.023	0.016	7.329	0.204	0.204	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.935	0.949	8.540	-0.064	-0.064	0.000	0.000	0.000	0.000
16	A	16	VAL	0	-0.009	-0.004	7.647	0.039	0.039	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.030	0.010	10.744	0.033	0.033	0.000	0.000	0.000	0.000
18	A	18	ASN	0	-0.056	-0.030	13.471	-0.051	-0.051	0.000	0.000	0.000	0.000
19	A	20	LEU	0	0.043	0.032	14.297	-0.036	-0.036	0.000	0.000	0.000	0.000
20	A	21	ILE	0	0.005	0.001	12.718	0.019	0.019	0.000	0.000	0.000	0.000
21	A	22	GLY	0	0.024	0.009	17.359	-0.018	-0.018	0.000	0.000	0.000	0.000
22	A	23	GLY	0	0.002	0.003	20.743	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	24	VAL	0	0.016	0.020	18.018	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	25	SER	0	-0.020	-0.021	17.793	0.023	0.023	0.000	0.000	0.000	0.000
25	A	26	PHE	0	-0.016	-0.003	12.626	-0.028	-0.028	0.000	0.000	0.000	0.000
26	A	27	THR	0	-0.010	-0.017	12.083	0.068	0.068	0.000	0.000	0.000	0.000
27	A	28	TYR	0	0.021	-0.007	6.719	-0.156	-0.156	0.000	0.000	0.000	0.000
28	A	31	THR	0	0.016	0.013	2.157	-4.983	-3.636	4.637	-2.211	-3.773	-0.022

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