FMO DATABASE

FMODB ID: R86J8

Calculation Name: 1T6F-A-Xray372

Preferred Name: Geminin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1T6F

Chain ID: A

ChEMBL ID: CHEMBL1293278

UniProt ID: O75496

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptAll
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	37
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-138789.678716
FMO2-HF: Nuclear repulsion	123655.291421
FMO2-HF: Total energy	-15134.387295
FMO2-MP2: Total energy	-15179.532229

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:THR)

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

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.
-43.715	-50.114	35.089	-16.365	-12.325	-0.065

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : -0.023

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	TYR	0	-0.005	0.007	2.167	-9.778	-5.880	3.580	-3.423	-4.056	0.033
4	A	4	GLU	-1	-0.796	-0.889	1.592	-38.350	-49.232	31.510	-12.782	-7.846	-0.098
5	A	5	ALA	0	0.002	0.007	3.577	2.022	2.478	0.000	-0.152	-0.304	0.000
6	A	6	LEU	0	0.003	-0.002	5.272	0.767	0.896	-0.001	-0.008	-0.119	0.000
7	A	7	LYS	1	0.903	0.959	7.283	1.080	1.080	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.807	-0.882	7.538	-1.229	-1.229	0.000	0.000	0.000	0.000
9	A	9	ASN	0	-0.039	-0.020	9.254	0.435	0.435	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.848	-0.929	11.234	-0.297	-0.297	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.804	0.886	11.220	1.341	1.341	0.000	0.000	0.000	0.000
12	A	12	LEU	0	0.009	-0.003	11.740	0.118	0.118	0.000	0.000	0.000	0.000
13	A	13	HIS	0	0.013	0.012	14.773	0.094	0.094	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.800	0.887	17.281	0.369	0.369	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.886	-0.932	16.988	-0.476	-0.476	0.000	0.000	0.000	0.000
16	A	16	ILE	0	-0.017	-0.009	17.989	0.043	0.043	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.815	-0.881	21.058	-0.227	-0.227	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.007	-0.005	22.819	0.006	0.006	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.825	0.901	20.764	0.399	0.399	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.866	-0.937	24.947	-0.190	-0.190	0.000	0.000	0.000	0.000
21	A	21	ASN	0	-0.099	-0.059	27.014	0.034	0.034	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.815	-0.881	28.183	-0.186	-0.186	0.000	0.000	0.000	0.000
23	A	23	ILE	0	0.002	-0.005	27.243	0.018	0.018	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.043	-0.020	30.932	0.014	0.014	0.000	0.000	0.000	0.000
25	A	25	ARG	1	0.868	0.912	29.533	0.188	0.188	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.033	0.021	32.044	0.009	0.009	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.919	0.966	31.700	0.140	0.140	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.798	0.883	36.751	0.095	0.095	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.933	-0.963	38.743	-0.108	-0.108	0.000	0.000	0.000	0.000
30	A	30	ASN	0	-0.023	-0.035	37.934	0.007	0.007	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.855	0.929	40.969	0.074	0.074	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.812	-0.895	42.909	-0.079	-0.079	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.007	-0.006	42.363	0.004	0.004	0.000	0.000	0.000	0.000
34	A	34	ALA	0	-0.035	-0.010	44.889	0.003	0.003	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.898	-0.942	46.724	-0.061	-0.061	0.000	0.000	0.000	0.000
36	A	36	VAL	0	-0.069	-0.014	48.980	0.003	0.003	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.036	-0.007	51.070	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:THR)