FMO DATABASE

FMODB ID: 6YKQZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-137990.958706
FMO2-HF: Nuclear repulsion	122857.180194
FMO2-HF: Total energy	-15133.778512
FMO2-MP2: Total energy	-15178.894023

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.
-42.467	-31.303	11.269	-10.336	-12.098	-0.022

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 : 0.047 / 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	TYR	0	-0.014	0.005	2.753	-5.377	-1.334	0.657	-2.026	-2.675	0.015
4	A	4	GLU	-1	-0.886	-0.949	2.034	-36.627	-30.532	10.604	-7.912	-8.787	-0.038
5	A	5	ALA	0	0.017	0.006	3.313	-0.577	0.318	0.009	-0.387	-0.517	0.001
6	A	6	LEU	0	-0.003	-0.009	4.899	0.425	0.556	-0.001	-0.011	-0.119	0.000
7	A	7	LYS	1	0.919	0.964	7.147	-0.225	-0.225	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.918	-0.955	7.547	-1.081	-1.081	0.000	0.000	0.000	0.000
9	A	9	ASN	0	-0.042	-0.026	8.982	0.236	0.236	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.897	-0.945	10.970	-0.030	-0.030	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.931	0.965	11.663	0.821	0.821	0.000	0.000	0.000	0.000
12	A	12	LEU	0	0.013	-0.002	11.411	0.056	0.056	0.000	0.000	0.000	0.000
13	A	13	HIS	0	0.025	0.016	14.847	0.039	0.039	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.842	0.912	17.008	0.132	0.132	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.965	-0.982	16.611	-0.383	-0.383	0.000	0.000	0.000	0.000
16	A	16	ILE	0	-0.021	-0.020	17.798	0.020	0.020	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.822	-0.875	20.965	-0.072	-0.072	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.070	-0.032	22.802	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.966	0.975	20.829	0.231	0.231	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.888	-0.935	24.745	-0.095	-0.095	0.000	0.000	0.000	0.000
21	A	21	ASN	0	-0.046	-0.040	26.892	0.016	0.016	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.978	-0.989	28.336	-0.119	-0.119	0.000	0.000	0.000	0.000
23	A	23	ILE	0	0.023	0.007	27.292	0.008	0.008	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.038	-0.018	30.949	0.007	0.007	0.000	0.000	0.000	0.000
25	A	25	ARG	1	0.943	0.965	30.256	0.091	0.091	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.064	0.039	32.190	0.004	0.004	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.917	0.960	32.399	0.068	0.068	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.907	0.962	36.872	0.045	0.045	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.904	-0.948	38.754	-0.059	-0.059	0.000	0.000	0.000	0.000
30	A	30	ASN	0	0.017	-0.008	37.883	0.003	0.003	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.903	0.957	41.043	0.038	0.038	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.935	-0.967	42.889	-0.038	-0.038	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.016	-0.017	42.406	0.002	0.002	0.000	0.000	0.000	0.000
34	A	34	ALA	0	-0.052	-0.025	44.729	0.001	0.001	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.978	-0.986	46.597	-0.030	-0.030	0.000	0.000	0.000	0.000
36	A	36	VAL	0	-0.083	-0.012	49.119	0.002	0.002	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.012	-0.005	51.222	0.002	0.002	0.000	0.000	0.000	0.000

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