FMO DATABASE

FMODB ID: ZVKQN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-138385.208182
FMO2-HF: Nuclear repulsion	123250.91136
FMO2-HF: Total energy	-15134.296822
FMO2-MP2: Total energy	-15179.446319

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.
-57.092	-60.621	35.659	-18.588	-13.54	-0.09

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 : -0.006 / q_NPA : -0.054

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	0.011	2.803	-5.893	-1.685	0.595	-2.097	-2.705	0.015
4	A	4	GLU	-1	-0.812	-0.881	1.623	-52.271	-60.966	35.059	-16.135	-10.229	-0.105
5	A	5	ALA	0	0.004	0.001	3.343	0.177	0.996	0.006	-0.345	-0.479	0.000
6	A	6	LEU	0	0.001	-0.008	4.902	0.541	0.680	-0.001	-0.011	-0.127	0.000
7	A	7	LYS	1	0.917	0.966	7.275	0.126	0.126	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.808	-0.879	7.475	-1.167	-1.167	0.000	0.000	0.000	0.000
9	A	9	ASN	0	-0.039	-0.026	8.995	0.308	0.308	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.879	-0.939	10.975	-0.109	-0.109	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.821	0.893	11.093	1.083	1.083	0.000	0.000	0.000	0.000
12	A	12	LEU	0	0.004	-0.009	11.593	0.070	0.070	0.000	0.000	0.000	0.000
13	A	13	HIS	0	0.016	0.011	14.723	0.053	0.053	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.815	0.898	17.021	0.198	0.198	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.871	-0.922	17.278	-0.378	-0.378	0.000	0.000	0.000	0.000
16	A	16	ILE	0	-0.032	-0.021	17.724	0.027	0.027	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.793	-0.861	20.972	-0.114	-0.114	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.008	0.003	22.820	0.000	0.000	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.834	0.901	20.763	0.289	0.289	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.870	-0.933	24.851	-0.113	-0.113	0.000	0.000	0.000	0.000
21	A	21	ASN	0	-0.108	-0.074	26.762	0.023	0.023	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.874	-0.919	28.434	-0.129	-0.129	0.000	0.000	0.000	0.000
23	A	23	ILE	0	0.016	-0.005	27.256	0.011	0.011	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.035	-0.012	30.955	0.009	0.009	0.000	0.000	0.000	0.000
25	A	25	ARG	1	0.888	0.927	29.949	0.120	0.120	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.042	0.028	32.148	0.005	0.005	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.926	0.972	32.062	0.084	0.084	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.808	0.890	36.877	0.058	0.058	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.922	-0.957	38.762	-0.073	-0.073	0.000	0.000	0.000	0.000
30	A	30	ASN	0	-0.030	-0.041	37.879	0.005	0.005	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.840	0.927	41.040	0.044	0.044	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.834	-0.900	42.892	-0.048	-0.048	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.012	-0.010	42.436	0.002	0.002	0.000	0.000	0.000	0.000
34	A	34	ALA	0	-0.042	-0.021	44.694	0.002	0.002	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.901	-0.947	46.601	-0.036	-0.036	0.000	0.000	0.000	0.000
36	A	36	VAL	0	-0.078	-0.009	49.042	0.002	0.002	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.004	-0.001	51.234	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)