FMO DATABASE

FMODB ID: 7GYRK

Calculation Name: 1LTT-C-Xray372

Preferred Name:

Target Type:

Ligand Name: beta-d-glucopyranose | beta-d-galactopyranose

Ligand 3-letter code: BGC | GAL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1LTT

Chain ID: C

ChEMBL ID:

UniProt ID: P06717

Base Structure: X-ray

Registration Date: 2023-03-13

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	41
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-157305.762243
FMO2-HF: Nuclear repulsion	139858.726025
FMO2-HF: Total energy	-17447.036218
FMO2-MP2: Total energy	-17497.736777

3D Structure Molmil

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(C:196:GLY)

Summations of interaction energy for fragment #1(C:196:GLY)

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.
2.248	4.607	-0.02	-1.164	-1.176	0.001

Interaction energy analysis for fragmet #1(C:196:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / q_NPA : 0.012

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	C	198	THR	0	0.002	-0.001	3.794	-0.916	1.156	-0.018	-1.111	-0.944	0.001
4	C	199	CYS	0	-0.008	-0.003	4.510	1.103	1.243	-0.001	-0.016	-0.123	0.000
5	C	200	ASN	0	-0.010	-0.005	3.862	1.090	1.237	-0.001	-0.037	-0.109	0.000
6	C	201	GLU	-1	-0.886	-0.939	7.074	-0.849	-0.849	0.000	0.000	0.000	0.000
7	C	202	GLU	-1	-0.829	-0.920	8.838	-0.422	-0.422	0.000	0.000	0.000	0.000
8	C	203	THR	0	-0.042	-0.011	9.722	0.371	0.371	0.000	0.000	0.000	0.000
9	C	204	GLN	0	-0.002	0.024	11.411	0.235	0.235	0.000	0.000	0.000	0.000
10	C	205	ASN	0	-0.035	-0.020	13.044	0.275	0.275	0.000	0.000	0.000	0.000
11	C	206	LEU	0	0.014	-0.001	13.868	0.156	0.156	0.000	0.000	0.000	0.000
12	C	207	SER	0	-0.037	-0.032	15.219	0.131	0.131	0.000	0.000	0.000	0.000
13	C	208	THR	0	-0.098	-0.068	16.892	0.097	0.097	0.000	0.000	0.000	0.000
14	C	209	ILE	0	0.017	0.013	18.306	0.081	0.081	0.000	0.000	0.000	0.000
15	C	210	TYR	0	0.039	0.028	20.558	0.057	0.057	0.000	0.000	0.000	0.000
16	C	211	LEU	0	-0.023	0.002	21.863	0.047	0.047	0.000	0.000	0.000	0.000
17	C	212	ARG	1	0.912	0.937	21.921	0.435	0.435	0.000	0.000	0.000	0.000
18	C	213	GLU	-1	-0.836	-0.907	24.999	-0.224	-0.224	0.000	0.000	0.000	0.000
19	C	214	TYR	0	0.008	0.003	26.437	0.030	0.030	0.000	0.000	0.000	0.000
20	C	215	GLN	0	0.002	-0.019	26.216	0.009	0.009	0.000	0.000	0.000	0.000
21	C	216	SER	0	0.000	0.012	29.465	0.024	0.024	0.000	0.000	0.000	0.000
22	C	217	LYS	1	0.823	0.899	29.730	0.249	0.249	0.000	0.000	0.000	0.000
23	C	218	VAL	0	0.055	0.027	32.060	0.013	0.013	0.000	0.000	0.000	0.000
24	C	219	LYS	1	0.934	0.975	30.760	0.227	0.227	0.000	0.000	0.000	0.000
25	C	220	ARG	1	0.949	0.978	34.757	0.172	0.172	0.000	0.000	0.000	0.000
26	C	221	GLN	0	-0.038	0.016	37.274	0.014	0.014	0.000	0.000	0.000	0.000
27	C	222	ILE	0	0.062	0.022	36.272	0.005	0.005	0.000	0.000	0.000	0.000
28	C	223	PHE	0	-0.036	-0.041	35.448	0.001	0.001	0.000	0.000	0.000	0.000
29	C	224	SER	0	-0.031	-0.041	40.299	0.006	0.006	0.000	0.000	0.000	0.000
30	C	225	ASP	-1	-0.910	-0.943	42.751	-0.111	-0.111	0.000	0.000	0.000	0.000
31	C	226	TYR	0	-0.087	-0.038	42.061	0.006	0.006	0.000	0.000	0.000	0.000
32	C	227	GLN	0	-0.100	-0.038	44.695	0.000	0.000	0.000	0.000	0.000	0.000
33	C	228	SER	0	0.013	0.005	46.366	0.004	0.004	0.000	0.000	0.000	0.000
34	C	229	GLU	-1	-0.921	-0.949	48.908	-0.090	-0.090	0.000	0.000	0.000	0.000
35	C	230	VAL	0	-0.033	-0.025	51.307	0.003	0.003	0.000	0.000	0.000	0.000
36	C	231	ASP	-1	-0.847	-0.917	53.839	-0.058	-0.058	0.000	0.000	0.000	0.000
37	C	232	ILE	0	-0.014	-0.033	52.417	0.001	0.001	0.000	0.000	0.000	0.000
38	C	233	TYR	0	0.031	0.015	56.625	0.002	0.002	0.000	0.000	0.000	0.000
39	C	234	ASN	0	-0.029	-0.021	60.166	0.000	0.000	0.000	0.000	0.000	0.000
40	C	235	ARG	1	0.909	0.977	51.570	0.072	0.072	0.000	0.000	0.000	0.000
41	C	236	ILE	0	-0.069	-0.020	55.183	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:196:GLY)