FMO DATABASE

FMODB ID: M3R7Z

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	OptH
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	-157141.785943
FMO2-HF: Nuclear repulsion	139695.160295
FMO2-HF: Total energy	-17446.625648
FMO2-MP2: Total energy	-17497.310256

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.
2.076	4.549	-0.02	-1.229	-1.225	0

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 : 0.039 / 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].
3	C	198	THR	0	0.025	0.021	3.794	-1.052	1.093	-0.018	-1.147	-0.980
4	C	199	CYS	0	-0.006	0.000	4.470	1.151	1.294	-0.001	-0.016	-0.126
5	C	200	ASN	0	0.016	0.008	3.591	1.018	1.203	-0.001	-0.066	-0.119
6	C	201	GLU	-1	-0.937	-0.963	7.063	-0.756	-0.756	0.000	0.000	0.000
7	C	202	GLU	-1	-0.879	-0.954	8.840	-0.433	-0.433	0.000	0.000	0.000
8	C	203	THR	0	-0.033	-0.003	9.949	0.390	0.390	0.000	0.000	0.000
9	C	204	GLN	0	-0.009	0.005	11.416	0.222	0.222	0.000	0.000	0.000
10	C	205	ASN	0	-0.020	-0.014	13.044	0.266	0.266	0.000	0.000	0.000
11	C	206	LEU	0	0.026	0.001	14.277	0.153	0.153	0.000	0.000	0.000
12	C	207	SER	0	-0.042	-0.021	15.307	0.136	0.136	0.000	0.000	0.000
13	C	208	THR	0	-0.074	-0.043	17.099	0.100	0.100	0.000	0.000	0.000
14	C	209	ILE	0	0.029	0.019	18.434	0.074	0.074	0.000	0.000	0.000
15	C	210	TYR	0	0.059	0.037	20.564	0.055	0.055	0.000	0.000	0.000
16	C	211	LEU	0	-0.035	-0.003	21.867	0.047	0.047	0.000	0.000	0.000
17	C	212	ARG	1	0.912	0.939	22.011	0.440	0.440	0.000	0.000	0.000
18	C	213	GLU	-1	-0.908	-0.947	25.004	-0.278	-0.278	0.000	0.000	0.000
19	C	214	TYR	0	-0.008	-0.003	26.442	0.031	0.031	0.000	0.000	0.000
20	C	215	GLN	0	-0.010	-0.032	26.451	0.012	0.012	0.000	0.000	0.000
21	C	216	SER	0	-0.005	0.007	29.474	0.025	0.025	0.000	0.000	0.000
22	C	217	LYS	1	0.904	0.948	31.245	0.215	0.215	0.000	0.000	0.000
23	C	218	VAL	0	0.053	0.030	32.180	0.013	0.013	0.000	0.000	0.000
24	C	219	LYS	1	0.954	0.980	31.031	0.224	0.224	0.000	0.000	0.000
25	C	220	ARG	1	0.935	0.969	34.840	0.171	0.171	0.000	0.000	0.000
26	C	221	GLN	0	-0.031	0.003	37.279	0.013	0.013	0.000	0.000	0.000
27	C	222	ILE	0	0.054	0.014	35.995	0.005	0.005	0.000	0.000	0.000
28	C	223	PHE	0	-0.045	-0.041	35.753	0.001	0.001	0.000	0.000	0.000
29	C	224	SER	0	-0.017	-0.020	40.299	0.006	0.006	0.000	0.000	0.000
30	C	225	ASP	-1	-0.911	-0.939	42.751	-0.111	-0.111	0.000	0.000	0.000
31	C	226	TYR	0	-0.086	-0.032	41.468	0.006	0.006	0.000	0.000	0.000
32	C	227	GLN	0	-0.088	-0.021	44.687	-0.001	-0.001	0.000	0.000	0.000
33	C	228	SER	0	0.000	-0.004	46.366	0.004	0.004	0.000	0.000	0.000
34	C	229	GLU	-1	-0.929	-0.967	49.044	-0.091	-0.091	0.000	0.000	0.000
35	C	230	VAL	0	-0.029	-0.021	51.441	0.003	0.003	0.000	0.000	0.000
36	C	231	ASP	-1	-0.863	-0.924	53.839	-0.058	-0.058	0.000	0.000	0.000
37	C	232	ILE	0	-0.023	-0.037	52.321	0.001	0.001	0.000	0.000	0.000
38	C	233	TYR	0	0.028	0.009	56.625	0.001	0.001	0.000	0.000	0.000
39	C	234	ASN	0	-0.014	-0.011	60.167	0.000	0.000	0.000	0.000	0.000
40	C	235	ARG	1	0.889	0.964	51.707	0.072	0.072	0.000	0.000	0.000
41	C	236	ILE	0	-0.033	-0.001	55.605	0.001	0.001	0.000	0.000	0.000

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