FMO DATABASE

FMODB ID: K3K63

Calculation Name: 1LTI-C-Xray372

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-alpha-d-galactopyranose

ligand 3-letter code: A2G

PDB ID: 1LTI

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:

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	41
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-156795.955377
FMO2-HF: Nuclear repulsion	139349.023108
FMO2-HF: Total energy	-17446.932269
FMO2-MP2: Total energy	-17497.62837

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(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.
-3.247	-3.394	11.325	-5.688	-5.49	-0.039

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 : -0.004 / q_NPA : -0.008

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	-0.018	-0.028	2.492	-2.147	1.278	0.981	-2.037	-2.369	-0.009
4	C	199	CYS	0	-0.012	-0.008	3.751	0.969	1.219	0.000	-0.043	-0.207	0.000
5	C	200	ASN	0	0.025	-0.005	1.878	-3.124	-7.168	10.345	-3.571	-2.730	-0.030
6	C	201	GLU	-1	-0.873	-0.895	4.504	-1.762	-1.540	-0.001	-0.037	-0.184	0.000
7	C	202	GLU	-1	-0.836	-0.921	6.092	-0.364	-0.364	0.000	0.000	0.000	0.000
8	C	203	THR	0	-0.013	-0.001	7.988	0.560	0.560	0.000	0.000	0.000	0.000
9	C	204	GLN	0	0.010	0.034	8.430	0.451	0.451	0.000	0.000	0.000	0.000
10	C	205	ASN	0	-0.012	-0.011	10.080	0.510	0.510	0.000	0.000	0.000	0.000
11	C	206	LEU	0	0.017	0.001	11.865	0.247	0.247	0.000	0.000	0.000	0.000
12	C	207	SER	0	-0.049	-0.041	12.672	0.203	0.203	0.000	0.000	0.000	0.000
13	C	208	THR	0	-0.084	-0.056	13.601	0.160	0.160	0.000	0.000	0.000	0.000
14	C	209	ILE	0	0.012	0.011	15.801	0.110	0.110	0.000	0.000	0.000	0.000
15	C	210	TYR	0	0.013	0.015	17.840	0.075	0.075	0.000	0.000	0.000	0.000
16	C	211	LEU	0	-0.017	-0.005	19.009	0.063	0.063	0.000	0.000	0.000	0.000
17	C	212	ARG	1	0.921	0.948	18.296	0.444	0.444	0.000	0.000	0.000	0.000
18	C	213	GLU	-1	-0.829	-0.891	22.194	-0.275	-0.275	0.000	0.000	0.000	0.000
19	C	214	TYR	0	0.009	-0.002	23.776	0.035	0.035	0.000	0.000	0.000	0.000
20	C	215	GLN	0	0.009	-0.016	23.070	0.010	0.010	0.000	0.000	0.000	0.000
21	C	216	SER	0	-0.009	0.009	26.416	0.029	0.029	0.000	0.000	0.000	0.000
22	C	217	LYS	1	0.855	0.908	27.321	0.276	0.276	0.000	0.000	0.000	0.000
23	C	218	VAL	0	0.016	0.014	29.005	0.015	0.015	0.000	0.000	0.000	0.000
24	C	219	LYS	1	0.941	0.979	27.420	0.213	0.213	0.000	0.000	0.000	0.000
25	C	220	ARG	1	0.947	0.973	32.199	0.188	0.188	0.000	0.000	0.000	0.000
26	C	221	GLN	0	-0.054	0.008	34.346	0.012	0.012	0.000	0.000	0.000	0.000
27	C	222	ILE	0	0.069	0.028	32.874	0.005	0.005	0.000	0.000	0.000	0.000
28	C	223	PHE	0	-0.029	-0.037	32.144	0.002	0.002	0.000	0.000	0.000	0.000
29	C	224	SER	0	-0.023	-0.027	37.034	0.003	0.003	0.000	0.000	0.000	0.000
30	C	225	ASP	-1	-0.920	-0.949	39.606	-0.095	-0.095	0.000	0.000	0.000	0.000
31	C	226	TYR	0	-0.089	-0.046	38.821	0.007	0.007	0.000	0.000	0.000	0.000
32	C	227	GLN	0	-0.095	-0.037	41.593	0.001	0.001	0.000	0.000	0.000	0.000
33	C	228	SER	0	0.014	0.009	43.232	0.004	0.004	0.000	0.000	0.000	0.000
34	C	229	GLU	-1	-0.891	-0.938	45.913	-0.093	-0.093	0.000	0.000	0.000	0.000
35	C	230	VAL	0	-0.065	-0.040	48.499	0.004	0.004	0.000	0.000	0.000	0.000
36	C	231	ASP	-1	-0.846	-0.917	50.956	-0.061	-0.061	0.000	0.000	0.000	0.000
37	C	232	ILE	0	0.006	-0.025	49.894	0.001	0.001	0.000	0.000	0.000	0.000
38	C	233	TYR	0	0.001	-0.003	53.847	0.001	0.001	0.000	0.000	0.000	0.000
39	C	234	ASN	0	-0.021	0.009	56.896	0.004	0.004	0.000	0.000	0.000	0.000
40	C	235	ARG	1	0.878	0.956	48.771	0.071	0.071	0.000	0.000	0.000	0.000
41	C	236	ILE	0	-0.025	-0.009	52.863	0.001	0.001	0.000	0.000	0.000	0.000

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