FMO DATABASE

FMODB ID: 3NY6L

Calculation Name: 1LTI-C-Xray307

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	43
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-159155.023856
FMO2-HF: Nuclear repulsion	141537.593617
FMO2-HF: Total energy	-17617.430239
FMO2-MP2: Total energy	-17668.707811

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:195:ACE )

Summations of interaction energy for fragment #1(C:195:ACE )

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.
-1.249	0.814	0.54	-1.231	-1.373	-0.006

Interaction energy analysis for fragmet #1(C:195:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.019

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	197	ASP	-1	-0.881	-0.961	3.832	-0.655	0.259	-0.006	-0.383	-0.526	0.000
4	C	198	THR	0	-0.040	-0.022	2.939	0.704	1.253	0.103	-0.282	-0.370	-0.001
5	C	199	CYS	0	-0.027	-0.022	4.341	-0.062	0.021	0.000	-0.016	-0.067	0.000
6	C	200	ASN	0	0.032	-0.015	2.862	-0.963	-0.446	0.443	-0.550	-0.410	-0.005
7	C	201	GLU	-1	-0.896	-0.884	5.841	-0.618	-0.618	0.000	0.000	0.000	0.000
8	C	202	GLU	-1	-0.867	-0.935	8.215	-0.026	-0.026	0.000	0.000	0.000	0.000
9	C	203	THR	0	-0.018	0.000	8.928	0.043	0.043	0.000	0.000	0.000	0.000
10	C	204	GLN	0	0.006	0.021	9.796	0.041	0.041	0.000	0.000	0.000	0.000
11	C	205	ASN	0	-0.013	-0.024	11.524	0.072	0.072	0.000	0.000	0.000	0.000
12	C	206	LEU	0	0.060	0.018	13.359	0.028	0.028	0.000	0.000	0.000	0.000
13	C	207	SER	0	-0.054	-0.037	13.694	0.028	0.028	0.000	0.000	0.000	0.000
14	C	208	THR	0	-0.071	-0.036	15.587	0.007	0.007	0.000	0.000	0.000	0.000
15	C	209	ILE	0	0.032	0.019	17.667	0.010	0.010	0.000	0.000	0.000	0.000
16	C	210	TYR	0	0.018	0.019	19.179	0.010	0.010	0.000	0.000	0.000	0.000
17	C	211	LEU	0	-0.024	-0.011	20.292	0.004	0.004	0.000	0.000	0.000	0.000
18	C	212	ARG	1	0.927	0.954	20.619	0.102	0.102	0.000	0.000	0.000	0.000
19	C	213	GLU	-1	-0.900	-0.935	23.646	-0.040	-0.040	0.000	0.000	0.000	0.000
20	C	214	TYR	0	0.000	-0.005	25.080	0.004	0.004	0.000	0.000	0.000	0.000
21	C	215	GLN	0	-0.009	-0.025	24.937	-0.003	-0.003	0.000	0.000	0.000	0.000
22	C	216	SER	0	0.005	0.015	27.897	0.002	0.002	0.000	0.000	0.000	0.000
23	C	217	LYS	1	0.904	0.944	29.847	0.016	0.016	0.000	0.000	0.000	0.000
24	C	218	VAL	0	0.024	0.017	30.135	0.002	0.002	0.000	0.000	0.000	0.000
25	C	219	LYS	1	0.957	0.983	30.280	0.048	0.048	0.000	0.000	0.000	0.000
26	C	220	ARG	1	0.940	0.970	33.734	0.020	0.020	0.000	0.000	0.000	0.000
27	C	221	GLN	0	-0.047	-0.002	35.757	0.003	0.003	0.000	0.000	0.000	0.000
28	C	222	ILE	0	0.067	0.020	34.408	0.000	0.000	0.000	0.000	0.000	0.000
29	C	223	PHE	0	-0.040	-0.035	34.593	-0.002	-0.002	0.000	0.000	0.000	0.000
30	C	224	SER	0	-0.018	-0.013	38.938	-0.001	-0.001	0.000	0.000	0.000	0.000
31	C	225	ASP	-1	-0.913	-0.942	41.392	-0.013	-0.013	0.000	0.000	0.000	0.000
32	C	226	TYR	0	-0.093	-0.048	40.160	0.000	0.000	0.000	0.000	0.000	0.000
33	C	227	GLN	0	-0.081	-0.015	43.687	-0.002	-0.002	0.000	0.000	0.000	0.000
34	C	228	SER	0	-0.016	-0.001	45.347	0.002	0.002	0.000	0.000	0.000	0.000
35	C	229	GLU	-1	-0.880	-0.949	47.991	-0.018	-0.018	0.000	0.000	0.000	0.000
36	C	230	VAL	0	-0.042	-0.034	50.941	0.000	0.000	0.000	0.000	0.000	0.000
37	C	231	ASP	-1	-0.881	-0.929	53.345	-0.012	-0.012	0.000	0.000	0.000	0.000
38	C	232	ILE	0	0.005	-0.022	52.137	0.000	0.000	0.000	0.000	0.000	0.000
39	C	233	TYR	0	0.004	-0.014	56.357	0.000	0.000	0.000	0.000	0.000	0.000
40	C	234	ASN	0	0.020	0.024	58.990	0.001	0.001	0.000	0.000	0.000	0.000
41	C	235	ARG	1	0.856	0.946	51.479	0.020	0.020	0.000	0.000	0.000	0.000
42	C	236	ILE	0	-0.052	-0.024	55.879	-0.001	-0.001	0.000	0.000	0.000	0.000
43	C	237	NME	0	0.017	0.020	59.519	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:195:ACE )