FMO DATABASE

FMODB ID: Q1K3Y

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	OptH
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	-156796.315149
FMO2-HF: Nuclear repulsion	139349.853418
FMO2-HF: Total energy	-17446.46173
FMO2-MP2: Total energy	-17497.195504

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.
-8.005	-11.848	16.706	-7.232	-5.632	-0.013

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 : -0.020 / q_NPA : -0.033

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	-0.032	-0.018	2.514	-4.564	-1.141	1.228	-2.161	-2.490	0.019
4	C	199	CYS	0	-0.027	-0.022	4.149	-1.380	-1.167	-0.001	-0.042	-0.171	0.000
5	C	200	ASN	0	0.041	-0.002	1.778	-2.623	-10.351	15.480	-4.986	-2.767	-0.032
6	C	201	GLU	-1	-0.903	-0.888	4.388	-1.453	-1.204	-0.001	-0.043	-0.204	0.000
7	C	202	GLU	-1	-0.867	-0.935	6.092	-0.041	-0.041	0.000	0.000	0.000	0.000
8	C	203	THR	0	-0.020	0.000	7.899	0.277	0.277	0.000	0.000	0.000	0.000
9	C	204	GLN	0	0.007	0.020	8.370	0.272	0.272	0.000	0.000	0.000	0.000
10	C	205	ASN	0	-0.015	-0.024	9.999	0.361	0.361	0.000	0.000	0.000	0.000
11	C	206	LEU	0	0.061	0.019	11.766	0.155	0.155	0.000	0.000	0.000	0.000
12	C	207	SER	0	-0.056	-0.037	12.690	0.134	0.134	0.000	0.000	0.000	0.000
13	C	208	THR	0	-0.071	-0.036	13.758	0.102	0.102	0.000	0.000	0.000	0.000
14	C	209	ILE	0	0.031	0.019	16.025	0.069	0.069	0.000	0.000	0.000	0.000
15	C	210	TYR	0	0.017	0.018	17.759	0.053	0.053	0.000	0.000	0.000	0.000
16	C	211	LEU	0	-0.025	-0.011	18.951	0.042	0.042	0.000	0.000	0.000	0.000
17	C	212	ARG	1	0.926	0.954	18.114	0.379	0.379	0.000	0.000	0.000	0.000
18	C	213	GLU	-1	-0.899	-0.934	22.130	-0.201	-0.201	0.000	0.000	0.000	0.000
19	C	214	TYR	0	0.001	-0.004	23.713	0.026	0.026	0.000	0.000	0.000	0.000
20	C	215	GLN	0	-0.011	-0.026	23.127	0.018	0.018	0.000	0.000	0.000	0.000
21	C	216	SER	0	0.005	0.015	26.398	0.019	0.019	0.000	0.000	0.000	0.000
22	C	217	LYS	1	0.906	0.944	28.406	0.146	0.146	0.000	0.000	0.000	0.000
23	C	218	VAL	0	0.028	0.019	28.974	0.010	0.010	0.000	0.000	0.000	0.000
24	C	219	LYS	1	0.954	0.982	27.919	0.173	0.173	0.000	0.000	0.000	0.000
25	C	220	ARG	1	0.939	0.969	32.117	0.120	0.120	0.000	0.000	0.000	0.000
26	C	221	GLN	0	-0.047	-0.003	34.329	0.011	0.011	0.000	0.000	0.000	0.000
27	C	222	ILE	0	0.069	0.021	32.743	0.003	0.003	0.000	0.000	0.000	0.000
28	C	223	PHE	0	-0.039	-0.034	32.349	0.000	0.000	0.000	0.000	0.000	0.000
29	C	224	SER	0	-0.019	-0.014	37.018	0.004	0.004	0.000	0.000	0.000	0.000
30	C	225	ASP	-1	-0.914	-0.942	39.589	-0.079	-0.079	0.000	0.000	0.000	0.000
31	C	226	TYR	0	-0.092	-0.048	38.209	0.004	0.004	0.000	0.000	0.000	0.000
32	C	227	GLN	0	-0.082	-0.015	41.580	-0.001	-0.001	0.000	0.000	0.000	0.000
33	C	228	SER	0	-0.016	-0.002	43.216	0.003	0.003	0.000	0.000	0.000	0.000
34	C	229	GLU	-1	-0.878	-0.949	45.996	-0.063	-0.063	0.000	0.000	0.000	0.000
35	C	230	VAL	0	-0.042	-0.033	48.519	0.002	0.002	0.000	0.000	0.000	0.000
36	C	231	ASP	-1	-0.882	-0.929	50.940	-0.040	-0.040	0.000	0.000	0.000	0.000
37	C	232	ILE	0	0.002	-0.025	49.701	0.001	0.001	0.000	0.000	0.000	0.000
38	C	233	TYR	0	0.004	-0.011	53.832	0.001	0.001	0.000	0.000	0.000	0.000
39	C	234	ASN	0	0.012	0.023	56.388	0.003	0.003	0.000	0.000	0.000	0.000
40	C	235	ARG	1	0.857	0.950	48.703	0.051	0.051	0.000	0.000	0.000	0.000
41	C	236	ILE	0	-0.020	-0.007	53.012	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)