FMO DATABASE

FMODB ID: Q1MYY

Calculation Name: 1XCT-P-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XCT

Chain ID: P

ChEMBL ID:

UniProt ID: P26661

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	OptAll
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	30
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-91666.878052
FMO2-HF: Nuclear repulsion	80596.731888
FMO2-HF: Total energy	-11070.146164
FMO2-MP2: Total energy	-11103.381873

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(P:16:ASN)

Summations of interaction energy for fragment #1(P:16:ASN)

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.
-10.745	-6.899	0.063	-1.435	-2.476	0.006

Interaction energy analysis for fragmet #1(P:16:ASN)

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 : 0.010

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

Sort

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	P	18	ARG	1	1.022	0.995	3.061	-9.948	-7.073	0.068	-1.361	-1.583	0.006
4	P	19	PRO	0	-0.017	0.009	4.319	-1.501	-1.338	-0.001	-0.013	-0.149	0.000
5	P	20	GLN	0	0.041	0.016	5.155	-1.328	-1.234	-0.001	-0.001	-0.091	0.000
6	P	21	ASP	-1	-0.855	-0.926	5.987	4.139	4.139	0.000	0.000	0.000	0.000
7	P	22	VAL	0	-0.021	-0.007	3.931	3.618	4.019	0.000	-0.047	-0.355	0.000
8	P	23	LYS	1	0.850	0.908	5.004	-3.716	-3.607	-0.001	-0.002	-0.107	0.000
9	P	24	PHE	0	0.042	0.032	7.064	-0.406	-0.406	0.000	0.000	0.000	0.000
10	P	25	PRO	0	0.013	0.036	7.755	-0.329	-0.329	0.000	0.000	0.000	0.000
11	P	26	GLY	0	0.022	-0.018	7.733	0.893	0.893	0.000	0.000	0.000	0.000
12	P	27	GLY	0	0.005	-0.005	8.708	-0.425	-0.425	0.000	0.000	0.000	0.000
13	P	28	GLY	0	0.015	-0.004	10.116	-0.017	-0.017	0.000	0.000	0.000	0.000
14	P	29	GLN	0	0.028	0.025	8.441	-0.015	-0.015	0.000	0.000	0.000	0.000
15	P	30	ILE	0	-0.063	-0.026	5.981	0.251	0.251	0.000	0.000	0.000	0.000
16	P	31	VAL	0	0.042	0.019	4.710	-0.382	-0.332	-0.001	-0.003	-0.046	0.000
17	P	32	GLY	0	0.073	0.029	5.725	-0.227	-0.227	0.000	0.000	0.000	0.000
18	P	33	GLY	0	0.000	-0.006	8.303	0.367	0.367	0.000	0.000	0.000	0.000
19	P	34	VAL	0	0.023	0.009	8.596	0.092	0.092	0.000	0.000	0.000	0.000
20	P	35	TYR	0	-0.007	0.002	4.857	0.076	0.230	-0.001	-0.008	-0.145	0.000
21	P	36	LEU	0	-0.059	-0.013	9.049	0.143	0.143	0.000	0.000	0.000	0.000
22	P	37	LEU	0	0.018	0.004	12.063	-0.007	-0.007	0.000	0.000	0.000	0.000
23	P	38	PRO	0	0.006	-0.003	15.329	-0.053	-0.053	0.000	0.000	0.000	0.000
24	P	39	ARG	1	0.960	0.977	18.397	-0.166	-0.166	0.000	0.000	0.000	0.000
25	P	40	ARG	1	0.973	0.982	18.982	-0.426	-0.426	0.000	0.000	0.000	0.000
26	P	41	GLY	0	0.033	0.020	19.270	0.000	0.000	0.000	0.000	0.000	0.000
27	P	42	PRO	0	0.015	0.012	18.106	0.026	0.026	0.000	0.000	0.000	0.000
28	P	43	ARG	1	0.843	0.919	11.801	-1.304	-1.304	0.000	0.000	0.000	0.000
29	P	44	LEU	0	0.024	0.018	12.777	-0.049	-0.049	0.000	0.000	0.000	0.000
30	P	45	GLY	0	0.005	0.023	13.253	-0.051	-0.051	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(P:16:ASN)