FMO DATABASE

FMODB ID: Q19QY

Calculation Name: 2XV5-A-Xray372

Preferred Name: Prelamin-A/C

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2XV5

Chain ID: A

ChEMBL ID: CHEMBL1293235

UniProt ID: P02545

Base Structure: X-ray

Registration Date: 2023-06-21

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	57
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-250902.127636
FMO2-HF: Nuclear repulsion	226224.024416
FMO2-HF: Total energy	-24678.10322
FMO2-MP2: Total energy	-24747.512561

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(A:326:GLY)

Summations of interaction energy for fragment #1(A:326: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.
-20.179	-17.384	8.51	-4.661	-6.644	0.019

Interaction energy analysis for fragmet #1(A:326:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.016

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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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	A	328	ALA	0	-0.023	-0.007	2.512	0.859	2.957	0.348	-1.072	-1.374	-0.004
4	A	329	ARG	1	0.984	0.967	2.161	-17.028	-16.865	8.151	-3.445	-4.869	0.022
5	A	330	GLU	-1	-0.809	-0.881	4.011	-4.610	-4.076	0.011	-0.144	-0.401	0.001
6	A	331	ARG	1	0.932	0.954	5.874	1.254	1.254	0.000	0.000	0.000	0.000
7	A	332	ASP	-1	-0.776	-0.850	6.809	0.887	0.887	0.000	0.000	0.000	0.000
8	A	333	THR	0	-0.007	-0.020	7.873	-0.281	-0.281	0.000	0.000	0.000	0.000
9	A	334	SER	0	0.016	0.014	9.890	-0.082	-0.082	0.000	0.000	0.000	0.000
10	A	335	ARG	1	0.866	0.913	11.358	-0.387	-0.387	0.000	0.000	0.000	0.000
11	A	336	ARG	1	0.827	0.895	11.087	-0.802	-0.802	0.000	0.000	0.000	0.000
12	A	337	LEU	0	0.059	0.031	13.047	-0.040	-0.040	0.000	0.000	0.000	0.000
13	A	338	LEU	0	0.009	0.001	15.539	-0.031	-0.031	0.000	0.000	0.000	0.000
14	A	339	ALA	0	-0.014	0.003	17.248	-0.021	-0.021	0.000	0.000	0.000	0.000
15	A	340	GLU	-1	-0.981	-0.996	18.692	0.232	0.232	0.000	0.000	0.000	0.000
16	A	341	LYS	1	0.928	0.958	20.286	-0.040	-0.040	0.000	0.000	0.000	0.000
17	A	342	GLU	-1	-0.829	-0.919	21.717	0.003	0.003	0.000	0.000	0.000	0.000
18	A	343	ARG	1	0.929	0.976	22.491	-0.179	-0.179	0.000	0.000	0.000	0.000
19	A	344	GLU	-1	-0.875	-0.926	24.927	0.071	0.071	0.000	0.000	0.000	0.000
20	A	345	MET	0	-0.010	-0.016	26.273	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	346	ALA	0	-0.070	-0.034	27.501	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	347	GLU	-1	-0.828	-0.904	29.240	0.081	0.081	0.000	0.000	0.000	0.000
23	A	348	MET	0	0.004	0.011	31.020	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	349	ARG	1	0.834	0.905	26.734	-0.025	-0.025	0.000	0.000	0.000	0.000
25	A	350	ALA	0	0.009	0.021	33.456	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	351	ARG	1	0.871	0.912	32.345	-0.065	-0.065	0.000	0.000	0.000	0.000
27	A	352	MET	0	0.003	0.001	36.737	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	353	GLN	0	-0.099	-0.052	37.631	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	354	GLN	0	-0.031	-0.023	39.346	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	355	GLN	0	-0.016	-0.015	40.453	0.001	0.001	0.000	0.000	0.000	0.000
31	A	356	LEU	0	-0.034	-0.016	40.657	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	357	ASP	-1	-0.853	-0.908	42.467	0.014	0.014	0.000	0.000	0.000	0.000
33	A	358	GLU	-1	-0.855	-0.918	45.292	0.026	0.026	0.000	0.000	0.000	0.000
34	A	359	TYR	0	-0.076	-0.038	46.997	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	360	GLN	0	-0.050	-0.050	47.590	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	361	GLU	-1	-0.907	-0.943	49.433	0.016	0.016	0.000	0.000	0.000	0.000
37	A	362	LEU	0	-0.017	-0.002	51.484	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	363	LEU	0	-0.043	-0.028	50.995	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	364	ASP	-1	-0.844	-0.905	52.307	0.006	0.006	0.000	0.000	0.000	0.000
40	A	365	ILE	0	-0.019	-0.010	55.111	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	366	LYS	1	0.751	0.869	57.147	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	367	LEU	0	0.007	-0.007	56.383	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	368	ALA	0	-0.003	-0.001	59.241	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	369	LEU	0	0.054	0.022	61.081	0.000	0.000	0.000	0.000	0.000	0.000
45	A	370	ASP	-1	-0.800	-0.886	62.297	0.004	0.004	0.000	0.000	0.000	0.000
46	A	371	MET	0	-0.065	-0.035	60.582	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	372	GLU	-1	-0.945	-0.968	64.786	0.007	0.007	0.000	0.000	0.000	0.000
48	A	373	ILE	0	-0.027	-0.017	66.524	0.000	0.000	0.000	0.000	0.000	0.000
49	A	374	HIS	0	-0.064	-0.031	68.309	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	375	ALA	0	0.015	0.005	69.639	0.000	0.000	0.000	0.000	0.000	0.000
51	A	376	TYR	0	0.010	0.002	71.327	0.000	0.000	0.000	0.000	0.000	0.000
52	A	377	ARG	1	0.936	0.965	72.847	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	378	LYS	1	0.833	0.892	73.895	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	379	LEU	0	-0.030	-0.001	75.613	0.000	0.000	0.000	0.000	0.000	0.000
55	A	380	LEU	0	-0.067	-0.025	77.422	0.000	0.000	0.000	0.000	0.000	0.000
56	A	381	GLU	-1	-0.875	-0.912	78.144	0.001	0.001	0.000	0.000	0.000	0.000
57	A	382	GLY	0	-0.033	-0.014	81.106	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:326:GLY)