FMO DATABASE

FMODB ID: K31N3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-251098.942919
FMO2-HF: Nuclear repulsion	226420.617765
FMO2-HF: Total energy	-24678.325153
FMO2-MP2: Total energy	-24747.713641

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.
-23.06	-26.487	13.985	-5.453	-5.104	0.027

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 : 0.062 / q_NPA : 0.031

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	A	328	ALA	0	-0.011	-0.004	3.623	1.114	2.490	-0.004	-0.664	-0.708	-0.001
4	A	329	ARG	1	0.958	0.953	1.943	-22.573	-28.112	13.976	-4.488	-3.948	0.030
5	A	330	GLU	-1	-0.828	-0.870	3.707	-4.133	-3.397	0.013	-0.301	-0.448	-0.002
6	A	331	ARG	1	0.959	0.976	6.450	1.965	1.965	0.000	0.000	0.000	0.000
7	A	332	ASP	-1	-0.758	-0.845	8.296	0.303	0.303	0.000	0.000	0.000	0.000
8	A	333	THR	0	-0.016	-0.035	8.377	0.095	0.095	0.000	0.000	0.000	0.000
9	A	334	SER	0	0.022	0.020	10.421	0.070	0.070	0.000	0.000	0.000	0.000
10	A	335	ARG	1	0.867	0.917	12.367	0.196	0.196	0.000	0.000	0.000	0.000
11	A	336	ARG	1	0.838	0.900	11.913	-0.186	-0.186	0.000	0.000	0.000	0.000
12	A	337	LEU	0	0.044	0.024	13.252	0.012	0.012	0.000	0.000	0.000	0.000
13	A	338	LEU	0	-0.012	-0.007	15.862	0.006	0.006	0.000	0.000	0.000	0.000
14	A	339	ALA	0	-0.001	-0.002	18.150	0.006	0.006	0.000	0.000	0.000	0.000
15	A	340	GLU	-1	-0.872	-0.929	19.503	0.095	0.095	0.000	0.000	0.000	0.000
16	A	341	LYS	1	0.837	0.894	20.628	0.068	0.068	0.000	0.000	0.000	0.000
17	A	342	GLU	-1	-0.802	-0.869	22.439	-0.082	-0.082	0.000	0.000	0.000	0.000
18	A	343	ARG	1	0.875	0.937	22.598	-0.051	-0.051	0.000	0.000	0.000	0.000
19	A	344	GLU	-1	-0.854	-0.918	25.849	0.016	0.016	0.000	0.000	0.000	0.000
20	A	345	MET	0	-0.012	-0.012	26.655	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	346	ALA	0	-0.048	-0.021	28.322	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	347	GLU	-1	-0.835	-0.904	30.133	0.022	0.022	0.000	0.000	0.000	0.000
23	A	348	MET	0	-0.012	-0.002	31.648	0.002	0.002	0.000	0.000	0.000	0.000
24	A	349	ARG	1	0.811	0.886	27.337	0.056	0.056	0.000	0.000	0.000	0.000
25	A	350	ALA	0	0.007	0.009	34.282	0.000	0.000	0.000	0.000	0.000	0.000
26	A	351	ARG	1	0.850	0.910	32.527	-0.012	-0.012	0.000	0.000	0.000	0.000
27	A	352	MET	0	0.013	-0.001	37.088	0.001	0.001	0.000	0.000	0.000	0.000
28	A	353	GLN	0	-0.091	-0.048	38.438	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	354	GLN	0	-0.023	-0.023	40.189	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	355	GLN	0	-0.005	-0.012	40.517	0.002	0.002	0.000	0.000	0.000	0.000
31	A	356	LEU	0	-0.051	-0.021	41.088	0.000	0.000	0.000	0.000	0.000	0.000
32	A	357	ASP	-1	-0.838	-0.907	43.532	-0.021	-0.021	0.000	0.000	0.000	0.000
33	A	358	GLU	-1	-0.870	-0.921	46.233	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	359	TYR	0	-0.061	-0.032	47.670	0.001	0.001	0.000	0.000	0.000	0.000
35	A	360	GLN	0	-0.061	-0.044	48.350	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	361	GLU	-1	-0.915	-0.957	50.190	-0.007	-0.007	0.000	0.000	0.000	0.000
37	A	362	LEU	0	-0.021	-0.010	52.273	0.001	0.001	0.000	0.000	0.000	0.000
38	A	363	LEU	0	-0.033	-0.020	51.365	0.000	0.000	0.000	0.000	0.000	0.000
39	A	364	ASP	-1	-0.848	-0.912	53.114	-0.017	-0.017	0.000	0.000	0.000	0.000
40	A	365	ILE	0	-0.027	-0.010	55.997	0.000	0.000	0.000	0.000	0.000	0.000
41	A	366	LYS	1	0.763	0.867	57.886	0.010	0.010	0.000	0.000	0.000	0.000
42	A	367	LEU	0	0.008	-0.009	56.719	0.000	0.000	0.000	0.000	0.000	0.000
43	A	368	ALA	0	-0.006	0.000	60.130	0.000	0.000	0.000	0.000	0.000	0.000
44	A	369	LEU	0	0.054	0.028	62.006	0.000	0.000	0.000	0.000	0.000	0.000
45	A	370	ASP	-1	-0.807	-0.886	62.838	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	371	MET	0	-0.067	-0.031	61.738	0.000	0.000	0.000	0.000	0.000	0.000
47	A	372	GLU	-1	-0.933	-0.958	65.969	-0.008	-0.008	0.000	0.000	0.000	0.000
48	A	373	ILE	0	-0.012	-0.006	67.240	0.000	0.000	0.000	0.000	0.000	0.000
49	A	374	HIS	0	-0.051	-0.025	69.211	0.000	0.000	0.000	0.000	0.000	0.000
50	A	375	ALA	0	0.007	-0.001	70.445	0.000	0.000	0.000	0.000	0.000	0.000
51	A	376	TYR	0	0.008	-0.004	72.148	0.000	0.000	0.000	0.000	0.000	0.000
52	A	377	ARG	1	0.869	0.916	73.715	0.008	0.008	0.000	0.000	0.000	0.000
53	A	378	LYS	1	0.821	0.896	74.586	0.010	0.010	0.000	0.000	0.000	0.000
54	A	379	LEU	0	-0.046	-0.012	76.449	0.000	0.000	0.000	0.000	0.000	0.000
55	A	380	LEU	0	-0.039	-0.018	78.181	0.000	0.000	0.000	0.000	0.000	0.000
56	A	381	GLU	-1	-0.814	-0.872	78.674	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	382	GLY	0	-0.038	-0.007	81.740	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)