FMO DATABASE

FMODB ID: R53R8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-250392.972378
FMO2-HF: Nuclear repulsion	225715.278107
FMO2-HF: Total energy	-24677.69427
FMO2-MP2: Total energy	-24747.093973

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.
-23.574	-23.93	13.752	-5.955	-7.441	0.017

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 : -0.022 / q_NPA : -0.014

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	-0.017	-0.015	2.470	0.492	2.825	0.431	-1.248	-1.517	-0.007
4	A	329	ARG	1	0.976	0.957	1.980	-19.795	-23.051	13.310	-4.522	-5.531	0.024
5	A	330	GLU	-1	-0.849	-0.917	4.002	-5.721	-5.154	0.011	-0.185	-0.393	0.000
6	A	331	ARG	1	0.937	0.957	5.707	1.633	1.633	0.000	0.000	0.000	0.000
7	A	332	ASP	-1	-0.799	-0.872	6.637	0.935	0.935	0.000	0.000	0.000	0.000
8	A	333	THR	0	-0.020	-0.017	8.002	-0.175	-0.175	0.000	0.000	0.000	0.000
9	A	334	SER	0	0.020	0.015	9.711	-0.039	-0.039	0.000	0.000	0.000	0.000
10	A	335	ARG	1	0.894	0.937	11.182	-0.266	-0.266	0.000	0.000	0.000	0.000
11	A	336	ARG	1	0.829	0.895	10.968	-0.686	-0.686	0.000	0.000	0.000	0.000
12	A	337	LEU	0	0.065	0.034	13.017	-0.030	-0.030	0.000	0.000	0.000	0.000
13	A	338	LEU	0	-0.008	-0.009	15.363	-0.020	-0.020	0.000	0.000	0.000	0.000
14	A	339	ALA	0	0.012	0.017	17.066	-0.012	-0.012	0.000	0.000	0.000	0.000
15	A	340	GLU	-1	-0.980	-0.992	18.515	0.209	0.209	0.000	0.000	0.000	0.000
16	A	341	LYS	1	0.964	0.976	20.104	0.008	0.008	0.000	0.000	0.000	0.000
17	A	342	GLU	-1	-0.962	-0.994	21.532	-0.041	-0.041	0.000	0.000	0.000	0.000
18	A	343	ARG	1	0.926	0.971	22.542	-0.148	-0.148	0.000	0.000	0.000	0.000
19	A	344	GLU	-1	-0.885	-0.926	24.748	0.058	0.058	0.000	0.000	0.000	0.000
20	A	345	MET	0	-0.023	-0.029	26.122	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	346	ALA	0	-0.073	-0.025	27.411	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	347	GLU	-1	-0.897	-0.958	29.065	0.068	0.068	0.000	0.000	0.000	0.000
23	A	348	MET	0	-0.004	0.005	30.852	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	349	ARG	1	0.948	0.970	27.103	0.004	0.004	0.000	0.000	0.000	0.000
25	A	350	ALA	0	0.007	0.020	33.276	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	351	ARG	1	0.947	0.961	33.467	-0.051	-0.051	0.000	0.000	0.000	0.000
27	A	352	MET	0	0.004	0.004	36.562	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	353	GLN	0	-0.104	-0.051	37.442	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	354	GLN	0	-0.022	-0.013	39.171	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	355	GLN	0	-0.008	-0.016	40.382	0.001	0.001	0.000	0.000	0.000	0.000
31	A	356	LEU	0	-0.022	-0.011	40.828	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	357	ASP	-1	-0.858	-0.910	42.450	0.005	0.005	0.000	0.000	0.000	0.000
33	A	358	GLU	-1	-0.864	-0.928	45.119	0.018	0.018	0.000	0.000	0.000	0.000
34	A	359	TYR	0	-0.077	-0.034	46.820	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	360	GLN	0	-0.050	-0.044	47.469	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	361	GLU	-1	-0.909	-0.942	49.259	0.010	0.010	0.000	0.000	0.000	0.000
37	A	362	LEU	0	-0.023	-0.003	51.311	0.000	0.000	0.000	0.000	0.000	0.000
38	A	363	LEU	0	-0.045	-0.032	50.785	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	364	ASP	-1	-0.848	-0.914	52.011	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	365	ILE	0	-0.014	-0.011	54.940	0.000	0.000	0.000	0.000	0.000	0.000
41	A	366	LYS	1	0.868	0.945	56.973	0.001	0.001	0.000	0.000	0.000	0.000
42	A	367	LEU	0	-0.011	-0.013	56.860	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	368	ALA	0	0.002	0.004	59.074	0.000	0.000	0.000	0.000	0.000	0.000
44	A	369	LEU	0	0.048	0.017	60.911	0.000	0.000	0.000	0.000	0.000	0.000
45	A	370	ASP	-1	-0.870	-0.944	62.367	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	371	MET	0	-0.081	-0.040	60.363	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	372	GLU	-1	-0.945	-0.970	64.290	0.003	0.003	0.000	0.000	0.000	0.000
48	A	373	ILE	0	-0.019	-0.010	66.150	0.000	0.000	0.000	0.000	0.000	0.000
49	A	374	HIS	0	-0.061	-0.033	68.137	0.000	0.000	0.000	0.000	0.000	0.000
50	A	375	ALA	0	0.002	-0.001	69.470	0.000	0.000	0.000	0.000	0.000	0.000
51	A	376	TYR	0	0.012	0.004	71.154	0.000	0.000	0.000	0.000	0.000	0.000
52	A	377	ARG	1	0.951	0.972	72.676	0.001	0.001	0.000	0.000	0.000	0.000
53	A	378	LYS	1	0.925	0.944	73.604	0.003	0.003	0.000	0.000	0.000	0.000
54	A	379	LEU	0	-0.033	-0.005	75.438	0.000	0.000	0.000	0.000	0.000	0.000
55	A	380	LEU	0	-0.084	-0.035	77.254	0.000	0.000	0.000	0.000	0.000	0.000
56	A	381	GLU	-1	-0.949	-0.944	78.264	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	382	GLY	0	-0.052	-0.028	80.936	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)