FMO DATABASE

FMODB ID: 2NQJR

Calculation Name: 3GEF-A-Xray372

Preferred Name: Prelamin-A/C

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3GEF

Chain ID: A

ChEMBL ID: CHEMBL1293235

UniProt ID: P02545

Base Structure: X-ray

Registration Date: 2023-09-23

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	118
LigandResidueName
LigandFragmentNumber	0
LigandCharge	CSD=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-939790.023983
FMO2-HF: Nuclear repulsion	893912.339204
FMO2-HF: Total energy	-45877.684779
FMO2-MP2: Total energy	-46011.983851

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:435:SER)

Summations of interaction energy for fragment #1(A:435:SER)

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.
-19.732	-18.785	11.726	-6.856	-5.816	-0.06

Interaction energy analysis for fragmet #1(A:435:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.005

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	437	SER	0	-0.003	-0.004	3.861	-0.524	2.014	-0.018	-1.417	-1.103	0.005
4	A	438	GLY	0	0.008	0.004	6.494	0.384	0.384	0.000	0.000	0.000	0.000
5	A	439	ARG	1	0.797	0.862	8.435	0.520	0.520	0.000	0.000	0.000	0.000
6	A	440	VAL	0	-0.031	-0.011	11.348	0.152	0.152	0.000	0.000	0.000	0.000
7	A	441	ALA	0	-0.009	-0.005	12.091	-0.159	-0.159	0.000	0.000	0.000	0.000
8	A	442	VAL	0	0.036	0.016	14.619	0.047	0.047	0.000	0.000	0.000	0.000
9	A	443	GLU	-1	-0.814	-0.860	17.385	-0.278	-0.278	0.000	0.000	0.000	0.000
10	A	444	GLU	-1	-0.856	-0.933	20.478	-0.230	-0.230	0.000	0.000	0.000	0.000
11	A	445	VAL	0	-0.019	-0.023	21.369	-0.047	-0.047	0.000	0.000	0.000	0.000
12	A	446	ASP	-1	-0.750	-0.846	24.119	-0.216	-0.216	0.000	0.000	0.000	0.000
13	A	447	GLU	-1	-0.836	-0.917	27.482	-0.221	-0.221	0.000	0.000	0.000	0.000
14	A	448	GLU	-1	-0.923	-0.941	29.440	-0.177	-0.177	0.000	0.000	0.000	0.000
15	A	449	GLY	0	0.032	0.012	28.023	0.003	0.003	0.000	0.000	0.000	0.000
16	A	450	LYS	1	0.816	0.885	28.507	0.195	0.195	0.000	0.000	0.000	0.000
17	A	451	PHE	0	-0.037	-0.026	25.620	-0.009	-0.009	0.000	0.000	0.000	0.000
18	A	452	VAL	0	0.006	0.022	19.935	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	453	ARG	1	0.817	0.882	22.169	0.307	0.307	0.000	0.000	0.000	0.000
20	A	454	LEU	0	-0.028	-0.009	16.002	-0.027	-0.027	0.000	0.000	0.000	0.000
21	A	455	ARG	1	0.850	0.885	17.756	0.355	0.355	0.000	0.000	0.000	0.000
22	A	456	ASN	0	-0.030	-0.017	15.949	-0.072	-0.072	0.000	0.000	0.000	0.000
23	A	457	LYS	1	0.915	0.962	11.969	0.696	0.696	0.000	0.000	0.000	0.000
24	A	458	SER	0	0.003	-0.007	13.820	0.049	0.049	0.000	0.000	0.000	0.000
25	A	459	ASN	0	0.019	-0.004	15.939	-0.020	-0.020	0.000	0.000	0.000	0.000
26	A	460	GLU	-1	-0.816	-0.882	12.705	0.038	0.038	0.000	0.000	0.000	0.000
27	A	461	ASP	-1	-0.792	-0.875	16.112	-0.315	-0.315	0.000	0.000	0.000	0.000
28	A	462	GLN	0	0.006	0.002	10.606	0.034	0.034	0.000	0.000	0.000	0.000
29	A	463	SER	0	0.003	-0.003	14.192	0.021	0.021	0.000	0.000	0.000	0.000
30	A	464	MET	0	-0.029	-0.016	12.839	-0.141	-0.141	0.000	0.000	0.000	0.000
31	A	465	GLY	0	0.016	0.029	14.393	-0.007	-0.007	0.000	0.000	0.000	0.000
32	A	466	ASN	0	-0.023	-0.032	14.272	-0.045	-0.045	0.000	0.000	0.000	0.000
33	A	467	TRP	0	0.016	0.031	9.425	-0.233	-0.233	0.000	0.000	0.000	0.000
34	A	468	GLN	0	-0.013	-0.011	11.906	0.196	0.196	0.000	0.000	0.000	0.000
35	A	469	ILE	0	-0.024	-0.010	13.819	-0.117	-0.117	0.000	0.000	0.000	0.000
36	A	470	LYS	1	0.897	0.973	12.101	1.216	1.216	0.000	0.000	0.000	0.000
37	A	471	ARG	1	0.822	0.892	16.856	0.371	0.371	0.000	0.000	0.000	0.000
38	A	472	GLN	0	-0.040	-0.039	19.915	-0.015	-0.015	0.000	0.000	0.000	0.000
39	A	473	ASN	0	-0.002	-0.002	21.691	-0.009	-0.009	0.000	0.000	0.000	0.000
40	A	474	GLY	0	0.028	0.003	25.351	0.015	0.015	0.000	0.000	0.000	0.000
41	A	475	ASP	-1	-0.922	-0.951	24.828	-0.242	-0.242	0.000	0.000	0.000	0.000
42	A	476	ASP	-1	-0.905	-0.941	26.210	-0.249	-0.249	0.000	0.000	0.000	0.000
43	A	477	PRO	0	-0.032	-0.025	24.735	-0.023	-0.023	0.000	0.000	0.000	0.000
44	A	478	LEU	0	-0.023	0.007	17.005	-0.020	-0.020	0.000	0.000	0.000	0.000
45	A	479	LEU	0	0.018	0.024	21.679	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	480	THR	0	-0.049	-0.048	16.750	-0.082	-0.082	0.000	0.000	0.000	0.000
47	A	481	TYR	0	0.018	0.024	18.560	0.035	0.035	0.000	0.000	0.000	0.000
48	A	482	TRP	0	0.023	-0.011	14.996	-0.124	-0.124	0.000	0.000	0.000	0.000
49	A	483	PHE	0	0.023	0.014	15.580	0.080	0.080	0.000	0.000	0.000	0.000
50	A	484	PRO	0	0.030	0.008	18.369	-0.017	-0.017	0.000	0.000	0.000	0.000
51	A	485	PRO	0	0.022	0.005	18.434	-0.033	-0.033	0.000	0.000	0.000	0.000
52	A	486	LYS	1	0.931	0.959	18.717	0.285	0.285	0.000	0.000	0.000	0.000
53	A	487	PHE	0	0.008	0.013	17.614	0.041	0.041	0.000	0.000	0.000	0.000
54	A	488	THR	0	0.032	0.008	17.398	-0.080	-0.080	0.000	0.000	0.000	0.000
55	A	489	LEU	0	-0.006	0.024	16.829	0.055	0.055	0.000	0.000	0.000	0.000
56	A	490	LYS	1	0.874	0.909	17.555	0.201	0.201	0.000	0.000	0.000	0.000
57	A	491	ALA	0	0.038	0.025	18.272	-0.025	-0.025	0.000	0.000	0.000	0.000
58	A	492	GLY	0	0.014	0.020	18.802	0.029	0.029	0.000	0.000	0.000	0.000
59	A	493	GLN	0	-0.075	-0.029	20.647	0.010	0.010	0.000	0.000	0.000	0.000
60	A	494	VAL	0	0.003	-0.012	20.542	-0.043	-0.043	0.000	0.000	0.000	0.000
61	A	495	VAL	0	-0.025	-0.008	19.484	0.007	0.007	0.000	0.000	0.000	0.000
62	A	496	THR	0	-0.006	-0.003	22.002	-0.037	-0.037	0.000	0.000	0.000	0.000
63	A	497	ILE	0	-0.071	-0.028	19.962	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	498	TRP	0	0.034	-0.003	23.820	0.000	0.000	0.000	0.000	0.000	0.000
65	A	499	ALA	0	0.011	0.008	26.801	-0.018	-0.018	0.000	0.000	0.000	0.000
66	A	500	ALA	0	-0.060	-0.036	28.362	0.016	0.016	0.000	0.000	0.000	0.000
67	A	501	GLY	0	-0.004	0.002	30.910	0.015	0.015	0.000	0.000	0.000	0.000
68	A	502	ALA	0	-0.041	-0.019	30.914	0.011	0.011	0.000	0.000	0.000	0.000
69	A	503	GLY	0	-0.018	-0.001	33.039	0.008	0.008	0.000	0.000	0.000	0.000
70	A	504	ALA	0	-0.003	0.011	31.757	0.008	0.008	0.000	0.000	0.000	0.000
71	A	505	THR	0	-0.032	-0.022	33.724	0.005	0.005	0.000	0.000	0.000	0.000
72	A	506	HIS	0	-0.007	-0.007	29.209	-0.019	-0.019	0.000	0.000	0.000	0.000
73	A	507	SER	0	0.022	0.006	29.193	0.021	0.021	0.000	0.000	0.000	0.000
74	A	508	PRO	0	-0.019	0.014	25.727	-0.015	-0.015	0.000	0.000	0.000	0.000
75	A	509	PRO	0	-0.037	-0.024	23.404	0.020	0.020	0.000	0.000	0.000	0.000
76	A	510	THR	0	0.026	-0.017	23.882	-0.031	-0.031	0.000	0.000	0.000	0.000
77	A	511	ASP	-1	-0.775	-0.850	25.626	-0.290	-0.290	0.000	0.000	0.000	0.000
78	A	512	LEU	0	-0.029	-0.018	21.623	0.009	0.009	0.000	0.000	0.000	0.000
79	A	513	VAL	0	0.030	0.013	25.641	0.003	0.003	0.000	0.000	0.000	0.000
80	A	514	TRP	0	0.028	0.013	21.958	-0.024	-0.024	0.000	0.000	0.000	0.000
81	A	515	LYS	1	0.941	0.959	25.631	0.283	0.283	0.000	0.000	0.000	0.000
82	A	516	ALA	0	-0.046	-0.041	27.532	-0.012	-0.012	0.000	0.000	0.000	0.000
83	A	517	GLN	0	0.037	0.045	25.424	0.003	0.003	0.000	0.000	0.000	0.000
84	A	518	ASN	0	-0.006	-0.027	28.399	-0.010	-0.010	0.000	0.000	0.000	0.000
85	A	519	THR	0	0.045	0.008	29.719	0.001	0.001	0.000	0.000	0.000	0.000
86	A	520	TRP	0	-0.024	-0.021	20.087	-0.034	-0.034	0.000	0.000	0.000	0.000
87	A	521	GLY	0	0.016	0.020	25.677	-0.018	-0.018	0.000	0.000	0.000	0.000
88	A	522	CSD	-1	-0.847	-0.905	27.768	-0.246	-0.246	0.000	0.000	0.000	0.000
89	A	523	GLY	0	0.053	0.014	30.268	0.008	0.008	0.000	0.000	0.000	0.000
90	A	524	ASN	0	0.002	-0.016	29.497	-0.011	-0.011	0.000	0.000	0.000	0.000
91	A	525	SER	0	0.027	0.006	25.189	0.001	0.001	0.000	0.000	0.000	0.000
92	A	526	LEU	0	0.011	0.034	24.257	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	527	ARG	1	0.786	0.850	13.359	0.731	0.731	0.000	0.000	0.000	0.000
94	A	528	THR	0	0.022	0.011	18.391	0.009	0.009	0.000	0.000	0.000	0.000
95	A	529	ALA	0	0.008	-0.003	13.257	0.005	0.005	0.000	0.000	0.000	0.000
96	A	530	LEU	0	-0.017	0.010	11.613	0.042	0.042	0.000	0.000	0.000	0.000
97	A	531	ILE	0	-0.018	-0.015	9.382	-0.198	-0.198	0.000	0.000	0.000	0.000
98	A	532	ASN	0	0.083	0.038	3.831	1.812	1.909	-0.001	-0.032	-0.063	0.000
99	A	533	SER	0	0.014	-0.010	8.429	0.141	0.141	0.000	0.000	0.000	0.000
100	A	534	THR	0	-0.059	-0.029	5.577	0.303	0.303	0.000	0.000	0.000	0.000
101	A	535	GLY	0	-0.020	-0.002	7.863	0.226	0.226	0.000	0.000	0.000	0.000
102	A	536	GLU	-1	-0.836	-0.907	1.882	-23.839	-25.527	11.745	-5.407	-4.650	-0.065
103	A	537	GLU	-1	-0.794	-0.871	5.963	-0.930	-0.930	0.000	0.000	0.000	0.000
104	A	538	VAL	0	-0.041	-0.026	5.479	-0.397	-0.397	0.000	0.000	0.000	0.000
105	A	539	ALA	0	-0.016	-0.003	7.651	0.333	0.333	0.000	0.000	0.000	0.000
106	A	540	MET	0	-0.049	-0.009	11.102	0.014	0.014	0.000	0.000	0.000	0.000
107	A	541	ARG	1	0.897	0.956	14.367	0.454	0.454	0.000	0.000	0.000	0.000
108	A	542	LYS	1	0.922	0.960	18.034	0.278	0.278	0.000	0.000	0.000	0.000
109	A	543	LEU	0	0.016	0.037	20.786	0.022	0.022	0.000	0.000	0.000	0.000
110	A	544	VAL	0	-0.015	-0.031	24.331	-0.009	-0.009	0.000	0.000	0.000	0.000
111	A	545	ARG	1	0.846	0.923	26.830	0.191	0.191	0.000	0.000	0.000	0.000
112	A	546	SER	0	-0.005	-0.013	30.661	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	547	VAL	0	0.001	0.011	27.708	0.002	0.002	0.000	0.000	0.000	0.000
114	A	548	THR	0	-0.004	0.004	30.928	0.010	0.010	0.000	0.000	0.000	0.000
115	A	549	VAL	0	-0.035	-0.022	29.283	-0.007	-0.007	0.000	0.000	0.000	0.000
116	A	550	VAL	0	-0.014	-0.004	31.720	0.003	0.003	0.000	0.000	0.000	0.000
117	A	551	GLU	-1	-0.944	-0.972	31.870	-0.049	-0.049	0.000	0.000	0.000	0.000
118	A	552	ASP	-1	-0.979	-0.980	33.996	-0.042	-0.042	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:435:SER)