FMO DATABASE

FMODB ID: 7672K

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

Total energy (hartree)

FMO2-HF: Electronic energy	-938147.623923
FMO2-HF: Nuclear repulsion	892270.209735
FMO2-HF: Total energy	-45877.414188
FMO2-MP2: Total energy	-46011.722552

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.
-23.672	-17.787	3.891	-5.1	-4.677	-0.044

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 : -0.037 / q_NPA : -0.001

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	-0.020	-0.012	3.797	-0.641	1.940	-0.019	-1.327	-1.235	0.008
4	A	438	GLY	0	-0.014	-0.004	6.103	0.277	0.277	0.000	0.000	0.000	0.000
5	A	439	ARG	1	0.796	0.867	8.190	0.190	0.190	0.000	0.000	0.000	0.000
6	A	440	VAL	0	-0.020	-0.011	11.299	0.140	0.140	0.000	0.000	0.000	0.000
7	A	441	ALA	0	-0.022	-0.002	12.301	-0.172	-0.172	0.000	0.000	0.000	0.000
8	A	442	VAL	0	0.062	0.026	14.873	0.043	0.043	0.000	0.000	0.000	0.000
9	A	443	GLU	-1	-0.838	-0.883	17.479	-0.283	-0.283	0.000	0.000	0.000	0.000
10	A	444	GLU	-1	-0.826	-0.903	20.411	-0.240	-0.240	0.000	0.000	0.000	0.000
11	A	445	VAL	0	-0.035	-0.022	21.337	-0.037	-0.037	0.000	0.000	0.000	0.000
12	A	446	ASP	-1	-0.770	-0.868	24.159	-0.234	-0.234	0.000	0.000	0.000	0.000
13	A	447	GLU	-1	-0.866	-0.934	27.754	-0.248	-0.248	0.000	0.000	0.000	0.000
14	A	448	GLU	-1	-0.899	-0.928	29.526	-0.186	-0.186	0.000	0.000	0.000	0.000
15	A	449	GLY	0	0.018	0.016	28.195	0.005	0.005	0.000	0.000	0.000	0.000
16	A	450	LYS	1	0.843	0.889	28.904	0.201	0.201	0.000	0.000	0.000	0.000
17	A	451	PHE	0	-0.040	-0.026	25.817	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	452	VAL	0	0.004	0.015	20.008	-0.012	-0.012	0.000	0.000	0.000	0.000
19	A	453	ARG	1	0.807	0.878	22.604	0.301	0.301	0.000	0.000	0.000	0.000
20	A	454	LEU	0	-0.022	-0.011	16.260	-0.044	-0.044	0.000	0.000	0.000	0.000
21	A	455	ARG	1	0.852	0.901	17.859	0.335	0.335	0.000	0.000	0.000	0.000
22	A	456	ASN	0	-0.029	-0.017	15.485	-0.092	-0.092	0.000	0.000	0.000	0.000
23	A	457	LYS	1	0.912	0.954	12.027	0.678	0.678	0.000	0.000	0.000	0.000
24	A	458	SER	0	-0.008	-0.005	13.366	0.064	0.064	0.000	0.000	0.000	0.000
25	A	459	ASN	0	0.036	0.002	15.462	-0.017	-0.017	0.000	0.000	0.000	0.000
26	A	460	GLU	-1	-0.814	-0.881	11.979	0.269	0.269	0.000	0.000	0.000	0.000
27	A	461	ASP	-1	-0.799	-0.882	15.274	-0.198	-0.198	0.000	0.000	0.000	0.000
28	A	462	GLN	0	0.006	0.001	10.698	0.049	0.049	0.000	0.000	0.000	0.000
29	A	463	SER	0	-0.014	-0.004	13.946	0.003	0.003	0.000	0.000	0.000	0.000
30	A	464	MET	0	-0.018	-0.013	13.450	-0.092	-0.092	0.000	0.000	0.000	0.000
31	A	465	GLY	0	0.024	0.026	15.058	-0.020	-0.020	0.000	0.000	0.000	0.000
32	A	466	ASN	0	-0.038	-0.034	14.968	-0.045	-0.045	0.000	0.000	0.000	0.000
33	A	467	TRP	0	0.004	0.029	9.925	-0.244	-0.244	0.000	0.000	0.000	0.000
34	A	468	GLN	0	0.005	-0.011	13.407	0.179	0.179	0.000	0.000	0.000	0.000
35	A	469	ILE	0	-0.021	0.000	14.523	-0.121	-0.121	0.000	0.000	0.000	0.000
36	A	470	LYS	1	0.921	0.979	12.796	1.285	1.285	0.000	0.000	0.000	0.000
37	A	471	ARG	1	0.857	0.914	17.284	0.404	0.404	0.000	0.000	0.000	0.000
38	A	472	GLN	0	-0.033	-0.035	19.797	-0.015	-0.015	0.000	0.000	0.000	0.000
39	A	473	ASN	0	0.006	0.008	21.529	-0.010	-0.010	0.000	0.000	0.000	0.000
40	A	474	GLY	0	0.055	0.022	25.111	0.014	0.014	0.000	0.000	0.000	0.000
41	A	475	ASP	-1	-0.938	-0.964	24.853	-0.315	-0.315	0.000	0.000	0.000	0.000
42	A	476	ASP	-1	-0.948	-0.960	26.450	-0.287	-0.287	0.000	0.000	0.000	0.000
43	A	477	PRO	0	-0.013	-0.009	24.875	-0.029	-0.029	0.000	0.000	0.000	0.000
44	A	478	LEU	0	-0.013	0.002	17.452	-0.021	-0.021	0.000	0.000	0.000	0.000
45	A	479	LEU	0	-0.002	0.012	21.782	0.017	0.017	0.000	0.000	0.000	0.000
46	A	480	THR	0	-0.027	-0.036	17.614	-0.085	-0.085	0.000	0.000	0.000	0.000
47	A	481	TYR	0	-0.003	0.018	19.417	0.051	0.051	0.000	0.000	0.000	0.000
48	A	482	TRP	0	0.022	-0.011	15.932	-0.108	-0.108	0.000	0.000	0.000	0.000
49	A	483	PHE	0	0.012	0.011	16.633	0.066	0.066	0.000	0.000	0.000	0.000
50	A	484	PRO	0	0.005	-0.007	19.436	0.004	0.004	0.000	0.000	0.000	0.000
51	A	485	PRO	0	0.036	0.008	19.394	-0.029	-0.029	0.000	0.000	0.000	0.000
52	A	486	LYS	1	0.930	0.960	19.366	0.183	0.183	0.000	0.000	0.000	0.000
53	A	487	PHE	0	0.009	0.014	18.498	0.046	0.046	0.000	0.000	0.000	0.000
54	A	488	THR	0	0.040	0.014	17.743	-0.044	-0.044	0.000	0.000	0.000	0.000
55	A	489	LEU	0	0.006	0.032	16.936	0.028	0.028	0.000	0.000	0.000	0.000
56	A	490	LYS	1	0.870	0.907	17.664	0.109	0.109	0.000	0.000	0.000	0.000
57	A	491	ALA	0	0.029	0.013	17.943	-0.037	-0.037	0.000	0.000	0.000	0.000
58	A	492	GLY	0	0.033	0.025	18.612	0.024	0.024	0.000	0.000	0.000	0.000
59	A	493	GLN	0	-0.082	-0.038	20.464	0.000	0.000	0.000	0.000	0.000	0.000
60	A	494	VAL	0	0.007	-0.008	20.486	-0.045	-0.045	0.000	0.000	0.000	0.000
61	A	495	VAL	0	-0.016	0.005	20.036	0.017	0.017	0.000	0.000	0.000	0.000
62	A	496	THR	0	0.004	-0.004	22.474	-0.044	-0.044	0.000	0.000	0.000	0.000
63	A	497	ILE	0	-0.065	-0.015	20.473	0.011	0.011	0.000	0.000	0.000	0.000
64	A	498	TRP	0	0.015	-0.022	24.396	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	499	ALA	0	0.019	0.016	27.749	-0.009	-0.009	0.000	0.000	0.000	0.000
66	A	500	ALA	0	-0.053	-0.037	28.635	0.020	0.020	0.000	0.000	0.000	0.000
67	A	501	GLY	0	-0.026	-0.014	31.341	0.016	0.016	0.000	0.000	0.000	0.000
68	A	502	ALA	0	-0.026	-0.004	31.488	0.010	0.010	0.000	0.000	0.000	0.000
69	A	503	GLY	0	-0.010	0.004	33.564	0.009	0.009	0.000	0.000	0.000	0.000
70	A	504	ALA	0	-0.013	0.010	32.095	0.009	0.009	0.000	0.000	0.000	0.000
71	A	505	THR	0	-0.029	-0.016	34.218	0.005	0.005	0.000	0.000	0.000	0.000
72	A	506	HIS	0	-0.002	-0.009	30.082	-0.015	-0.015	0.000	0.000	0.000	0.000
73	A	507	SER	0	0.027	0.002	30.061	0.022	0.022	0.000	0.000	0.000	0.000
74	A	508	PRO	0	-0.027	0.026	26.354	-0.012	-0.012	0.000	0.000	0.000	0.000
75	A	509	PRO	0	-0.033	-0.029	23.822	0.018	0.018	0.000	0.000	0.000	0.000
76	A	510	THR	0	0.013	-0.042	24.283	-0.027	-0.027	0.000	0.000	0.000	0.000
77	A	511	ASP	-1	-0.781	-0.842	26.239	-0.258	-0.258	0.000	0.000	0.000	0.000
78	A	512	LEU	0	-0.044	-0.027	22.482	0.012	0.012	0.000	0.000	0.000	0.000
79	A	513	VAL	0	0.056	0.039	26.500	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	514	TRP	0	0.005	-0.003	22.938	-0.024	-0.024	0.000	0.000	0.000	0.000
81	A	515	LYS	1	0.933	0.949	26.353	0.260	0.260	0.000	0.000	0.000	0.000
82	A	516	ALA	0	-0.050	-0.040	28.206	-0.012	-0.012	0.000	0.000	0.000	0.000
83	A	517	GLN	0	0.067	0.054	26.162	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	518	ASN	0	-0.004	-0.024	29.316	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	519	THR	0	0.054	0.023	30.000	0.002	0.002	0.000	0.000	0.000	0.000
86	A	520	TRP	0	-0.018	-0.013	20.691	-0.039	-0.039	0.000	0.000	0.000	0.000
87	A	521	GLY	0	-0.009	0.001	25.933	-0.027	-0.027	0.000	0.000	0.000	0.000
88	A	522	CSD	-1	-0.846	-0.914	28.228	-0.257	-0.257	0.000	0.000	0.000	0.000
89	A	523	GLY	0	0.033	-0.005	30.252	0.001	0.001	0.000	0.000	0.000	0.000
90	A	524	ASN	0	-0.005	-0.019	29.557	-0.007	-0.007	0.000	0.000	0.000	0.000
91	A	525	SER	0	0.029	0.009	24.488	-0.005	-0.005	0.000	0.000	0.000	0.000
92	A	526	LEU	0	0.017	0.036	23.981	-0.011	-0.011	0.000	0.000	0.000	0.000
93	A	527	ARG	1	0.770	0.841	13.067	0.953	0.953	0.000	0.000	0.000	0.000
94	A	528	THR	0	0.017	0.014	18.364	0.007	0.007	0.000	0.000	0.000	0.000
95	A	529	ALA	0	0.009	0.002	13.096	0.001	0.001	0.000	0.000	0.000	0.000
96	A	530	LEU	0	-0.003	0.013	12.012	0.096	0.096	0.000	0.000	0.000	0.000
97	A	531	ILE	0	-0.029	-0.024	9.945	-0.280	-0.280	0.000	0.000	0.000	0.000
98	A	532	ASN	0	0.096	0.039	5.034	1.139	1.139	0.000	0.000	0.000	0.000
99	A	533	SER	0	0.022	-0.011	9.579	0.086	0.086	0.000	0.000	0.000	0.000
100	A	534	THR	0	-0.036	-0.009	6.090	0.370	0.370	0.000	0.000	0.000	0.000
101	A	535	GLY	0	-0.015	-0.001	8.869	0.181	0.181	0.000	0.000	0.000	0.000
102	A	536	GLU	-1	-0.907	-0.947	2.208	-26.678	-23.374	3.910	-3.773	-3.442	-0.052
103	A	537	GLU	-1	-0.806	-0.869	6.708	-1.004	-1.004	0.000	0.000	0.000	0.000
104	A	538	VAL	0	-0.017	-0.019	5.696	-0.525	-0.525	0.000	0.000	0.000	0.000
105	A	539	ALA	0	-0.021	-0.005	7.965	0.373	0.373	0.000	0.000	0.000	0.000
106	A	540	MET	0	-0.027	-0.004	11.470	0.010	0.010	0.000	0.000	0.000	0.000
107	A	541	ARG	1	0.905	0.958	14.651	0.500	0.500	0.000	0.000	0.000	0.000
108	A	542	LYS	1	0.927	0.962	18.291	0.383	0.383	0.000	0.000	0.000	0.000
109	A	543	LEU	0	-0.018	0.008	20.693	0.025	0.025	0.000	0.000	0.000	0.000
110	A	544	VAL	0	-0.020	-0.024	24.071	-0.009	-0.009	0.000	0.000	0.000	0.000
111	A	545	ARG	1	0.867	0.940	26.602	0.226	0.226	0.000	0.000	0.000	0.000
112	A	546	SER	0	-0.032	-0.028	30.352	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	547	VAL	0	0.019	0.014	27.726	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	548	THR	0	0.008	0.010	30.995	0.013	0.013	0.000	0.000	0.000	0.000
115	A	549	VAL	0	-0.035	-0.018	29.392	-0.010	-0.010	0.000	0.000	0.000	0.000
116	A	550	VAL	0	-0.009	-0.007	31.358	0.007	0.007	0.000	0.000	0.000	0.000
117	A	551	GLU	-1	-0.953	-0.972	31.587	-0.099	-0.099	0.000	0.000	0.000	0.000
118	A	552	ASP	-1	-0.984	-0.986	33.710	-0.089	-0.089	0.000	0.000	0.000	0.000

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