FMO DATABASE

FMODB ID: MNYVZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-937719.739193
FMO2-HF: Nuclear repulsion	891843.070079
FMO2-HF: Total energy	-45876.669114
FMO2-MP2: Total energy	-46011.073637

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.
-20.843	-13.732	1.547	-4.538	-4.12	-0.031

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 : -0.016 / q_NPA : 0.012

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	-0.019	-0.016	3.797	-0.575	2.189	-0.020	-1.449	-1.295	0.009
4	A	438	GLY	0	-0.021	-0.013	6.174	0.268	0.268	0.000	0.000	0.000	0.000
5	A	439	ARG	1	0.792	0.872	8.194	0.249	0.249	0.000	0.000	0.000	0.000
6	A	440	VAL	0	-0.020	-0.006	11.315	0.147	0.147	0.000	0.000	0.000	0.000
7	A	441	ALA	0	-0.017	0.000	12.332	-0.175	-0.175	0.000	0.000	0.000	0.000
8	A	442	VAL	0	0.046	0.014	14.906	0.039	0.039	0.000	0.000	0.000	0.000
9	A	443	GLU	-1	-0.880	-0.933	17.525	-0.306	-0.306	0.000	0.000	0.000	0.000
10	A	444	GLU	-1	-0.875	-0.942	20.448	-0.251	-0.251	0.000	0.000	0.000	0.000
11	A	445	VAL	0	-0.055	-0.032	21.450	-0.041	-0.041	0.000	0.000	0.000	0.000
12	A	446	ASP	-1	-0.783	-0.878	24.189	-0.246	-0.246	0.000	0.000	0.000	0.000
13	A	447	GLU	-1	-0.966	-0.990	27.782	-0.253	-0.253	0.000	0.000	0.000	0.000
14	A	448	GLU	-1	-0.961	-0.974	29.550	-0.196	-0.196	0.000	0.000	0.000	0.000
15	A	449	GLY	0	-0.027	-0.001	28.224	0.003	0.003	0.000	0.000	0.000	0.000
16	A	450	LYS	1	0.975	0.970	28.935	0.203	0.203	0.000	0.000	0.000	0.000
17	A	451	PHE	0	-0.037	-0.021	25.781	-0.009	-0.009	0.000	0.000	0.000	0.000
18	A	452	VAL	0	0.008	0.017	20.025	-0.012	-0.012	0.000	0.000	0.000	0.000
19	A	453	ARG	1	0.898	0.960	22.644	0.312	0.312	0.000	0.000	0.000	0.000
20	A	454	LEU	0	-0.033	-0.019	16.465	-0.045	-0.045	0.000	0.000	0.000	0.000
21	A	455	ARG	1	0.857	0.910	17.890	0.355	0.355	0.000	0.000	0.000	0.000
22	A	456	ASN	0	-0.032	-0.007	15.668	-0.094	-0.094	0.000	0.000	0.000	0.000
23	A	457	LYS	1	0.920	0.949	12.856	0.654	0.654	0.000	0.000	0.000	0.000
24	A	458	SER	0	-0.010	-0.002	13.440	0.067	0.067	0.000	0.000	0.000	0.000
25	A	459	ASN	0	0.024	-0.005	15.536	-0.012	-0.012	0.000	0.000	0.000	0.000
26	A	460	GLU	-1	-0.793	-0.888	11.978	0.264	0.264	0.000	0.000	0.000	0.000
27	A	461	ASP	-1	-0.824	-0.910	15.336	-0.213	-0.213	0.000	0.000	0.000	0.000
28	A	462	GLN	0	0.004	0.015	9.868	0.014	0.014	0.000	0.000	0.000	0.000
29	A	463	SER	0	-0.023	-0.012	13.378	0.006	0.006	0.000	0.000	0.000	0.000
30	A	464	MET	0	-0.015	-0.023	12.632	-0.095	-0.095	0.000	0.000	0.000	0.000
31	A	465	GLY	0	0.017	0.019	14.442	-0.017	-0.017	0.000	0.000	0.000	0.000
32	A	466	ASN	0	-0.040	-0.027	14.548	-0.060	-0.060	0.000	0.000	0.000	0.000
33	A	467	TRP	0	0.007	0.032	9.503	-0.274	-0.274	0.000	0.000	0.000	0.000
34	A	468	GLN	0	0.003	-0.014	13.462	0.290	0.290	0.000	0.000	0.000	0.000
35	A	469	ILE	0	-0.018	0.002	14.561	-0.128	-0.128	0.000	0.000	0.000	0.000
36	A	470	LYS	1	0.939	0.981	12.477	1.350	1.350	0.000	0.000	0.000	0.000
37	A	471	ARG	1	0.878	0.934	17.308	0.421	0.421	0.000	0.000	0.000	0.000
38	A	472	GLN	0	-0.049	-0.044	19.768	-0.014	-0.014	0.000	0.000	0.000	0.000
39	A	473	ASN	0	0.025	0.014	21.541	-0.011	-0.011	0.000	0.000	0.000	0.000
40	A	474	GLY	0	0.041	0.013	25.123	0.015	0.015	0.000	0.000	0.000	0.000
41	A	475	ASP	-1	-0.937	-0.965	24.855	-0.320	-0.320	0.000	0.000	0.000	0.000
42	A	476	ASP	-1	-0.942	-0.959	26.439	-0.297	-0.297	0.000	0.000	0.000	0.000
43	A	477	PRO	0	-0.023	-0.010	24.881	-0.030	-0.030	0.000	0.000	0.000	0.000
44	A	478	LEU	0	-0.016	0.001	17.619	-0.022	-0.022	0.000	0.000	0.000	0.000
45	A	479	LEU	0	-0.008	0.009	21.806	0.017	0.017	0.000	0.000	0.000	0.000
46	A	480	THR	0	-0.014	-0.026	17.662	-0.081	-0.081	0.000	0.000	0.000	0.000
47	A	481	TYR	0	-0.023	0.012	19.401	0.075	0.075	0.000	0.000	0.000	0.000
48	A	482	TRP	0	0.035	0.000	15.888	-0.110	-0.110	0.000	0.000	0.000	0.000
49	A	483	PHE	0	-0.011	-0.003	16.805	0.069	0.069	0.000	0.000	0.000	0.000
50	A	484	PRO	0	0.009	-0.004	19.404	0.004	0.004	0.000	0.000	0.000	0.000
51	A	485	PRO	0	0.043	0.008	18.934	-0.033	-0.033	0.000	0.000	0.000	0.000
52	A	486	LYS	1	0.935	0.965	18.660	0.197	0.197	0.000	0.000	0.000	0.000
53	A	487	PHE	0	0.009	0.016	18.008	0.046	0.046	0.000	0.000	0.000	0.000
54	A	488	THR	0	0.032	0.013	17.213	-0.046	-0.046	0.000	0.000	0.000	0.000
55	A	489	LEU	0	0.007	0.029	16.812	0.032	0.032	0.000	0.000	0.000	0.000
56	A	490	LYS	1	0.903	0.938	17.461	0.126	0.126	0.000	0.000	0.000	0.000
57	A	491	ALA	0	0.044	0.026	18.023	-0.040	-0.040	0.000	0.000	0.000	0.000
58	A	492	GLY	0	0.032	0.016	18.683	0.025	0.025	0.000	0.000	0.000	0.000
59	A	493	GLN	0	-0.094	-0.040	20.544	0.000	0.000	0.000	0.000	0.000	0.000
60	A	494	VAL	0	0.011	-0.006	20.499	-0.047	-0.047	0.000	0.000	0.000	0.000
61	A	495	VAL	0	-0.021	0.005	20.012	0.018	0.018	0.000	0.000	0.000	0.000
62	A	496	THR	0	0.014	-0.004	22.497	-0.047	-0.047	0.000	0.000	0.000	0.000
63	A	497	ILE	0	-0.062	-0.011	20.491	0.011	0.011	0.000	0.000	0.000	0.000
64	A	498	TRP	0	0.012	-0.023	24.439	-0.009	-0.009	0.000	0.000	0.000	0.000
65	A	499	ALA	0	0.019	0.010	27.790	-0.010	-0.010	0.000	0.000	0.000	0.000
66	A	500	ALA	0	-0.058	-0.038	28.673	0.020	0.020	0.000	0.000	0.000	0.000
67	A	501	GLY	0	-0.012	-0.005	31.379	0.017	0.017	0.000	0.000	0.000	0.000
68	A	502	ALA	0	-0.048	-0.015	31.551	0.011	0.011	0.000	0.000	0.000	0.000
69	A	503	GLY	0	-0.012	-0.001	33.602	0.009	0.009	0.000	0.000	0.000	0.000
70	A	504	ALA	0	-0.007	0.013	32.167	0.010	0.010	0.000	0.000	0.000	0.000
71	A	505	THR	0	-0.028	-0.013	34.261	0.006	0.006	0.000	0.000	0.000	0.000
72	A	506	HIS	0	0.001	-0.012	29.983	-0.016	-0.016	0.000	0.000	0.000	0.000
73	A	507	SER	0	0.031	0.006	29.769	0.023	0.023	0.000	0.000	0.000	0.000
74	A	508	PRO	0	-0.033	0.024	25.875	-0.013	-0.013	0.000	0.000	0.000	0.000
75	A	509	PRO	0	-0.044	-0.037	23.297	0.019	0.019	0.000	0.000	0.000	0.000
76	A	510	THR	0	0.033	-0.025	23.984	-0.029	-0.029	0.000	0.000	0.000	0.000
77	A	511	ASP	-1	-0.790	-0.850	26.235	-0.267	-0.267	0.000	0.000	0.000	0.000
78	A	512	LEU	0	-0.044	-0.030	22.401	0.011	0.011	0.000	0.000	0.000	0.000
79	A	513	VAL	0	0.044	0.033	26.473	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	514	TRP	0	0.014	0.006	23.382	-0.023	-0.023	0.000	0.000	0.000	0.000
81	A	515	LYS	1	0.946	0.949	26.393	0.269	0.269	0.000	0.000	0.000	0.000
82	A	516	ALA	0	-0.063	-0.041	28.242	-0.011	-0.011	0.000	0.000	0.000	0.000
83	A	517	GLN	0	0.088	0.070	26.312	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	518	ASN	0	0.004	-0.022	29.349	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	519	THR	0	0.036	0.013	29.878	0.002	0.002	0.000	0.000	0.000	0.000
86	A	520	TRP	0	-0.022	-0.018	20.905	-0.036	-0.036	0.000	0.000	0.000	0.000
87	A	521	GLY	0	-0.008	-0.004	25.957	-0.025	-0.025	0.000	0.000	0.000	0.000
88	A	522	CSD	-1	-0.874	-0.924	28.251	-0.260	-0.260	0.000	0.000	0.000	0.000
89	A	523	GLY	0	0.029	-0.007	30.266	0.001	0.001	0.000	0.000	0.000	0.000
90	A	524	ASN	0	-0.015	-0.027	29.570	-0.007	-0.007	0.000	0.000	0.000	0.000
91	A	525	SER	0	0.002	0.004	24.579	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	526	LEU	0	0.050	0.045	23.994	-0.011	-0.011	0.000	0.000	0.000	0.000
93	A	527	ARG	1	0.779	0.867	13.200	0.957	0.957	0.000	0.000	0.000	0.000
94	A	528	THR	0	0.022	0.013	18.157	0.004	0.004	0.000	0.000	0.000	0.000
95	A	529	ALA	0	-0.002	-0.001	13.070	0.003	0.003	0.000	0.000	0.000	0.000
96	A	530	LEU	0	0.001	0.013	12.077	0.097	0.097	0.000	0.000	0.000	0.000
97	A	531	ILE	0	-0.040	-0.021	9.881	-0.276	-0.276	0.000	0.000	0.000	0.000
98	A	532	ASN	0	0.103	0.043	5.065	1.356	1.356	0.000	0.000	0.000	0.000
99	A	533	SER	0	0.003	-0.018	9.606	-0.024	-0.024	0.000	0.000	0.000	0.000
100	A	534	THR	0	-0.059	-0.020	6.435	-0.103	-0.103	0.000	0.000	0.000	0.000
101	A	535	GLY	0	0.016	0.006	8.879	0.221	0.221	0.000	0.000	0.000	0.000
102	A	536	GLU	-1	-0.900	-0.942	2.491	-23.753	-19.406	1.567	-3.089	-2.825	-0.040
103	A	537	GLU	-1	-0.832	-0.905	6.731	-1.031	-1.031	0.000	0.000	0.000	0.000
104	A	538	VAL	0	-0.016	-0.018	5.781	-0.509	-0.509	0.000	0.000	0.000	0.000
105	A	539	ALA	0	-0.024	-0.007	7.997	0.382	0.382	0.000	0.000	0.000	0.000
106	A	540	MET	0	-0.028	-0.003	11.497	0.013	0.013	0.000	0.000	0.000	0.000
107	A	541	ARG	1	0.933	0.975	14.671	0.511	0.511	0.000	0.000	0.000	0.000
108	A	542	LYS	1	0.938	0.962	18.310	0.416	0.416	0.000	0.000	0.000	0.000
109	A	543	LEU	0	-0.007	0.009	20.706	0.025	0.025	0.000	0.000	0.000	0.000
110	A	544	VAL	0	-0.009	-0.012	24.008	-0.008	-0.008	0.000	0.000	0.000	0.000
111	A	545	ARG	1	0.964	0.993	26.609	0.227	0.227	0.000	0.000	0.000	0.000
112	A	546	SER	0	-0.040	-0.034	30.358	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	547	VAL	0	0.027	0.019	27.803	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	548	THR	0	0.004	0.004	30.992	0.013	0.013	0.000	0.000	0.000	0.000
115	A	549	VAL	0	-0.029	-0.008	29.778	-0.010	-0.010	0.000	0.000	0.000	0.000
116	A	550	VAL	0	-0.008	-0.008	31.337	0.007	0.007	0.000	0.000	0.000	0.000
117	A	551	GLU	-1	-0.957	-0.977	31.659	-0.105	-0.105	0.000	0.000	0.000	0.000
118	A	552	ASP	-1	-0.988	-0.987	33.713	-0.093	-0.093	0.000	0.000	0.000	0.000

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