FMO DATABASE

FMODB ID: 6G34Z

Calculation Name: 1L3K-A-Xray372

Preferred Name: Heterogeneous nuclear ribonucleoprotein A1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1L3K

Chain ID: A

ChEMBL ID: CHEMBL1955709

UniProt ID: P09651

Base Structure: X-ray

Registration Date: 2023-09-26

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	163
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1591964.504983
FMO2-HF: Nuclear repulsion	1526374.286736
FMO2-HF: Total energy	-65590.218247
FMO2-MP2: Total energy	-65782.045009

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:8:LYS)

Summations of interaction energy for fragment #1(A:8:LYS)

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.
-26.816	-20.958	1.635	-2.504	-4.99	-0.015

Interaction energy analysis for fragmet #1(A:8:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.962 / q_NPA : 0.979

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

Sort

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	10	PRO	0	0.024	-0.003	2.667	-10.260	-7.288	0.619	-1.511	-2.081	-0.007
4	A	11	GLU	-1	-0.813	-0.912	4.773	-36.630	-36.380	-0.001	-0.010	-0.239	0.000
5	A	12	GLN	0	-0.045	-0.023	5.692	1.975	1.975	0.000	0.000	0.000	0.000
6	A	13	LEU	0	-0.037	-0.022	7.486	2.452	2.452	0.000	0.000	0.000	0.000
7	A	14	ARG	1	0.814	0.910	2.457	53.024	54.846	1.013	-0.781	-2.055	-0.007
8	A	15	LYS	1	0.816	0.919	7.846	28.429	28.429	0.000	0.000	0.000	0.000
9	A	16	LEU	0	0.014	0.010	10.859	1.119	1.119	0.000	0.000	0.000	0.000
10	A	17	PHE	0	-0.001	-0.011	14.374	-0.018	-0.018	0.000	0.000	0.000	0.000
11	A	18	ILE	0	0.001	0.003	16.581	0.472	0.472	0.000	0.000	0.000	0.000
12	A	19	GLY	0	0.047	0.017	19.725	0.269	0.269	0.000	0.000	0.000	0.000
13	A	20	GLY	0	0.034	0.014	23.293	0.099	0.099	0.000	0.000	0.000	0.000
14	A	21	LEU	0	-0.012	-0.009	21.264	0.268	0.268	0.000	0.000	0.000	0.000
15	A	22	SER	0	0.007	0.006	25.517	0.538	0.538	0.000	0.000	0.000	0.000
16	A	23	PHE	0	-0.056	-0.029	26.853	-0.305	-0.305	0.000	0.000	0.000	0.000
17	A	24	GLU	-1	-0.908	-0.969	28.516	-9.809	-9.809	0.000	0.000	0.000	0.000
18	A	25	THR	0	-0.078	-0.037	22.461	-0.051	-0.051	0.000	0.000	0.000	0.000
19	A	26	THR	0	-0.038	-0.040	23.342	-0.085	-0.085	0.000	0.000	0.000	0.000
20	A	27	ASP	-1	-0.816	-0.911	18.310	-15.392	-15.392	0.000	0.000	0.000	0.000
21	A	28	GLU	-1	-0.853	-0.932	18.669	-14.366	-14.366	0.000	0.000	0.000	0.000
22	A	29	SER	0	-0.038	-0.031	20.341	-0.272	-0.272	0.000	0.000	0.000	0.000
23	A	30	LEU	0	-0.005	-0.014	17.698	0.028	0.028	0.000	0.000	0.000	0.000
24	A	31	ARG	1	0.877	0.902	11.850	20.681	20.681	0.000	0.000	0.000	0.000
25	A	32	SER	0	-0.028	-0.028	16.911	-0.253	-0.253	0.000	0.000	0.000	0.000
26	A	33	HIS	0	-0.077	-0.033	19.408	0.333	0.333	0.000	0.000	0.000	0.000
27	A	34	PHE	0	0.012	-0.009	15.109	0.067	0.067	0.000	0.000	0.000	0.000
28	A	35	GLU	-1	-0.822	-0.900	13.504	-20.088	-20.088	0.000	0.000	0.000	0.000
29	A	36	GLN	0	-0.078	-0.026	15.370	0.139	0.139	0.000	0.000	0.000	0.000
30	A	37	TRP	0	-0.046	-0.027	15.594	0.354	0.354	0.000	0.000	0.000	0.000
31	A	38	GLY	0	0.029	0.002	11.650	-0.806	-0.806	0.000	0.000	0.000	0.000
32	A	39	THR	0	-0.039	-0.021	8.256	1.127	1.127	0.000	0.000	0.000	0.000
33	A	40	LEU	0	-0.016	0.000	8.724	-2.251	-2.251	0.000	0.000	0.000	0.000
34	A	41	THR	0	-0.029	-0.020	4.501	-0.374	-0.307	-0.001	-0.004	-0.062	0.000
35	A	42	ASP	-1	-0.913	-0.965	7.935	-23.452	-23.452	0.000	0.000	0.000	0.000
36	A	43	CYS	0	-0.078	-0.019	10.735	0.401	0.401	0.000	0.000	0.000	0.000
37	A	44	VAL	0	0.001	0.034	14.124	0.763	0.763	0.000	0.000	0.000	0.000
38	A	45	VAL	0	-0.015	0.001	17.054	0.159	0.159	0.000	0.000	0.000	0.000
39	A	46	MET	0	-0.048	-0.019	20.001	-0.028	-0.028	0.000	0.000	0.000	0.000
40	A	47	ARG	1	0.942	0.970	22.198	12.868	12.868	0.000	0.000	0.000	0.000
41	A	48	ASP	-1	-0.827	-0.912	25.364	-10.353	-10.353	0.000	0.000	0.000	0.000
42	A	49	PRO	0	-0.012	-0.006	26.623	-0.033	-0.033	0.000	0.000	0.000	0.000
43	A	50	ASN	0	-0.033	-0.011	27.793	0.081	0.081	0.000	0.000	0.000	0.000
44	A	51	THR	0	-0.055	-0.063	31.352	0.110	0.110	0.000	0.000	0.000	0.000
45	A	52	LYS	1	0.934	0.990	27.616	10.615	10.615	0.000	0.000	0.000	0.000
46	A	53	ARG	1	0.986	0.987	28.406	8.907	8.907	0.000	0.000	0.000	0.000
47	A	54	SER	0	0.033	0.029	26.018	-0.308	-0.308	0.000	0.000	0.000	0.000
48	A	55	ARG	1	0.922	0.952	24.308	12.740	12.740	0.000	0.000	0.000	0.000
49	A	56	GLY	0	0.012	0.008	26.220	0.114	0.114	0.000	0.000	0.000	0.000
50	A	57	PHE	0	-0.051	-0.025	20.838	0.051	0.051	0.000	0.000	0.000	0.000
51	A	58	GLY	0	0.055	0.021	19.324	0.188	0.188	0.000	0.000	0.000	0.000
52	A	59	PHE	0	-0.089	-0.025	11.945	0.298	0.298	0.000	0.000	0.000	0.000
53	A	60	VAL	0	0.053	0.033	12.958	0.131	0.131	0.000	0.000	0.000	0.000
54	A	61	THR	0	-0.003	-0.013	6.684	0.071	0.071	0.000	0.000	0.000	0.000
55	A	62	TYR	0	0.037	0.006	8.016	0.057	0.057	0.000	0.000	0.000	0.000
56	A	63	ALA	0	0.008	0.010	4.301	-5.010	-4.902	-0.001	-0.009	-0.097	0.000
57	A	64	THR	0	-0.064	-0.054	3.690	-7.659	-7.020	0.006	-0.189	-0.456	-0.001
58	A	65	VAL	0	-0.003	-0.033	5.764	2.522	2.522	0.000	0.000	0.000	0.000
59	A	66	GLU	-1	-0.904	-0.939	8.383	-20.133	-20.133	0.000	0.000	0.000	0.000
60	A	67	GLU	-1	-0.760	-0.859	8.105	-27.708	-27.708	0.000	0.000	0.000	0.000
61	A	68	VAL	0	-0.017	0.009	9.484	1.638	1.638	0.000	0.000	0.000	0.000
62	A	69	ASP	-1	-0.798	-0.887	12.018	-18.441	-18.441	0.000	0.000	0.000	0.000
63	A	70	ALA	0	-0.025	0.001	13.823	1.445	1.445	0.000	0.000	0.000	0.000
64	A	71	ALA	0	0.032	0.011	14.730	1.161	1.161	0.000	0.000	0.000	0.000
65	A	72	MET	0	-0.080	-0.023	15.944	1.144	1.144	0.000	0.000	0.000	0.000
66	A	73	ASN	0	-0.027	-0.019	17.974	1.232	1.232	0.000	0.000	0.000	0.000
67	A	74	ALA	0	-0.017	0.012	19.478	0.685	0.685	0.000	0.000	0.000	0.000
68	A	75	ARG	1	0.738	0.862	20.845	13.983	13.983	0.000	0.000	0.000	0.000
69	A	76	PRO	0	-0.033	-0.042	23.085	0.260	0.260	0.000	0.000	0.000	0.000
70	A	77	HIS	0	0.060	0.041	19.552	0.456	0.456	0.000	0.000	0.000	0.000
71	A	78	LYS	1	0.832	0.904	23.862	9.959	9.959	0.000	0.000	0.000	0.000
72	A	79	VAL	0	0.068	0.038	21.834	-0.060	-0.060	0.000	0.000	0.000	0.000
73	A	80	ASP	-1	-0.747	-0.841	24.898	-11.687	-11.687	0.000	0.000	0.000	0.000
74	A	81	GLY	0	-0.001	-0.004	27.484	0.337	0.337	0.000	0.000	0.000	0.000
75	A	82	ARG	1	0.890	0.950	28.154	10.297	10.297	0.000	0.000	0.000	0.000
76	A	83	VAL	0	-0.027	-0.008	26.982	-0.299	-0.299	0.000	0.000	0.000	0.000
77	A	84	VAL	0	-0.010	0.006	21.917	0.167	0.167	0.000	0.000	0.000	0.000
78	A	85	GLU	-1	-0.852	-0.934	23.437	-12.007	-12.007	0.000	0.000	0.000	0.000
79	A	86	PRO	0	-0.004	-0.007	18.204	-0.246	-0.246	0.000	0.000	0.000	0.000
80	A	87	LYS	1	0.821	0.909	18.489	13.085	13.085	0.000	0.000	0.000	0.000
81	A	88	ARG	1	0.809	0.859	12.892	18.433	18.433	0.000	0.000	0.000	0.000
82	A	89	ALA	0	-0.029	-0.001	12.797	1.102	1.102	0.000	0.000	0.000	0.000
83	A	90	VAL	0	-0.013	-0.003	14.827	0.032	0.032	0.000	0.000	0.000	0.000
84	A	91	SER	0	0.025	0.021	15.111	-0.674	-0.674	0.000	0.000	0.000	0.000
85	A	103	THR	0	-0.024	-0.023	22.844	-0.059	-0.059	0.000	0.000	0.000	0.000
86	A	104	VAL	0	0.007	0.003	24.588	0.466	0.466	0.000	0.000	0.000	0.000
87	A	105	LYS	1	0.929	0.979	25.108	9.619	9.619	0.000	0.000	0.000	0.000
88	A	106	LYS	1	0.843	0.929	27.324	9.104	9.104	0.000	0.000	0.000	0.000
89	A	107	ILE	0	0.014	0.023	24.131	-0.303	-0.303	0.000	0.000	0.000	0.000
90	A	108	PHE	0	-0.022	-0.007	27.399	0.476	0.476	0.000	0.000	0.000	0.000
91	A	109	VAL	0	0.044	0.016	26.546	-0.497	-0.497	0.000	0.000	0.000	0.000
92	A	110	GLY	0	0.012	-0.010	27.876	0.466	0.466	0.000	0.000	0.000	0.000
93	A	111	GLY	0	0.035	0.012	28.105	-0.324	-0.324	0.000	0.000	0.000	0.000
94	A	112	ILE	0	0.004	0.003	28.940	-0.028	-0.028	0.000	0.000	0.000	0.000
95	A	113	LYS	1	0.875	0.957	31.170	9.303	9.303	0.000	0.000	0.000	0.000
96	A	114	GLU	-1	-0.761	-0.895	34.531	-7.222	-7.222	0.000	0.000	0.000	0.000
97	A	115	ASP	-1	-0.875	-0.941	35.107	-8.082	-8.082	0.000	0.000	0.000	0.000
98	A	116	THR	0	-0.050	-0.024	30.708	-0.154	-0.154	0.000	0.000	0.000	0.000
99	A	117	GLU	-1	-0.792	-0.892	33.874	-7.670	-7.670	0.000	0.000	0.000	0.000
100	A	118	GLU	-1	-0.839	-0.920	33.237	-8.760	-8.760	0.000	0.000	0.000	0.000
101	A	119	HIS	0	0.063	0.022	32.597	-0.156	-0.156	0.000	0.000	0.000	0.000
102	A	120	HIS	0	0.065	0.051	29.918	-0.287	-0.287	0.000	0.000	0.000	0.000
103	A	121	LEU	0	-0.026	-0.020	28.397	-0.414	-0.414	0.000	0.000	0.000	0.000
104	A	122	ARG	1	0.872	0.916	27.856	8.698	8.698	0.000	0.000	0.000	0.000
105	A	123	ASP	-1	-0.859	-0.923	27.815	-9.873	-9.873	0.000	0.000	0.000	0.000
106	A	124	TYR	0	-0.064	-0.034	19.898	-0.593	-0.593	0.000	0.000	0.000	0.000
107	A	125	PHE	0	0.006	-0.032	22.943	-0.440	-0.440	0.000	0.000	0.000	0.000
108	A	126	GLU	-1	-0.935	-0.964	24.154	-10.481	-10.481	0.000	0.000	0.000	0.000
109	A	127	GLN	0	-0.084	-0.053	21.106	-0.470	-0.470	0.000	0.000	0.000	0.000
110	A	128	TYR	0	-0.038	-0.018	17.105	-1.003	-1.003	0.000	0.000	0.000	0.000
111	A	129	GLY	0	0.019	0.003	21.131	-0.414	-0.414	0.000	0.000	0.000	0.000
112	A	130	LYS	1	0.878	0.949	23.945	9.984	9.984	0.000	0.000	0.000	0.000
113	A	131	ILE	0	-0.012	-0.010	27.373	-0.013	-0.013	0.000	0.000	0.000	0.000
114	A	132	GLU	-1	-0.913	-0.981	29.674	-9.190	-9.190	0.000	0.000	0.000	0.000
115	A	133	VAL	0	-0.028	-0.022	32.402	0.310	0.310	0.000	0.000	0.000	0.000
116	A	134	ILE	0	-0.010	0.008	30.963	-0.348	-0.348	0.000	0.000	0.000	0.000
117	A	135	GLU	-1	-0.866	-0.921	33.769	-8.143	-8.143	0.000	0.000	0.000	0.000
118	A	136	ILE	0	0.042	0.009	34.729	-0.207	-0.207	0.000	0.000	0.000	0.000
119	A	137	MET	0	-0.045	-0.005	35.980	0.250	0.250	0.000	0.000	0.000	0.000
120	A	138	THR	0	0.036	0.010	38.220	-0.043	-0.043	0.000	0.000	0.000	0.000
121	A	139	ASP	-1	-0.870	-0.923	41.454	-6.777	-6.777	0.000	0.000	0.000	0.000
122	A	140	ARG	1	0.906	0.955	43.957	6.509	6.509	0.000	0.000	0.000	0.000
123	A	141	GLY	0	-0.008	0.004	46.514	0.134	0.134	0.000	0.000	0.000	0.000
124	A	142	SER	0	-0.037	-0.054	46.720	0.071	0.071	0.000	0.000	0.000	0.000
125	A	143	GLY	0	-0.003	0.005	45.688	0.062	0.062	0.000	0.000	0.000	0.000
126	A	144	LYS	1	0.819	0.898	43.318	6.866	6.866	0.000	0.000	0.000	0.000
127	A	145	LYS	1	0.838	0.925	37.197	7.729	7.729	0.000	0.000	0.000	0.000
128	A	146	ARG	1	0.920	0.949	38.149	7.770	7.770	0.000	0.000	0.000	0.000
129	A	147	GLY	0	-0.010	0.013	34.885	-0.069	-0.069	0.000	0.000	0.000	0.000
130	A	148	PHE	0	-0.071	-0.050	32.355	-0.230	-0.230	0.000	0.000	0.000	0.000
131	A	149	ALA	0	0.020	0.017	31.544	0.313	0.313	0.000	0.000	0.000	0.000
132	A	150	PHE	0	-0.027	-0.022	31.091	-0.308	-0.308	0.000	0.000	0.000	0.000
133	A	151	VAL	0	0.020	0.026	28.011	0.241	0.241	0.000	0.000	0.000	0.000
134	A	152	THR	0	-0.029	-0.023	29.114	-0.256	-0.256	0.000	0.000	0.000	0.000
135	A	153	PHE	0	0.044	0.015	25.015	0.143	0.143	0.000	0.000	0.000	0.000
136	A	154	ASP	-1	-0.853	-0.925	27.514	-10.483	-10.483	0.000	0.000	0.000	0.000
137	A	155	ASP	-1	-0.769	-0.874	23.070	-12.758	-12.758	0.000	0.000	0.000	0.000
138	A	156	HIS	0	-0.045	-0.038	20.297	0.118	0.118	0.000	0.000	0.000	0.000
139	A	157	ASP	-1	-0.716	-0.820	17.781	-16.808	-16.808	0.000	0.000	0.000	0.000
140	A	158	SER	0	0.009	0.006	19.350	-0.691	-0.691	0.000	0.000	0.000	0.000
141	A	159	VAL	0	0.003	0.006	20.667	-0.326	-0.326	0.000	0.000	0.000	0.000
142	A	160	ASP	-1	-0.844	-0.911	17.508	-14.907	-14.907	0.000	0.000	0.000	0.000
143	A	161	LYS	1	0.865	0.938	15.614	14.516	14.516	0.000	0.000	0.000	0.000
144	A	162	ILE	0	-0.010	0.005	16.503	-0.465	-0.465	0.000	0.000	0.000	0.000
145	A	163	VAL	0	-0.078	-0.045	18.602	-0.122	-0.122	0.000	0.000	0.000	0.000
146	A	164	ILE	0	-0.034	-0.006	12.212	-0.171	-0.171	0.000	0.000	0.000	0.000
147	A	165	GLN	0	-0.034	0.003	13.632	-2.148	-2.148	0.000	0.000	0.000	0.000
148	A	166	LYS	1	0.887	0.938	12.646	18.657	18.657	0.000	0.000	0.000	0.000
149	A	167	TYR	0	-0.016	-0.017	14.321	0.360	0.360	0.000	0.000	0.000	0.000
150	A	168	HIS	0	0.080	0.060	17.995	-0.019	-0.019	0.000	0.000	0.000	0.000
151	A	169	THR	0	-0.018	-0.004	20.782	0.445	0.445	0.000	0.000	0.000	0.000
152	A	170	VAL	0	0.043	0.017	22.804	-0.062	-0.062	0.000	0.000	0.000	0.000
153	A	171	ASN	0	-0.010	-0.010	26.012	0.143	0.143	0.000	0.000	0.000	0.000
154	A	172	GLY	0	0.017	0.017	26.616	0.235	0.235	0.000	0.000	0.000	0.000
155	A	173	HIS	0	-0.023	-0.003	27.277	0.191	0.191	0.000	0.000	0.000	0.000
156	A	174	ASN	0	-0.002	-0.004	22.107	-0.716	-0.716	0.000	0.000	0.000	0.000
157	A	175	CYS	0	-0.068	-0.034	23.898	0.436	0.436	0.000	0.000	0.000	0.000
158	A	176	GLU	-1	-0.838	-0.891	23.455	-11.007	-11.007	0.000	0.000	0.000	0.000
159	A	177	VAL	0	0.002	-0.004	22.558	0.465	0.465	0.000	0.000	0.000	0.000
160	A	178	ARG	1	0.841	0.917	23.249	10.287	10.287	0.000	0.000	0.000	0.000
161	A	179	LYS	1	0.896	0.942	20.875	14.238	14.238	0.000	0.000	0.000	0.000
162	A	180	ALA	0	-0.028	-0.013	25.610	0.228	0.228	0.000	0.000	0.000	0.000
163	A	181	LEU	0	0.000	0.003	29.373	0.040	0.040	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:LYS)