FMO DATABASE

FMODB ID: 2LKMR

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1591695.541526
FMO2-HF: Nuclear repulsion	1526106.372895
FMO2-HF: Total energy	-65589.168631
FMO2-MP2: Total energy	-65780.929857

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.
-31.129	-26.244	1.241	-2.029	-4.096	-0.017

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 : 0.946 / q_NPA : 0.956

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	0.020	0.000	2.963	-10.987	-8.825	0.181	-0.952	-1.391	-0.004
4	A	11	GLU	-1	-0.884	-0.953	4.922	-38.825	-38.825	0.000	0.000	0.000	0.000
5	A	12	GLN	0	-0.046	-0.023	5.823	1.878	1.878	0.000	0.000	0.000	0.000
6	A	13	LEU	0	-0.035	-0.024	7.651	2.587	2.587	0.000	0.000	0.000	0.000
7	A	14	ARG	1	0.839	0.921	2.710	52.676	54.729	1.056	-0.902	-2.207	-0.012
8	A	15	LYS	1	0.897	0.980	7.855	26.658	26.658	0.000	0.000	0.000	0.000
9	A	16	LEU	0	0.009	0.007	10.847	1.169	1.169	0.000	0.000	0.000	0.000
10	A	17	PHE	0	-0.016	-0.016	14.349	-0.170	-0.170	0.000	0.000	0.000	0.000
11	A	18	ILE	0	0.010	0.003	17.036	0.484	0.484	0.000	0.000	0.000	0.000
12	A	19	GLY	0	0.035	0.013	20.002	0.247	0.247	0.000	0.000	0.000	0.000
13	A	20	GLY	0	0.048	0.019	23.489	0.105	0.105	0.000	0.000	0.000	0.000
14	A	21	LEU	0	-0.012	-0.005	21.805	0.267	0.267	0.000	0.000	0.000	0.000
15	A	22	SER	0	0.013	0.007	26.028	0.514	0.514	0.000	0.000	0.000	0.000
16	A	23	PHE	0	-0.053	-0.035	27.339	-0.301	-0.301	0.000	0.000	0.000	0.000
17	A	24	GLU	-1	-0.917	-0.968	28.880	-9.897	-9.897	0.000	0.000	0.000	0.000
18	A	25	THR	0	-0.079	-0.050	23.045	-0.049	-0.049	0.000	0.000	0.000	0.000
19	A	26	THR	0	-0.047	-0.037	23.827	-0.026	-0.026	0.000	0.000	0.000	0.000
20	A	27	ASP	-1	-0.806	-0.905	18.551	-15.733	-15.733	0.000	0.000	0.000	0.000
21	A	28	GLU	-1	-0.896	-0.958	19.066	-14.522	-14.522	0.000	0.000	0.000	0.000
22	A	29	SER	0	-0.036	-0.048	20.604	-0.312	-0.312	0.000	0.000	0.000	0.000
23	A	30	LEU	0	0.010	-0.005	18.206	0.016	0.016	0.000	0.000	0.000	0.000
24	A	31	ARG	1	0.881	0.914	11.982	20.898	20.898	0.000	0.000	0.000	0.000
25	A	32	SER	0	-0.016	-0.013	17.113	-0.246	-0.246	0.000	0.000	0.000	0.000
26	A	33	HIS	0	-0.063	-0.014	19.566	0.349	0.349	0.000	0.000	0.000	0.000
27	A	34	PHE	0	0.012	-0.008	15.420	0.074	0.074	0.000	0.000	0.000	0.000
28	A	35	GLU	-1	-0.840	-0.919	13.760	-19.694	-19.694	0.000	0.000	0.000	0.000
29	A	36	GLN	0	-0.070	-0.024	15.443	0.018	0.018	0.000	0.000	0.000	0.000
30	A	37	TRP	0	-0.056	-0.024	15.548	0.325	0.325	0.000	0.000	0.000	0.000
31	A	38	GLY	0	0.022	-0.004	11.635	-0.772	-0.772	0.000	0.000	0.000	0.000
32	A	39	THR	0	-0.023	-0.008	8.073	1.073	1.073	0.000	0.000	0.000	0.000
33	A	40	LEU	0	-0.010	0.002	8.814	-2.237	-2.237	0.000	0.000	0.000	0.000
34	A	41	THR	0	-0.094	-0.055	4.844	-1.036	-1.036	0.000	0.000	0.000	0.000
35	A	42	ASP	-1	-0.857	-0.946	8.258	-23.822	-23.822	0.000	0.000	0.000	0.000
36	A	43	CYS	0	-0.095	-0.026	11.057	0.492	0.492	0.000	0.000	0.000	0.000
37	A	44	VAL	0	0.006	0.037	14.553	0.752	0.752	0.000	0.000	0.000	0.000
38	A	45	VAL	0	-0.008	0.006	17.193	0.166	0.166	0.000	0.000	0.000	0.000
39	A	46	MET	0	-0.052	-0.028	19.994	-0.031	-0.031	0.000	0.000	0.000	0.000
40	A	47	ARG	1	0.939	0.959	22.082	12.853	12.853	0.000	0.000	0.000	0.000
41	A	48	ASP	-1	-0.865	-0.934	25.291	-10.470	-10.470	0.000	0.000	0.000	0.000
42	A	49	PRO	0	-0.019	-0.009	26.774	-0.057	-0.057	0.000	0.000	0.000	0.000
43	A	50	ASN	0	-0.015	-0.003	27.850	0.011	0.011	0.000	0.000	0.000	0.000
44	A	51	THR	0	-0.048	-0.044	31.459	0.094	0.094	0.000	0.000	0.000	0.000
45	A	52	LYS	1	0.968	1.003	27.951	10.769	10.769	0.000	0.000	0.000	0.000
46	A	53	ARG	1	0.989	0.991	28.484	8.984	8.984	0.000	0.000	0.000	0.000
47	A	54	SER	0	0.026	0.025	26.513	-0.313	-0.313	0.000	0.000	0.000	0.000
48	A	55	ARG	1	0.933	0.962	24.064	12.854	12.854	0.000	0.000	0.000	0.000
49	A	56	GLY	0	0.013	0.009	26.385	0.109	0.109	0.000	0.000	0.000	0.000
50	A	57	PHE	0	-0.052	-0.029	20.734	0.050	0.050	0.000	0.000	0.000	0.000
51	A	58	GLY	0	0.055	0.021	19.493	0.180	0.180	0.000	0.000	0.000	0.000
52	A	59	PHE	0	-0.100	-0.035	11.689	0.398	0.398	0.000	0.000	0.000	0.000
53	A	60	VAL	0	0.077	0.047	13.400	0.135	0.135	0.000	0.000	0.000	0.000
54	A	61	THR	0	0.005	-0.008	7.129	0.728	0.728	0.000	0.000	0.000	0.000
55	A	62	TYR	0	0.027	0.005	8.415	-0.074	-0.074	0.000	0.000	0.000	0.000
56	A	63	ALA	0	0.011	0.012	4.485	-5.275	-5.180	-0.001	-0.008	-0.086	0.000
57	A	64	THR	0	-0.054	-0.028	3.733	-7.601	-7.026	0.005	-0.167	-0.412	-0.001
58	A	65	VAL	0	0.023	-0.020	5.806	2.297	2.297	0.000	0.000	0.000	0.000
59	A	66	GLU	-1	-0.900	-0.936	8.478	-19.090	-19.090	0.000	0.000	0.000	0.000
60	A	67	GLU	-1	-0.795	-0.902	8.307	-27.549	-27.549	0.000	0.000	0.000	0.000
61	A	68	VAL	0	-0.023	0.004	9.534	1.552	1.552	0.000	0.000	0.000	0.000
62	A	69	ASP	-1	-0.840	-0.920	12.130	-18.087	-18.087	0.000	0.000	0.000	0.000
63	A	70	ALA	0	-0.027	0.001	13.875	1.390	1.390	0.000	0.000	0.000	0.000
64	A	71	ALA	0	0.037	0.015	14.803	1.116	1.116	0.000	0.000	0.000	0.000
65	A	72	MET	0	-0.076	-0.014	16.023	1.116	1.116	0.000	0.000	0.000	0.000
66	A	73	ASN	0	-0.027	-0.013	18.055	1.167	1.167	0.000	0.000	0.000	0.000
67	A	74	ALA	0	-0.021	0.010	19.551	0.675	0.675	0.000	0.000	0.000	0.000
68	A	75	ARG	1	0.732	0.853	20.744	13.810	13.810	0.000	0.000	0.000	0.000
69	A	76	PRO	0	-0.033	-0.043	23.191	0.260	0.260	0.000	0.000	0.000	0.000
70	A	77	HIS	0	0.037	0.013	19.571	0.428	0.428	0.000	0.000	0.000	0.000
71	A	78	LYS	1	0.859	0.938	24.253	10.011	10.011	0.000	0.000	0.000	0.000
72	A	79	VAL	0	0.063	0.034	22.236	-0.056	-0.056	0.000	0.000	0.000	0.000
73	A	80	ASP	-1	-0.751	-0.821	25.307	-11.673	-11.673	0.000	0.000	0.000	0.000
74	A	81	GLY	0	0.004	-0.013	27.878	0.336	0.336	0.000	0.000	0.000	0.000
75	A	82	ARG	1	0.871	0.931	28.663	10.290	10.290	0.000	0.000	0.000	0.000
76	A	83	VAL	0	-0.043	-0.017	27.210	-0.287	-0.287	0.000	0.000	0.000	0.000
77	A	84	VAL	0	-0.012	0.006	22.472	0.169	0.169	0.000	0.000	0.000	0.000
78	A	85	GLU	-1	-0.938	-0.989	23.296	-11.782	-11.782	0.000	0.000	0.000	0.000
79	A	86	PRO	0	-0.009	-0.013	18.375	-0.277	-0.277	0.000	0.000	0.000	0.000
80	A	87	LYS	1	0.901	0.954	18.482	13.245	13.245	0.000	0.000	0.000	0.000
81	A	88	ARG	1	0.818	0.884	12.846	18.236	18.236	0.000	0.000	0.000	0.000
82	A	89	ALA	0	-0.037	-0.006	12.922	1.066	1.066	0.000	0.000	0.000	0.000
83	A	90	VAL	0	-0.016	-0.004	14.935	0.049	0.049	0.000	0.000	0.000	0.000
84	A	91	SER	0	0.018	0.010	15.318	-0.651	-0.651	0.000	0.000	0.000	0.000
85	A	103	THR	0	-0.006	-0.015	22.862	-0.120	-0.120	0.000	0.000	0.000	0.000
86	A	104	VAL	0	0.000	0.003	24.734	0.459	0.459	0.000	0.000	0.000	0.000
87	A	105	LYS	1	0.973	0.987	25.247	9.724	9.724	0.000	0.000	0.000	0.000
88	A	106	LYS	1	0.945	0.997	27.459	9.124	9.124	0.000	0.000	0.000	0.000
89	A	107	ILE	0	0.007	0.016	24.194	-0.296	-0.296	0.000	0.000	0.000	0.000
90	A	108	PHE	0	-0.039	-0.014	27.541	0.459	0.459	0.000	0.000	0.000	0.000
91	A	109	VAL	0	0.049	0.016	26.682	-0.483	-0.483	0.000	0.000	0.000	0.000
92	A	110	GLY	0	0.015	-0.013	28.172	0.452	0.452	0.000	0.000	0.000	0.000
93	A	111	GLY	0	0.052	0.020	28.440	-0.305	-0.305	0.000	0.000	0.000	0.000
94	A	112	ILE	0	-0.007	0.004	29.559	-0.025	-0.025	0.000	0.000	0.000	0.000
95	A	113	LYS	1	0.899	0.980	31.671	9.095	9.095	0.000	0.000	0.000	0.000
96	A	114	GLU	-1	-0.839	-0.944	34.993	-7.186	-7.186	0.000	0.000	0.000	0.000
97	A	115	ASP	-1	-0.929	-0.967	36.041	-7.725	-7.725	0.000	0.000	0.000	0.000
98	A	116	THR	0	-0.034	-0.014	31.197	-0.190	-0.190	0.000	0.000	0.000	0.000
99	A	117	GLU	-1	-0.776	-0.889	34.370	-7.719	-7.719	0.000	0.000	0.000	0.000
100	A	118	GLU	-1	-0.838	-0.910	33.458	-8.504	-8.504	0.000	0.000	0.000	0.000
101	A	119	HIS	0	0.030	0.003	32.604	-0.171	-0.171	0.000	0.000	0.000	0.000
102	A	120	HIS	0	0.049	0.031	30.289	-0.283	-0.283	0.000	0.000	0.000	0.000
103	A	121	LEU	0	-0.014	-0.013	28.550	-0.387	-0.387	0.000	0.000	0.000	0.000
104	A	122	ARG	1	0.880	0.902	27.861	8.544	8.544	0.000	0.000	0.000	0.000
105	A	123	ASP	-1	-0.862	-0.917	27.821	-9.712	-9.712	0.000	0.000	0.000	0.000
106	A	124	TYR	0	-0.073	-0.026	19.843	-0.496	-0.496	0.000	0.000	0.000	0.000
107	A	125	PHE	0	0.010	-0.030	22.929	-0.438	-0.438	0.000	0.000	0.000	0.000
108	A	126	GLU	-1	-0.926	-0.964	24.156	-10.435	-10.435	0.000	0.000	0.000	0.000
109	A	127	GLN	0	-0.057	-0.022	21.129	-0.416	-0.416	0.000	0.000	0.000	0.000
110	A	128	TYR	0	-0.025	-0.014	17.061	-0.891	-0.891	0.000	0.000	0.000	0.000
111	A	129	GLY	0	-0.006	-0.009	21.132	-0.459	-0.459	0.000	0.000	0.000	0.000
112	A	130	LYS	1	0.978	1.011	23.944	9.676	9.676	0.000	0.000	0.000	0.000
113	A	131	ILE	0	-0.007	-0.007	27.541	-0.009	-0.009	0.000	0.000	0.000	0.000
114	A	132	GLU	-1	-1.010	-1.006	29.674	-9.023	-9.023	0.000	0.000	0.000	0.000
115	A	133	VAL	0	-0.024	-0.024	32.408	0.303	0.303	0.000	0.000	0.000	0.000
116	A	134	ILE	0	-0.022	-0.005	31.286	-0.345	-0.345	0.000	0.000	0.000	0.000
117	A	135	GLU	-1	-0.923	-0.959	33.771	-7.863	-7.863	0.000	0.000	0.000	0.000
118	A	136	ILE	0	0.030	0.010	34.642	-0.208	-0.208	0.000	0.000	0.000	0.000
119	A	137	MET	0	-0.061	-0.010	35.923	0.233	0.233	0.000	0.000	0.000	0.000
120	A	138	THR	0	0.027	0.008	38.337	0.032	0.032	0.000	0.000	0.000	0.000
121	A	139	ASP	-1	-0.907	-0.956	41.672	-6.747	-6.747	0.000	0.000	0.000	0.000
122	A	140	ARG	1	0.917	0.957	44.243	6.496	6.496	0.000	0.000	0.000	0.000
123	A	141	GLY	0	-0.013	-0.004	46.664	0.132	0.132	0.000	0.000	0.000	0.000
124	A	142	SER	0	-0.037	-0.030	47.091	0.068	0.068	0.000	0.000	0.000	0.000
125	A	143	GLY	0	0.007	0.009	45.930	0.067	0.067	0.000	0.000	0.000	0.000
126	A	144	LYS	1	0.955	0.982	43.595	6.486	6.486	0.000	0.000	0.000	0.000
127	A	145	LYS	1	0.846	0.930	37.653	7.614	7.614	0.000	0.000	0.000	0.000
128	A	146	ARG	1	0.927	0.952	38.472	7.729	7.729	0.000	0.000	0.000	0.000
129	A	147	GLY	0	-0.012	0.010	35.323	-0.071	-0.071	0.000	0.000	0.000	0.000
130	A	148	PHE	0	-0.076	-0.056	32.572	-0.232	-0.232	0.000	0.000	0.000	0.000
131	A	149	ALA	0	0.031	0.024	31.628	0.299	0.299	0.000	0.000	0.000	0.000
132	A	150	PHE	0	-0.024	-0.023	31.103	-0.315	-0.315	0.000	0.000	0.000	0.000
133	A	151	VAL	0	0.020	0.023	27.997	0.235	0.235	0.000	0.000	0.000	0.000
134	A	152	THR	0	-0.028	-0.019	29.113	-0.284	-0.284	0.000	0.000	0.000	0.000
135	A	153	PHE	0	0.022	-0.001	25.067	0.152	0.152	0.000	0.000	0.000	0.000
136	A	154	ASP	-1	-0.814	-0.913	27.412	-10.569	-10.569	0.000	0.000	0.000	0.000
137	A	155	ASP	-1	-0.805	-0.890	23.169	-12.591	-12.591	0.000	0.000	0.000	0.000
138	A	156	HIS	0	-0.051	-0.043	20.488	0.186	0.186	0.000	0.000	0.000	0.000
139	A	157	ASP	-1	-0.741	-0.841	17.873	-16.688	-16.688	0.000	0.000	0.000	0.000
140	A	158	SER	0	-0.003	-0.003	19.454	-0.480	-0.480	0.000	0.000	0.000	0.000
141	A	159	VAL	0	0.005	0.006	20.673	-0.294	-0.294	0.000	0.000	0.000	0.000
142	A	160	ASP	-1	-0.886	-0.945	17.625	-14.827	-14.827	0.000	0.000	0.000	0.000
143	A	161	LYS	1	0.906	0.951	15.658	14.340	14.340	0.000	0.000	0.000	0.000
144	A	162	ILE	0	-0.003	0.011	16.503	-0.415	-0.415	0.000	0.000	0.000	0.000
145	A	163	VAL	0	-0.081	-0.047	18.603	-0.098	-0.098	0.000	0.000	0.000	0.000
146	A	164	ILE	0	-0.052	-0.013	12.856	-0.189	-0.189	0.000	0.000	0.000	0.000
147	A	165	GLN	0	-0.029	0.008	13.607	-2.113	-2.113	0.000	0.000	0.000	0.000
148	A	166	LYS	1	0.908	0.950	12.792	18.482	18.482	0.000	0.000	0.000	0.000
149	A	167	TYR	0	-0.012	-0.011	14.584	0.371	0.371	0.000	0.000	0.000	0.000
150	A	168	HIS	0	0.049	0.017	18.523	-0.052	-0.052	0.000	0.000	0.000	0.000
151	A	169	THR	0	-0.023	-0.006	21.325	0.375	0.375	0.000	0.000	0.000	0.000
152	A	170	VAL	0	0.043	0.016	23.495	-0.069	-0.069	0.000	0.000	0.000	0.000
153	A	171	ASN	0	-0.006	-0.009	26.577	0.168	0.168	0.000	0.000	0.000	0.000
154	A	172	GLY	0	0.011	0.018	27.377	0.200	0.200	0.000	0.000	0.000	0.000
155	A	173	HIS	0	-0.036	-0.015	27.901	0.109	0.109	0.000	0.000	0.000	0.000
156	A	174	ASN	0	-0.012	-0.013	22.566	-0.661	-0.661	0.000	0.000	0.000	0.000
157	A	175	CYS	0	-0.061	-0.027	24.345	0.408	0.408	0.000	0.000	0.000	0.000
158	A	176	GLU	-1	-0.900	-0.931	23.749	-10.789	-10.789	0.000	0.000	0.000	0.000
159	A	177	VAL	0	0.011	0.000	22.678	0.437	0.437	0.000	0.000	0.000	0.000
160	A	178	ARG	1	0.908	0.969	23.249	9.992	9.992	0.000	0.000	0.000	0.000
161	A	179	LYS	1	0.958	0.985	20.861	14.079	14.079	0.000	0.000	0.000	0.000
162	A	180	ALA	0	-0.028	-0.009	25.841	0.233	0.233	0.000	0.000	0.000	0.000
163	A	181	LEU	0	-0.010	-0.004	29.597	0.061	0.061	0.000	0.000	0.000	0.000

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