FMO DATABASE

FMODB ID: ZN2ZN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1588704.53405
FMO2-HF: Nuclear repulsion	1523113.798539
FMO2-HF: Total energy	-65590.735511
FMO2-MP2: Total energy	-65782.595597

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.
-36.61	-28.966	1.306	-3.238	-5.709	-0.02

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 : 0.964 / q_NPA : 0.984

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	0.012	-0.011	2.890	-8.904	-5.991	0.253	-1.527	-1.638	-0.005
4	A	11	GLU	-1	-0.762	-0.875	4.947	-43.288	-43.028	-0.001	-0.008	-0.251	0.000
5	A	12	GLN	0	-0.042	-0.029	5.974	1.248	1.248	0.000	0.000	0.000	0.000
6	A	13	LEU	0	-0.016	-0.015	7.526	2.110	2.110	0.000	0.000	0.000	0.000
7	A	14	ARG	1	0.761	0.880	2.585	53.919	56.194	0.860	-0.828	-2.306	-0.007
8	A	15	LYS	1	0.802	0.905	7.585	29.549	29.549	0.000	0.000	0.000	0.000
9	A	16	LEU	0	0.022	0.015	10.279	1.329	1.329	0.000	0.000	0.000	0.000
10	A	17	PHE	0	0.009	-0.004	13.766	0.091	0.091	0.000	0.000	0.000	0.000
11	A	18	ILE	0	-0.012	-0.004	16.283	0.384	0.384	0.000	0.000	0.000	0.000
12	A	19	GLY	0	0.032	0.011	19.344	0.277	0.277	0.000	0.000	0.000	0.000
13	A	20	GLY	0	0.029	0.004	22.992	0.053	0.053	0.000	0.000	0.000	0.000
14	A	21	LEU	0	0.004	0.006	21.002	0.223	0.223	0.000	0.000	0.000	0.000
15	A	22	SER	0	-0.014	-0.007	25.221	0.528	0.528	0.000	0.000	0.000	0.000
16	A	23	PHE	0	-0.063	-0.037	26.669	-0.304	-0.304	0.000	0.000	0.000	0.000
17	A	24	GLU	-1	-0.878	-0.963	27.944	-9.953	-9.953	0.000	0.000	0.000	0.000
18	A	25	THR	0	-0.086	-0.038	22.272	-0.029	-0.029	0.000	0.000	0.000	0.000
19	A	26	THR	0	0.013	0.011	23.351	-0.124	-0.124	0.000	0.000	0.000	0.000
20	A	27	ASP	-1	-0.745	-0.872	18.425	-15.006	-15.006	0.000	0.000	0.000	0.000
21	A	28	GLU	-1	-0.839	-0.928	18.294	-14.813	-14.813	0.000	0.000	0.000	0.000
22	A	29	SER	0	-0.043	-0.027	19.971	-0.331	-0.331	0.000	0.000	0.000	0.000
23	A	30	LEU	0	-0.008	-0.012	17.336	-0.025	-0.025	0.000	0.000	0.000	0.000
24	A	31	ARG	1	0.862	0.894	11.309	21.602	21.602	0.000	0.000	0.000	0.000
25	A	32	SER	0	-0.023	-0.033	16.510	-0.334	-0.334	0.000	0.000	0.000	0.000
26	A	33	HIS	0	-0.065	-0.030	19.102	0.430	0.430	0.000	0.000	0.000	0.000
27	A	34	PHE	0	0.012	-0.016	14.717	0.084	0.084	0.000	0.000	0.000	0.000
28	A	35	GLU	-1	-0.812	-0.896	13.236	-20.593	-20.593	0.000	0.000	0.000	0.000
29	A	36	GLN	0	-0.076	-0.026	15.033	0.067	0.067	0.000	0.000	0.000	0.000
30	A	37	TRP	0	-0.044	-0.023	15.214	0.585	0.585	0.000	0.000	0.000	0.000
31	A	38	GLY	0	0.007	0.000	11.504	-0.763	-0.763	0.000	0.000	0.000	0.000
32	A	39	THR	0	-0.031	-0.036	7.938	1.290	1.290	0.000	0.000	0.000	0.000
33	A	40	LEU	0	-0.024	-0.001	8.057	-3.068	-3.068	0.000	0.000	0.000	0.000
34	A	41	THR	0	-0.020	-0.005	3.933	1.082	1.199	0.000	-0.017	-0.100	0.000
35	A	42	ASP	-1	-0.872	-0.956	7.407	-23.425	-23.425	0.000	0.000	0.000	0.000
36	A	43	CYS	0	-0.061	-0.023	10.052	0.477	0.477	0.000	0.000	0.000	0.000
37	A	44	VAL	0	-0.018	0.025	13.500	0.698	0.698	0.000	0.000	0.000	0.000
38	A	45	VAL	0	-0.035	-0.014	16.633	0.148	0.148	0.000	0.000	0.000	0.000
39	A	46	MET	0	-0.036	-0.012	19.609	-0.047	-0.047	0.000	0.000	0.000	0.000
40	A	47	ARG	1	0.838	0.899	21.734	13.412	13.412	0.000	0.000	0.000	0.000
41	A	48	ASP	-1	-0.768	-0.851	24.929	-10.348	-10.348	0.000	0.000	0.000	0.000
42	A	49	PRO	0	0.007	0.009	26.179	0.015	0.015	0.000	0.000	0.000	0.000
43	A	50	ASN	0	-0.060	-0.031	27.435	0.208	0.208	0.000	0.000	0.000	0.000
44	A	51	THR	0	-0.035	-0.063	31.181	0.039	0.039	0.000	0.000	0.000	0.000
45	A	52	LYS	1	0.856	0.931	27.230	10.612	10.612	0.000	0.000	0.000	0.000
46	A	53	ARG	1	0.986	0.999	27.626	8.981	8.981	0.000	0.000	0.000	0.000
47	A	54	SER	0	0.043	0.037	25.477	-0.294	-0.294	0.000	0.000	0.000	0.000
48	A	55	ARG	1	0.876	0.914	24.404	12.763	12.763	0.000	0.000	0.000	0.000
49	A	56	GLY	0	0.037	0.023	26.296	0.130	0.130	0.000	0.000	0.000	0.000
50	A	57	PHE	0	-0.063	-0.032	20.745	0.031	0.031	0.000	0.000	0.000	0.000
51	A	58	GLY	0	0.045	0.021	19.141	0.210	0.210	0.000	0.000	0.000	0.000
52	A	59	PHE	0	-0.081	-0.021	11.581	0.374	0.374	0.000	0.000	0.000	0.000
53	A	60	VAL	0	0.043	0.025	12.668	0.154	0.154	0.000	0.000	0.000	0.000
54	A	61	THR	0	-0.021	0.000	6.434	0.022	0.022	0.000	0.000	0.000	0.000
55	A	62	TYR	0	0.027	0.014	7.341	0.194	0.194	0.000	0.000	0.000	0.000
56	A	63	ALA	0	0.013	0.009	3.727	-5.820	-5.606	0.001	-0.031	-0.184	0.000
57	A	64	THR	0	-0.064	-0.053	2.902	-11.516	-9.670	0.194	-0.824	-1.216	-0.008
58	A	65	VAL	0	-0.018	-0.040	5.125	2.304	2.323	-0.001	-0.003	-0.014	0.000
59	A	66	GLU	-1	-0.889	-0.935	8.027	-20.589	-20.589	0.000	0.000	0.000	0.000
60	A	67	GLU	-1	-0.749	-0.845	7.441	-29.580	-29.580	0.000	0.000	0.000	0.000
61	A	68	VAL	0	-0.008	0.009	9.189	1.637	1.637	0.000	0.000	0.000	0.000
62	A	69	ASP	-1	-0.801	-0.891	11.543	-18.711	-18.711	0.000	0.000	0.000	0.000
63	A	70	ALA	0	-0.040	-0.012	13.432	1.484	1.484	0.000	0.000	0.000	0.000
64	A	71	ALA	0	0.031	0.017	14.297	1.142	1.142	0.000	0.000	0.000	0.000
65	A	72	MET	0	-0.078	-0.023	15.330	1.200	1.200	0.000	0.000	0.000	0.000
66	A	73	ASN	0	-0.020	-0.019	17.507	1.294	1.294	0.000	0.000	0.000	0.000
67	A	74	ALA	0	0.003	0.017	19.268	0.656	0.656	0.000	0.000	0.000	0.000
68	A	75	ARG	1	0.746	0.854	20.311	14.064	14.064	0.000	0.000	0.000	0.000
69	A	76	PRO	0	-0.027	-0.026	22.780	0.260	0.260	0.000	0.000	0.000	0.000
70	A	77	HIS	0	0.053	0.047	19.199	0.456	0.456	0.000	0.000	0.000	0.000
71	A	78	LYS	1	0.840	0.896	23.524	10.152	10.152	0.000	0.000	0.000	0.000
72	A	79	VAL	0	0.073	0.049	21.292	0.174	0.174	0.000	0.000	0.000	0.000
73	A	80	ASP	-1	-0.742	-0.835	24.269	-11.786	-11.786	0.000	0.000	0.000	0.000
74	A	81	GLY	0	0.009	0.009	26.963	0.347	0.347	0.000	0.000	0.000	0.000
75	A	82	ARG	1	0.865	0.935	27.837	10.429	10.429	0.000	0.000	0.000	0.000
76	A	83	VAL	0	-0.018	-0.008	26.841	-0.284	-0.284	0.000	0.000	0.000	0.000
77	A	84	VAL	0	-0.035	-0.005	21.805	0.125	0.125	0.000	0.000	0.000	0.000
78	A	85	GLU	-1	-0.842	-0.925	23.111	-12.170	-12.170	0.000	0.000	0.000	0.000
79	A	86	PRO	0	0.002	-0.001	17.759	-0.304	-0.304	0.000	0.000	0.000	0.000
80	A	87	LYS	1	0.819	0.900	18.147	13.217	13.217	0.000	0.000	0.000	0.000
81	A	88	ARG	1	0.807	0.866	12.716	18.654	18.654	0.000	0.000	0.000	0.000
82	A	89	ALA	0	-0.020	0.004	12.583	1.182	1.182	0.000	0.000	0.000	0.000
83	A	90	VAL	0	-0.010	0.001	14.593	0.036	0.036	0.000	0.000	0.000	0.000
84	A	91	SER	0	0.022	0.022	15.220	-0.599	-0.599	0.000	0.000	0.000	0.000
85	A	103	THR	0	0.022	0.013	22.343	-0.141	-0.141	0.000	0.000	0.000	0.000
86	A	104	VAL	0	-0.005	-0.003	24.033	0.476	0.476	0.000	0.000	0.000	0.000
87	A	105	LYS	1	0.909	0.961	25.378	9.593	9.593	0.000	0.000	0.000	0.000
88	A	106	LYS	1	0.832	0.920	27.788	9.000	9.000	0.000	0.000	0.000	0.000
89	A	107	ILE	0	0.021	0.014	24.193	-0.308	-0.308	0.000	0.000	0.000	0.000
90	A	108	PHE	0	-0.022	-0.012	27.437	0.466	0.466	0.000	0.000	0.000	0.000
91	A	109	VAL	0	0.027	0.006	26.366	-0.492	-0.492	0.000	0.000	0.000	0.000
92	A	110	GLY	0	0.009	-0.003	28.168	0.472	0.472	0.000	0.000	0.000	0.000
93	A	111	GLY	0	0.032	0.013	28.330	-0.367	-0.367	0.000	0.000	0.000	0.000
94	A	112	ILE	0	-0.002	0.000	29.304	0.080	0.080	0.000	0.000	0.000	0.000
95	A	113	LYS	1	0.885	0.948	31.384	9.171	9.171	0.000	0.000	0.000	0.000
96	A	114	GLU	-1	-0.744	-0.870	34.941	-7.218	-7.218	0.000	0.000	0.000	0.000
97	A	115	ASP	-1	-0.887	-0.928	35.147	-8.103	-8.103	0.000	0.000	0.000	0.000
98	A	116	THR	0	-0.044	-0.022	31.054	-0.092	-0.092	0.000	0.000	0.000	0.000
99	A	117	GLU	-1	-0.804	-0.903	34.205	-7.656	-7.656	0.000	0.000	0.000	0.000
100	A	118	GLU	-1	-0.860	-0.937	33.484	-8.821	-8.821	0.000	0.000	0.000	0.000
101	A	119	HIS	0	0.063	0.033	32.459	-0.175	-0.175	0.000	0.000	0.000	0.000
102	A	120	HIS	0	0.055	0.048	30.435	-0.297	-0.297	0.000	0.000	0.000	0.000
103	A	121	LEU	0	-0.026	-0.021	28.601	-0.413	-0.413	0.000	0.000	0.000	0.000
104	A	122	ARG	1	0.837	0.899	27.622	8.790	8.790	0.000	0.000	0.000	0.000
105	A	123	ASP	-1	-0.872	-0.937	27.386	-9.877	-9.877	0.000	0.000	0.000	0.000
106	A	124	TYR	0	-0.070	-0.030	20.087	-0.585	-0.585	0.000	0.000	0.000	0.000
107	A	125	PHE	0	0.015	-0.022	22.841	-0.441	-0.441	0.000	0.000	0.000	0.000
108	A	126	GLU	-1	-0.896	-0.952	23.839	-10.346	-10.346	0.000	0.000	0.000	0.000
109	A	127	GLN	0	-0.058	-0.034	21.011	-0.490	-0.490	0.000	0.000	0.000	0.000
110	A	128	TYR	0	-0.030	-0.007	17.057	-0.946	-0.946	0.000	0.000	0.000	0.000
111	A	129	GLY	0	0.013	-0.007	20.895	-0.456	-0.456	0.000	0.000	0.000	0.000
112	A	130	LYS	1	0.821	0.895	23.845	9.971	9.971	0.000	0.000	0.000	0.000
113	A	131	ILE	0	-0.003	-0.001	27.387	0.021	0.021	0.000	0.000	0.000	0.000
114	A	132	GLU	-1	-0.828	-0.914	29.491	-9.242	-9.242	0.000	0.000	0.000	0.000
115	A	133	VAL	0	-0.029	-0.020	32.126	0.320	0.320	0.000	0.000	0.000	0.000
116	A	134	ILE	0	-0.006	0.009	30.667	-0.370	-0.370	0.000	0.000	0.000	0.000
117	A	135	GLU	-1	-0.849	-0.908	33.579	-8.205	-8.205	0.000	0.000	0.000	0.000
118	A	136	ILE	0	0.046	0.009	34.671	-0.161	-0.161	0.000	0.000	0.000	0.000
119	A	137	MET	0	-0.037	0.005	36.004	0.272	0.272	0.000	0.000	0.000	0.000
120	A	138	THR	0	0.035	0.019	38.102	-0.021	-0.021	0.000	0.000	0.000	0.000
121	A	139	ASP	-1	-0.855	-0.919	41.583	-6.726	-6.726	0.000	0.000	0.000	0.000
122	A	140	ARG	1	0.896	0.950	44.330	6.426	6.426	0.000	0.000	0.000	0.000
123	A	141	GLY	0	-0.014	0.003	46.908	0.136	0.136	0.000	0.000	0.000	0.000
124	A	142	SER	0	-0.050	-0.056	47.369	0.088	0.088	0.000	0.000	0.000	0.000
125	A	143	GLY	0	0.001	0.004	45.807	0.032	0.032	0.000	0.000	0.000	0.000
126	A	144	LYS	1	0.833	0.898	43.507	6.854	6.854	0.000	0.000	0.000	0.000
127	A	145	LYS	1	0.839	0.911	37.537	7.707	7.707	0.000	0.000	0.000	0.000
128	A	146	ARG	1	0.904	0.942	38.461	7.655	7.655	0.000	0.000	0.000	0.000
129	A	147	GLY	0	-0.007	0.010	35.129	-0.080	-0.080	0.000	0.000	0.000	0.000
130	A	148	PHE	0	-0.051	-0.037	32.580	-0.246	-0.246	0.000	0.000	0.000	0.000
131	A	149	ALA	0	0.009	0.014	31.621	0.318	0.318	0.000	0.000	0.000	0.000
132	A	150	PHE	0	-0.026	-0.015	30.975	-0.287	-0.287	0.000	0.000	0.000	0.000
133	A	151	VAL	0	0.015	0.016	27.918	0.212	0.212	0.000	0.000	0.000	0.000
134	A	152	THR	0	-0.022	-0.021	29.192	-0.198	-0.198	0.000	0.000	0.000	0.000
135	A	153	PHE	0	0.026	0.010	25.158	0.142	0.142	0.000	0.000	0.000	0.000
136	A	154	ASP	-1	-0.845	-0.916	27.182	-10.604	-10.604	0.000	0.000	0.000	0.000
137	A	155	ASP	-1	-0.761	-0.861	22.757	-12.765	-12.765	0.000	0.000	0.000	0.000
138	A	156	HIS	0	-0.057	-0.032	20.464	0.147	0.147	0.000	0.000	0.000	0.000
139	A	157	ASP	-1	-0.722	-0.835	17.562	-16.890	-16.890	0.000	0.000	0.000	0.000
140	A	158	SER	0	0.001	-0.004	19.303	-0.637	-0.637	0.000	0.000	0.000	0.000
141	A	159	VAL	0	-0.011	-0.002	20.824	-0.283	-0.283	0.000	0.000	0.000	0.000
142	A	160	ASP	-1	-0.843	-0.917	17.646	-14.759	-14.759	0.000	0.000	0.000	0.000
143	A	161	LYS	1	0.849	0.924	15.417	14.586	14.586	0.000	0.000	0.000	0.000
144	A	162	ILE	0	-0.018	0.007	16.485	-0.447	-0.447	0.000	0.000	0.000	0.000
145	A	163	VAL	0	-0.064	-0.045	18.511	-0.068	-0.068	0.000	0.000	0.000	0.000
146	A	164	ILE	0	-0.027	-0.001	12.130	-0.197	-0.197	0.000	0.000	0.000	0.000
147	A	165	GLN	0	-0.020	0.009	13.960	-2.082	-2.082	0.000	0.000	0.000	0.000
148	A	166	LYS	1	0.858	0.915	13.144	18.073	18.073	0.000	0.000	0.000	0.000
149	A	167	TYR	0	-0.001	0.000	14.858	0.262	0.262	0.000	0.000	0.000	0.000
150	A	168	HIS	0	0.107	0.073	18.226	0.024	0.024	0.000	0.000	0.000	0.000
151	A	169	THR	0	-0.059	-0.032	20.922	0.246	0.246	0.000	0.000	0.000	0.000
152	A	170	VAL	0	0.050	0.036	23.176	-0.047	-0.047	0.000	0.000	0.000	0.000
153	A	171	ASN	0	-0.014	-0.033	26.468	0.118	0.118	0.000	0.000	0.000	0.000
154	A	172	GLY	0	0.025	0.024	26.654	0.228	0.228	0.000	0.000	0.000	0.000
155	A	173	HIS	0	-0.021	0.001	27.116	0.153	0.153	0.000	0.000	0.000	0.000
156	A	174	ASN	0	0.013	0.001	22.165	-0.692	-0.692	0.000	0.000	0.000	0.000
157	A	175	CYS	0	-0.083	-0.037	24.082	0.460	0.460	0.000	0.000	0.000	0.000
158	A	176	GLU	-1	-0.818	-0.872	23.641	-11.061	-11.061	0.000	0.000	0.000	0.000
159	A	177	VAL	0	-0.006	-0.018	22.592	0.413	0.413	0.000	0.000	0.000	0.000
160	A	178	ARG	1	0.816	0.894	23.338	10.279	10.279	0.000	0.000	0.000	0.000
161	A	179	LYS	1	0.871	0.916	21.092	14.066	14.066	0.000	0.000	0.000	0.000
162	A	180	ALA	0	-0.026	-0.009	25.532	0.225	0.225	0.000	0.000	0.000	0.000
163	A	181	LEU	0	0.002	0.010	29.345	0.076	0.076	0.000	0.000	0.000	0.000

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