FMO DATABASE

FMODB ID: G6G41

Calculation Name: 5IM0-B-Xray372

Preferred Name: Heterogeneous nuclear ribonucleoprotein D0

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5IM0

Chain ID: B

ChEMBL ID: CHEMBL4296009

UniProt ID: Q14103

Base Structure: X-ray

Registration Date: 2023-09-19

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	82
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-548673.854874
FMO2-HF: Nuclear repulsion	515589.098379
FMO2-HF: Total energy	-33084.756495
FMO2-MP2: Total energy	-33179.065345

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(B:76:MET)

Summations of interaction energy for fragment #1(B:76:MET)

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.
-20.893	-16.111	8.707	-6.343	-7.148	-0.048

Interaction energy analysis for fragmet #1(B:76:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : 0.011

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	B	78	GLY	0	-0.003	-0.006	3.360	-1.026	1.515	0.027	-1.416	-1.153	0.003
4	B	79	LYS	1	0.892	0.958	5.093	0.452	0.521	-0.001	-0.005	-0.064	0.000
5	B	80	MET	0	-0.039	-0.011	8.231	0.149	0.149	0.000	0.000	0.000	0.000
6	B	81	PHE	0	0.007	-0.003	11.337	0.034	0.034	0.000	0.000	0.000	0.000
7	B	82	ILE	0	-0.011	-0.008	14.670	-0.035	-0.035	0.000	0.000	0.000	0.000
8	B	83	GLY	0	0.057	0.019	17.680	0.032	0.032	0.000	0.000	0.000	0.000
9	B	84	GLY	0	0.009	0.008	21.023	-0.025	-0.025	0.000	0.000	0.000	0.000
10	B	85	LEU	0	0.037	0.026	20.473	-0.011	-0.011	0.000	0.000	0.000	0.000
11	B	86	SER	0	-0.015	-0.018	24.397	0.018	0.018	0.000	0.000	0.000	0.000
12	B	87	TRP	0	-0.032	-0.034	27.376	-0.005	-0.005	0.000	0.000	0.000	0.000
13	B	88	ASP	-1	-0.802	-0.869	29.944	-0.173	-0.173	0.000	0.000	0.000	0.000
14	B	89	THR	0	-0.048	-0.023	23.544	-0.018	-0.018	0.000	0.000	0.000	0.000
15	B	90	THR	0	0.001	-0.040	25.866	0.000	0.000	0.000	0.000	0.000	0.000
16	B	91	LYS	1	0.838	0.887	18.276	0.351	0.351	0.000	0.000	0.000	0.000
17	B	92	LYS	1	0.855	0.914	21.364	0.330	0.330	0.000	0.000	0.000	0.000
18	B	93	ASP	-1	-0.723	-0.817	22.164	-0.313	-0.313	0.000	0.000	0.000	0.000
19	B	94	LEU	0	0.003	0.000	18.148	-0.037	-0.037	0.000	0.000	0.000	0.000
20	B	95	LYS	1	0.841	0.903	15.244	0.628	0.628	0.000	0.000	0.000	0.000
21	B	96	ASP	-1	-0.773	-0.856	17.885	-0.515	-0.515	0.000	0.000	0.000	0.000
22	B	97	TYR	0	-0.091	-0.056	18.765	-0.007	-0.007	0.000	0.000	0.000	0.000
23	B	98	PHE	0	0.030	-0.008	14.676	-0.019	-0.019	0.000	0.000	0.000	0.000
24	B	99	SER	0	0.001	-0.025	14.504	-0.164	-0.164	0.000	0.000	0.000	0.000
25	B	100	LYS	1	0.843	0.939	15.206	0.490	0.490	0.000	0.000	0.000	0.000
26	B	101	PHE	0	0.002	0.007	12.797	0.022	0.022	0.000	0.000	0.000	0.000
27	B	102	GLY	0	0.017	0.024	10.327	-0.279	-0.279	0.000	0.000	0.000	0.000
28	B	103	GLU	-1	-0.889	-0.942	9.629	-1.324	-1.324	0.000	0.000	0.000	0.000
29	B	104	VAL	0	-0.022	-0.003	9.736	-0.386	-0.386	0.000	0.000	0.000	0.000
30	B	105	VAL	0	0.068	0.044	8.157	0.222	0.222	0.000	0.000	0.000	0.000
31	B	106	ASP	-1	-0.822	-0.909	11.413	-0.223	-0.223	0.000	0.000	0.000	0.000
32	B	107	CYS	0	-0.036	0.009	13.440	-0.079	-0.079	0.000	0.000	0.000	0.000
33	B	108	THR	0	-0.025	-0.019	15.985	0.082	0.082	0.000	0.000	0.000	0.000
34	B	109	LEU	0	0.092	0.054	18.819	-0.011	-0.011	0.000	0.000	0.000	0.000
35	B	110	LYS	1	0.894	0.948	21.277	0.029	0.029	0.000	0.000	0.000	0.000
36	B	111	LEU	0	0.045	0.017	22.811	0.007	0.007	0.000	0.000	0.000	0.000
37	B	112	ASP	-1	-0.783	-0.863	26.401	-0.004	-0.004	0.000	0.000	0.000	0.000
38	B	113	PRO	0	-0.052	-0.038	27.661	-0.006	-0.006	0.000	0.000	0.000	0.000
39	B	114	ILE	0	0.005	0.021	30.019	0.001	0.001	0.000	0.000	0.000	0.000
40	B	115	THR	0	-0.022	-0.029	32.999	-0.005	-0.005	0.000	0.000	0.000	0.000
41	B	116	GLY	0	0.033	0.025	30.513	-0.006	-0.006	0.000	0.000	0.000	0.000
42	B	117	ARG	1	0.943	0.968	30.074	0.042	0.042	0.000	0.000	0.000	0.000
43	B	118	SER	0	0.037	0.015	26.542	0.009	0.009	0.000	0.000	0.000	0.000
44	B	119	ARG	1	0.802	0.875	24.679	0.031	0.031	0.000	0.000	0.000	0.000
45	B	120	GLY	0	0.051	0.041	25.856	0.011	0.011	0.000	0.000	0.000	0.000
46	B	121	PHE	0	-0.059	-0.035	19.977	0.002	0.002	0.000	0.000	0.000	0.000
47	B	122	GLY	0	0.038	0.017	19.148	0.011	0.011	0.000	0.000	0.000	0.000
48	B	123	PHE	0	-0.072	-0.036	13.977	0.047	0.047	0.000	0.000	0.000	0.000
49	B	124	VAL	0	0.016	0.011	11.649	0.014	0.014	0.000	0.000	0.000	0.000
50	B	125	LEU	0	-0.009	0.003	7.510	0.147	0.147	0.000	0.000	0.000	0.000
51	B	126	PHE	0	0.022	-0.007	7.599	0.206	0.206	0.000	0.000	0.000	0.000
52	B	127	LYS	1	0.868	0.928	4.981	2.094	2.094	0.000	0.000	0.000	0.000
53	B	128	GLU	-1	-0.804	-0.908	1.893	-18.227	-19.247	7.481	-3.421	-3.040	-0.042
54	B	129	SER	0	-0.004	-0.017	2.591	-1.607	1.153	1.199	-1.410	-2.550	-0.009
55	B	130	GLU	-1	-0.834	-0.911	4.026	-4.609	-4.177	0.001	-0.091	-0.341	0.000
56	B	131	SER	0	-0.070	-0.045	6.945	0.708	0.708	0.000	0.000	0.000	0.000
57	B	132	VAL	0	0.003	-0.005	6.878	0.578	0.578	0.000	0.000	0.000	0.000
58	B	133	ASP	-1	-0.835	-0.893	8.031	-0.777	-0.777	0.000	0.000	0.000	0.000
59	B	134	LYS	1	0.915	0.952	9.408	2.067	2.067	0.000	0.000	0.000	0.000
60	B	135	VAL	0	-0.025	-0.001	12.591	0.168	0.168	0.000	0.000	0.000	0.000
61	B	136	MET	0	-0.091	-0.052	12.470	0.167	0.167	0.000	0.000	0.000	0.000
62	B	137	ASP	-1	-0.875	-0.917	14.869	-0.375	-0.375	0.000	0.000	0.000	0.000
63	B	138	GLN	0	-0.022	-0.004	16.761	0.028	0.028	0.000	0.000	0.000	0.000
64	B	139	LYS	1	0.815	0.880	19.111	0.364	0.364	0.000	0.000	0.000	0.000
65	B	140	GLU	-1	-0.818	-0.878	21.668	-0.216	-0.216	0.000	0.000	0.000	0.000
66	B	141	HIS	0	0.030	0.027	17.597	-0.042	-0.042	0.000	0.000	0.000	0.000
67	B	142	LYS	1	0.834	0.893	22.303	0.291	0.291	0.000	0.000	0.000	0.000
68	B	143	LEU	0	-0.022	0.001	22.187	-0.029	-0.029	0.000	0.000	0.000	0.000
69	B	144	ASN	0	-0.023	-0.030	25.615	0.001	0.001	0.000	0.000	0.000	0.000
70	B	145	GLY	0	0.021	0.024	28.970	0.017	0.017	0.000	0.000	0.000	0.000
71	B	146	LYS	1	0.802	0.892	26.555	0.170	0.170	0.000	0.000	0.000	0.000
72	B	147	VAL	0	0.036	0.017	25.197	-0.022	-0.022	0.000	0.000	0.000	0.000
73	B	148	ILE	0	-0.071	-0.027	20.541	0.020	0.020	0.000	0.000	0.000	0.000
74	B	149	ASP	-1	-0.811	-0.909	20.744	-0.171	-0.171	0.000	0.000	0.000	0.000
75	B	150	PRO	0	0.010	0.010	15.380	0.027	0.027	0.000	0.000	0.000	0.000
76	B	151	LYS	1	0.831	0.905	14.943	0.202	0.202	0.000	0.000	0.000	0.000
77	B	152	ARG	1	0.919	0.923	8.486	0.399	0.399	0.000	0.000	0.000	0.000
78	B	153	ALA	0	0.021	0.005	9.273	0.106	0.106	0.000	0.000	0.000	0.000
79	B	154	LYS	1	0.957	0.973	9.363	-0.904	-0.904	0.000	0.000	0.000	0.000
80	B	155	ALA	0	-0.008	0.004	11.835	0.007	0.007	0.000	0.000	0.000	0.000
81	B	156	MET	0	-0.075	-0.026	14.578	-0.078	-0.078	0.000	0.000	0.000	0.000
82	B	157	ALA	0	0.024	0.031	16.563	0.054	0.054	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(B:76:MET)