FMO DATABASE

FMODB ID: 17K3Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-547788.238821
FMO2-HF: Nuclear repulsion	514703.682585
FMO2-HF: Total energy	-33084.556235
FMO2-MP2: Total energy	-33178.834847

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.
-16.24	-8.924	1.169	-3.806	-4.679	-0.021

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 : 0.019 / q_NPA : 0.018

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	B	78	GLY	0	-0.012	-0.008	2.725	-2.805	0.313	0.453	-1.878	-1.693	-0.005
4	B	79	LYS	1	0.927	0.977	4.945	0.389	0.439	-0.001	-0.005	-0.044	0.000
5	B	80	MET	0	-0.024	-0.007	8.241	0.174	0.174	0.000	0.000	0.000	0.000
6	B	81	PHE	0	-0.003	-0.005	11.419	0.027	0.027	0.000	0.000	0.000	0.000
7	B	82	ILE	0	-0.009	-0.010	14.575	-0.027	-0.027	0.000	0.000	0.000	0.000
8	B	83	GLY	0	0.052	0.023	17.649	0.035	0.035	0.000	0.000	0.000	0.000
9	B	84	GLY	0	0.010	0.006	21.062	-0.023	-0.023	0.000	0.000	0.000	0.000
10	B	85	LEU	0	0.048	0.029	20.387	-0.007	-0.007	0.000	0.000	0.000	0.000
11	B	86	SER	0	-0.006	-0.021	24.406	0.017	0.017	0.000	0.000	0.000	0.000
12	B	87	TRP	0	-0.024	-0.028	27.394	-0.008	-0.008	0.000	0.000	0.000	0.000
13	B	88	ASP	-1	-0.820	-0.881	29.794	-0.179	-0.179	0.000	0.000	0.000	0.000
14	B	89	THR	0	-0.048	-0.006	23.508	-0.019	-0.019	0.000	0.000	0.000	0.000
15	B	90	THR	0	-0.023	-0.047	25.734	0.004	0.004	0.000	0.000	0.000	0.000
16	B	91	LYS	1	0.842	0.888	18.297	0.347	0.347	0.000	0.000	0.000	0.000
17	B	92	LYS	1	0.864	0.914	21.196	0.317	0.317	0.000	0.000	0.000	0.000
18	B	93	ASP	-1	-0.729	-0.831	22.541	-0.309	-0.309	0.000	0.000	0.000	0.000
19	B	94	LEU	0	-0.008	-0.003	17.772	-0.037	-0.037	0.000	0.000	0.000	0.000
20	B	95	LYS	1	0.892	0.926	14.961	0.684	0.684	0.000	0.000	0.000	0.000
21	B	96	ASP	-1	-0.783	-0.860	18.072	-0.505	-0.505	0.000	0.000	0.000	0.000
22	B	97	TYR	0	-0.048	-0.038	18.586	-0.022	-0.022	0.000	0.000	0.000	0.000
23	B	98	PHE	0	0.004	-0.021	14.542	-0.023	-0.023	0.000	0.000	0.000	0.000
24	B	99	SER	0	0.009	-0.013	14.929	-0.171	-0.171	0.000	0.000	0.000	0.000
25	B	100	LYS	1	0.865	0.953	15.928	0.474	0.474	0.000	0.000	0.000	0.000
26	B	101	PHE	0	-0.022	-0.005	13.263	0.025	0.025	0.000	0.000	0.000	0.000
27	B	102	GLY	0	0.012	0.024	11.049	-0.279	-0.279	0.000	0.000	0.000	0.000
28	B	103	GLU	-1	-0.899	-0.947	9.742	-1.280	-1.280	0.000	0.000	0.000	0.000
29	B	104	VAL	0	-0.014	-0.005	10.047	-0.343	-0.343	0.000	0.000	0.000	0.000
30	B	105	VAL	0	0.026	0.016	8.136	0.195	0.195	0.000	0.000	0.000	0.000
31	B	106	ASP	-1	-0.847	-0.920	11.479	-0.207	-0.207	0.000	0.000	0.000	0.000
32	B	107	CYS	0	-0.066	-0.003	13.519	-0.091	-0.091	0.000	0.000	0.000	0.000
33	B	108	THR	0	-0.016	-0.012	15.938	0.084	0.084	0.000	0.000	0.000	0.000
34	B	109	LEU	0	0.075	0.041	18.710	-0.014	-0.014	0.000	0.000	0.000	0.000
35	B	110	LYS	1	0.925	0.966	20.937	0.038	0.038	0.000	0.000	0.000	0.000
36	B	111	LEU	0	0.032	0.009	22.511	0.001	0.001	0.000	0.000	0.000	0.000
37	B	112	ASP	-1	-0.825	-0.877	26.157	-0.007	-0.007	0.000	0.000	0.000	0.000
38	B	113	PRO	0	-0.014	-0.020	27.408	-0.006	-0.006	0.000	0.000	0.000	0.000
39	B	114	ILE	0	0.009	0.018	29.715	0.000	0.000	0.000	0.000	0.000	0.000
40	B	115	THR	0	-0.014	-0.026	32.900	-0.006	-0.006	0.000	0.000	0.000	0.000
41	B	116	GLY	0	0.035	0.026	30.242	-0.006	-0.006	0.000	0.000	0.000	0.000
42	B	117	ARG	1	0.922	0.964	30.366	0.046	0.046	0.000	0.000	0.000	0.000
43	B	118	SER	0	0.040	0.008	26.818	0.006	0.006	0.000	0.000	0.000	0.000
44	B	119	ARG	1	0.816	0.886	24.751	0.034	0.034	0.000	0.000	0.000	0.000
45	B	120	GLY	0	0.039	0.036	25.675	0.010	0.010	0.000	0.000	0.000	0.000
46	B	121	PHE	0	-0.050	-0.035	20.032	0.001	0.001	0.000	0.000	0.000	0.000
47	B	122	GLY	0	0.033	0.011	19.041	0.013	0.013	0.000	0.000	0.000	0.000
48	B	123	PHE	0	-0.077	-0.027	13.958	0.040	0.040	0.000	0.000	0.000	0.000
49	B	124	VAL	0	0.017	0.009	11.723	0.020	0.020	0.000	0.000	0.000	0.000
50	B	125	LEU	0	-0.028	-0.005	7.666	0.079	0.079	0.000	0.000	0.000	0.000
51	B	126	PHE	0	0.036	-0.004	7.524	0.264	0.264	0.000	0.000	0.000	0.000
52	B	127	LYS	1	0.958	0.983	5.245	1.697	1.697	0.000	0.000	0.000	0.000
53	B	128	GLU	-1	-0.816	-0.918	2.758	-13.071	-11.058	0.232	-1.085	-1.160	-0.012
54	B	129	SER	0	-0.058	-0.021	2.639	0.840	2.648	0.486	-0.784	-1.510	-0.004
55	B	130	GLU	-1	-0.822	-0.925	4.178	-5.005	-4.678	-0.001	-0.054	-0.272	0.000
56	B	131	SER	0	-0.064	-0.054	7.144	0.735	0.735	0.000	0.000	0.000	0.000
57	B	132	VAL	0	-0.014	-0.017	7.012	0.596	0.596	0.000	0.000	0.000	0.000
58	B	133	ASP	-1	-0.797	-0.875	8.200	-0.928	-0.928	0.000	0.000	0.000	0.000
59	B	134	LYS	1	0.957	0.991	10.568	1.679	1.679	0.000	0.000	0.000	0.000
60	B	135	VAL	0	-0.026	-0.009	12.655	0.181	0.181	0.000	0.000	0.000	0.000
61	B	136	MET	0	-0.097	-0.056	12.475	0.176	0.176	0.000	0.000	0.000	0.000
62	B	137	ASP	-1	-0.893	-0.929	14.876	-0.548	-0.548	0.000	0.000	0.000	0.000
63	B	138	GLN	0	-0.087	-0.036	16.866	0.042	0.042	0.000	0.000	0.000	0.000
64	B	139	LYS	1	0.876	0.918	19.257	0.357	0.357	0.000	0.000	0.000	0.000
65	B	140	GLU	-1	-0.804	-0.881	21.845	-0.235	-0.235	0.000	0.000	0.000	0.000
66	B	141	HIS	0	0.023	0.031	17.511	-0.038	-0.038	0.000	0.000	0.000	0.000
67	B	142	LYS	1	0.832	0.897	22.236	0.290	0.290	0.000	0.000	0.000	0.000
68	B	143	LEU	0	-0.022	-0.012	21.860	-0.031	-0.031	0.000	0.000	0.000	0.000
69	B	144	ASN	0	-0.023	-0.021	25.314	0.000	0.000	0.000	0.000	0.000	0.000
70	B	145	GLY	0	0.001	0.012	28.691	0.017	0.017	0.000	0.000	0.000	0.000
71	B	146	LYS	1	0.841	0.921	26.648	0.178	0.178	0.000	0.000	0.000	0.000
72	B	147	VAL	0	0.026	0.015	24.968	-0.023	-0.023	0.000	0.000	0.000	0.000
73	B	148	ILE	0	-0.067	-0.029	20.176	0.017	0.017	0.000	0.000	0.000	0.000
74	B	149	ASP	-1	-0.820	-0.921	20.299	-0.202	-0.202	0.000	0.000	0.000	0.000
75	B	150	PRO	0	-0.006	0.007	15.283	0.028	0.028	0.000	0.000	0.000	0.000
76	B	151	LYS	1	0.837	0.907	14.787	0.228	0.228	0.000	0.000	0.000	0.000
77	B	152	ARG	1	0.903	0.911	8.641	0.480	0.480	0.000	0.000	0.000	0.000
78	B	153	ALA	0	0.033	0.011	9.196	0.100	0.100	0.000	0.000	0.000	0.000
79	B	154	LYS	1	0.959	0.972	9.173	-0.750	-0.750	0.000	0.000	0.000	0.000
80	B	155	ALA	0	-0.035	-0.009	11.745	-0.001	-0.001	0.000	0.000	0.000	0.000
81	B	156	MET	0	-0.073	-0.018	14.520	-0.066	-0.066	0.000	0.000	0.000	0.000
82	B	157	ALA	0	0.042	0.035	16.492	0.067	0.067	0.000	0.000	0.000	0.000

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