FMO DATABASE

FMODB ID: V5L61

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

Total energy (hartree)

FMO2-HF: Electronic energy	-547348.837242
FMO2-HF: Nuclear repulsion	514264.627211
FMO2-HF: Total energy	-33084.210031
FMO2-MP2: Total energy	-33178.447242

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.
-11.367	-5.945	1.032	-2.847	-3.606	-0.01

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 : 0.018 / q_NPA : 0.014

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	-0.016	-0.010	2.640	-3.130	-0.025	0.644	-1.945	-1.804	-0.007
4	B	79	LYS	1	0.920	0.977	4.853	0.270	0.320	-0.001	-0.007	-0.042	0.000
5	B	80	MET	0	-0.027	-0.010	8.119	0.203	0.203	0.000	0.000	0.000	0.000
6	B	81	PHE	0	0.000	-0.004	11.299	0.017	0.017	0.000	0.000	0.000	0.000
7	B	82	ILE	0	-0.006	-0.005	14.615	-0.025	-0.025	0.000	0.000	0.000	0.000
8	B	83	GLY	0	0.045	0.018	17.529	0.029	0.029	0.000	0.000	0.000	0.000
9	B	84	GLY	0	0.053	0.024	20.933	-0.022	-0.022	0.000	0.000	0.000	0.000
10	B	85	LEU	0	0.026	0.029	20.289	-0.007	-0.007	0.000	0.000	0.000	0.000
11	B	86	SER	0	-0.007	-0.015	24.299	0.016	0.016	0.000	0.000	0.000	0.000
12	B	87	TRP	0	-0.028	-0.030	27.296	-0.008	-0.008	0.000	0.000	0.000	0.000
13	B	88	ASP	-1	-0.840	-0.895	29.692	-0.152	-0.152	0.000	0.000	0.000	0.000
14	B	89	THR	0	-0.033	-0.003	23.479	-0.019	-0.019	0.000	0.000	0.000	0.000
15	B	90	THR	0	0.009	0.010	25.668	0.000	0.000	0.000	0.000	0.000	0.000
16	B	91	LYS	1	0.922	0.951	18.874	0.308	0.308	0.000	0.000	0.000	0.000
17	B	92	LYS	1	0.896	0.934	21.149	0.270	0.270	0.000	0.000	0.000	0.000
18	B	93	ASP	-1	-0.751	-0.870	22.513	-0.286	-0.286	0.000	0.000	0.000	0.000
19	B	94	LEU	0	-0.023	-0.013	17.846	-0.031	-0.031	0.000	0.000	0.000	0.000
20	B	95	LYS	1	0.932	0.944	15.828	0.617	0.617	0.000	0.000	0.000	0.000
21	B	96	ASP	-1	-0.797	-0.879	18.316	-0.482	-0.482	0.000	0.000	0.000	0.000
22	B	97	TYR	0	-0.068	-0.072	18.611	-0.024	-0.024	0.000	0.000	0.000	0.000
23	B	98	PHE	0	-0.007	-0.025	14.492	-0.018	-0.018	0.000	0.000	0.000	0.000
24	B	99	SER	0	0.017	-0.007	15.054	-0.160	-0.160	0.000	0.000	0.000	0.000
25	B	100	LYS	1	0.867	0.952	16.336	0.429	0.429	0.000	0.000	0.000	0.000
26	B	101	PHE	0	-0.023	-0.005	13.440	0.028	0.028	0.000	0.000	0.000	0.000
27	B	102	GLY	0	0.015	0.026	11.457	-0.245	-0.245	0.000	0.000	0.000	0.000
28	B	103	GLU	-1	-0.913	-0.952	10.140	-1.181	-1.181	0.000	0.000	0.000	0.000
29	B	104	VAL	0	-0.031	-0.015	10.431	-0.322	-0.322	0.000	0.000	0.000	0.000
30	B	105	VAL	0	-0.011	0.000	8.238	0.160	0.160	0.000	0.000	0.000	0.000
31	B	106	ASP	-1	-0.875	-0.950	11.560	-0.202	-0.202	0.000	0.000	0.000	0.000
32	B	107	CYS	0	-0.087	-0.020	13.472	-0.083	-0.083	0.000	0.000	0.000	0.000
33	B	108	THR	0	-0.044	-0.021	15.876	0.079	0.079	0.000	0.000	0.000	0.000
34	B	109	LEU	0	0.084	0.036	18.628	-0.009	-0.009	0.000	0.000	0.000	0.000
35	B	110	LYS	1	0.921	0.967	20.856	0.022	0.022	0.000	0.000	0.000	0.000
36	B	111	LEU	0	0.030	0.005	22.397	0.002	0.002	0.000	0.000	0.000	0.000
37	B	112	ASP	-1	-0.904	-0.953	26.047	0.006	0.006	0.000	0.000	0.000	0.000
38	B	113	PRO	0	-0.027	-0.024	27.477	-0.006	-0.006	0.000	0.000	0.000	0.000
39	B	114	ILE	0	0.018	0.020	29.604	-0.001	-0.001	0.000	0.000	0.000	0.000
40	B	115	THR	0	0.011	0.001	32.777	-0.007	-0.007	0.000	0.000	0.000	0.000
41	B	116	GLY	0	0.037	0.028	30.139	-0.006	-0.006	0.000	0.000	0.000	0.000
42	B	117	ARG	1	0.933	0.968	30.262	0.032	0.032	0.000	0.000	0.000	0.000
43	B	118	SER	0	0.023	0.004	26.962	0.007	0.007	0.000	0.000	0.000	0.000
44	B	119	ARG	1	0.872	0.935	24.644	0.018	0.018	0.000	0.000	0.000	0.000
45	B	120	GLY	0	0.042	0.040	25.552	0.011	0.011	0.000	0.000	0.000	0.000
46	B	121	PHE	0	-0.039	-0.031	20.131	0.002	0.002	0.000	0.000	0.000	0.000
47	B	122	GLY	0	0.021	0.005	18.929	0.008	0.008	0.000	0.000	0.000	0.000
48	B	123	PHE	0	-0.065	-0.023	13.531	0.043	0.043	0.000	0.000	0.000	0.000
49	B	124	VAL	0	0.025	0.014	11.547	0.015	0.015	0.000	0.000	0.000	0.000
50	B	125	LEU	0	-0.032	-0.007	7.523	0.092	0.092	0.000	0.000	0.000	0.000
51	B	126	PHE	0	0.037	-0.004	7.528	0.229	0.229	0.000	0.000	0.000	0.000
52	B	127	LYS	1	1.002	0.998	5.990	1.363	1.363	0.000	0.000	0.000	0.000
53	B	128	GLU	-1	-0.863	-0.929	3.674	-8.843	-8.295	0.004	-0.263	-0.288	-0.001
54	B	129	SER	0	-0.070	-0.027	2.565	1.988	3.452	0.386	-0.607	-1.243	-0.002
55	B	130	GLU	-1	-0.799	-0.917	4.671	-3.955	-3.700	-0.001	-0.025	-0.229	0.000
56	B	131	SER	0	-0.063	-0.054	7.310	0.666	0.666	0.000	0.000	0.000	0.000
57	B	132	VAL	0	-0.024	-0.023	6.971	0.553	0.553	0.000	0.000	0.000	0.000
58	B	133	ASP	-1	-0.818	-0.907	8.468	-0.775	-0.775	0.000	0.000	0.000	0.000
59	B	134	LYS	1	0.951	0.989	10.903	1.417	1.417	0.000	0.000	0.000	0.000
60	B	135	VAL	0	-0.021	-0.004	12.610	0.160	0.160	0.000	0.000	0.000	0.000
61	B	136	MET	0	-0.113	-0.060	12.329	0.173	0.173	0.000	0.000	0.000	0.000
62	B	137	ASP	-1	-0.892	-0.928	14.780	-0.478	-0.478	0.000	0.000	0.000	0.000
63	B	138	GLN	0	-0.083	-0.042	16.893	0.034	0.034	0.000	0.000	0.000	0.000
64	B	139	LYS	1	0.870	0.923	19.186	0.287	0.287	0.000	0.000	0.000	0.000
65	B	140	GLU	-1	-0.838	-0.916	21.773	-0.205	-0.205	0.000	0.000	0.000	0.000
66	B	141	HIS	0	0.028	0.059	17.593	-0.034	-0.034	0.000	0.000	0.000	0.000
67	B	142	LYS	1	0.880	0.938	22.160	0.256	0.256	0.000	0.000	0.000	0.000
68	B	143	LEU	0	-0.028	-0.016	21.769	-0.029	-0.029	0.000	0.000	0.000	0.000
69	B	144	ASN	0	-0.026	-0.023	25.242	0.014	0.014	0.000	0.000	0.000	0.000
70	B	145	GLY	0	0.000	0.009	28.620	0.015	0.015	0.000	0.000	0.000	0.000
71	B	146	LYS	1	0.841	0.913	26.785	0.143	0.143	0.000	0.000	0.000	0.000
72	B	147	VAL	0	0.023	0.009	24.927	-0.022	-0.022	0.000	0.000	0.000	0.000
73	B	148	ILE	0	-0.078	-0.031	20.041	0.013	0.013	0.000	0.000	0.000	0.000
74	B	149	ASP	-1	-0.890	-0.964	20.182	-0.154	-0.154	0.000	0.000	0.000	0.000
75	B	150	PRO	0	-0.015	-0.006	15.209	0.024	0.024	0.000	0.000	0.000	0.000
76	B	151	LYS	1	0.953	0.981	14.652	0.085	0.085	0.000	0.000	0.000	0.000
77	B	152	ARG	1	0.915	0.936	8.463	0.263	0.263	0.000	0.000	0.000	0.000
78	B	153	ALA	0	0.039	0.013	9.038	0.087	0.087	0.000	0.000	0.000	0.000
79	B	154	LYS	1	0.960	0.974	8.925	-0.875	-0.875	0.000	0.000	0.000	0.000
80	B	155	ALA	0	-0.044	-0.015	11.465	-0.018	-0.018	0.000	0.000	0.000	0.000
81	B	156	MET	0	-0.071	-0.018	14.370	-0.073	-0.073	0.000	0.000	0.000	0.000
82	B	157	ALA	0	0.041	0.034	16.337	0.066	0.066	0.000	0.000	0.000	0.000

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