FMO DATABASE

FMODB ID: VRGQ1

Calculation Name: 3S9G-A-Xray372

Preferred Name: Protein HEXIM1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3S9G

Chain ID: A

ChEMBL ID: CHEMBL3120044

UniProt ID: O94992

Base Structure: X-ray

Registration Date: 2023-06-19

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
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-438993.594631
FMO2-HF: Nuclear repulsion	403387.851235
FMO2-HF: Total energy	-35605.743396
FMO2-MP2: Total energy	-35709.713059

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:266:ASP)

Summations of interaction energy for fragment #1(A:266:ASP)

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.
53.645	57.631	2.331	-2.535	-3.782	0.001

Interaction energy analysis for fragmet #1(A:266:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.930 / q_NPA : -0.977

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	A	268	SER	0	-0.023	-0.029	3.170	-3.443	-1.243	0.065	-1.125	-1.140	0.000
4	A	269	GLU	-1	-0.884	-0.934	4.803	24.412	24.586	-0.001	-0.005	-0.168	0.000
5	A	270	THR	0	-0.033	-0.025	3.970	-1.307	-0.949	0.000	-0.069	-0.289	0.000
6	A	271	TYR	0	0.027	0.022	2.024	-2.095	-1.108	2.266	-1.261	-1.991	0.001
7	A	272	GLU	-1	-0.825	-0.913	4.198	22.748	23.015	0.001	-0.075	-0.194	0.000
8	A	273	ARG	1	0.798	0.899	7.241	-25.853	-25.853	0.000	0.000	0.000	0.000
9	A	274	TYR	0	0.040	0.018	5.897	-2.360	-2.360	0.000	0.000	0.000	0.000
10	A	275	HIS	0	0.014	0.008	7.074	-1.820	-1.820	0.000	0.000	0.000	0.000
11	A	276	THR	0	-0.016	-0.022	8.897	-3.115	-3.115	0.000	0.000	0.000	0.000
12	A	277	GLU	-1	-0.932	-0.976	11.372	22.398	22.398	0.000	0.000	0.000	0.000
13	A	278	SER	0	0.012	0.013	10.762	-1.873	-1.873	0.000	0.000	0.000	0.000
14	A	279	LEU	0	-0.015	0.000	12.878	-1.381	-1.381	0.000	0.000	0.000	0.000
15	A	280	GLN	0	-0.063	-0.037	15.202	-1.873	-1.873	0.000	0.000	0.000	0.000
16	A	281	ASN	0	-0.117	-0.050	14.567	-0.979	-0.979	0.000	0.000	0.000	0.000
17	A	282	MET	0	0.009	0.041	16.946	-0.290	-0.290	0.000	0.000	0.000	0.000
18	A	283	SER	0	-0.040	-0.057	19.341	-0.652	-0.652	0.000	0.000	0.000	0.000
19	A	284	LYS	1	0.997	0.975	22.226	-10.737	-10.737	0.000	0.000	0.000	0.000
20	A	285	GLN	0	-0.009	-0.031	23.795	0.253	0.253	0.000	0.000	0.000	0.000
21	A	286	GLU	-1	-0.841	-0.875	20.690	13.835	13.835	0.000	0.000	0.000	0.000
22	A	287	LEU	0	0.073	0.038	17.489	0.198	0.198	0.000	0.000	0.000	0.000
23	A	288	ILE	0	-0.047	-0.024	20.480	0.002	0.002	0.000	0.000	0.000	0.000
24	A	289	LYS	1	0.900	0.951	22.286	-12.126	-12.126	0.000	0.000	0.000	0.000
25	A	290	GLU	-1	-0.872	-0.947	16.102	16.209	16.209	0.000	0.000	0.000	0.000
26	A	291	TYR	0	-0.017	0.005	18.737	0.313	0.313	0.000	0.000	0.000	0.000
27	A	292	LEU	0	0.002	-0.003	19.992	-0.174	-0.174	0.000	0.000	0.000	0.000
28	A	293	GLU	-1	-1.045	-1.017	17.192	14.728	14.728	0.000	0.000	0.000	0.000
29	A	294	LEU	0	0.027	0.009	14.587	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	295	GLU	-1	-0.895	-0.950	18.762	11.377	11.377	0.000	0.000	0.000	0.000
31	A	296	LYS	1	0.911	0.959	22.011	-12.127	-12.127	0.000	0.000	0.000	0.000
32	A	297	SER	0	-0.054	-0.031	17.438	-0.394	-0.394	0.000	0.000	0.000	0.000
33	A	298	LEU	0	0.081	0.043	19.969	0.058	0.058	0.000	0.000	0.000	0.000
34	A	299	SER	0	-0.023	0.003	21.176	-0.368	-0.368	0.000	0.000	0.000	0.000
35	A	300	ARG	1	0.966	0.990	20.631	-12.780	-12.780	0.000	0.000	0.000	0.000
36	A	301	MET	0	-0.012	-0.026	17.604	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	302	GLU	-1	-0.954	-0.970	22.523	10.888	10.888	0.000	0.000	0.000	0.000
38	A	303	ASP	-1	-0.885	-0.941	25.115	9.690	9.690	0.000	0.000	0.000	0.000
39	A	304	GLU	-1	-0.954	-0.970	23.502	11.446	11.446	0.000	0.000	0.000	0.000
40	A	305	ASN	0	0.024	0.003	24.327	-0.516	-0.516	0.000	0.000	0.000	0.000
41	A	306	ASN	0	0.004	0.007	26.105	-0.176	-0.176	0.000	0.000	0.000	0.000
42	A	307	ARG	1	0.887	0.954	27.875	-10.146	-10.146	0.000	0.000	0.000	0.000
43	A	308	LEU	0	0.001	-0.011	24.923	-0.292	-0.292	0.000	0.000	0.000	0.000
44	A	309	ARG	1	0.886	0.934	28.265	-9.889	-9.889	0.000	0.000	0.000	0.000
45	A	310	LEU	0	-0.043	-0.014	30.607	-0.280	-0.280	0.000	0.000	0.000	0.000
46	A	311	GLU	-1	-0.934	-0.977	31.990	8.766	8.766	0.000	0.000	0.000	0.000
47	A	312	SER	0	-0.012	-0.013	30.623	-0.217	-0.217	0.000	0.000	0.000	0.000
48	A	313	LYS	1	0.956	0.988	32.735	-8.010	-8.010	0.000	0.000	0.000	0.000
49	A	314	ARG	1	0.961	0.983	35.656	-8.248	-8.248	0.000	0.000	0.000	0.000
50	A	315	LEU	0	-0.011	-0.017	33.877	-0.229	-0.229	0.000	0.000	0.000	0.000
51	A	319	ASP	-1	-0.841	-0.921	35.510	8.008	8.008	0.000	0.000	0.000	0.000
52	A	320	ALA	0	0.008	0.017	37.483	-0.188	-0.188	0.000	0.000	0.000	0.000
53	A	321	ARG	1	0.910	0.976	40.313	-6.990	-6.990	0.000	0.000	0.000	0.000
54	A	322	VAL	0	0.012	-0.003	37.429	-0.141	-0.141	0.000	0.000	0.000	0.000
55	A	323	ARG	1	0.909	0.959	40.782	-7.087	-7.087	0.000	0.000	0.000	0.000
56	A	324	GLU	-1	-0.886	-0.962	42.675	6.458	6.458	0.000	0.000	0.000	0.000
57	A	325	LEU	0	-0.039	-0.034	43.014	-0.135	-0.135	0.000	0.000	0.000	0.000
58	A	326	GLU	-1	-0.931	-0.962	42.232	7.047	7.047	0.000	0.000	0.000	0.000
59	A	327	LEU	0	-0.035	-0.008	45.236	-0.090	-0.090	0.000	0.000	0.000	0.000
60	A	328	GLU	-1	-0.832	-0.882	48.398	5.686	5.686	0.000	0.000	0.000	0.000
61	A	329	LEU	0	-0.014	-0.019	45.478	-0.111	-0.111	0.000	0.000	0.000	0.000
62	A	330	ASP	-1	-0.913	-0.953	47.991	6.412	6.412	0.000	0.000	0.000	0.000
63	A	331	ARG	1	0.758	0.863	50.567	-5.695	-5.695	0.000	0.000	0.000	0.000
64	A	332	LEU	0	-0.009	-0.013	52.942	-0.108	-0.108	0.000	0.000	0.000	0.000
65	A	333	ARG	1	0.923	0.960	46.115	-6.610	-6.610	0.000	0.000	0.000	0.000
66	A	334	ALA	0	-0.021	-0.005	53.575	-0.062	-0.062	0.000	0.000	0.000	0.000
67	A	335	GLU	-1	-0.858	-0.934	55.987	5.118	5.118	0.000	0.000	0.000	0.000
68	A	336	ASN	0	-0.015	-0.015	55.762	-0.137	-0.137	0.000	0.000	0.000	0.000
69	A	337	LEU	0	-0.043	-0.010	55.823	-0.063	-0.063	0.000	0.000	0.000	0.000
70	A	338	GLN	0	-0.004	-0.004	58.368	-0.018	-0.018	0.000	0.000	0.000	0.000
71	A	339	LEU	0	0.105	0.058	61.503	-0.059	-0.059	0.000	0.000	0.000	0.000
72	A	340	LEU	0	-0.069	-0.016	58.726	-0.065	-0.065	0.000	0.000	0.000	0.000
73	A	341	THR	0	-0.082	-0.056	61.385	-0.060	-0.060	0.000	0.000	0.000	0.000
74	A	342	GLU	-1	-0.903	-0.957	64.072	4.734	4.734	0.000	0.000	0.000	0.000
75	A	343	ASN	0	-0.045	-0.037	64.788	-0.130	-0.130	0.000	0.000	0.000	0.000
76	A	344	GLU	-1	-0.947	-0.963	64.753	4.809	4.809	0.000	0.000	0.000	0.000
77	A	345	LEU	0	-0.015	-0.001	67.274	-0.081	-0.081	0.000	0.000	0.000	0.000
78	A	346	HIS	0	-0.065	-0.047	70.066	-0.059	-0.059	0.000	0.000	0.000	0.000
79	A	347	ARG	1	0.793	0.901	69.491	-4.433	-4.433	0.000	0.000	0.000	0.000
80	A	348	GLN	0	0.016	-0.011	71.110	-0.032	-0.032	0.000	0.000	0.000	0.000
81	A	349	GLN	0	-0.079	-0.024	72.716	-0.055	-0.055	0.000	0.000	0.000	0.000
82	A	350	GLU	-1	-0.871	-0.905	75.628	4.223	4.223	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:266:ASP)