FMO DATABASE

FMODB ID: GN251

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

Total energy (hartree)

FMO2-HF: Electronic energy	-439211.56411
FMO2-HF: Nuclear repulsion	403604.287631
FMO2-HF: Total energy	-35607.276479
FMO2-MP2: Total energy	-35711.12605

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.
21.821	20.99	14.821	-7.206	-6.786	0.06

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 : -0.849 / q_NPA : -0.931

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	-0.019	3.437	-0.850	1.154	0.030	-0.996	-1.039	0.002
4	A	269	GLU	-1	-0.888	-0.943	5.422	28.462	28.462	0.000	0.000	0.000	0.000
5	A	270	THR	0	-0.021	-0.031	1.714	-22.845	-27.714	12.924	-4.733	-3.322	0.056
6	A	271	TYR	0	-0.018	0.001	2.240	-4.273	-2.467	1.844	-1.458	-2.192	0.002
7	A	272	GLU	-1	-0.829	-0.927	3.583	22.319	22.547	0.023	-0.019	-0.233	0.000
8	A	273	ARG	1	0.777	0.883	7.150	-29.128	-29.128	0.000	0.000	0.000	0.000
9	A	274	TYR	0	0.019	0.007	5.489	-3.378	-3.378	0.000	0.000	0.000	0.000
10	A	275	HIS	0	-0.003	0.003	7.144	-2.697	-2.697	0.000	0.000	0.000	0.000
11	A	276	THR	0	-0.013	-0.035	8.794	-3.081	-3.081	0.000	0.000	0.000	0.000
12	A	277	GLU	-1	-0.836	-0.892	10.783	21.944	21.944	0.000	0.000	0.000	0.000
13	A	278	SER	0	-0.037	-0.010	10.860	-2.401	-2.401	0.000	0.000	0.000	0.000
14	A	279	LEU	0	-0.012	-0.020	12.760	-1.798	-1.798	0.000	0.000	0.000	0.000
15	A	280	GLN	0	-0.082	-0.034	14.902	-1.877	-1.877	0.000	0.000	0.000	0.000
16	A	281	ASN	0	-0.103	-0.051	14.646	-1.391	-1.391	0.000	0.000	0.000	0.000
17	A	282	MET	0	0.005	0.032	16.554	-0.344	-0.344	0.000	0.000	0.000	0.000
18	A	283	SER	0	-0.029	-0.049	19.161	-0.608	-0.608	0.000	0.000	0.000	0.000
19	A	284	LYS	1	0.972	0.971	22.155	-11.065	-11.065	0.000	0.000	0.000	0.000
20	A	285	GLN	0	0.020	-0.005	23.990	0.317	0.317	0.000	0.000	0.000	0.000
21	A	286	GLU	-1	-0.849	-0.881	20.814	13.722	13.722	0.000	0.000	0.000	0.000
22	A	287	LEU	0	0.042	0.026	17.582	0.109	0.109	0.000	0.000	0.000	0.000
23	A	288	ILE	0	-0.020	-0.013	20.655	0.056	0.056	0.000	0.000	0.000	0.000
24	A	289	LYS	1	0.813	0.903	20.772	-14.028	-14.028	0.000	0.000	0.000	0.000
25	A	290	GLU	-1	-0.775	-0.893	16.854	14.715	14.715	0.000	0.000	0.000	0.000
26	A	291	TYR	0	-0.101	-0.059	19.231	0.388	0.388	0.000	0.000	0.000	0.000
27	A	292	LEU	0	0.032	0.009	20.402	-0.156	-0.156	0.000	0.000	0.000	0.000
28	A	293	GLU	-1	-0.899	-0.937	19.291	12.433	12.433	0.000	0.000	0.000	0.000
29	A	294	LEU	0	0.008	0.003	15.505	0.066	0.066	0.000	0.000	0.000	0.000
30	A	295	GLU	-1	-0.843	-0.911	19.070	11.411	11.411	0.000	0.000	0.000	0.000
31	A	296	LYS	1	0.805	0.901	22.427	-12.256	-12.256	0.000	0.000	0.000	0.000
32	A	297	SER	0	-0.029	-0.022	18.155	-0.423	-0.423	0.000	0.000	0.000	0.000
33	A	298	LEU	0	0.005	0.028	20.230	0.004	0.004	0.000	0.000	0.000	0.000
34	A	299	SER	0	0.074	0.028	21.550	-0.100	-0.100	0.000	0.000	0.000	0.000
35	A	300	ARG	1	0.896	0.945	20.587	-12.828	-12.828	0.000	0.000	0.000	0.000
36	A	301	MET	0	-0.015	-0.006	17.195	-0.088	-0.088	0.000	0.000	0.000	0.000
37	A	302	GLU	-1	-0.960	-0.977	22.868	10.636	10.636	0.000	0.000	0.000	0.000
38	A	303	ASP	-1	-0.830	-0.920	25.301	9.263	9.263	0.000	0.000	0.000	0.000
39	A	304	GLU	-1	-0.884	-0.920	24.667	10.676	10.676	0.000	0.000	0.000	0.000
40	A	305	ASN	0	0.000	0.001	23.921	-0.523	-0.523	0.000	0.000	0.000	0.000
41	A	306	ASN	0	-0.027	-0.027	26.458	-0.252	-0.252	0.000	0.000	0.000	0.000
42	A	307	ARG	1	0.774	0.870	27.861	-10.047	-10.047	0.000	0.000	0.000	0.000
43	A	308	LEU	0	0.008	-0.002	25.552	-0.273	-0.273	0.000	0.000	0.000	0.000
44	A	309	ARG	1	0.895	0.943	28.435	-9.836	-9.836	0.000	0.000	0.000	0.000
45	A	310	LEU	0	-0.035	-0.009	30.939	-0.257	-0.257	0.000	0.000	0.000	0.000
46	A	311	GLU	-1	-0.889	-0.944	32.491	8.682	8.682	0.000	0.000	0.000	0.000
47	A	312	SER	0	0.047	0.016	31.070	-0.087	-0.087	0.000	0.000	0.000	0.000
48	A	313	LYS	1	0.909	0.983	33.219	-7.870	-7.870	0.000	0.000	0.000	0.000
49	A	314	ARG	1	0.904	0.933	35.564	-8.290	-8.290	0.000	0.000	0.000	0.000
50	A	315	LEU	0	-0.017	-0.002	33.804	-0.201	-0.201	0.000	0.000	0.000	0.000
51	A	319	ASP	-1	-0.822	-0.909	35.753	7.849	7.849	0.000	0.000	0.000	0.000
52	A	320	ALA	0	-0.011	-0.001	37.683	-0.181	-0.181	0.000	0.000	0.000	0.000
53	A	321	ARG	1	0.856	0.917	40.682	-6.818	-6.818	0.000	0.000	0.000	0.000
54	A	322	VAL	0	0.020	-0.001	38.053	-0.139	-0.139	0.000	0.000	0.000	0.000
55	A	323	ARG	1	0.856	0.912	41.224	-6.912	-6.912	0.000	0.000	0.000	0.000
56	A	324	GLU	-1	-0.831	-0.904	43.160	6.377	6.377	0.000	0.000	0.000	0.000
57	A	325	LEU	0	-0.020	-0.008	43.199	-0.138	-0.138	0.000	0.000	0.000	0.000
58	A	326	GLU	-1	-0.798	-0.882	42.873	6.850	6.850	0.000	0.000	0.000	0.000
59	A	327	LEU	0	-0.071	-0.022	45.644	-0.089	-0.089	0.000	0.000	0.000	0.000
60	A	328	GLU	-1	-0.772	-0.861	48.527	5.585	5.585	0.000	0.000	0.000	0.000
61	A	329	LEU	0	-0.014	-0.005	45.805	-0.100	-0.100	0.000	0.000	0.000	0.000
62	A	330	ASP	-1	-0.844	-0.914	47.718	6.384	6.384	0.000	0.000	0.000	0.000
63	A	331	ARG	1	0.693	0.815	50.602	-5.588	-5.588	0.000	0.000	0.000	0.000
64	A	332	LEU	0	0.014	0.010	52.610	-0.109	-0.109	0.000	0.000	0.000	0.000
65	A	333	ARG	1	0.761	0.851	45.751	-6.591	-6.591	0.000	0.000	0.000	0.000
66	A	334	ALA	0	-0.007	0.001	53.626	-0.074	-0.074	0.000	0.000	0.000	0.000
67	A	335	GLU	-1	-0.818	-0.893	56.155	5.173	5.173	0.000	0.000	0.000	0.000
68	A	336	ASN	0	-0.029	-0.035	56.304	-0.145	-0.145	0.000	0.000	0.000	0.000
69	A	337	LEU	0	-0.025	-0.001	55.802	-0.049	-0.049	0.000	0.000	0.000	0.000
70	A	338	GLN	0	-0.074	-0.039	58.421	-0.021	-0.021	0.000	0.000	0.000	0.000
71	A	339	LEU	0	0.080	0.042	61.607	-0.071	-0.071	0.000	0.000	0.000	0.000
72	A	340	LEU	0	-0.031	0.009	59.011	-0.076	-0.076	0.000	0.000	0.000	0.000
73	A	341	THR	0	-0.066	-0.049	61.686	-0.066	-0.066	0.000	0.000	0.000	0.000
74	A	342	GLU	-1	-0.849	-0.923	64.239	4.719	4.719	0.000	0.000	0.000	0.000
75	A	343	ASN	0	-0.073	-0.061	65.328	-0.130	-0.130	0.000	0.000	0.000	0.000
76	A	344	GLU	-1	-0.936	-0.958	65.432	4.700	4.700	0.000	0.000	0.000	0.000
77	A	345	LEU	0	-0.034	-0.005	67.483	-0.079	-0.079	0.000	0.000	0.000	0.000
78	A	346	HIS	0	-0.053	-0.056	70.087	-0.055	-0.055	0.000	0.000	0.000	0.000
79	A	347	ARG	1	0.817	0.906	69.843	-4.373	-4.373	0.000	0.000	0.000	0.000
80	A	348	GLN	0	-0.012	-0.017	70.993	-0.036	-0.036	0.000	0.000	0.000	0.000
81	A	349	GLN	0	-0.060	-0.011	72.953	-0.061	-0.061	0.000	0.000	0.000	0.000
82	A	350	GLU	-1	-0.885	-0.911	75.817	4.133	4.133	0.000	0.000	0.000	0.000

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