FMO DATABASE

FMODB ID: 9Y5L2

Calculation Name: 3S9G-A-Xray313

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	84
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-442831.689348
FMO2-HF: Nuclear repulsion	407055.005345
FMO2-HF: Total energy	-35776.684002
FMO2-MP2: Total energy	-35881.198021

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:265:ACE )

Summations of interaction energy for fragment #1(A:265:ACE )

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.
1.869	3.675	2.567	-2.066	-2.308	-0.011

Interaction energy analysis for fragmet #1(A:265:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.015

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	267	PHE	0	-0.019	0.011	3.846	1.273	2.106	-0.005	-0.409	-0.419	-0.001
4	A	268	SER	0	-0.039	-0.036	4.343	0.003	0.056	0.000	-0.019	-0.034	0.000
5	A	269	GLU	-1	-0.881	-0.933	5.299	0.452	0.452	0.000	0.000	0.000	0.000
6	A	270	THR	0	-0.029	-0.022	7.499	-0.026	-0.026	0.000	0.000	0.000	0.000
7	A	271	TYR	0	0.032	0.029	2.828	-0.985	-0.162	2.572	-1.629	-1.767	-0.010
8	A	272	GLU	-1	-0.824	-0.915	4.643	1.291	1.388	0.000	-0.009	-0.088	0.000
9	A	273	ARG	1	0.800	0.901	6.629	-0.128	-0.128	0.000	0.000	0.000	0.000
10	A	274	TYR	0	0.041	0.019	6.971	0.000	0.000	0.000	0.000	0.000	0.000
11	A	275	HIS	0	0.015	0.007	6.046	-0.074	-0.074	0.000	0.000	0.000	0.000
12	A	276	THR	0	-0.019	-0.024	8.096	-0.038	-0.038	0.000	0.000	0.000	0.000
13	A	277	GLU	-1	-0.930	-0.975	11.117	-0.125	-0.125	0.000	0.000	0.000	0.000
14	A	278	SER	0	0.010	0.013	10.567	-0.019	-0.019	0.000	0.000	0.000	0.000
15	A	279	LEU	0	-0.009	0.001	11.259	0.001	0.001	0.000	0.000	0.000	0.000
16	A	280	GLN	0	-0.067	-0.038	14.146	-0.022	-0.022	0.000	0.000	0.000	0.000
17	A	281	ASN	0	-0.117	-0.049	15.408	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	282	MET	0	0.009	0.041	15.348	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	283	SER	0	-0.040	-0.058	18.368	0.010	0.010	0.000	0.000	0.000	0.000
20	A	284	LYS	1	0.997	0.975	20.619	-0.055	-0.055	0.000	0.000	0.000	0.000
21	A	285	GLN	0	-0.009	-0.030	21.946	0.008	0.008	0.000	0.000	0.000	0.000
22	A	286	GLU	-1	-0.840	-0.875	19.187	0.023	0.023	0.000	0.000	0.000	0.000
23	A	287	LEU	0	0.073	0.039	15.799	0.010	0.010	0.000	0.000	0.000	0.000
24	A	288	ILE	0	-0.047	-0.024	18.405	0.017	0.017	0.000	0.000	0.000	0.000
25	A	289	LYS	1	0.903	0.952	20.283	-0.038	-0.038	0.000	0.000	0.000	0.000
26	A	290	GLU	-1	-0.875	-0.948	14.039	0.099	0.099	0.000	0.000	0.000	0.000
27	A	291	TYR	0	-0.017	0.005	16.397	0.029	0.029	0.000	0.000	0.000	0.000
28	A	292	LEU	0	0.003	-0.002	17.647	0.008	0.008	0.000	0.000	0.000	0.000
29	A	293	GLU	-1	-1.042	-1.016	14.909	0.130	0.130	0.000	0.000	0.000	0.000
30	A	294	LEU	0	0.024	0.008	12.058	0.008	0.008	0.000	0.000	0.000	0.000
31	A	295	GLU	-1	-0.900	-0.951	16.242	0.166	0.166	0.000	0.000	0.000	0.000
32	A	296	LYS	1	0.917	0.961	19.459	-0.104	-0.104	0.000	0.000	0.000	0.000
33	A	297	SER	0	-0.056	-0.031	14.931	-0.014	-0.014	0.000	0.000	0.000	0.000
34	A	298	LEU	0	0.083	0.044	17.418	0.006	0.006	0.000	0.000	0.000	0.000
35	A	299	SER	0	-0.023	0.003	18.630	-0.013	-0.013	0.000	0.000	0.000	0.000
36	A	300	ARG	1	0.968	0.991	18.238	-0.149	-0.149	0.000	0.000	0.000	0.000
37	A	301	MET	0	-0.016	-0.027	15.181	0.006	0.006	0.000	0.000	0.000	0.000
38	A	302	GLU	-1	-0.952	-0.970	20.114	0.168	0.168	0.000	0.000	0.000	0.000
39	A	303	ASP	-1	-0.884	-0.940	22.692	0.104	0.104	0.000	0.000	0.000	0.000
40	A	304	GLU	-1	-0.953	-0.970	21.324	0.121	0.121	0.000	0.000	0.000	0.000
41	A	305	ASN	0	0.023	0.003	21.819	-0.014	-0.014	0.000	0.000	0.000	0.000
42	A	306	ASN	0	0.003	0.007	23.661	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	307	ARG	1	0.888	0.954	25.721	-0.095	-0.095	0.000	0.000	0.000	0.000
44	A	308	LEU	0	0.000	-0.011	22.563	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	309	ARG	1	0.885	0.934	25.692	-0.129	-0.129	0.000	0.000	0.000	0.000
46	A	310	LEU	0	-0.042	-0.014	28.097	-0.007	-0.007	0.000	0.000	0.000	0.000
47	A	311	GLU	-1	-0.933	-0.977	29.623	0.064	0.064	0.000	0.000	0.000	0.000
48	A	312	SER	0	-0.015	-0.014	28.169	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	313	LYS	1	0.958	0.989	30.285	-0.074	-0.074	0.000	0.000	0.000	0.000
50	A	314	ARG	1	0.961	0.984	33.147	-0.060	-0.060	0.000	0.000	0.000	0.000
51	A	315	LEU	0	-0.011	-0.018	31.545	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	319	ASP	-1	-0.841	-0.921	33.052	0.063	0.063	0.000	0.000	0.000	0.000
53	A	320	ALA	0	0.009	0.017	35.041	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	321	ARG	1	0.911	0.977	37.954	-0.038	-0.038	0.000	0.000	0.000	0.000
55	A	322	VAL	0	0.013	-0.003	35.082	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	323	ARG	1	0.909	0.959	38.425	-0.045	-0.045	0.000	0.000	0.000	0.000
57	A	324	GLU	-1	-0.888	-0.962	40.248	0.034	0.034	0.000	0.000	0.000	0.000
58	A	325	LEU	0	-0.039	-0.034	40.722	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	326	GLU	-1	-0.931	-0.962	40.029	0.035	0.035	0.000	0.000	0.000	0.000
60	A	327	LEU	0	-0.033	-0.008	42.913	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	328	GLU	-1	-0.831	-0.882	46.022	0.024	0.024	0.000	0.000	0.000	0.000
62	A	329	LEU	0	-0.014	-0.018	43.268	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	330	ASP	-1	-0.913	-0.953	45.751	0.030	0.030	0.000	0.000	0.000	0.000
64	A	331	ARG	1	0.757	0.863	48.326	-0.024	-0.024	0.000	0.000	0.000	0.000
65	A	332	LEU	0	-0.010	-0.014	50.761	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	333	ARG	1	0.923	0.960	44.034	-0.028	-0.028	0.000	0.000	0.000	0.000
67	A	334	ALA	0	-0.022	-0.005	51.445	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	335	GLU	-1	-0.856	-0.934	53.844	0.018	0.018	0.000	0.000	0.000	0.000
69	A	336	ASN	0	-0.016	-0.016	53.704	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	337	LEU	0	-0.042	-0.010	53.860	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	338	GLN	0	-0.005	-0.004	56.359	0.000	0.000	0.000	0.000	0.000	0.000
72	A	339	LEU	0	0.107	0.059	59.364	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	340	LEU	0	-0.071	-0.016	56.880	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	341	THR	0	-0.087	-0.059	59.476	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	342	GLU	-1	-0.901	-0.956	62.168	0.014	0.014	0.000	0.000	0.000	0.000
76	A	343	ASN	0	-0.045	-0.037	62.850	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	344	GLU	-1	-0.952	-0.964	63.461	0.010	0.010	0.000	0.000	0.000	0.000
78	A	345	LEU	0	-0.009	0.001	65.507	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	346	HIS	0	-0.067	-0.047	68.219	0.000	0.000	0.000	0.000	0.000	0.000
80	A	347	ARG	1	0.794	0.905	67.899	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	348	GLN	0	0.026	-0.006	69.441	0.000	0.000	0.000	0.000	0.000	0.000
82	A	349	GLN	0	-0.082	-0.028	71.111	0.000	0.000	0.000	0.000	0.000	0.000
83	A	350	GLU	-1	-0.858	-0.916	73.960	0.008	0.008	0.000	0.000	0.000	0.000
84	A	351	NME	0	-0.020	0.005	75.840	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:265:ACE )