FMO DATABASE

FMODB ID: 14LNZ

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:

Apendix: None

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

Total energy (hartree)

FMO2-HF: Electronic energy	-438735.371179
FMO2-HF: Nuclear repulsion	403128.74205
FMO2-HF: Total energy	-35606.629129
FMO2-MP2: Total energy	-35710.54085

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.
50.034	54.218	2.423	-2.653	-3.953	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 : -0.948 / q_NPA : -0.988

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	-0.016	-0.020	3.193	-4.383	-2.137	0.057	-1.149	-1.153	0.000
4	A	269	GLU	-1	-0.879	-0.938	4.845	24.811	24.989	-0.001	-0.005	-0.171	0.000
5	A	270	THR	0	-0.002	-0.018	3.798	-1.058	-0.669	0.001	-0.107	-0.283	0.001
6	A	271	TYR	0	-0.011	0.009	2.036	-1.858	-0.757	2.365	-1.318	-2.148	0.000
7	A	272	GLU	-1	-0.820	-0.917	4.182	23.253	23.523	0.001	-0.074	-0.198	0.000
8	A	273	ARG	1	0.777	0.902	7.236	-26.229	-26.229	0.000	0.000	0.000	0.000
9	A	274	TYR	0	0.044	0.021	5.817	-2.423	-2.423	0.000	0.000	0.000	0.000
10	A	275	HIS	0	0.018	0.014	6.986	-1.679	-1.679	0.000	0.000	0.000	0.000
11	A	276	THR	0	-0.016	-0.041	8.793	-3.054	-3.054	0.000	0.000	0.000	0.000
12	A	277	GLU	-1	-0.897	-0.943	11.338	22.216	22.216	0.000	0.000	0.000	0.000
13	A	278	SER	0	-0.006	0.003	10.719	-2.199	-2.199	0.000	0.000	0.000	0.000
14	A	279	LEU	0	0.002	0.002	12.787	-1.401	-1.401	0.000	0.000	0.000	0.000
15	A	280	GLN	0	-0.073	-0.040	15.122	-1.835	-1.835	0.000	0.000	0.000	0.000
16	A	281	ASN	0	-0.134	-0.056	14.273	-1.326	-1.326	0.000	0.000	0.000	0.000
17	A	282	MET	0	0.009	0.032	16.750	-0.249	-0.249	0.000	0.000	0.000	0.000
18	A	283	SER	0	-0.037	-0.059	19.232	-0.667	-0.667	0.000	0.000	0.000	0.000
19	A	284	LYS	1	0.988	0.976	22.199	-10.794	-10.794	0.000	0.000	0.000	0.000
20	A	285	GLN	0	0.019	-0.017	23.823	0.345	0.345	0.000	0.000	0.000	0.000
21	A	286	GLU	-1	-0.861	-0.884	20.825	13.608	13.608	0.000	0.000	0.000	0.000
22	A	287	LEU	0	0.064	0.042	17.423	0.239	0.239	0.000	0.000	0.000	0.000
23	A	288	ILE	0	-0.034	-0.023	20.506	0.023	0.023	0.000	0.000	0.000	0.000
24	A	289	LYS	1	0.916	0.961	22.556	-12.708	-12.708	0.000	0.000	0.000	0.000
25	A	290	GLU	-1	-0.884	-0.950	16.196	16.187	16.187	0.000	0.000	0.000	0.000
26	A	291	TYR	0	-0.090	-0.061	18.750	0.419	0.419	0.000	0.000	0.000	0.000
27	A	292	LEU	0	0.008	0.003	20.007	-0.163	-0.163	0.000	0.000	0.000	0.000
28	A	293	GLU	-1	-0.938	-0.949	18.793	13.433	13.433	0.000	0.000	0.000	0.000
29	A	294	LEU	0	0.023	0.008	14.868	0.057	0.057	0.000	0.000	0.000	0.000
30	A	295	GLU	-1	-0.839	-0.905	18.768	11.549	11.549	0.000	0.000	0.000	0.000
31	A	296	LYS	1	0.817	0.899	22.016	-12.547	-12.547	0.000	0.000	0.000	0.000
32	A	297	SER	0	-0.017	-0.007	17.755	-0.414	-0.414	0.000	0.000	0.000	0.000
33	A	298	LEU	0	0.044	0.031	19.907	0.060	0.060	0.000	0.000	0.000	0.000
34	A	299	SER	0	0.039	0.021	21.172	-0.179	-0.179	0.000	0.000	0.000	0.000
35	A	300	ARG	1	0.897	0.953	20.171	-13.136	-13.136	0.000	0.000	0.000	0.000
36	A	301	MET	0	-0.019	-0.024	16.899	-0.087	-0.087	0.000	0.000	0.000	0.000
37	A	302	GLU	-1	-0.966	-0.971	22.509	10.743	10.743	0.000	0.000	0.000	0.000
38	A	303	ASP	-1	-0.874	-0.939	25.104	9.586	9.586	0.000	0.000	0.000	0.000
39	A	304	GLU	-1	-0.886	-0.915	23.891	11.200	11.200	0.000	0.000	0.000	0.000
40	A	305	ASN	0	0.022	0.002	23.763	-0.587	-0.587	0.000	0.000	0.000	0.000
41	A	306	ASN	0	0.004	0.007	26.086	-0.265	-0.265	0.000	0.000	0.000	0.000
42	A	307	ARG	1	0.792	0.876	27.364	-10.290	-10.290	0.000	0.000	0.000	0.000
43	A	308	LEU	0	0.014	-0.007	24.943	-0.267	-0.267	0.000	0.000	0.000	0.000
44	A	309	ARG	1	0.884	0.931	28.080	-9.946	-9.946	0.000	0.000	0.000	0.000
45	A	310	LEU	0	-0.041	-0.010	30.585	-0.284	-0.284	0.000	0.000	0.000	0.000
46	A	311	GLU	-1	-0.906	-0.950	31.878	8.895	8.895	0.000	0.000	0.000	0.000
47	A	312	SER	0	0.022	0.000	30.572	-0.079	-0.079	0.000	0.000	0.000	0.000
48	A	313	LYS	1	0.936	0.976	32.708	-8.019	-8.019	0.000	0.000	0.000	0.000
49	A	314	ARG	1	0.945	0.983	35.631	-8.274	-8.274	0.000	0.000	0.000	0.000
50	A	315	LEU	0	-0.010	-0.017	33.628	-0.230	-0.230	0.000	0.000	0.000	0.000
51	A	319	ASP	-1	-0.858	-0.933	35.473	8.019	8.019	0.000	0.000	0.000	0.000
52	A	320	ALA	0	0.011	0.019	37.454	-0.182	-0.182	0.000	0.000	0.000	0.000
53	A	321	ARG	1	0.847	0.937	40.281	-6.955	-6.955	0.000	0.000	0.000	0.000
54	A	322	VAL	0	0.032	0.003	37.529	-0.144	-0.144	0.000	0.000	0.000	0.000
55	A	323	ARG	1	0.910	0.958	40.750	-7.074	-7.074	0.000	0.000	0.000	0.000
56	A	324	GLU	-1	-0.845	-0.932	42.646	6.489	6.489	0.000	0.000	0.000	0.000
57	A	325	LEU	0	-0.023	-0.018	42.575	-0.136	-0.136	0.000	0.000	0.000	0.000
58	A	326	GLU	-1	-0.842	-0.919	42.662	6.956	6.956	0.000	0.000	0.000	0.000
59	A	327	LEU	0	-0.048	-0.010	45.204	-0.084	-0.084	0.000	0.000	0.000	0.000
60	A	328	GLU	-1	-0.785	-0.850	48.367	5.678	5.678	0.000	0.000	0.000	0.000
61	A	329	LEU	0	-0.015	-0.010	45.412	-0.113	-0.113	0.000	0.000	0.000	0.000
62	A	330	ASP	-1	-0.869	-0.924	47.816	6.414	6.414	0.000	0.000	0.000	0.000
63	A	331	ARG	1	0.697	0.804	50.567	-5.682	-5.682	0.000	0.000	0.000	0.000
64	A	332	LEU	0	-0.015	-0.009	52.775	-0.102	-0.102	0.000	0.000	0.000	0.000
65	A	333	ARG	1	0.779	0.864	45.576	-6.679	-6.679	0.000	0.000	0.000	0.000
66	A	334	ALA	0	-0.012	-0.003	53.575	-0.064	-0.064	0.000	0.000	0.000	0.000
67	A	335	GLU	-1	-0.836	-0.903	55.987	5.188	5.188	0.000	0.000	0.000	0.000
68	A	336	ASN	0	-0.008	-0.017	55.289	-0.163	-0.163	0.000	0.000	0.000	0.000
69	A	337	LEU	0	-0.029	-0.005	55.843	-0.065	-0.065	0.000	0.000	0.000	0.000
70	A	338	GLN	0	-0.034	-0.016	58.368	-0.017	-0.017	0.000	0.000	0.000	0.000
71	A	339	LEU	0	0.069	0.041	61.634	-0.063	-0.063	0.000	0.000	0.000	0.000
72	A	340	LEU	0	-0.064	-0.015	58.760	-0.070	-0.070	0.000	0.000	0.000	0.000
73	A	341	THR	0	-0.067	-0.048	61.441	-0.055	-0.055	0.000	0.000	0.000	0.000
74	A	342	GLU	-1	-0.870	-0.945	64.072	4.758	4.758	0.000	0.000	0.000	0.000
75	A	343	ASN	0	-0.046	-0.033	64.277	-0.147	-0.147	0.000	0.000	0.000	0.000
76	A	344	GLU	-1	-0.942	-0.964	65.031	4.780	4.780	0.000	0.000	0.000	0.000
77	A	345	LEU	0	-0.022	0.006	67.252	-0.082	-0.082	0.000	0.000	0.000	0.000
78	A	346	HIS	0	-0.056	-0.057	70.058	-0.055	-0.055	0.000	0.000	0.000	0.000
79	A	347	ARG	1	0.815	0.917	69.666	-4.418	-4.418	0.000	0.000	0.000	0.000
80	A	348	GLN	0	-0.024	-0.029	70.905	-0.040	-0.040	0.000	0.000	0.000	0.000
81	A	349	GLN	0	-0.064	-0.011	72.694	-0.058	-0.058	0.000	0.000	0.000	0.000
82	A	350	GLU	-1	-0.866	-0.909	75.658	4.206	4.206	0.000	0.000	0.000	0.000

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