FMO DATABASE

FMODB ID: LNGJ9

Calculation Name: 3MTS-A-Xray372

Preferred Name: Histone-lysine N-methyltransferase SUV39H1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3MTS

Chain ID: A

ChEMBL ID: CHEMBL1795118

UniProt ID: O43463

Base Structure: X-ray

Registration Date: 2023-09-22

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	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	62
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-395869.823743
FMO2-HF: Nuclear repulsion	368464.976901
FMO2-HF: Total energy	-27404.846842
FMO2-MP2: Total energy	-27485.346486

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:43:GLY)

Summations of interaction energy for fragment #1(A:43:GLY)

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.
0.673	2.91	0.343	-1.143	-1.437	-0.005

Interaction energy analysis for fragmet #1(A:43:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.039 / q_NPA : 0.027

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	45	VAL	0	0.007	-0.002	3.786	-0.076	1.046	-0.016	-0.491	-0.615	0.001
4	A	46	GLU	-1	-0.877	-0.940	6.668	0.071	0.071	0.000	0.000	0.000	0.000
5	A	47	TYR	0	-0.063	-0.066	9.390	0.084	0.084	0.000	0.000	0.000	0.000
6	A	48	LEU	0	-0.047	-0.020	10.582	-0.072	-0.072	0.000	0.000	0.000	0.000
7	A	49	CYS	0	-0.002	-0.010	13.122	0.042	0.042	0.000	0.000	0.000	0.000
8	A	50	ASP	-1	-0.832	-0.916	15.501	-0.174	-0.174	0.000	0.000	0.000	0.000
9	A	51	TYR	0	-0.142	-0.102	15.909	-0.037	-0.037	0.000	0.000	0.000	0.000
10	A	52	LYS	1	0.914	0.984	17.156	0.267	0.267	0.000	0.000	0.000	0.000
11	A	53	LYS	1	0.830	0.916	18.956	0.168	0.168	0.000	0.000	0.000	0.000
12	A	54	ILE	0	-0.041	0.002	20.762	0.023	0.023	0.000	0.000	0.000	0.000
13	A	55	ARG	1	0.944	0.961	21.458	0.127	0.127	0.000	0.000	0.000	0.000
14	A	56	GLU	-1	-0.815	-0.924	23.592	-0.149	-0.149	0.000	0.000	0.000	0.000
15	A	57	GLN	0	-0.025	-0.009	16.099	0.001	0.001	0.000	0.000	0.000	0.000
16	A	58	GLU	-1	-0.851	-0.905	17.608	-0.229	-0.229	0.000	0.000	0.000	0.000
17	A	59	TYR	0	-0.015	-0.016	14.185	-0.030	-0.030	0.000	0.000	0.000	0.000
18	A	60	TYR	0	0.009	-0.030	11.928	0.033	0.033	0.000	0.000	0.000	0.000
19	A	61	LEU	0	0.014	0.036	12.043	-0.060	-0.060	0.000	0.000	0.000	0.000
20	A	62	VAL	0	-0.005	-0.011	6.560	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	63	LYS	1	0.890	0.962	9.552	0.254	0.254	0.000	0.000	0.000	0.000
22	A	64	TRP	0	-0.048	-0.033	3.018	-1.582	-0.641	0.358	-0.597	-0.702	-0.006
23	A	65	ARG	1	0.901	0.927	5.373	-0.045	-0.045	0.000	0.000	0.000	0.000
24	A	66	GLY	0	-0.039	-0.021	5.660	0.127	0.127	0.000	0.000	0.000	0.000
25	A	67	TYR	0	-0.006	0.015	5.432	0.079	0.079	0.000	0.000	0.000	0.000
26	A	68	PRO	0	0.034	0.006	9.641	-0.036	-0.036	0.000	0.000	0.000	0.000
27	A	69	ASP	-1	-0.827	-0.909	12.449	-0.224	-0.224	0.000	0.000	0.000	0.000
28	A	70	SER	0	-0.044	-0.042	14.402	-0.026	-0.026	0.000	0.000	0.000	0.000
29	A	71	GLU	-1	-0.913	-0.933	11.518	-0.079	-0.079	0.000	0.000	0.000	0.000
30	A	72	SER	0	-0.057	-0.021	10.526	-0.039	-0.039	0.000	0.000	0.000	0.000
31	A	73	THR	0	0.007	-0.005	8.665	0.039	0.039	0.000	0.000	0.000	0.000
32	A	74	TRP	0	-0.029	-0.029	10.571	-0.076	-0.076	0.000	0.000	0.000	0.000
33	A	75	GLU	-1	-0.806	-0.891	7.512	-0.751	-0.751	0.000	0.000	0.000	0.000
34	A	76	PRO	0	-0.012	0.004	10.765	0.033	0.033	0.000	0.000	0.000	0.000
35	A	77	ARG	1	0.928	0.945	11.423	0.380	0.380	0.000	0.000	0.000	0.000
36	A	78	GLN	0	0.016	0.006	12.066	-0.091	-0.091	0.000	0.000	0.000	0.000
37	A	79	ASN	0	-0.009	0.007	7.586	0.069	0.069	0.000	0.000	0.000	0.000
38	A	80	LEU	0	-0.028	0.005	6.954	-0.365	-0.365	0.000	0.000	0.000	0.000
39	A	81	LYS	1	1.000	0.993	3.633	2.053	2.227	0.001	-0.055	-0.120	0.000
40	A	82	CYS	0	-0.019	0.007	8.896	0.166	0.166	0.000	0.000	0.000	0.000
41	A	83	VAL	0	0.060	0.011	10.520	0.065	0.065	0.000	0.000	0.000	0.000
42	A	84	ARG	1	0.942	0.969	14.108	0.157	0.157	0.000	0.000	0.000	0.000
43	A	85	ILE	0	0.072	0.037	11.546	0.042	0.042	0.000	0.000	0.000	0.000
44	A	86	LEU	0	0.037	0.028	12.428	0.031	0.031	0.000	0.000	0.000	0.000
45	A	87	LYS	1	0.921	0.967	15.323	0.224	0.224	0.000	0.000	0.000	0.000
46	A	88	GLN	0	-0.029	-0.028	17.677	0.025	0.025	0.000	0.000	0.000	0.000
47	A	89	PHE	0	0.046	0.030	16.243	0.015	0.015	0.000	0.000	0.000	0.000
48	A	90	HIS	0	0.057	0.034	17.789	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	91	LYS	1	0.773	0.872	20.642	0.140	0.140	0.000	0.000	0.000	0.000
50	A	92	ASP	-1	-0.774	-0.862	21.338	-0.131	-0.131	0.000	0.000	0.000	0.000
51	A	93	LEU	0	0.011	0.010	21.226	0.014	0.014	0.000	0.000	0.000	0.000
52	A	94	GLU	-1	-0.811	-0.889	23.589	-0.106	-0.106	0.000	0.000	0.000	0.000
53	A	95	ARG	1	0.854	0.900	24.653	0.124	0.124	0.000	0.000	0.000	0.000
54	A	96	GLU	-1	-0.875	-0.909	26.431	-0.102	-0.102	0.000	0.000	0.000	0.000
55	A	97	LEU	0	0.031	0.008	25.765	0.008	0.008	0.000	0.000	0.000	0.000
56	A	98	LEU	0	-0.006	0.003	29.364	0.008	0.008	0.000	0.000	0.000	0.000
57	A	99	ARG	1	0.925	0.961	28.114	0.097	0.097	0.000	0.000	0.000	0.000
58	A	100	ARG	1	0.840	0.888	27.450	0.112	0.112	0.000	0.000	0.000	0.000
59	A	101	HIS	0	-0.014	-0.001	33.583	0.001	0.001	0.000	0.000	0.000	0.000
60	A	102	HIS	0	0.031	0.004	35.301	0.005	0.005	0.000	0.000	0.000	0.000
61	A	103	ARG	1	0.870	0.959	36.894	0.068	0.068	0.000	0.000	0.000	0.000
62	A	104	SER	0	-0.029	0.000	37.478	0.005	0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:43:GLY)