FMO DATABASE

FMODB ID: 9G3Y2

Calculation Name: 4EVX-A-Xray372

Preferred Name:

Target Type:

Ligand Name: n-dimethyl-lysine

ligand 3-letter code: MLY

PDB ID: 4EVX

Chain ID: A

ChEMBL ID:

UniProt ID: Q8ZLC6

Base Structure: X-ray

Registration Date: 2023-06-20

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	97
LigandCharge	MLY=1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-715706.96045
FMO2-HF: Nuclear repulsion	675605.606295
FMO2-HF: Total energy	-40101.354155
FMO2-MP2: Total energy	-40216.650257

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:7:ARG)

Summations of interaction energy for fragment #1(A:7:ARG)

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.
-99.485	-98.91	13.378	-6.431	-7.523	-0.066

Interaction energy analysis for fragmet #1(A:7:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.937 / q_NPA : 0.947

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

Sort

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	9	SER	0	-0.049	-0.038	3.364	-1.103	0.588	0.006	-0.836	-0.861	-0.001
4	A	10	SER	0	0.049	0.009	5.930	0.439	0.439	0.000	0.000	0.000	0.000
5	A	11	ALA	0	0.007	0.003	7.486	1.186	1.186	0.000	0.000	0.000	0.000
6	A	12	CSO	0	-0.010	0.013	7.964	1.183	1.183	0.000	0.000	0.000	0.000
7	A	13	ILE	0	0.036	0.006	4.789	1.019	1.079	-0.001	-0.004	-0.055	0.000
8	A	14	ALA	0	-0.015	-0.012	9.216	1.243	1.243	0.000	0.000	0.000	0.000
9	A	15	PHE	0	-0.006	0.006	12.355	1.335	1.335	0.000	0.000	0.000	0.000
10	A	16	ILE	0	0.022	0.007	10.905	1.084	1.084	0.000	0.000	0.000	0.000
11	A	17	MLY	1	0.833	0.889	10.957	21.929	21.929	0.000	0.000	0.000	0.000
12	A	18	GLN	0	-0.070	-0.012	15.112	0.910	0.910	0.000	0.000	0.000	0.000
13	A	19	TRP	0	-0.035	-0.017	17.550	1.202	1.202	0.000	0.000	0.000	0.000
14	A	20	GLN	0	-0.062	-0.020	16.670	0.693	0.693	0.000	0.000	0.000	0.000
15	A	21	GLY	0	0.004	0.008	18.265	-0.275	-0.275	0.000	0.000	0.000	0.000
16	A	22	LEU	0	-0.012	-0.009	17.466	-0.658	-0.658	0.000	0.000	0.000	0.000
17	A	23	SER	0	-0.016	-0.005	20.047	0.718	0.718	0.000	0.000	0.000	0.000
18	A	24	LEU	0	0.009	-0.004	20.250	-0.590	-0.590	0.000	0.000	0.000	0.000
19	A	25	GLU	-1	-0.902	-0.948	22.157	-11.094	-11.094	0.000	0.000	0.000	0.000
20	A	26	MLY	1	0.821	0.918	22.396	12.257	12.257	0.000	0.000	0.000	0.000
21	A	27	TYR	0	-0.001	-0.011	21.804	0.626	0.626	0.000	0.000	0.000	0.000
22	A	28	ARG	1	0.884	0.941	24.592	10.340	10.340	0.000	0.000	0.000	0.000
23	A	29	ASP	-1	-0.807	-0.901	23.843	-12.334	-12.334	0.000	0.000	0.000	0.000
24	A	30	ARG	1	0.957	0.959	26.370	10.088	10.088	0.000	0.000	0.000	0.000
25	A	31	GLN	0	-0.073	-0.037	25.911	0.286	0.286	0.000	0.000	0.000	0.000
26	A	32	GLY	0	0.015	0.022	28.306	0.124	0.124	0.000	0.000	0.000	0.000
27	A	33	ASN	0	-0.018	-0.004	22.779	0.132	0.132	0.000	0.000	0.000	0.000
28	A	34	TRP	0	0.001	-0.009	22.615	0.282	0.282	0.000	0.000	0.000	0.000
29	A	35	VAL	0	-0.001	0.004	19.218	-0.675	-0.675	0.000	0.000	0.000	0.000
30	A	36	ILE	0	0.022	0.012	17.485	0.691	0.691	0.000	0.000	0.000	0.000
31	A	37	GLY	0	0.041	0.021	16.732	-0.999	-0.999	0.000	0.000	0.000	0.000
32	A	38	TYR	0	-0.019	-0.028	13.999	1.426	1.426	0.000	0.000	0.000	0.000
33	A	39	GLY	0	-0.026	-0.016	15.823	-0.730	-0.730	0.000	0.000	0.000	0.000
34	A	40	HIS	1	0.902	0.943	11.891	21.969	21.969	0.000	0.000	0.000	0.000
35	A	41	MET	0	-0.011	-0.008	15.739	1.086	1.086	0.000	0.000	0.000	0.000
36	A	42	LEU	0	-0.042	-0.013	16.233	-0.809	-0.809	0.000	0.000	0.000	0.000
37	A	43	THR	0	-0.038	-0.052	15.969	0.610	0.610	0.000	0.000	0.000	0.000
38	A	44	PRO	0	-0.013	-0.028	18.712	0.388	0.388	0.000	0.000	0.000	0.000
39	A	45	ASP	-1	-0.907	-0.950	21.726	-12.434	-12.434	0.000	0.000	0.000	0.000
40	A	46	GLU	-1	-0.877	-0.901	16.797	-17.441	-17.441	0.000	0.000	0.000	0.000
41	A	47	THR	0	0.006	-0.013	21.136	0.282	0.282	0.000	0.000	0.000	0.000
42	A	48	LEU	0	-0.042	0.006	17.756	0.539	0.539	0.000	0.000	0.000	0.000
43	A	49	THR	0	0.040	0.004	22.420	0.170	0.170	0.000	0.000	0.000	0.000
44	A	50	PHE	0	0.024	0.012	23.128	-0.046	-0.046	0.000	0.000	0.000	0.000
45	A	51	ILE	0	-0.022	-0.006	16.457	-0.338	-0.338	0.000	0.000	0.000	0.000
46	A	52	THR	0	0.024	0.005	17.412	0.323	0.323	0.000	0.000	0.000	0.000
47	A	53	PRO	0	0.052	0.003	17.284	-0.731	-0.731	0.000	0.000	0.000	0.000
48	A	54	ASP	-1	-0.899	-0.937	13.756	-20.194	-20.194	0.000	0.000	0.000	0.000
49	A	55	GLN	0	0.017	0.008	12.707	-1.146	-1.146	0.000	0.000	0.000	0.000
50	A	56	ALA	0	0.007	0.007	13.136	-1.097	-1.097	0.000	0.000	0.000	0.000
51	A	57	GLU	-1	-0.810	-0.880	9.915	-24.138	-24.138	0.000	0.000	0.000	0.000
52	A	58	ALA	0	-0.004	-0.006	8.571	-2.598	-2.598	0.000	0.000	0.000	0.000
53	A	59	PHE	0	0.030	0.008	8.339	-2.645	-2.645	0.000	0.000	0.000	0.000
54	A	60	LEU	0	-0.003	0.022	9.834	-0.619	-0.619	0.000	0.000	0.000	0.000
55	A	61	LEU	0	-0.013	-0.015	5.102	-2.143	-2.143	0.000	0.000	0.000	0.000
56	A	62	ASP	-1	-0.887	-0.933	5.601	-39.666	-39.666	0.000	0.000	0.000	0.000
57	A	63	ASP	-1	-0.821	-0.892	6.603	-24.967	-24.967	0.000	0.000	0.000	0.000
58	A	64	LEU	0	-0.036	-0.023	6.630	0.688	0.688	0.000	0.000	0.000	0.000
59	A	65	ASN	0	-0.026	-0.036	1.859	-31.450	-33.170	13.374	-5.369	-6.286	-0.065
60	A	66	SER	0	0.002	0.016	4.650	1.252	1.353	-0.001	-0.015	-0.085	0.000
61	A	67	CYS	0	-0.049	-0.031	7.582	3.021	3.021	0.000	0.000	0.000	0.000
62	A	68	ASP	-1	-0.828	-0.914	5.234	-36.472	-36.472	0.000	0.000	0.000	0.000
63	A	69	ILE	0	-0.009	-0.002	4.889	2.123	2.123	0.000	0.000	0.000	0.000
64	A	70	LEU	0	-0.013	-0.011	8.017	3.029	3.029	0.000	0.000	0.000	0.000
65	A	71	LEU	0	-0.030	-0.004	10.100	2.145	2.145	0.000	0.000	0.000	0.000
66	A	72	GLN	0	0.009	0.021	9.443	-0.354	-0.354	0.000	0.000	0.000	0.000
67	A	73	ASN	0	-0.011	-0.025	11.459	1.466	1.466	0.000	0.000	0.000	0.000
68	A	74	CYS	0	-0.024	0.009	14.127	1.401	1.401	0.000	0.000	0.000	0.000
69	A	75	LEU	0	-0.038	-0.022	14.246	1.213	1.213	0.000	0.000	0.000	0.000
70	A	76	PRO	0	0.017	0.015	14.404	-0.898	-0.898	0.000	0.000	0.000	0.000
71	A	77	GLU	-1	-0.933	-0.968	15.259	-14.397	-14.397	0.000	0.000	0.000	0.000
72	A	78	LEU	0	-0.056	-0.011	12.845	0.214	0.214	0.000	0.000	0.000	0.000
73	A	79	ASN	0	-0.003	-0.027	11.553	-2.516	-2.516	0.000	0.000	0.000	0.000
74	A	80	ASP	-1	-0.849	-0.902	10.958	-19.504	-19.504	0.000	0.000	0.000	0.000
75	A	81	ARG	1	0.917	0.916	3.908	35.504	35.947	0.000	-0.207	-0.236	0.000
76	A	82	PHE	0	0.001	0.017	9.315	-1.042	-1.042	0.000	0.000	0.000	0.000
77	A	83	GLN	0	0.003	-0.006	11.936	0.173	0.173	0.000	0.000	0.000	0.000
78	A	84	ARG	1	0.802	0.880	6.753	30.311	30.311	0.000	0.000	0.000	0.000
79	A	85	GLU	-1	-0.779	-0.871	6.492	-32.231	-32.231	0.000	0.000	0.000	0.000
80	A	86	THR	0	-0.037	-0.030	9.698	0.779	0.779	0.000	0.000	0.000	0.000
81	A	87	LEU	0	-0.003	0.011	12.698	0.833	0.833	0.000	0.000	0.000	0.000
82	A	88	ILE	0	0.026	0.012	7.652	0.654	0.654	0.000	0.000	0.000	0.000
83	A	89	ALA	0	0.011	0.004	11.471	0.583	0.583	0.000	0.000	0.000	0.000
84	A	90	LEU	0	-0.022	-0.003	13.442	0.960	0.960	0.000	0.000	0.000	0.000
85	A	91	MET	0	0.017	0.006	12.536	1.042	1.042	0.000	0.000	0.000	0.000
86	A	92	PHE	0	-0.018	-0.002	12.582	0.694	0.694	0.000	0.000	0.000	0.000
87	A	93	SER	0	-0.085	-0.058	15.414	1.100	1.100	0.000	0.000	0.000	0.000
88	A	94	ILE	0	0.008	0.000	18.651	0.825	0.825	0.000	0.000	0.000	0.000
89	A	95	GLY	0	-0.011	0.003	18.672	0.586	0.586	0.000	0.000	0.000	0.000
90	A	96	HIS	1	0.858	0.955	15.016	18.520	18.520	0.000	0.000	0.000	0.000
91	A	97	GLN	0	0.042	0.037	20.275	0.661	0.661	0.000	0.000	0.000	0.000
92	A	98	ARG	1	0.852	0.920	20.003	13.913	13.913	0.000	0.000	0.000	0.000
93	A	99	PHE	0	0.000	-0.008	24.085	0.456	0.456	0.000	0.000	0.000	0.000
94	A	100	LEU	0	0.006	0.009	27.170	-0.189	-0.189	0.000	0.000	0.000	0.000
95	A	101	SER	0	0.038	0.007	28.017	0.205	0.205	0.000	0.000	0.000	0.000
96	A	102	LEU	0	-0.009	-0.002	29.906	0.013	0.013	0.000	0.000	0.000	0.000
97	A	103	ILE	0	-0.016	0.006	30.639	0.114	0.114	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:ARG)