FMO DATABASE

FMODB ID: LJ1L9

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	OptH
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	-715589.398308
FMO2-HF: Nuclear repulsion	675488.435839
FMO2-HF: Total energy	-40100.962469
FMO2-MP2: Total energy	-40216.261848

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.
-91.238	-86.666	5.095	-3.746	-5.922	-0.035

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 : 0.973 / q_NPA : 0.975

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	-0.085	-0.065	3.294	-1.880	0.094	0.011	-1.012	-0.973	-0.002
4	A	10	SER	0	0.039	0.004	5.880	0.572	0.572	0.000	0.000	0.000	0.000
5	A	11	ALA	0	0.013	0.005	7.452	1.244	1.244	0.000	0.000	0.000	0.000
6	A	12	CSO	0	-0.003	0.015	7.807	1.245	1.245	0.000	0.000	0.000	0.000
7	A	13	ILE	0	0.030	0.008	4.861	1.151	1.151	0.000	0.000	0.000	0.000
8	A	14	ALA	0	-0.020	-0.016	9.097	1.348	1.348	0.000	0.000	0.000	0.000
9	A	15	PHE	0	-0.018	0.001	12.263	1.427	1.427	0.000	0.000	0.000	0.000
10	A	16	ILE	0	0.025	0.011	10.586	1.136	1.136	0.000	0.000	0.000	0.000
11	A	17	MLY	1	0.814	0.879	10.553	22.739	22.739	0.000	0.000	0.000	0.000
12	A	18	GLN	0	-0.036	0.014	14.994	0.743	0.743	0.000	0.000	0.000	0.000
13	A	19	TRP	0	-0.042	-0.024	17.424	1.147	1.147	0.000	0.000	0.000	0.000
14	A	20	GLN	0	-0.047	-0.015	16.474	0.725	0.725	0.000	0.000	0.000	0.000
15	A	21	GLY	0	0.006	0.009	18.136	-0.299	-0.299	0.000	0.000	0.000	0.000
16	A	22	LEU	0	-0.008	-0.003	17.430	-0.667	-0.667	0.000	0.000	0.000	0.000
17	A	23	SER	0	-0.024	-0.012	19.930	0.995	0.995	0.000	0.000	0.000	0.000
18	A	24	LEU	0	0.004	-0.009	19.975	-0.595	-0.595	0.000	0.000	0.000	0.000
19	A	25	GLU	-1	-0.913	-0.953	21.994	-11.169	-11.169	0.000	0.000	0.000	0.000
20	A	26	MLY	1	0.848	0.942	22.936	12.123	12.123	0.000	0.000	0.000	0.000
21	A	27	TYR	0	0.005	-0.008	22.397	0.434	0.434	0.000	0.000	0.000	0.000
22	A	28	ARG	1	0.889	0.948	25.202	10.309	10.309	0.000	0.000	0.000	0.000
23	A	29	ASP	-1	-0.828	-0.916	24.364	-12.403	-12.403	0.000	0.000	0.000	0.000
24	A	30	ARG	1	0.958	0.966	26.996	10.045	10.045	0.000	0.000	0.000	0.000
25	A	31	GLN	0	-0.073	-0.040	26.976	0.272	0.272	0.000	0.000	0.000	0.000
26	A	32	GLY	0	0.010	0.020	28.944	0.122	0.122	0.000	0.000	0.000	0.000
27	A	33	ASN	0	0.008	0.008	23.345	0.158	0.158	0.000	0.000	0.000	0.000
28	A	34	TRP	0	0.009	-0.004	23.190	0.268	0.268	0.000	0.000	0.000	0.000
29	A	35	VAL	0	-0.014	0.000	19.915	-0.673	-0.673	0.000	0.000	0.000	0.000
30	A	36	ILE	0	0.026	0.015	17.813	0.685	0.685	0.000	0.000	0.000	0.000
31	A	37	GLY	0	0.041	0.020	17.014	-0.991	-0.991	0.000	0.000	0.000	0.000
32	A	38	TYR	0	0.018	0.001	14.133	1.188	1.188	0.000	0.000	0.000	0.000
33	A	39	GLY	0	-0.026	-0.017	15.585	-0.699	-0.699	0.000	0.000	0.000	0.000
34	A	40	HIS	1	0.903	0.940	12.808	21.502	21.502	0.000	0.000	0.000	0.000
35	A	41	MET	0	-0.017	-0.013	16.401	1.071	1.071	0.000	0.000	0.000	0.000
36	A	42	LEU	0	-0.032	-0.012	16.767	-0.840	-0.840	0.000	0.000	0.000	0.000
37	A	43	THR	0	-0.036	-0.033	16.338	0.634	0.634	0.000	0.000	0.000	0.000
38	A	44	PRO	0	-0.012	-0.027	19.082	0.360	0.360	0.000	0.000	0.000	0.000
39	A	45	ASP	-1	-0.892	-0.941	21.958	-12.263	-12.263	0.000	0.000	0.000	0.000
40	A	46	GLU	-1	-0.915	-0.937	16.955	-17.522	-17.522	0.000	0.000	0.000	0.000
41	A	47	THR	0	-0.012	-0.018	21.421	0.269	0.269	0.000	0.000	0.000	0.000
42	A	48	LEU	0	-0.038	0.007	18.140	0.529	0.529	0.000	0.000	0.000	0.000
43	A	49	THR	0	0.029	-0.011	22.471	0.212	0.212	0.000	0.000	0.000	0.000
44	A	50	PHE	0	0.026	0.009	22.949	-0.017	-0.017	0.000	0.000	0.000	0.000
45	A	51	ILE	0	-0.015	-0.001	16.353	-0.319	-0.319	0.000	0.000	0.000	0.000
46	A	52	THR	0	0.013	0.001	16.880	0.309	0.309	0.000	0.000	0.000	0.000
47	A	53	PRO	0	0.048	0.002	16.909	-0.740	-0.740	0.000	0.000	0.000	0.000
48	A	54	ASP	-1	-0.876	-0.928	13.390	-21.621	-21.621	0.000	0.000	0.000	0.000
49	A	55	GLN	0	0.003	0.003	12.309	-1.185	-1.185	0.000	0.000	0.000	0.000
50	A	56	ALA	0	-0.004	-0.003	12.808	-1.035	-1.035	0.000	0.000	0.000	0.000
51	A	57	GLU	-1	-0.818	-0.897	9.699	-25.964	-25.964	0.000	0.000	0.000	0.000
52	A	58	ALA	0	-0.009	-0.008	8.232	-2.624	-2.624	0.000	0.000	0.000	0.000
53	A	59	PHE	0	0.027	0.006	8.490	-2.356	-2.356	0.000	0.000	0.000	0.000
54	A	60	LEU	0	0.001	0.022	9.467	-0.369	-0.369	0.000	0.000	0.000	0.000
55	A	61	LEU	0	-0.019	-0.018	4.961	-2.213	-2.213	0.000	0.000	0.000	0.000
56	A	62	ASP	-1	-0.899	-0.940	6.211	-37.697	-37.697	0.000	0.000	0.000	0.000
57	A	63	ASP	-1	-0.811	-0.890	7.237	-24.943	-24.943	0.000	0.000	0.000	0.000
58	A	64	LEU	0	-0.046	-0.030	6.309	0.831	0.831	0.000	0.000	0.000	0.000
59	A	65	ASN	0	-0.037	-0.048	2.306	-17.217	-15.127	5.083	-2.638	-4.536	-0.033
60	A	66	SER	0	0.002	0.020	5.200	0.948	1.030	-0.001	-0.002	-0.079	0.000
61	A	67	CYS	0	-0.054	-0.035	8.070	2.856	2.856	0.000	0.000	0.000	0.000
62	A	68	ASP	-1	-0.861	-0.944	4.826	-37.228	-37.078	-0.001	-0.005	-0.144	0.000
63	A	69	ILE	0	-0.005	-0.001	4.801	2.100	2.100	0.000	0.000	0.000	0.000
64	A	70	LEU	0	-0.025	-0.019	8.325	2.925	2.925	0.000	0.000	0.000	0.000
65	A	71	LEU	0	-0.029	0.001	10.041	2.058	2.058	0.000	0.000	0.000	0.000
66	A	72	GLN	0	-0.029	-0.020	9.050	-1.017	-1.017	0.000	0.000	0.000	0.000
67	A	73	ASN	0	-0.004	-0.018	11.569	1.584	1.584	0.000	0.000	0.000	0.000
68	A	74	CYS	0	-0.024	0.014	14.524	1.278	1.278	0.000	0.000	0.000	0.000
69	A	75	LEU	0	-0.049	-0.031	14.222	1.164	1.164	0.000	0.000	0.000	0.000
70	A	76	PRO	0	0.007	0.010	14.574	-0.862	-0.862	0.000	0.000	0.000	0.000
71	A	77	GLU	-1	-0.939	-0.969	15.311	-14.154	-14.154	0.000	0.000	0.000	0.000
72	A	78	LEU	0	-0.058	-0.008	12.822	0.147	0.147	0.000	0.000	0.000	0.000
73	A	79	ASN	0	0.034	-0.005	11.462	-2.667	-2.667	0.000	0.000	0.000	0.000
74	A	80	ASP	-1	-0.886	-0.933	10.870	-19.217	-19.217	0.000	0.000	0.000	0.000
75	A	81	ARG	1	0.992	0.967	3.679	34.997	35.273	0.003	-0.089	-0.190	0.000
76	A	82	PHE	0	-0.001	0.021	9.109	-1.084	-1.084	0.000	0.000	0.000	0.000
77	A	83	GLN	0	0.041	0.007	11.669	-0.183	-0.183	0.000	0.000	0.000	0.000
78	A	84	ARG	1	0.868	0.947	7.410	28.179	28.179	0.000	0.000	0.000	0.000
79	A	85	GLU	-1	-0.772	-0.865	6.492	-32.086	-32.086	0.000	0.000	0.000	0.000
80	A	86	THR	0	-0.059	-0.031	9.769	0.872	0.872	0.000	0.000	0.000	0.000
81	A	87	LEU	0	0.020	0.019	12.836	0.788	0.788	0.000	0.000	0.000	0.000
82	A	88	ILE	0	0.027	0.013	7.608	0.694	0.694	0.000	0.000	0.000	0.000
83	A	89	ALA	0	0.008	0.002	11.426	0.571	0.571	0.000	0.000	0.000	0.000
84	A	90	LEU	0	-0.019	-0.001	13.373	0.962	0.962	0.000	0.000	0.000	0.000
85	A	91	MET	0	0.007	0.001	12.493	1.037	1.037	0.000	0.000	0.000	0.000
86	A	92	PHE	0	-0.027	-0.004	12.530	0.675	0.675	0.000	0.000	0.000	0.000
87	A	93	SER	0	-0.068	-0.052	15.262	1.085	1.085	0.000	0.000	0.000	0.000
88	A	94	ILE	0	0.000	-0.002	18.518	0.818	0.818	0.000	0.000	0.000	0.000
89	A	95	GLY	0	-0.008	0.002	18.504	0.590	0.590	0.000	0.000	0.000	0.000
90	A	96	HIS	1	0.858	0.961	15.175	18.236	18.236	0.000	0.000	0.000	0.000
91	A	97	GLN	0	0.033	0.024	20.140	0.744	0.744	0.000	0.000	0.000	0.000
92	A	98	ARG	1	0.849	0.918	19.805	13.845	13.845	0.000	0.000	0.000	0.000
93	A	99	PHE	0	0.003	-0.007	23.834	0.456	0.456	0.000	0.000	0.000	0.000
94	A	100	LEU	0	0.006	0.010	26.887	-0.198	-0.198	0.000	0.000	0.000	0.000
95	A	101	SER	0	0.029	0.003	27.872	0.201	0.201	0.000	0.000	0.000	0.000
96	A	102	LEU	0	-0.023	-0.008	29.777	0.006	0.006	0.000	0.000	0.000	0.000
97	A	103	ILE	0	0.003	0.015	30.549	0.150	0.150	0.000	0.000	0.000	0.000

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