FMO DATABASE

FMODB ID: M35MZ

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	OptAll
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	-718233.74693
FMO2-HF: Nuclear repulsion	678132.143107
FMO2-HF: Total energy	-40101.603823
FMO2-MP2: Total energy	-40216.916123

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.
-94.312	-93.93	14.151	-7.076	-7.456	-0.07

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 : 0.941 / 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	-0.039	3.391	-1.597	0.013	0.013	-0.865	-0.758	-0.001
4	A	10	SER	0	0.028	-0.004	6.147	0.275	0.275	0.000	0.000	0.000	0.000
5	A	11	ALA	0	0.012	0.009	7.412	1.251	1.251	0.000	0.000	0.000	0.000
6	A	12	CSO	0	-0.030	-0.009	7.982	1.119	1.119	0.000	0.000	0.000	0.000
7	A	13	ILE	0	0.043	0.013	4.387	1.020	1.093	-0.001	-0.004	-0.068	0.000
8	A	14	ALA	0	-0.011	-0.009	8.913	1.271	1.271	0.000	0.000	0.000	0.000
9	A	15	PHE	0	-0.010	-0.004	11.966	1.268	1.268	0.000	0.000	0.000	0.000
10	A	16	ILE	0	0.015	0.001	10.927	1.053	1.053	0.000	0.000	0.000	0.000
11	A	17	MLY	1	0.839	0.890	10.460	21.592	21.592	0.000	0.000	0.000	0.000
12	A	18	GLN	0	-0.087	-0.018	14.716	0.812	0.812	0.000	0.000	0.000	0.000
13	A	19	TRP	0	-0.030	-0.009	17.392	1.233	1.233	0.000	0.000	0.000	0.000
14	A	20	GLN	0	-0.069	-0.030	16.066	0.738	0.738	0.000	0.000	0.000	0.000
15	A	21	GLY	0	0.024	0.014	17.570	-0.373	-0.373	0.000	0.000	0.000	0.000
16	A	22	LEU	0	-0.025	-0.012	16.872	-0.596	-0.596	0.000	0.000	0.000	0.000
17	A	23	SER	0	-0.005	0.001	19.528	0.666	0.666	0.000	0.000	0.000	0.000
18	A	24	LEU	0	-0.006	-0.008	19.599	-0.569	-0.569	0.000	0.000	0.000	0.000
19	A	25	GLU	-1	-0.886	-0.944	21.703	-10.940	-10.940	0.000	0.000	0.000	0.000
20	A	26	MLY	1	0.797	0.914	22.130	12.237	12.237	0.000	0.000	0.000	0.000
21	A	27	TYR	0	0.004	-0.002	21.400	0.667	0.667	0.000	0.000	0.000	0.000
22	A	28	ARG	1	0.885	0.929	24.487	10.384	10.384	0.000	0.000	0.000	0.000
23	A	29	ASP	-1	-0.773	-0.874	23.847	-12.196	-12.196	0.000	0.000	0.000	0.000
24	A	30	ARG	1	0.927	0.942	26.025	10.028	10.028	0.000	0.000	0.000	0.000
25	A	31	GLN	0	-0.055	-0.027	25.414	0.380	0.380	0.000	0.000	0.000	0.000
26	A	32	GLY	0	0.013	0.023	27.842	0.230	0.230	0.000	0.000	0.000	0.000
27	A	33	ASN	0	-0.043	-0.027	22.633	0.148	0.148	0.000	0.000	0.000	0.000
28	A	34	TRP	0	0.029	0.003	22.520	0.266	0.266	0.000	0.000	0.000	0.000
29	A	35	VAL	0	0.003	0.011	19.123	-0.667	-0.667	0.000	0.000	0.000	0.000
30	A	36	ILE	0	0.018	0.018	17.268	0.670	0.670	0.000	0.000	0.000	0.000
31	A	37	GLY	0	0.045	0.017	16.226	-0.977	-0.977	0.000	0.000	0.000	0.000
32	A	38	TYR	0	-0.041	-0.042	13.224	1.447	1.447	0.000	0.000	0.000	0.000
33	A	39	GLY	0	0.007	-0.007	16.108	-0.484	-0.484	0.000	0.000	0.000	0.000
34	A	40	HIS	1	0.876	0.951	12.032	21.777	21.777	0.000	0.000	0.000	0.000
35	A	41	MET	0	-0.029	-0.016	15.482	0.944	0.944	0.000	0.000	0.000	0.000
36	A	42	LEU	0	-0.052	-0.021	16.343	-0.794	-0.794	0.000	0.000	0.000	0.000
37	A	43	THR	0	-0.028	-0.049	16.422	0.698	0.698	0.000	0.000	0.000	0.000
38	A	44	PRO	0	-0.025	-0.030	19.184	0.374	0.374	0.000	0.000	0.000	0.000
39	A	45	ASP	-1	-0.896	-0.942	21.754	-12.425	-12.425	0.000	0.000	0.000	0.000
40	A	46	GLU	-1	-0.838	-0.895	16.592	-17.380	-17.380	0.000	0.000	0.000	0.000
41	A	47	THR	0	-0.024	-0.024	21.123	0.143	0.143	0.000	0.000	0.000	0.000
42	A	48	LEU	0	-0.022	0.010	17.636	0.508	0.508	0.000	0.000	0.000	0.000
43	A	49	THR	0	0.012	-0.009	22.286	0.209	0.209	0.000	0.000	0.000	0.000
44	A	50	PHE	0	0.025	0.015	22.885	0.014	0.014	0.000	0.000	0.000	0.000
45	A	51	ILE	0	-0.029	-0.011	16.211	-0.328	-0.328	0.000	0.000	0.000	0.000
46	A	52	THR	0	-0.021	-0.032	17.385	0.307	0.307	0.000	0.000	0.000	0.000
47	A	53	PRO	0	0.053	0.002	16.721	-0.666	-0.666	0.000	0.000	0.000	0.000
48	A	54	ASP	-1	-0.824	-0.890	13.520	-19.084	-19.084	0.000	0.000	0.000	0.000
49	A	55	GLN	0	0.015	0.016	12.506	-1.358	-1.358	0.000	0.000	0.000	0.000
50	A	56	ALA	0	0.016	0.025	12.803	-0.981	-0.981	0.000	0.000	0.000	0.000
51	A	57	GLU	-1	-0.807	-0.874	9.171	-23.555	-23.555	0.000	0.000	0.000	0.000
52	A	58	ALA	0	-0.009	-0.010	8.319	-2.743	-2.743	0.000	0.000	0.000	0.000
53	A	59	PHE	0	0.031	0.005	8.112	-2.653	-2.653	0.000	0.000	0.000	0.000
54	A	60	LEU	0	-0.009	0.013	9.517	-0.243	-0.243	0.000	0.000	0.000	0.000
55	A	61	LEU	0	-0.026	-0.020	4.414	-2.293	-2.100	-0.001	-0.016	-0.176	0.000
56	A	62	ASP	-1	-0.891	-0.935	5.411	-37.165	-37.165	0.000	0.000	0.000	0.000
57	A	63	ASP	-1	-0.784	-0.876	6.866	-23.656	-23.656	0.000	0.000	0.000	0.000
58	A	64	LEU	0	-0.018	-0.006	6.796	0.330	0.330	0.000	0.000	0.000	0.000
59	A	65	ASN	0	-0.040	-0.043	1.783	-32.346	-34.422	14.141	-5.956	-6.109	-0.069
60	A	66	SER	0	0.018	0.018	4.679	1.231	1.329	-0.001	-0.025	-0.071	0.000
61	A	67	CYS	0	-0.061	-0.037	7.913	3.161	3.161	0.000	0.000	0.000	0.000
62	A	68	ASP	-1	-0.824	-0.896	5.314	-36.070	-36.070	0.000	0.000	0.000	0.000
63	A	69	ILE	0	-0.005	0.001	5.434	2.226	2.226	0.000	0.000	0.000	0.000
64	A	70	LEU	0	0.005	-0.001	8.015	2.762	2.762	0.000	0.000	0.000	0.000
65	A	71	LEU	0	-0.003	0.000	10.375	1.970	1.970	0.000	0.000	0.000	0.000
66	A	72	GLN	0	-0.017	0.008	9.032	-0.066	-0.066	0.000	0.000	0.000	0.000
67	A	73	ASN	0	-0.009	-0.013	11.105	1.271	1.271	0.000	0.000	0.000	0.000
68	A	74	CYS	0	-0.048	-0.016	13.933	1.555	1.555	0.000	0.000	0.000	0.000
69	A	75	LEU	0	-0.016	-0.008	14.766	1.209	1.209	0.000	0.000	0.000	0.000
70	A	76	PRO	0	0.013	0.014	14.428	-0.863	-0.863	0.000	0.000	0.000	0.000
71	A	77	GLU	-1	-0.918	-0.962	14.608	-14.810	-14.810	0.000	0.000	0.000	0.000
72	A	78	LEU	0	-0.032	-0.001	12.935	0.160	0.160	0.000	0.000	0.000	0.000
73	A	79	ASN	0	-0.021	-0.030	11.890	-2.662	-2.662	0.000	0.000	0.000	0.000
74	A	80	ASP	-1	-0.823	-0.886	11.576	-19.950	-19.950	0.000	0.000	0.000	0.000
75	A	81	ARG	1	0.851	0.889	3.732	37.312	37.796	0.000	-0.210	-0.274	0.000
76	A	82	PHE	0	-0.007	0.010	9.722	-0.692	-0.692	0.000	0.000	0.000	0.000
77	A	83	GLN	0	0.002	-0.008	12.369	0.476	0.476	0.000	0.000	0.000	0.000
78	A	84	ARG	1	0.764	0.857	7.053	30.201	30.201	0.000	0.000	0.000	0.000
79	A	85	GLU	-1	-0.716	-0.834	7.065	-31.684	-31.684	0.000	0.000	0.000	0.000
80	A	86	THR	0	-0.031	-0.016	9.656	0.804	0.804	0.000	0.000	0.000	0.000
81	A	87	LEU	0	0.016	0.011	13.105	0.823	0.823	0.000	0.000	0.000	0.000
82	A	88	ILE	0	0.000	0.001	8.033	0.567	0.567	0.000	0.000	0.000	0.000
83	A	89	ALA	0	0.018	0.009	11.763	0.463	0.463	0.000	0.000	0.000	0.000
84	A	90	LEU	0	-0.023	0.004	13.639	0.894	0.894	0.000	0.000	0.000	0.000
85	A	91	MET	0	0.016	0.007	12.832	0.945	0.945	0.000	0.000	0.000	0.000
86	A	92	PHE	0	-0.011	-0.003	12.235	0.596	0.596	0.000	0.000	0.000	0.000
87	A	93	SER	0	-0.087	-0.058	15.501	1.057	1.057	0.000	0.000	0.000	0.000
88	A	94	ILE	0	-0.002	0.002	18.706	0.754	0.754	0.000	0.000	0.000	0.000
89	A	95	GLY	0	-0.007	0.003	18.396	0.565	0.565	0.000	0.000	0.000	0.000
90	A	96	HIS	1	0.820	0.920	14.389	18.545	18.545	0.000	0.000	0.000	0.000
91	A	97	GLN	0	0.034	0.029	19.678	0.487	0.487	0.000	0.000	0.000	0.000
92	A	98	ARG	1	0.850	0.916	19.869	13.882	13.882	0.000	0.000	0.000	0.000
93	A	99	PHE	0	0.012	0.000	24.192	0.438	0.438	0.000	0.000	0.000	0.000
94	A	100	LEU	0	0.009	0.010	26.820	-0.189	-0.189	0.000	0.000	0.000	0.000
95	A	101	SER	0	0.033	0.010	27.804	0.191	0.191	0.000	0.000	0.000	0.000
96	A	102	LEU	0	0.000	0.013	29.701	-0.020	-0.020	0.000	0.000	0.000	0.000
97	A	103	ILE	0	-0.031	-0.015	30.071	0.159	0.159	0.000	0.000	0.000	0.000

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