FMO DATABASE

FMODB ID: YYQY2

Calculation Name: 4EVX-A-Xray321

Preferred Name:

Target Type:

Ligand Name: n-dimethyl-lysine | s-hydroxycysteine

Ligand 3-letter code: MLY | CSO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4EVX

Chain ID: A

ChEMBL ID:

UniProt ID: Q8ZLC6

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

Apendix: None

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. 1.20200129
Remarks	Structural optimization was performed under the unconstrained condition of hydrogen and heavy atoms fixed using MOE with Auto-FMO protocol as OptH.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	99
LigandResidueName
LigandFragmentNumber	0
LigandCharge	MLY=1
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-721188.7667
FMO2-HF: Nuclear repulsion	680916.865247
FMO2-HF: Total energy	-40271.901452
FMO2-MP2: Total energy	-40387.741194

3D Structure Molmil

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:6:ACE )

Summations of interaction energy for fragment #1(A:6:ACE )

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.
0.974	2.151	0.001	-0.487	-0.691	-0.001

Interaction energy analysis for fragmet #1(A:6:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.010

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	8	PHE	0	0.029	0.023	3.829	0.586	1.586	-0.005	-0.424	-0.571	-0.001
4	A	9	SER	0	-0.082	-0.063	4.905	0.192	0.259	0.000	-0.005	-0.062	0.000
5	A	10	SER	0	0.038	0.003	7.503	0.114	0.114	0.000	0.000	0.000	0.000
6	A	11	ALA	0	0.014	0.007	8.073	0.037	0.037	0.000	0.000	0.000	0.000
7	A	12	CSO	0	-0.001	0.016	9.558	0.039	0.039	0.000	0.000	0.000	0.000
8	A	13	ILE	0	0.024	0.005	5.219	0.043	0.043	0.000	0.000	0.000	0.000
9	A	14	ALA	0	-0.015	-0.015	9.816	0.009	0.009	0.000	0.000	0.000	0.000
10	A	15	PHE	0	-0.017	0.001	12.870	-0.010	-0.010	0.000	0.000	0.000	0.000
11	A	16	ILE	0	0.023	0.010	11.542	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	17	MLY	1	0.814	0.879	10.058	-0.450	-0.450	0.000	0.000	0.000	0.000
13	A	18	GLN	0	-0.034	0.015	15.092	0.003	0.003	0.000	0.000	0.000	0.000
14	A	19	TRP	0	-0.043	-0.024	17.849	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	20	GLN	0	-0.046	-0.016	16.445	-0.022	-0.022	0.000	0.000	0.000	0.000
16	A	21	GLY	0	0.006	0.009	17.835	0.019	0.019	0.000	0.000	0.000	0.000
17	A	22	LEU	0	-0.007	-0.003	16.191	0.006	0.006	0.000	0.000	0.000	0.000
18	A	23	SER	0	-0.024	-0.012	18.979	-0.016	-0.016	0.000	0.000	0.000	0.000
19	A	24	LEU	0	0.001	-0.010	18.743	0.010	0.010	0.000	0.000	0.000	0.000
20	A	25	GLU	-1	-0.910	-0.952	21.277	0.084	0.084	0.000	0.000	0.000	0.000
21	A	26	MLY	1	0.848	0.942	23.331	-0.073	-0.073	0.000	0.000	0.000	0.000
22	A	27	TYR	0	0.005	-0.008	22.319	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	28	ARG	1	0.888	0.948	25.755	-0.038	-0.038	0.000	0.000	0.000	0.000
24	A	29	ASP	-1	-0.826	-0.915	25.359	0.033	0.033	0.000	0.000	0.000	0.000
25	A	30	ARG	1	0.958	0.966	27.559	-0.018	-0.018	0.000	0.000	0.000	0.000
26	A	31	GLN	0	-0.073	-0.040	28.523	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	32	GLY	0	0.009	0.020	30.106	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	33	ASN	0	0.010	0.007	25.229	0.001	0.001	0.000	0.000	0.000	0.000
29	A	34	TRP	0	0.010	-0.004	24.750	0.003	0.003	0.000	0.000	0.000	0.000
30	A	35	VAL	0	-0.013	0.001	20.272	0.000	0.000	0.000	0.000	0.000	0.000
31	A	36	ILE	0	0.025	0.014	18.115	0.001	0.001	0.000	0.000	0.000	0.000
32	A	37	GLY	0	0.041	0.019	16.474	0.007	0.007	0.000	0.000	0.000	0.000
33	A	38	TYR	0	0.014	0.000	13.031	-0.028	-0.028	0.000	0.000	0.000	0.000
34	A	39	GLY	0	-0.020	-0.015	15.743	-0.014	-0.014	0.000	0.000	0.000	0.000
35	A	40	HIS	1	0.902	0.940	14.611	-0.131	-0.131	0.000	0.000	0.000	0.000
36	A	41	MET	0	-0.019	-0.014	16.973	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	42	LEU	0	-0.033	-0.012	18.892	0.005	0.005	0.000	0.000	0.000	0.000
38	A	43	THR	0	-0.036	-0.033	19.622	-0.015	-0.015	0.000	0.000	0.000	0.000
39	A	44	PRO	0	-0.012	-0.026	22.230	0.004	0.004	0.000	0.000	0.000	0.000
40	A	45	ASP	-1	-0.892	-0.941	25.500	0.034	0.034	0.000	0.000	0.000	0.000
41	A	46	GLU	-1	-0.915	-0.936	19.397	0.106	0.106	0.000	0.000	0.000	0.000
42	A	47	THR	0	-0.013	-0.018	24.102	0.001	0.001	0.000	0.000	0.000	0.000
43	A	48	LEU	0	-0.038	0.008	19.678	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	49	THR	0	0.026	-0.012	24.047	-0.009	-0.009	0.000	0.000	0.000	0.000
45	A	50	PHE	0	0.029	0.010	23.196	0.000	0.000	0.000	0.000	0.000	0.000
46	A	51	ILE	0	-0.019	-0.002	16.382	0.004	0.004	0.000	0.000	0.000	0.000
47	A	52	THR	0	0.017	0.001	16.757	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	53	PRO	0	0.045	0.001	15.968	0.013	0.013	0.000	0.000	0.000	0.000
49	A	54	ASP	-1	-0.875	-0.928	12.359	0.551	0.551	0.000	0.000	0.000	0.000
50	A	55	GLN	0	0.003	0.003	11.809	0.043	0.043	0.000	0.000	0.000	0.000
51	A	56	ALA	0	0.000	-0.002	13.005	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	57	GLU	-1	-0.822	-0.898	8.045	0.649	0.649	0.000	0.000	0.000	0.000
53	A	58	ALA	0	-0.009	-0.008	8.216	0.071	0.071	0.000	0.000	0.000	0.000
54	A	59	PHE	0	0.028	0.006	9.160	-0.047	-0.047	0.000	0.000	0.000	0.000
55	A	60	LEU	0	0.000	0.022	9.390	-0.066	-0.066	0.000	0.000	0.000	0.000
56	A	61	LEU	0	-0.025	-0.022	3.530	-0.157	0.000	0.006	-0.054	-0.109	0.000
57	A	62	ASP	-1	-0.894	-0.937	6.901	-0.116	-0.116	0.000	0.000	0.000	0.000
58	A	63	ASP	-1	-0.810	-0.890	9.298	-0.017	-0.017	0.000	0.000	0.000	0.000
59	A	64	LEU	0	-0.048	-0.031	7.790	-0.062	-0.062	0.000	0.000	0.000	0.000
60	A	65	ASN	0	-0.036	-0.047	4.596	-0.421	-0.468	0.000	-0.004	0.051	0.000
61	A	66	SER	0	0.003	0.020	8.605	-0.045	-0.045	0.000	0.000	0.000	0.000
62	A	67	CYS	0	-0.054	-0.035	12.198	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	68	ASP	-1	-0.865	-0.946	10.153	-0.599	-0.599	0.000	0.000	0.000	0.000
64	A	69	ILE	0	0.000	0.002	10.688	0.004	0.004	0.000	0.000	0.000	0.000
65	A	70	LEU	0	-0.027	-0.020	13.523	0.027	0.027	0.000	0.000	0.000	0.000
66	A	71	LEU	0	-0.032	-0.001	14.982	0.019	0.019	0.000	0.000	0.000	0.000
67	A	72	GLN	0	-0.029	-0.019	14.408	-0.041	-0.041	0.000	0.000	0.000	0.000
68	A	73	ASN	0	-0.001	-0.017	16.966	0.013	0.013	0.000	0.000	0.000	0.000
69	A	74	CYS	0	-0.025	0.014	19.805	0.020	0.020	0.000	0.000	0.000	0.000
70	A	75	LEU	0	-0.048	-0.031	19.327	0.015	0.015	0.000	0.000	0.000	0.000
71	A	76	PRO	0	0.007	0.011	19.998	-0.023	-0.023	0.000	0.000	0.000	0.000
72	A	77	GLU	-1	-0.940	-0.970	20.837	-0.143	-0.143	0.000	0.000	0.000	0.000
73	A	78	LEU	0	-0.058	-0.008	18.081	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	79	ASN	0	0.035	-0.005	17.059	-0.057	-0.057	0.000	0.000	0.000	0.000
75	A	80	ASP	-1	-0.887	-0.934	16.270	-0.255	-0.255	0.000	0.000	0.000	0.000
76	A	81	ARG	1	0.993	0.968	7.355	0.967	0.967	0.000	0.000	0.000	0.000
77	A	82	PHE	0	-0.001	0.021	13.569	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	83	GLN	0	0.042	0.008	15.545	0.018	0.018	0.000	0.000	0.000	0.000
79	A	84	ARG	1	0.865	0.946	12.672	0.414	0.414	0.000	0.000	0.000	0.000
80	A	85	GLU	-1	-0.769	-0.864	9.227	-0.451	-0.451	0.000	0.000	0.000	0.000
81	A	86	THR	0	-0.060	-0.031	13.154	0.054	0.054	0.000	0.000	0.000	0.000
82	A	87	LEU	0	0.023	0.020	16.639	0.029	0.029	0.000	0.000	0.000	0.000
83	A	88	ILE	0	0.023	0.012	11.550	0.025	0.025	0.000	0.000	0.000	0.000
84	A	89	ALA	0	0.008	0.002	14.683	0.035	0.035	0.000	0.000	0.000	0.000
85	A	90	LEU	0	-0.016	0.000	15.658	0.024	0.024	0.000	0.000	0.000	0.000
86	A	91	MET	0	0.008	0.001	16.340	0.019	0.019	0.000	0.000	0.000	0.000
87	A	92	PHE	0	-0.031	-0.005	13.810	0.014	0.014	0.000	0.000	0.000	0.000
88	A	93	SER	0	-0.067	-0.052	17.244	0.016	0.016	0.000	0.000	0.000	0.000
89	A	94	ILE	0	0.002	-0.001	20.186	0.008	0.008	0.000	0.000	0.000	0.000
90	A	95	GLY	0	-0.008	0.002	20.763	0.004	0.004	0.000	0.000	0.000	0.000
91	A	96	HIS	1	0.850	0.957	16.775	-0.028	-0.028	0.000	0.000	0.000	0.000
92	A	97	GLN	0	0.041	0.026	21.365	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	98	ARG	1	0.849	0.918	20.661	-0.022	-0.022	0.000	0.000	0.000	0.000
94	A	99	PHE	0	0.001	-0.008	24.309	-0.007	-0.007	0.000	0.000	0.000	0.000
95	A	100	LEU	0	0.006	0.010	26.920	0.003	0.003	0.000	0.000	0.000	0.000
96	A	101	SER	0	0.035	0.006	27.698	0.002	0.002	0.000	0.000	0.000	0.000
97	A	102	LEU	0	-0.016	-0.009	29.684	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	103	ILE	0	-0.015	0.002	30.529	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	104	NME	0	0.003	0.009	30.709	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:6:ACE )