FMO DATABASE

FMODB ID: R5298

Calculation Name: 1XL3-C-Xray372

Preferred Name:

Target Type:

Ligand Name: n-dimethyl-lysine

ligand 3-letter code: MLY

PDB ID: 1XL3

Chain ID: C

ChEMBL ID:

UniProt ID: P69968

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	91
LigandCharge	MLY=1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-665440.96813
FMO2-HF: Nuclear repulsion	627315.508005
FMO2-HF: Total energy	-38125.460125
FMO2-MP2: Total energy	-38234.606821

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(C:2:ALA)

Summations of interaction energy for fragment #1(C:2:ALA)

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.
-6.428	-4.751	-0.018	-0.808	-0.85	0.002

Interaction energy analysis for fragmet #1(C:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.044 / q_NPA : -0.028

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	C	4	ASP	-1	-0.821	-0.890	3.852	-0.552	1.192	-0.017	-0.798	-0.929	0.002
4	C	5	LEU	0	0.001	-0.002	5.609	0.192	0.192	0.000	0.000	0.000	0.000
5	C	6	SER	0	-0.102	-0.082	8.815	0.102	0.102	0.000	0.000	0.000	0.000
6	C	7	GLU	-1	-0.857	-0.928	5.088	-4.636	-4.703	-0.001	-0.010	0.079	0.000
7	C	8	PHE	0	0.016	0.020	9.314	0.284	0.284	0.000	0.000	0.000	0.000
8	C	9	MET	0	-0.040	-0.024	10.833	0.218	0.218	0.000	0.000	0.000	0.000
9	C	10	GLY	0	0.019	0.005	12.680	0.130	0.130	0.000	0.000	0.000	0.000
10	C	11	ASP	-1	-0.774	-0.858	10.969	-1.353	-1.353	0.000	0.000	0.000	0.000
11	C	12	ILE	0	-0.053	-0.028	14.126	0.150	0.150	0.000	0.000	0.000	0.000
12	C	13	VAL	0	-0.052	-0.027	16.831	0.082	0.082	0.000	0.000	0.000	0.000
13	C	14	ALA	0	0.006	0.003	17.110	0.063	0.063	0.000	0.000	0.000	0.000
14	C	15	LEU	0	-0.043	-0.020	18.015	0.061	0.061	0.000	0.000	0.000	0.000
15	C	16	VAL	0	-0.071	-0.048	19.817	0.053	0.053	0.000	0.000	0.000	0.000
16	C	17	ASP	-1	-0.968	-0.973	21.997	-0.305	-0.305	0.000	0.000	0.000	0.000
17	C	18	MLY	1	0.783	0.896	22.026	0.375	0.375	0.000	0.000	0.000	0.000
18	C	19	ARG	1	0.911	0.958	24.317	0.251	0.251	0.000	0.000	0.000	0.000
19	C	20	TRP	0	-0.081	-0.040	27.476	-0.003	-0.003	0.000	0.000	0.000	0.000
20	C	21	ALA	0	0.042	0.016	22.899	-0.003	-0.003	0.000	0.000	0.000	0.000
21	C	22	GLY	0	0.017	-0.012	23.342	0.032	0.032	0.000	0.000	0.000	0.000
22	C	23	ILE	0	0.017	0.003	22.357	-0.027	-0.027	0.000	0.000	0.000	0.000
23	C	24	HIS	0	-0.022	-0.031	19.733	-0.003	-0.003	0.000	0.000	0.000	0.000
24	C	25	ASP	-1	-0.789	-0.862	18.017	-0.446	-0.446	0.000	0.000	0.000	0.000
25	C	26	ILE	0	-0.003	-0.017	17.361	-0.064	-0.064	0.000	0.000	0.000	0.000
26	C	27	GLU	-1	-0.821	-0.907	16.550	-0.359	-0.359	0.000	0.000	0.000	0.000
27	C	28	HIS	0	-0.093	-0.050	12.041	0.018	0.018	0.000	0.000	0.000	0.000
28	C	29	LEU	0	0.006	-0.001	12.111	-0.140	-0.140	0.000	0.000	0.000	0.000
29	C	30	ALA	0	-0.005	0.011	11.362	-0.140	-0.140	0.000	0.000	0.000	0.000
30	C	31	ASN	0	-0.013	-0.033	10.964	0.027	0.027	0.000	0.000	0.000	0.000
31	C	32	ALA	0	-0.003	0.023	7.504	-0.038	-0.038	0.000	0.000	0.000	0.000
32	C	33	PHE	0	-0.044	-0.028	6.057	-0.693	-0.693	0.000	0.000	0.000	0.000
33	C	34	SER	0	-0.066	-0.014	6.915	0.311	0.311	0.000	0.000	0.000	0.000
34	C	35	LEU	0	-0.002	0.000	8.835	0.202	0.202	0.000	0.000	0.000	0.000
35	C	36	PRO	0	-0.041	-0.026	11.592	0.014	0.014	0.000	0.000	0.000	0.000
36	C	37	THR	0	-0.025	-0.055	13.852	0.042	0.042	0.000	0.000	0.000	0.000
37	C	38	PRO	0	0.063	0.041	17.238	-0.044	-0.044	0.000	0.000	0.000	0.000
38	C	39	GLU	-1	-0.729	-0.840	19.748	-0.051	-0.051	0.000	0.000	0.000	0.000
39	C	40	ILE	0	-0.096	-0.053	14.954	-0.016	-0.016	0.000	0.000	0.000	0.000
40	C	41	MLY	1	0.940	0.973	14.121	0.197	0.197	0.000	0.000	0.000	0.000
41	C	42	VAL	0	0.074	0.058	17.425	-0.036	-0.036	0.000	0.000	0.000	0.000
42	C	43	ARG	1	0.879	0.938	19.167	0.080	0.080	0.000	0.000	0.000	0.000
43	C	44	PHE	0	0.016	0.018	13.068	-0.008	-0.008	0.000	0.000	0.000	0.000
44	C	45	TYR	0	0.060	0.020	17.242	-0.054	-0.054	0.000	0.000	0.000	0.000
45	C	46	GLN	0	-0.034	-0.017	19.907	0.010	0.010	0.000	0.000	0.000	0.000
46	C	47	ASP	-1	-0.853	-0.933	19.497	-0.178	-0.178	0.000	0.000	0.000	0.000
47	C	48	LEU	0	0.000	0.023	16.516	-0.004	-0.004	0.000	0.000	0.000	0.000
48	C	49	MLY	1	0.870	0.932	19.827	0.185	0.185	0.000	0.000	0.000	0.000
49	C	50	ARG	1	0.789	0.880	23.379	0.183	0.183	0.000	0.000	0.000	0.000
50	C	51	MET	0	-0.027	-0.009	16.973	0.017	0.017	0.000	0.000	0.000	0.000
51	C	52	PHE	0	0.051	0.014	18.365	0.012	0.012	0.000	0.000	0.000	0.000
52	C	53	ARG	1	0.934	0.971	23.536	0.170	0.170	0.000	0.000	0.000	0.000
53	C	54	LEU	0	-0.075	-0.043	25.440	0.022	0.022	0.000	0.000	0.000	0.000
54	C	55	PHE	0	0.011	0.023	19.589	0.007	0.007	0.000	0.000	0.000	0.000
55	C	56	PRO	0	-0.001	-0.006	25.740	0.015	0.015	0.000	0.000	0.000	0.000
56	C	57	LEU	0	0.015	-0.016	28.173	-0.012	-0.012	0.000	0.000	0.000	0.000
57	C	58	GLY	0	-0.036	-0.019	30.034	-0.004	-0.004	0.000	0.000	0.000	0.000
58	C	59	VAL	0	-0.009	0.007	24.223	-0.001	-0.001	0.000	0.000	0.000	0.000
59	C	60	PHE	0	-0.002	-0.005	25.285	-0.020	-0.020	0.000	0.000	0.000	0.000
60	C	61	SER	0	-0.010	-0.017	27.710	0.011	0.011	0.000	0.000	0.000	0.000
61	C	62	ASP	-1	-0.874	-0.913	29.827	-0.176	-0.176	0.000	0.000	0.000	0.000
62	C	63	GLU	-1	-0.819	-0.900	31.419	-0.181	-0.181	0.000	0.000	0.000	0.000
63	C	64	GLU	-1	-0.876	-0.943	32.699	-0.170	-0.170	0.000	0.000	0.000	0.000
64	C	65	GLN	0	0.061	0.026	28.598	-0.021	-0.021	0.000	0.000	0.000	0.000
65	C	66	ARG	1	0.832	0.927	28.082	0.176	0.176	0.000	0.000	0.000	0.000
66	C	67	GLN	0	-0.067	-0.055	28.483	-0.006	-0.006	0.000	0.000	0.000	0.000
67	C	68	ASN	0	-0.018	-0.009	27.287	0.010	0.010	0.000	0.000	0.000	0.000
68	C	69	LEU	0	0.013	0.024	22.016	-0.002	-0.002	0.000	0.000	0.000	0.000
69	C	70	LEU	0	-0.001	-0.019	25.037	-0.009	-0.009	0.000	0.000	0.000	0.000
70	C	71	GLN	0	-0.030	-0.022	26.902	0.010	0.010	0.000	0.000	0.000	0.000
71	C	72	MET	0	-0.015	0.012	24.272	0.013	0.013	0.000	0.000	0.000	0.000
72	C	73	CYS	0	-0.050	-0.020	22.632	-0.016	-0.016	0.000	0.000	0.000	0.000
73	C	74	GLN	0	-0.038	-0.004	23.639	0.000	0.000	0.000	0.000	0.000	0.000
74	C	75	ASN	0	0.067	0.013	26.070	0.021	0.021	0.000	0.000	0.000	0.000
75	C	76	ALA	0	0.014	0.025	20.809	0.007	0.007	0.000	0.000	0.000	0.000
76	C	77	ILE	0	-0.048	-0.032	22.737	0.006	0.006	0.000	0.000	0.000	0.000
77	C	78	ASP	-1	-0.857	-0.923	23.920	-0.136	-0.136	0.000	0.000	0.000	0.000
78	C	79	MET	0	0.002	0.016	19.554	0.005	0.005	0.000	0.000	0.000	0.000
79	C	80	ALA	0	-0.012	-0.018	20.959	0.008	0.008	0.000	0.000	0.000	0.000
80	C	81	ILE	0	-0.027	-0.021	22.561	0.014	0.014	0.000	0.000	0.000	0.000
81	C	82	GLU	-1	-0.918	-0.951	25.710	-0.108	-0.108	0.000	0.000	0.000	0.000
82	C	83	SER	0	0.001	0.011	22.446	0.006	0.006	0.000	0.000	0.000	0.000
83	C	84	GLU	-1	-0.954	-0.993	23.466	-0.068	-0.068	0.000	0.000	0.000	0.000
84	C	85	GLU	-1	-0.991	-1.000	24.625	-0.055	-0.055	0.000	0.000	0.000	0.000
85	C	86	GLU	-1	-0.962	-0.988	26.612	-0.081	-0.081	0.000	0.000	0.000	0.000
86	C	87	GLU	-1	-0.981	-0.982	21.409	-0.042	-0.042	0.000	0.000	0.000	0.000
87	C	88	LEU	0	-0.076	-0.030	26.182	0.015	0.015	0.000	0.000	0.000	0.000
88	C	89	SER	0	-0.118	-0.058	28.965	0.005	0.005	0.000	0.000	0.000	0.000
89	C	90	GLU	-1	-0.967	-0.980	30.767	-0.013	-0.013	0.000	0.000	0.000	0.000
90	C	91	LEU	0	-0.069	-0.032	31.069	0.004	0.004	0.000	0.000	0.000	0.000
91	C	92	ASP	-1	-0.998	-1.000	29.308	0.030	0.030	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:2:ALA)