FMO DATABASE

FMODB ID: ZY86N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-665279.195007
FMO2-HF: Nuclear repulsion	627154.660868
FMO2-HF: Total energy	-38124.534139
FMO2-MP2: Total energy	-38233.740893

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.
-3.382	-2.11	-0.016	-0.537	-0.72	0

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 : -0.071 / q_NPA : -0.056

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].
3	C	4	ASP	-1	-0.882	-0.943	3.852	-0.698	0.663	-0.015	-0.525	-0.822
4	C	5	LEU	0	-0.012	-0.002	5.515	0.387	0.387	0.000	0.000	0.000
5	C	6	SER	0	-0.071	-0.045	8.958	0.115	0.115	0.000	0.000	0.000
6	C	7	GLU	-1	-0.834	-0.925	4.987	-4.503	-4.592	-0.001	-0.012	0.102
7	C	8	PHE	0	0.027	0.032	9.251	0.260	0.260	0.000	0.000	0.000
8	C	9	MET	0	-0.039	-0.028	10.833	0.164	0.164	0.000	0.000	0.000
9	C	10	GLY	0	0.015	0.004	12.566	0.092	0.092	0.000	0.000	0.000
10	C	11	ASP	-1	-0.790	-0.847	10.924	-0.767	-0.767	0.000	0.000	0.000
11	C	12	ILE	0	-0.057	-0.029	14.126	0.107	0.107	0.000	0.000	0.000
12	C	13	VAL	0	-0.055	-0.028	16.831	0.049	0.049	0.000	0.000	0.000
13	C	14	ALA	0	0.011	-0.001	17.013	0.039	0.039	0.000	0.000	0.000
14	C	15	LEU	0	-0.055	-0.021	18.117	0.040	0.040	0.000	0.000	0.000
15	C	16	VAL	0	-0.069	-0.048	19.769	0.035	0.035	0.000	0.000	0.000
16	C	17	ASP	-1	-0.972	-0.975	21.998	-0.197	-0.197	0.000	0.000	0.000
17	C	18	MLY	1	0.791	0.895	21.910	0.164	0.164	0.000	0.000	0.000
18	C	19	ARG	1	0.912	0.956	24.105	0.144	0.144	0.000	0.000	0.000
19	C	20	TRP	0	-0.072	-0.046	27.299	-0.001	-0.001	0.000	0.000	0.000
20	C	21	ALA	0	0.052	0.023	23.026	-0.001	-0.001	0.000	0.000	0.000
21	C	22	GLY	0	0.032	-0.020	23.399	0.015	0.015	0.000	0.000	0.000
22	C	23	ILE	0	0.031	0.009	22.685	-0.013	-0.013	0.000	0.000	0.000
23	C	24	HIS	0	0.037	0.009	19.723	0.000	0.000	0.000	0.000	0.000
24	C	25	ASP	-1	-0.807	-0.868	18.153	-0.166	-0.166	0.000	0.000	0.000
25	C	26	ILE	0	-0.027	-0.022	17.521	-0.028	-0.028	0.000	0.000	0.000
26	C	27	GLU	-1	-0.852	-0.956	17.004	0.031	0.031	0.000	0.000	0.000
27	C	28	HIS	0	-0.051	-0.020	12.021	0.112	0.112	0.000	0.000	0.000
28	C	29	LEU	0	0.005	-0.002	12.350	-0.021	-0.021	0.000	0.000	0.000
29	C	30	ALA	0	0.002	0.012	11.902	0.018	0.018	0.000	0.000	0.000
30	C	31	ASN	0	-0.009	-0.024	11.473	0.196	0.196	0.000	0.000	0.000
31	C	32	ALA	0	-0.016	0.012	7.828	0.194	0.194	0.000	0.000	0.000
32	C	33	PHE	0	-0.048	-0.030	6.756	0.280	0.280	0.000	0.000	0.000
33	C	34	SER	0	-0.086	-0.022	7.942	0.178	0.178	0.000	0.000	0.000
34	C	35	LEU	0	0.008	0.010	9.819	0.133	0.133	0.000	0.000	0.000
35	C	36	PRO	0	-0.023	-0.015	12.869	-0.056	-0.056	0.000	0.000	0.000
36	C	37	THR	0	0.004	-0.009	14.789	-0.024	-0.024	0.000	0.000	0.000
37	C	38	PRO	0	0.055	0.035	18.233	0.011	0.011	0.000	0.000	0.000
38	C	39	GLU	-1	-0.744	-0.890	20.750	0.242	0.242	0.000	0.000	0.000
39	C	40	ILE	0	-0.089	-0.051	15.592	-0.018	-0.018	0.000	0.000	0.000
40	C	41	MLY	1	0.944	0.973	15.043	-0.350	-0.350	0.000	0.000	0.000
41	C	42	VAL	0	0.070	0.055	18.426	-0.032	-0.032	0.000	0.000	0.000
42	C	43	ARG	1	0.900	0.947	19.454	-0.228	-0.228	0.000	0.000	0.000
43	C	44	PHE	0	0.022	0.021	12.972	-0.022	-0.022	0.000	0.000	0.000
44	C	45	TYR	0	0.065	0.026	17.747	-0.043	-0.043	0.000	0.000	0.000
45	C	46	GLN	0	-0.022	-0.016	20.620	-0.018	-0.018	0.000	0.000	0.000
46	C	47	ASP	-1	-0.968	-0.995	19.456	0.090	0.090	0.000	0.000	0.000
47	C	48	LEU	0	-0.004	0.016	16.787	-0.022	-0.022	0.000	0.000	0.000
48	C	49	MLY	1	0.931	0.980	20.023	-0.022	-0.022	0.000	0.000	0.000
49	C	50	ARG	1	0.887	0.938	23.599	-0.058	-0.058	0.000	0.000	0.000
50	C	51	MET	0	-0.022	-0.006	16.958	-0.005	-0.005	0.000	0.000	0.000
51	C	52	PHE	0	0.054	0.015	18.683	-0.008	-0.008	0.000	0.000	0.000
52	C	53	ARG	1	0.905	0.962	23.536	0.011	0.011	0.000	0.000	0.000
53	C	54	LEU	0	-0.063	-0.038	25.402	0.004	0.004	0.000	0.000	0.000
54	C	55	PHE	0	0.009	0.019	19.648	-0.002	-0.002	0.000	0.000	0.000
55	C	56	PRO	0	-0.005	-0.008	25.716	0.007	0.007	0.000	0.000	0.000
56	C	57	LEU	0	0.018	-0.015	28.165	-0.008	-0.008	0.000	0.000	0.000
57	C	58	GLY	0	-0.029	-0.015	29.929	-0.003	-0.003	0.000	0.000	0.000
58	C	59	VAL	0	-0.010	0.010	24.120	-0.006	-0.006	0.000	0.000	0.000
59	C	60	PHE	0	0.004	-0.003	25.031	-0.012	-0.012	0.000	0.000	0.000
60	C	61	SER	0	0.014	0.014	27.710	0.001	0.001	0.000	0.000	0.000
61	C	62	ASP	-1	-0.895	-0.935	29.827	-0.081	-0.081	0.000	0.000	0.000
62	C	63	GLU	-1	-0.860	-0.925	31.419	-0.057	-0.057	0.000	0.000	0.000
63	C	64	GLU	-1	-0.884	-0.952	32.833	-0.061	-0.061	0.000	0.000	0.000
64	C	65	GLN	0	0.086	0.044	28.543	-0.003	-0.003	0.000	0.000	0.000
65	C	66	ARG	1	0.856	0.952	28.195	0.056	0.056	0.000	0.000	0.000
66	C	67	GLN	0	-0.085	-0.072	28.745	0.008	0.008	0.000	0.000	0.000
67	C	68	ASN	0	-0.010	-0.009	27.415	0.015	0.015	0.000	0.000	0.000
68	C	69	LEU	0	-0.010	0.020	22.309	0.006	0.006	0.000	0.000	0.000
69	C	70	LEU	0	-0.011	-0.033	25.435	0.009	0.009	0.000	0.000	0.000
70	C	71	GLN	0	-0.037	-0.022	27.378	0.010	0.010	0.000	0.000	0.000
71	C	72	MET	0	-0.018	0.028	24.475	0.011	0.011	0.000	0.000	0.000
72	C	73	CYS	0	-0.034	-0.011	22.973	0.006	0.006	0.000	0.000	0.000
73	C	74	GLN	0	-0.048	-0.020	24.210	0.009	0.009	0.000	0.000	0.000
74	C	75	ASN	0	0.067	0.018	26.499	0.012	0.012	0.000	0.000	0.000
75	C	76	ALA	0	0.017	0.025	21.439	0.007	0.007	0.000	0.000	0.000
76	C	77	ILE	0	-0.063	-0.039	23.466	0.016	0.016	0.000	0.000	0.000
77	C	78	ASP	-1	-0.879	-0.936	24.731	0.045	0.045	0.000	0.000	0.000
78	C	79	MET	0	-0.003	0.024	20.491	0.007	0.007	0.000	0.000	0.000
79	C	80	ALA	0	-0.037	-0.030	21.781	0.011	0.011	0.000	0.000	0.000
80	C	81	ILE	0	-0.016	-0.018	23.405	0.016	0.016	0.000	0.000	0.000
81	C	82	GLU	-1	-0.906	-0.945	26.642	0.054	0.054	0.000	0.000	0.000
82	C	83	SER	0	-0.020	0.003	23.186	0.010	0.010	0.000	0.000	0.000
83	C	84	GLU	-1	-0.982	-1.006	24.278	0.158	0.158	0.000	0.000	0.000
84	C	85	GLU	-1	-0.975	-0.994	25.607	0.081	0.081	0.000	0.000	0.000
85	C	86	GLU	-1	-0.978	-0.999	27.438	0.079	0.079	0.000	0.000	0.000
86	C	87	GLU	-1	-0.975	-0.985	22.424	0.202	0.202	0.000	0.000	0.000
87	C	88	LEU	0	-0.091	-0.038	27.101	0.004	0.004	0.000	0.000	0.000
88	C	89	SER	0	-0.120	-0.040	29.936	-0.010	-0.010	0.000	0.000	0.000
89	C	90	GLU	-1	-0.953	-0.976	31.662	0.080	0.080	0.000	0.000	0.000
90	C	91	LEU	0	-0.091	-0.043	31.994	0.006	0.006	0.000	0.000	0.000
91	C	92	ASP	-1	-0.979	-0.987	30.091	0.125	0.125	0.000	0.000	0.000

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