FMO DATABASE

FMODB ID: Q16YY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-668023.83273
FMO2-HF: Nuclear repulsion	629897.955884
FMO2-HF: Total energy	-38125.876846
FMO2-MP2: Total energy	-38235.049648

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.
-5.838	-4.375	-0.014	-0.705	-0.743	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 : -0.037 / q_NPA : -0.026

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	-0.828	-0.894	3.873	-0.204	1.305	-0.013	-0.700	-0.795	0.002
4	C	5	LEU	0	-0.028	-0.012	5.744	0.077	0.077	0.000	0.000	0.000	0.000
5	C	6	SER	0	-0.092	-0.081	8.906	0.057	0.057	0.000	0.000	0.000	0.000
6	C	7	GLU	-1	-0.855	-0.917	5.176	-3.809	-3.855	-0.001	-0.005	0.052	0.000
7	C	8	PHE	0	0.030	0.021	9.287	0.244	0.244	0.000	0.000	0.000	0.000
8	C	9	MET	0	-0.040	-0.020	10.964	0.189	0.189	0.000	0.000	0.000	0.000
9	C	10	GLY	0	0.014	0.002	12.819	0.108	0.108	0.000	0.000	0.000	0.000
10	C	11	ASP	-1	-0.780	-0.858	11.228	-1.323	-1.323	0.000	0.000	0.000	0.000
11	C	12	ILE	0	-0.032	-0.016	14.447	0.130	0.130	0.000	0.000	0.000	0.000
12	C	13	VAL	0	-0.046	-0.024	16.939	0.078	0.078	0.000	0.000	0.000	0.000
13	C	14	ALA	0	-0.001	-0.001	17.291	0.058	0.058	0.000	0.000	0.000	0.000
14	C	15	LEU	0	-0.041	-0.021	18.145	0.057	0.057	0.000	0.000	0.000	0.000
15	C	16	VAL	0	-0.042	-0.020	20.063	0.049	0.049	0.000	0.000	0.000	0.000
16	C	17	ASP	-1	-0.889	-0.931	22.389	-0.273	-0.273	0.000	0.000	0.000	0.000
17	C	18	MLY	1	0.790	0.896	22.211	0.402	0.402	0.000	0.000	0.000	0.000
18	C	19	ARG	1	0.811	0.892	24.404	0.262	0.262	0.000	0.000	0.000	0.000
19	C	20	TRP	0	-0.052	-0.036	27.615	-0.006	-0.006	0.000	0.000	0.000	0.000
20	C	21	ALA	0	0.005	0.016	23.010	-0.006	-0.006	0.000	0.000	0.000	0.000
21	C	22	GLY	0	0.016	-0.008	23.379	0.034	0.034	0.000	0.000	0.000	0.000
22	C	23	ILE	0	0.016	0.006	21.986	-0.028	-0.028	0.000	0.000	0.000	0.000
23	C	24	HIS	0	-0.019	-0.027	19.643	-0.009	-0.009	0.000	0.000	0.000	0.000
24	C	25	ASP	-1	-0.803	-0.875	17.959	-0.489	-0.489	0.000	0.000	0.000	0.000
25	C	26	ILE	0	-0.004	-0.007	17.437	-0.063	-0.063	0.000	0.000	0.000	0.000
26	C	27	GLU	-1	-0.805	-0.913	16.274	-0.431	-0.431	0.000	0.000	0.000	0.000
27	C	28	HIS	0	-0.101	-0.050	12.008	-0.031	-0.031	0.000	0.000	0.000	0.000
28	C	29	LEU	0	0.018	0.005	11.997	-0.158	-0.158	0.000	0.000	0.000	0.000
29	C	30	ALA	0	0.001	0.006	11.332	-0.141	-0.141	0.000	0.000	0.000	0.000
30	C	31	ASN	0	-0.023	-0.031	11.109	0.033	0.033	0.000	0.000	0.000	0.000
31	C	32	ALA	0	0.003	0.022	7.660	-0.101	-0.101	0.000	0.000	0.000	0.000
32	C	33	PHE	0	-0.041	-0.020	6.163	-0.776	-0.776	0.000	0.000	0.000	0.000
33	C	34	SER	0	-0.058	-0.030	6.754	0.342	0.342	0.000	0.000	0.000	0.000
34	C	35	LEU	0	-0.032	-0.007	8.561	0.274	0.274	0.000	0.000	0.000	0.000
35	C	36	PRO	0	-0.025	-0.019	11.422	0.022	0.022	0.000	0.000	0.000	0.000
36	C	37	THR	0	-0.018	-0.026	13.477	0.051	0.051	0.000	0.000	0.000	0.000
37	C	38	PRO	0	0.087	0.047	17.097	-0.044	-0.044	0.000	0.000	0.000	0.000
38	C	39	GLU	-1	-0.675	-0.806	19.488	-0.113	-0.113	0.000	0.000	0.000	0.000
39	C	40	ILE	0	-0.105	-0.058	14.560	-0.010	-0.010	0.000	0.000	0.000	0.000
40	C	41	MLY	1	0.929	0.983	14.031	0.308	0.308	0.000	0.000	0.000	0.000
41	C	42	VAL	0	0.049	0.033	17.434	-0.027	-0.027	0.000	0.000	0.000	0.000
42	C	43	ARG	1	0.781	0.883	19.420	0.110	0.110	0.000	0.000	0.000	0.000
43	C	44	PHE	0	0.027	0.017	13.466	-0.008	-0.008	0.000	0.000	0.000	0.000
44	C	45	TYR	0	0.061	0.018	17.201	-0.050	-0.050	0.000	0.000	0.000	0.000
45	C	46	GLN	0	-0.022	-0.004	19.936	0.017	0.017	0.000	0.000	0.000	0.000
46	C	47	ASP	-1	-0.841	-0.914	19.232	-0.189	-0.189	0.000	0.000	0.000	0.000
47	C	48	LEU	0	-0.005	0.014	16.477	0.003	0.003	0.000	0.000	0.000	0.000
48	C	49	MLY	1	0.860	0.927	19.761	0.201	0.201	0.000	0.000	0.000	0.000
49	C	50	ARG	1	0.770	0.861	23.137	0.195	0.195	0.000	0.000	0.000	0.000
50	C	51	MET	0	-0.025	-0.007	17.035	0.023	0.023	0.000	0.000	0.000	0.000
51	C	52	PHE	0	0.046	0.006	18.524	0.016	0.016	0.000	0.000	0.000	0.000
52	C	53	ARG	1	0.933	0.964	23.539	0.171	0.171	0.000	0.000	0.000	0.000
53	C	54	LEU	0	-0.061	-0.035	25.040	0.020	0.020	0.000	0.000	0.000	0.000
54	C	55	PHE	0	0.010	0.020	19.431	0.011	0.011	0.000	0.000	0.000	0.000
55	C	56	PRO	0	-0.015	-0.005	25.661	0.013	0.013	0.000	0.000	0.000	0.000
56	C	57	LEU	0	0.019	-0.023	28.174	-0.011	-0.011	0.000	0.000	0.000	0.000
57	C	58	GLY	0	-0.018	-0.004	30.057	-0.006	-0.006	0.000	0.000	0.000	0.000
58	C	59	VAL	0	-0.031	-0.002	24.290	0.000	0.000	0.000	0.000	0.000	0.000
59	C	60	PHE	0	0.001	-0.005	25.062	-0.024	-0.024	0.000	0.000	0.000	0.000
60	C	61	SER	0	-0.029	-0.033	27.605	0.013	0.013	0.000	0.000	0.000	0.000
61	C	62	ASP	-1	-0.849	-0.900	29.609	-0.176	-0.176	0.000	0.000	0.000	0.000
62	C	63	GLU	-1	-0.806	-0.892	31.089	-0.182	-0.182	0.000	0.000	0.000	0.000
63	C	64	GLU	-1	-0.895	-0.941	32.555	-0.175	-0.175	0.000	0.000	0.000	0.000
64	C	65	GLN	0	0.056	0.018	28.593	-0.023	-0.023	0.000	0.000	0.000	0.000
65	C	66	ARG	1	0.824	0.927	27.850	0.174	0.174	0.000	0.000	0.000	0.000
66	C	67	GLN	0	-0.061	-0.056	28.353	-0.009	-0.009	0.000	0.000	0.000	0.000
67	C	68	ASN	0	-0.025	-0.010	27.405	0.010	0.010	0.000	0.000	0.000	0.000
68	C	69	LEU	0	0.035	0.027	21.933	-0.002	-0.002	0.000	0.000	0.000	0.000
69	C	70	LEU	0	-0.008	-0.009	25.051	-0.010	-0.010	0.000	0.000	0.000	0.000
70	C	71	GLN	0	-0.020	-0.013	26.946	0.008	0.008	0.000	0.000	0.000	0.000
71	C	72	MET	0	-0.023	-0.003	24.631	0.011	0.011	0.000	0.000	0.000	0.000
72	C	73	CYS	0	-0.041	-0.021	22.483	-0.023	-0.023	0.000	0.000	0.000	0.000
73	C	74	GLN	0	-0.071	-0.034	23.768	0.000	0.000	0.000	0.000	0.000	0.000
74	C	75	ASN	0	0.060	0.014	26.098	0.017	0.017	0.000	0.000	0.000	0.000
75	C	76	ALA	0	0.032	0.025	20.725	0.005	0.005	0.000	0.000	0.000	0.000
76	C	77	ILE	0	-0.061	-0.029	22.427	0.002	0.002	0.000	0.000	0.000	0.000
77	C	78	ASP	-1	-0.838	-0.908	23.904	-0.158	-0.158	0.000	0.000	0.000	0.000
78	C	79	MET	0	0.009	0.018	19.671	0.004	0.004	0.000	0.000	0.000	0.000
79	C	80	ALA	0	-0.004	-0.011	20.853	0.005	0.005	0.000	0.000	0.000	0.000
80	C	81	ILE	0	-0.023	-0.015	22.487	0.014	0.014	0.000	0.000	0.000	0.000
81	C	82	GLU	-1	-0.938	-0.961	25.737	-0.139	-0.139	0.000	0.000	0.000	0.000
82	C	83	SER	0	0.015	0.009	22.063	0.003	0.003	0.000	0.000	0.000	0.000
83	C	84	GLU	-1	-0.957	-0.994	23.352	-0.108	-0.108	0.000	0.000	0.000	0.000
84	C	85	GLU	-1	-0.971	-0.995	24.546	-0.077	-0.077	0.000	0.000	0.000	0.000
85	C	86	GLU	-1	-0.968	-0.986	26.338	-0.120	-0.120	0.000	0.000	0.000	0.000
86	C	87	GLU	-1	-0.969	-0.980	21.122	-0.115	-0.115	0.000	0.000	0.000	0.000
87	C	88	LEU	0	-0.085	-0.034	25.743	0.017	0.017	0.000	0.000	0.000	0.000
88	C	89	SER	0	-0.090	-0.045	28.663	0.008	0.008	0.000	0.000	0.000	0.000
89	C	90	GLU	-1	-0.976	-0.989	30.720	-0.039	-0.039	0.000	0.000	0.000	0.000
90	C	91	LEU	0	-0.067	-0.035	30.991	0.003	0.003	0.000	0.000	0.000	0.000
91	C	92	ASP	-1	-1.010	-0.999	28.872	-0.001	-0.001	0.000	0.000	0.000	0.000

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