FMO DATABASE

FMODB ID: YVGL2

Calculation Name: 3BED-A-Xray372

Preferred Name:

Target Type:

Ligand Name: n-dimethyl-lysine

ligand 3-letter code: MLY

PDB ID: 3BED

Chain ID: A

ChEMBL ID:

UniProt ID: Q838I6

Base Structure: X-ray

Registration Date: 2023-09-23

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	132
LigandCharge	MLY=1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-999018.633735
FMO2-HF: Nuclear repulsion	949280.936796
FMO2-HF: Total energy	-49737.69694
FMO2-MP2: Total energy	-49876.216939

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:1:MET)

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

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.
-16.976	-7.623	12.84	-6.759	-15.431	-0.047

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : 0.025

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	3	PRO	0	0.010	0.008	2.221	-1.844	0.967	1.045	-1.254	-2.602	0.005
4	A	4	LYS	1	0.911	0.950	2.501	-2.229	-1.795	2.473	-1.042	-1.864	-0.015
5	A	5	LEU	0	0.013	0.015	2.160	-1.205	-1.530	3.634	-0.550	-2.758	0.005
6	A	6	ILE	0	-0.018	-0.019	4.443	0.562	0.657	-0.001	-0.020	-0.074	0.000
7	A	7	LEU	0	0.019	0.027	7.915	-0.186	-0.186	0.000	0.000	0.000	0.000
8	A	8	MET	0	-0.042	-0.026	10.402	0.095	0.095	0.000	0.000	0.000	0.000
9	A	9	SER	0	-0.014	-0.005	13.872	-0.031	-0.031	0.000	0.000	0.000	0.000
10	A	10	HIS	0	-0.042	-0.049	17.212	0.037	0.037	0.000	0.000	0.000	0.000
11	A	11	GLY	0	0.004	0.004	20.700	0.004	0.004	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.751	0.829	18.989	-0.067	-0.067	0.000	0.000	0.000	0.000
13	A	13	MET	0	0.023	0.024	16.346	0.027	0.027	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.023	0.016	13.229	0.000	0.000	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.753	-0.845	13.419	0.056	0.056	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.777	-0.879	15.208	0.134	0.134	0.000	0.000	0.000	0.000
17	A	17	THR	0	-0.044	-0.012	11.690	0.012	0.012	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.008	0.013	9.203	-0.021	-0.021	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.021	0.020	12.124	0.117	0.117	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.033	-0.042	15.073	0.051	0.051	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.017	-0.024	8.742	-0.054	-0.054	0.000	0.000	0.000	0.000
22	A	22	GLN	0	-0.028	-0.018	10.064	-0.062	-0.062	0.000	0.000	0.000	0.000
23	A	23	MET	0	-0.075	-0.031	12.296	0.071	0.071	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.066	-0.028	13.338	-0.057	-0.057	0.000	0.000	0.000	0.000
25	A	25	VAL	0	-0.034	-0.021	8.260	-0.046	-0.046	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.008	0.018	10.105	0.260	0.260	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.961	-1.003	10.136	1.337	1.337	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.028	-0.010	5.910	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.012	0.019	5.210	1.203	1.203	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.869	-0.923	5.260	0.603	0.603	0.000	0.000	0.000	0.000
31	A	31	ALA	0	0.001	-0.009	5.758	-0.173	-0.070	-0.001	-0.004	-0.097	0.000
32	A	32	ALA	0	0.009	0.026	7.600	0.065	0.065	0.000	0.000	0.000	0.000
33	A	33	ILE	0	0.006	-0.012	10.247	-0.125	-0.125	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.047	-0.027	13.013	0.021	0.021	0.000	0.000	0.000	0.000
35	A	35	SER	0	0.010	-0.016	15.654	-0.044	-0.044	0.000	0.000	0.000	0.000
36	A	36	MET	0	-0.083	-0.022	18.368	0.013	0.013	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.017	-0.038	21.171	0.002	0.002	0.000	0.000	0.000	0.000
38	A	38	ALA	0	-0.006	-0.011	24.623	-0.014	-0.014	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.877	-0.953	27.800	-0.054	-0.054	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.837	-0.854	23.361	-0.081	-0.081	0.000	0.000	0.000	0.000
41	A	41	GLY	0	0.045	0.021	25.751	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.002	-0.004	23.353	-0.011	-0.011	0.000	0.000	0.000	0.000
43	A	43	SER	0	0.036	0.006	23.587	-0.009	-0.009	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.043	0.037	24.190	0.001	0.001	0.000	0.000	0.000	0.000
45	A	45	THR	0	0.018	-0.007	19.098	0.000	0.000	0.000	0.000	0.000	0.000
46	A	46	GLN	0	-0.012	-0.030	19.225	-0.005	-0.005	0.000	0.000	0.000	0.000
47	A	47	ALA	0	-0.026	-0.006	19.941	-0.010	-0.010	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.841	0.900	17.867	0.080	0.080	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.040	0.021	12.734	0.004	0.004	0.000	0.000	0.000	0.000
50	A	50	ALA	0	-0.012	-0.012	15.577	-0.015	-0.015	0.000	0.000	0.000	0.000
51	A	51	ALA	0	-0.037	-0.015	18.011	0.007	0.007	0.000	0.000	0.000	0.000
52	A	52	ILE	0	0.020	0.014	11.509	0.012	0.012	0.000	0.000	0.000	0.000
53	A	53	LEU	0	0.030	0.006	11.586	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.860	0.942	14.260	0.118	0.118	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.931	-0.947	14.709	0.090	0.090	0.000	0.000	0.000	0.000
56	A	56	ALA	0	-0.031	-0.011	10.948	0.022	0.022	0.000	0.000	0.000	0.000
57	A	57	GLY	0	0.024	0.018	12.966	-0.012	-0.012	0.000	0.000	0.000	0.000
58	A	58	ASN	0	-0.049	-0.037	13.542	-0.122	-0.122	0.000	0.000	0.000	0.000
59	A	59	VAL	0	0.026	0.020	9.187	0.029	0.029	0.000	0.000	0.000	0.000
60	A	60	PRO	0	-0.005	-0.001	7.043	-0.043	-0.043	0.000	0.000	0.000	0.000
61	A	61	THR	0	-0.009	-0.003	6.264	-0.042	-0.042	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.015	-0.013	4.543	-0.002	0.104	-0.001	-0.005	-0.100	0.000
63	A	63	VAL	0	-0.002	-0.002	6.187	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	64	LEU	0	0.004	0.010	6.656	-0.042	-0.042	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.018	-0.009	9.830	0.145	0.145	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.729	-0.844	13.582	-0.317	-0.317	0.000	0.000	0.000	0.000
67	A	67	LEU	0	-0.026	-0.014	16.449	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	68	MLY	1	1.023	0.986	18.808	0.389	0.389	0.000	0.000	0.000	0.000
69	A	69	GLY	0	-0.017	0.000	19.626	0.026	0.026	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.043	0.038	21.198	0.029	0.029	0.000	0.000	0.000	0.000
71	A	71	THR	0	-0.004	-0.014	20.561	-0.027	-0.027	0.000	0.000	0.000	0.000
72	A	72	PRO	0	0.058	0.022	17.157	-0.010	-0.010	0.000	0.000	0.000	0.000
73	A	73	CYS	0	0.040	0.028	16.123	-0.049	-0.049	0.000	0.000	0.000	0.000
74	A	74	ASN	0	-0.071	-0.040	17.202	-0.045	-0.045	0.000	0.000	0.000	0.000
75	A	75	VAL	0	0.012	0.002	17.538	0.000	0.000	0.000	0.000	0.000	0.000
76	A	76	ALA	0	0.028	0.010	13.532	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	77	MET	0	-0.025	-0.013	15.465	-0.030	-0.030	0.000	0.000	0.000	0.000
78	A	78	MET	0	-0.058	-0.026	17.508	0.018	0.018	0.000	0.000	0.000	0.000
79	A	79	ALA	0	0.036	0.029	15.513	0.015	0.015	0.000	0.000	0.000	0.000
80	A	80	MET	0	0.004	0.005	14.112	-0.016	-0.016	0.000	0.000	0.000	0.000
81	A	81	GLY	0	-0.033	0.003	16.473	0.005	0.005	0.000	0.000	0.000	0.000
82	A	82	THR	0	-0.110	-0.062	18.491	0.043	0.043	0.000	0.000	0.000	0.000
83	A	83	TYR	0	-0.026	-0.014	13.858	0.028	0.028	0.000	0.000	0.000	0.000
84	A	84	PRO	0	0.032	0.017	14.701	-0.066	-0.066	0.000	0.000	0.000	0.000
85	A	85	GLN	0	-0.041	-0.018	10.980	-0.075	-0.075	0.000	0.000	0.000	0.000
86	A	86	LEU	0	0.026	0.027	9.715	-0.169	-0.169	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.729	0.816	9.109	0.954	0.954	0.000	0.000	0.000	0.000
88	A	88	VAL	0	0.026	-0.006	10.011	-0.034	-0.034	0.000	0.000	0.000	0.000
89	A	89	VAL	0	0.004	0.022	10.050	0.034	0.034	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.032	-0.029	12.039	0.037	0.037	0.000	0.000	0.000	0.000
91	A	91	GLY	0	-0.002	0.010	14.687	-0.011	-0.011	0.000	0.000	0.000	0.000
92	A	92	LEU	0	-0.072	-0.037	10.553	-0.006	-0.006	0.000	0.000	0.000	0.000
93	A	93	ASN	0	0.035	-0.003	12.973	0.072	0.072	0.000	0.000	0.000	0.000
94	A	94	LEU	0	0.051	0.008	12.101	-0.100	-0.100	0.000	0.000	0.000	0.000
95	A	95	ALA	0	0.044	0.032	11.550	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	96	MET	0	-0.030	0.032	9.251	-0.088	-0.088	0.000	0.000	0.000	0.000
97	A	97	ALA	0	0.022	0.008	7.281	-0.408	-0.408	0.000	0.000	0.000	0.000
98	A	98	ILE	0	0.004	-0.003	7.034	0.013	0.013	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.829	-0.904	7.211	-1.151	-1.151	0.000	0.000	0.000	0.000
100	A	100	ALA	0	-0.058	-0.037	3.482	-1.437	-1.097	0.012	-0.070	-0.280	0.000
101	A	101	ALA	0	-0.023	-0.015	2.524	-5.857	-3.325	1.596	-1.622	-2.507	-0.023
102	A	102	VAL	0	-0.010	0.002	4.122	0.756	1.306	0.002	-0.084	-0.469	0.000
103	A	103	SER	0	0.003	0.018	3.519	-0.045	0.688	0.017	-0.207	-0.543	-0.001
104	A	104	PRO	0	-0.018	-0.019	2.467	-5.032	-3.682	2.823	-1.628	-2.545	-0.020
105	A	105	VAL	0	-0.047	-0.012	3.924	0.380	0.547	-0.001	0.012	-0.178	0.000
106	A	106	GLU	-1	-0.871	-0.953	4.044	-1.898	-1.695	0.001	-0.064	-0.140	0.000
107	A	107	ASN	0	-0.014	-0.005	5.896	0.011	0.011	0.000	0.000	0.000	0.000
108	A	108	VAL	0	0.070	0.025	6.337	-0.321	-0.321	0.000	0.000	0.000	0.000
109	A	109	ASP	-1	-0.825	-0.875	7.412	-0.982	-0.982	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.933	-0.969	8.977	-1.218	-1.218	0.000	0.000	0.000	0.000
111	A	111	LEU	0	0.028	0.013	2.530	-0.214	-0.035	1.242	-0.217	-1.204	0.002
112	A	112	ALA	0	0.004	0.001	6.841	0.071	0.071	0.000	0.000	0.000	0.000
113	A	113	ALA	0	-0.005	0.004	9.125	0.162	0.162	0.000	0.000	0.000	0.000
114	A	114	TYR	0	-0.061	-0.050	7.515	0.183	0.183	0.000	0.000	0.000	0.000
115	A	115	LEU	0	0.031	0.005	4.432	0.116	0.191	-0.001	-0.004	-0.070	0.000
116	A	116	THR	0	-0.043	-0.031	9.004	0.239	0.239	0.000	0.000	0.000	0.000
117	A	117	GLN	0	-0.016	0.006	12.502	0.199	0.199	0.000	0.000	0.000	0.000
118	A	118	ILE	0	0.007	0.011	9.913	0.116	0.116	0.000	0.000	0.000	0.000
119	A	119	GLY	0	0.006	-0.021	12.307	0.110	0.110	0.000	0.000	0.000	0.000
120	A	120	GLN	0	-0.047	-0.040	13.705	0.071	0.071	0.000	0.000	0.000	0.000
121	A	121	SER	0	-0.017	-0.027	15.787	0.081	0.081	0.000	0.000	0.000	0.000
122	A	122	ALA	0	-0.035	0.002	15.021	0.051	0.051	0.000	0.000	0.000	0.000
123	A	123	VAL	0	-0.087	-0.034	17.109	0.053	0.053	0.000	0.000	0.000	0.000
124	A	124	THR	0	-0.004	-0.014	20.207	0.003	0.003	0.000	0.000	0.000	0.000
125	A	125	THR	0	-0.044	-0.022	23.420	0.007	0.007	0.000	0.000	0.000	0.000
126	A	126	ILE	0	-0.005	0.009	23.008	-0.007	-0.007	0.000	0.000	0.000	0.000
127	A	127	ASP	-1	-0.927	-0.961	27.115	-0.108	-0.108	0.000	0.000	0.000	0.000
128	A	128	LEU	0	-0.012	-0.013	29.765	0.005	0.005	0.000	0.000	0.000	0.000
129	A	129	PRO	0	0.020	0.000	30.844	0.001	0.001	0.000	0.000	0.000	0.000
130	A	130	GLU	-1	-0.923	-0.940	33.638	-0.065	-0.065	0.000	0.000	0.000	0.000
131	A	131	LEU	0	-0.022	-0.015	34.147	0.000	0.000	0.000	0.000	0.000	0.000
132	A	132	THR	0	-0.092	-0.040	38.416	0.006	0.006	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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