FMO DATABASE

FMODB ID: 4JV4N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-995800.756549
FMO2-HF: Nuclear repulsion	946063.83884
FMO2-HF: Total energy	-49736.917708
FMO2-MP2: Total energy	-49875.637531

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.
-16.55	-11.01	16.831	-7.263	-15.107	-0.058

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 : 0.006 / q_NPA : 0.027

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	-0.009	-0.003	2.455	-1.286	1.280	0.425	-0.906	-2.085	0.005
4	A	4	LYS	1	0.996	1.004	2.425	-1.462	-1.566	3.326	-1.239	-1.983	-0.018
5	A	5	LEU	0	0.028	0.025	2.063	-0.873	-1.719	4.348	-0.603	-2.900	0.004
6	A	6	ILE	0	-0.012	-0.006	4.534	0.597	0.687	-0.001	-0.017	-0.071	0.000
7	A	7	LEU	0	0.011	0.022	7.827	-0.173	-0.173	0.000	0.000	0.000	0.000
8	A	8	MET	0	-0.025	-0.013	10.477	0.124	0.124	0.000	0.000	0.000	0.000
9	A	9	SER	0	-0.003	-0.003	13.920	-0.040	-0.040	0.000	0.000	0.000	0.000
10	A	10	HIS	0	-0.050	-0.053	17.221	0.053	0.053	0.000	0.000	0.000	0.000
11	A	11	GLY	0	-0.024	-0.010	20.438	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.778	0.867	19.264	0.062	0.062	0.000	0.000	0.000	0.000
13	A	13	MET	0	0.043	0.032	16.535	0.019	0.019	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.026	0.019	13.329	-0.017	-0.017	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.850	-0.926	13.878	-0.085	-0.085	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.795	-0.907	15.412	-0.045	-0.045	0.000	0.000	0.000	0.000
17	A	17	THR	0	-0.049	-0.029	12.088	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.009	0.003	9.233	-0.069	-0.069	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.028	0.029	12.237	0.063	0.063	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.017	-0.027	15.342	0.054	0.054	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.020	-0.024	8.761	-0.056	-0.056	0.000	0.000	0.000	0.000
22	A	22	GLN	0	-0.006	-0.004	10.480	-0.055	-0.055	0.000	0.000	0.000	0.000
23	A	23	MET	0	-0.075	-0.026	12.655	0.099	0.099	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.076	-0.026	13.051	-0.012	-0.012	0.000	0.000	0.000	0.000
25	A	25	VAL	0	-0.024	-0.024	8.220	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	26	GLY	0	-0.002	0.010	10.570	0.180	0.180	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.956	-0.995	10.452	1.010	1.010	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.034	-0.019	5.966	0.079	0.079	0.000	0.000	0.000	0.000
29	A	29	ALA	0	-0.017	0.012	5.656	0.464	0.464	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.900	-0.951	5.941	0.716	0.716	0.000	0.000	0.000	0.000
31	A	31	ALA	0	-0.040	-0.025	5.823	-0.184	-0.184	0.000	0.000	0.000	0.000
32	A	32	ALA	0	-0.007	0.013	7.634	0.138	0.138	0.000	0.000	0.000	0.000
33	A	33	ILE	0	0.030	0.006	10.124	-0.148	-0.148	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.054	-0.027	12.885	0.053	0.053	0.000	0.000	0.000	0.000
35	A	35	SER	0	0.053	0.026	15.621	-0.051	-0.051	0.000	0.000	0.000	0.000
36	A	36	MET	0	-0.062	-0.022	18.568	0.024	0.024	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.005	-0.009	21.220	0.001	0.001	0.000	0.000	0.000	0.000
38	A	38	ALA	0	-0.002	-0.014	24.533	-0.010	-0.010	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.896	-0.953	27.852	-0.093	-0.093	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.877	-0.899	23.067	-0.136	-0.136	0.000	0.000	0.000	0.000
41	A	41	GLY	0	0.032	0.012	26.010	0.002	0.002	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.013	-0.002	23.636	-0.010	-0.010	0.000	0.000	0.000	0.000
43	A	43	SER	0	0.030	0.011	23.992	-0.010	-0.010	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.058	0.036	24.367	0.000	0.000	0.000	0.000	0.000	0.000
45	A	45	THR	0	0.006	-0.014	19.499	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	46	GLN	0	-0.009	-0.029	19.581	-0.005	-0.005	0.000	0.000	0.000	0.000
47	A	47	ALA	0	-0.021	-0.002	19.996	-0.008	-0.008	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.863	0.929	18.219	0.145	0.145	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.043	0.026	12.949	0.001	0.001	0.000	0.000	0.000	0.000
50	A	50	ALA	0	-0.033	-0.019	15.593	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	51	ALA	0	-0.030	-0.019	17.603	0.010	0.010	0.000	0.000	0.000	0.000
52	A	52	ILE	0	0.032	0.026	11.553	0.026	0.026	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.022	-0.022	11.699	0.008	0.008	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.890	0.939	14.077	0.130	0.130	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.946	-0.952	14.467	0.148	0.148	0.000	0.000	0.000	0.000
56	A	56	ALA	0	-0.016	0.000	11.066	0.044	0.044	0.000	0.000	0.000	0.000
57	A	57	GLY	0	0.015	0.016	13.191	0.014	0.014	0.000	0.000	0.000	0.000
58	A	58	ASN	0	-0.044	-0.030	13.368	-0.137	-0.137	0.000	0.000	0.000	0.000
59	A	59	VAL	0	-0.002	-0.002	8.460	0.042	0.042	0.000	0.000	0.000	0.000
60	A	60	PRO	0	-0.010	-0.009	7.076	-0.063	-0.063	0.000	0.000	0.000	0.000
61	A	61	THR	0	-0.013	-0.006	6.118	-0.067	-0.067	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.012	-0.001	4.852	0.191	0.191	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.006	-0.008	6.417	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.002	0.000	6.751	-0.009	-0.009	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.001	-0.016	10.010	0.137	0.137	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.728	-0.860	13.724	-0.419	-0.419	0.000	0.000	0.000	0.000
67	A	67	LEU	0	-0.018	-0.002	16.478	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	68	MLY	1	1.025	0.981	19.175	0.425	0.425	0.000	0.000	0.000	0.000
69	A	69	GLY	0	-0.025	-0.005	20.098	0.027	0.027	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.041	0.031	21.399	0.033	0.033	0.000	0.000	0.000	0.000
71	A	71	THR	0	-0.007	-0.010	21.077	-0.022	-0.022	0.000	0.000	0.000	0.000
72	A	72	PRO	0	0.059	0.024	17.524	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	73	CYS	0	0.052	0.027	16.513	-0.046	-0.046	0.000	0.000	0.000	0.000
74	A	74	ASN	0	-0.054	-0.031	17.593	-0.040	-0.040	0.000	0.000	0.000	0.000
75	A	75	VAL	0	0.000	0.000	17.675	0.006	0.006	0.000	0.000	0.000	0.000
76	A	76	ALA	0	0.043	0.024	13.697	0.006	0.006	0.000	0.000	0.000	0.000
77	A	77	MET	0	-0.034	-0.026	15.677	-0.019	-0.019	0.000	0.000	0.000	0.000
78	A	78	MET	0	-0.054	-0.024	17.640	0.022	0.022	0.000	0.000	0.000	0.000
79	A	79	ALA	0	0.032	0.028	15.619	0.023	0.023	0.000	0.000	0.000	0.000
80	A	80	MET	0	-0.013	-0.008	14.315	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	81	GLY	0	-0.026	0.005	16.584	0.009	0.009	0.000	0.000	0.000	0.000
82	A	82	THR	0	-0.088	-0.041	18.772	0.044	0.044	0.000	0.000	0.000	0.000
83	A	83	TYR	0	-0.012	-0.009	13.917	0.038	0.038	0.000	0.000	0.000	0.000
84	A	84	PRO	0	0.051	0.029	14.915	-0.065	-0.065	0.000	0.000	0.000	0.000
85	A	85	GLN	0	-0.056	-0.021	11.090	-0.104	-0.104	0.000	0.000	0.000	0.000
86	A	86	LEU	0	0.027	0.034	9.838	-0.170	-0.170	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.755	0.844	9.581	0.948	0.948	0.000	0.000	0.000	0.000
88	A	88	VAL	0	0.027	-0.002	10.011	-0.081	-0.081	0.000	0.000	0.000	0.000
89	A	89	VAL	0	0.018	0.024	9.937	0.054	0.054	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.034	-0.018	12.281	0.011	0.011	0.000	0.000	0.000	0.000
91	A	91	GLY	0	-0.005	-0.003	14.873	-0.028	-0.028	0.000	0.000	0.000	0.000
92	A	92	LEU	0	-0.051	-0.013	10.816	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	93	ASN	0	0.056	0.006	13.047	0.025	0.025	0.000	0.000	0.000	0.000
94	A	94	LEU	0	0.049	0.008	12.315	-0.114	-0.114	0.000	0.000	0.000	0.000
95	A	95	ALA	0	0.041	0.030	11.691	-0.072	-0.072	0.000	0.000	0.000	0.000
96	A	96	MET	0	-0.021	0.020	9.535	-0.116	-0.116	0.000	0.000	0.000	0.000
97	A	97	ALA	0	0.004	0.005	7.620	-0.434	-0.434	0.000	0.000	0.000	0.000
98	A	98	ILE	0	0.016	0.001	7.040	-0.228	-0.228	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.865	-0.951	7.266	-1.567	-1.567	0.000	0.000	0.000	0.000
100	A	100	ALA	0	-0.065	-0.036	3.694	-1.178	-0.917	0.004	-0.053	-0.211	0.000
101	A	101	ALA	0	-0.039	-0.019	2.542	-6.692	-4.319	1.041	-1.403	-2.011	-0.020
102	A	102	VAL	0	0.016	0.011	3.788	-0.297	0.357	0.009	-0.172	-0.491	-0.001
103	A	103	SER	0	-0.026	0.010	3.459	0.197	1.134	0.033	-0.289	-0.681	-0.001
104	A	104	PRO	0	0.017	-0.003	2.372	-3.921	-5.152	7.497	-2.581	-3.686	-0.028
105	A	105	VAL	0	-0.042	-0.015	3.465	0.683	0.734	-0.004	0.194	-0.241	0.000
106	A	106	GLU	-1	-0.886	-0.961	3.967	-1.502	-1.250	0.001	-0.077	-0.176	0.000
107	A	107	ASN	0	-0.001	-0.004	6.102	-0.047	-0.047	0.000	0.000	0.000	0.000
108	A	108	VAL	0	0.056	0.019	6.735	-0.261	-0.261	0.000	0.000	0.000	0.000
109	A	109	ASP	-1	-0.822	-0.888	7.775	-0.966	-0.966	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.963	-0.975	9.260	-1.083	-1.083	0.000	0.000	0.000	0.000
111	A	111	LEU	0	0.007	0.002	2.974	-0.418	0.119	0.152	-0.117	-0.571	0.001
112	A	112	ALA	0	0.011	-0.008	7.091	0.035	0.035	0.000	0.000	0.000	0.000
113	A	113	ALA	0	-0.005	0.009	9.452	0.147	0.147	0.000	0.000	0.000	0.000
114	A	114	TYR	0	-0.022	-0.011	7.463	0.266	0.266	0.000	0.000	0.000	0.000
115	A	115	LEU	0	0.022	0.003	5.026	0.167	0.167	0.000	0.000	0.000	0.000
116	A	116	THR	0	-0.026	-0.016	9.476	0.216	0.216	0.000	0.000	0.000	0.000
117	A	117	GLN	0	-0.028	-0.016	12.914	0.203	0.203	0.000	0.000	0.000	0.000
118	A	118	ILE	0	0.008	0.016	10.282	0.111	0.111	0.000	0.000	0.000	0.000
119	A	119	GLY	0	0.014	-0.011	12.659	0.115	0.115	0.000	0.000	0.000	0.000
120	A	120	GLN	0	-0.058	-0.042	13.993	0.097	0.097	0.000	0.000	0.000	0.000
121	A	121	SER	0	-0.011	-0.011	16.512	0.089	0.089	0.000	0.000	0.000	0.000
122	A	122	ALA	0	-0.049	-0.006	15.305	0.054	0.054	0.000	0.000	0.000	0.000
123	A	123	VAL	0	-0.072	-0.020	17.410	0.052	0.052	0.000	0.000	0.000	0.000
124	A	124	THR	0	0.006	-0.001	20.417	0.012	0.012	0.000	0.000	0.000	0.000
125	A	125	THR	0	-0.056	-0.033	23.620	0.012	0.012	0.000	0.000	0.000	0.000
126	A	126	ILE	0	-0.023	-0.011	23.407	-0.002	-0.002	0.000	0.000	0.000	0.000
127	A	127	ASP	-1	-0.935	-0.961	27.465	-0.165	-0.165	0.000	0.000	0.000	0.000
128	A	128	LEU	0	-0.039	-0.020	30.150	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	129	PRO	0	0.047	0.021	31.212	0.000	0.000	0.000	0.000	0.000	0.000
130	A	130	GLU	-1	-0.939	-0.963	33.599	-0.109	-0.109	0.000	0.000	0.000	0.000
131	A	131	LEU	0	-0.024	-0.022	34.363	0.001	0.001	0.000	0.000	0.000	0.000
132	A	132	THR	0	-0.055	-0.016	38.716	0.007	0.007	0.000	0.000	0.000	0.000

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