FMO DATABASE

FMODB ID: 5JVKZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-996290.748793
FMO2-HF: Nuclear repulsion	946553.325168
FMO2-HF: Total energy	-49737.423624
FMO2-MP2: Total energy	-49876.083867

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.
-15.672	-9.812	18.265	-7.704	-16.418	-0.059

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 : -0.002 / q_NPA : 0.023

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	0.006	0.000	2.319	-1.509	1.161	0.715	-1.038	-2.347	0.005
4	A	4	LYS	1	0.943	0.977	2.468	-1.706	-1.786	3.778	-1.419	-2.280	-0.019
5	A	5	LEU	0	0.010	0.019	2.100	-1.135	-1.781	4.181	-0.591	-2.943	0.005
6	A	6	ILE	0	-0.016	-0.012	4.491	0.547	0.640	-0.001	-0.017	-0.075	0.000
7	A	7	LEU	0	0.011	0.022	7.770	-0.177	-0.177	0.000	0.000	0.000	0.000
8	A	8	MET	0	-0.026	-0.010	10.405	0.100	0.100	0.000	0.000	0.000	0.000
9	A	9	SER	0	0.004	0.006	13.822	-0.035	-0.035	0.000	0.000	0.000	0.000
10	A	10	HIS	0	-0.056	-0.064	17.126	0.040	0.040	0.000	0.000	0.000	0.000
11	A	11	GLY	0	-0.018	-0.006	20.366	0.000	0.000	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.756	0.831	19.240	-0.026	-0.026	0.000	0.000	0.000	0.000
13	A	13	MET	0	0.035	0.028	16.418	0.022	0.022	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.024	0.015	13.348	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.778	-0.877	13.880	0.014	0.014	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.772	-0.879	15.460	0.073	0.073	0.000	0.000	0.000	0.000
17	A	17	THR	0	-0.043	-0.012	11.911	0.004	0.004	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.008	0.005	9.350	-0.036	-0.036	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.016	0.022	12.224	0.087	0.087	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.018	-0.034	15.229	0.050	0.050	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.022	-0.030	8.801	-0.048	-0.048	0.000	0.000	0.000	0.000
22	A	22	GLN	0	-0.015	-0.005	10.404	-0.072	-0.072	0.000	0.000	0.000	0.000
23	A	23	MET	0	-0.075	-0.025	12.664	0.083	0.083	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.079	-0.031	13.346	-0.040	-0.040	0.000	0.000	0.000	0.000
25	A	25	VAL	0	-0.020	-0.020	8.326	-0.013	-0.013	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.001	0.014	10.605	0.182	0.182	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.959	-0.996	10.564	1.161	1.161	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.032	-0.018	6.304	0.028	0.028	0.000	0.000	0.000	0.000
29	A	29	ALA	0	-0.005	0.017	5.761	0.806	0.806	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.867	-0.938	5.567	0.894	0.894	0.000	0.000	0.000	0.000
31	A	31	ALA	0	-0.017	-0.013	5.902	-0.132	-0.036	-0.001	-0.003	-0.091	0.000
32	A	32	ALA	0	-0.006	0.013	7.720	0.081	0.081	0.000	0.000	0.000	0.000
33	A	33	ILE	0	0.019	-0.004	10.127	-0.121	-0.121	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.049	-0.022	12.885	0.031	0.031	0.000	0.000	0.000	0.000
35	A	35	SER	0	0.032	0.006	15.577	-0.045	-0.045	0.000	0.000	0.000	0.000
36	A	36	MET	0	-0.080	-0.028	18.530	0.015	0.015	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.015	-0.042	21.149	0.001	0.001	0.000	0.000	0.000	0.000
38	A	38	ALA	0	-0.008	-0.015	24.480	-0.011	-0.011	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.889	-0.952	27.782	-0.059	-0.059	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.862	-0.856	23.651	-0.088	-0.088	0.000	0.000	0.000	0.000
41	A	41	GLY	0	0.053	0.023	25.938	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.012	0.004	23.558	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	43	SER	0	0.037	0.014	23.878	-0.009	-0.009	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.047	0.033	24.279	0.000	0.000	0.000	0.000	0.000	0.000
45	A	45	THR	0	0.017	-0.016	19.278	0.000	0.000	0.000	0.000	0.000	0.000
46	A	46	GLN	0	-0.013	-0.033	19.490	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	47	ALA	0	-0.024	-0.002	19.906	-0.009	-0.009	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.839	0.903	18.141	0.090	0.090	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.040	0.019	12.791	0.004	0.004	0.000	0.000	0.000	0.000
50	A	50	ALA	0	-0.026	-0.015	15.527	-0.011	-0.011	0.000	0.000	0.000	0.000
51	A	51	ALA	0	-0.030	-0.014	17.557	0.004	0.004	0.000	0.000	0.000	0.000
52	A	52	ILE	0	0.028	0.021	11.527	0.019	0.019	0.000	0.000	0.000	0.000
53	A	53	LEU	0	0.004	-0.007	11.511	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.871	0.928	14.024	0.113	0.113	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.941	-0.948	14.694	0.104	0.104	0.000	0.000	0.000	0.000
56	A	56	ALA	0	-0.019	-0.002	11.087	0.030	0.030	0.000	0.000	0.000	0.000
57	A	57	GLY	0	0.009	0.014	13.209	-0.009	-0.009	0.000	0.000	0.000	0.000
58	A	58	ASN	0	-0.045	-0.027	13.316	-0.120	-0.120	0.000	0.000	0.000	0.000
59	A	59	VAL	0	0.022	0.009	8.658	0.016	0.016	0.000	0.000	0.000	0.000
60	A	60	PRO	0	0.003	-0.001	7.028	-0.031	-0.031	0.000	0.000	0.000	0.000
61	A	61	THR	0	-0.023	-0.010	5.989	-0.052	-0.052	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.014	-0.005	4.564	0.057	0.159	-0.001	-0.005	-0.096	0.000
63	A	63	VAL	0	-0.003	-0.006	6.253	0.026	0.026	0.000	0.000	0.000	0.000
64	A	64	LEU	0	0.000	0.002	6.648	-0.016	-0.016	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.001	-0.020	9.844	0.136	0.136	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.738	-0.863	13.565	-0.326	-0.326	0.000	0.000	0.000	0.000
67	A	67	LEU	0	-0.018	0.000	16.339	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	68	MLY	1	1.025	0.987	19.008	0.373	0.373	0.000	0.000	0.000	0.000
69	A	69	GLY	0	-0.015	-0.003	19.901	0.025	0.025	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.046	0.035	21.231	0.029	0.029	0.000	0.000	0.000	0.000
71	A	71	THR	0	-0.007	-0.009	20.905	-0.021	-0.021	0.000	0.000	0.000	0.000
72	A	72	PRO	0	0.056	0.024	17.456	-0.010	-0.010	0.000	0.000	0.000	0.000
73	A	73	CYS	0	0.046	0.027	16.331	-0.043	-0.043	0.000	0.000	0.000	0.000
74	A	74	ASN	0	-0.075	-0.049	17.415	-0.042	-0.042	0.000	0.000	0.000	0.000
75	A	75	VAL	0	0.010	0.010	17.630	0.001	0.001	0.000	0.000	0.000	0.000
76	A	76	ALA	0	0.039	0.020	13.556	0.000	0.000	0.000	0.000	0.000	0.000
77	A	77	MET	0	-0.030	-0.025	15.504	-0.024	-0.024	0.000	0.000	0.000	0.000
78	A	78	MET	0	-0.054	-0.023	17.397	0.016	0.016	0.000	0.000	0.000	0.000
79	A	79	ALA	0	0.037	0.031	15.461	0.017	0.017	0.000	0.000	0.000	0.000
80	A	80	MET	0	-0.019	-0.010	14.118	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	81	GLY	0	-0.027	0.005	16.391	0.003	0.003	0.000	0.000	0.000	0.000
82	A	82	THR	0	-0.094	-0.045	18.612	0.039	0.039	0.000	0.000	0.000	0.000
83	A	83	TYR	0	-0.022	-0.014	13.759	0.028	0.028	0.000	0.000	0.000	0.000
84	A	84	PRO	0	0.049	0.026	14.744	-0.058	-0.058	0.000	0.000	0.000	0.000
85	A	85	GLN	0	-0.060	-0.026	11.013	-0.078	-0.078	0.000	0.000	0.000	0.000
86	A	86	LEU	0	0.026	0.033	9.698	-0.162	-0.162	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.745	0.826	9.220	0.923	0.923	0.000	0.000	0.000	0.000
88	A	88	VAL	0	0.025	-0.006	9.793	-0.064	-0.064	0.000	0.000	0.000	0.000
89	A	89	VAL	0	0.011	0.022	10.243	0.044	0.044	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.029	-0.016	12.058	0.021	0.021	0.000	0.000	0.000	0.000
91	A	91	GLY	0	-0.001	0.000	14.687	-0.027	-0.027	0.000	0.000	0.000	0.000
92	A	92	LEU	0	-0.060	-0.022	10.546	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	93	ASN	0	0.052	0.006	12.897	0.048	0.048	0.000	0.000	0.000	0.000
94	A	94	LEU	0	0.059	0.012	12.201	-0.094	-0.094	0.000	0.000	0.000	0.000
95	A	95	ALA	0	0.045	0.034	11.622	-0.040	-0.040	0.000	0.000	0.000	0.000
96	A	96	MET	0	-0.039	0.025	9.470	-0.094	-0.094	0.000	0.000	0.000	0.000
97	A	97	ALA	0	0.012	0.008	7.513	-0.382	-0.382	0.000	0.000	0.000	0.000
98	A	98	ILE	0	0.014	-0.007	7.002	-0.111	-0.111	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.846	-0.909	7.320	-1.238	-1.238	0.000	0.000	0.000	0.000
100	A	100	ALA	0	-0.049	-0.030	3.584	-1.138	-0.844	0.007	-0.061	-0.239	0.000
101	A	101	ALA	0	-0.045	-0.020	2.569	-6.231	-3.781	1.014	-1.418	-2.046	-0.020
102	A	102	VAL	0	0.016	0.009	4.007	0.354	0.929	0.005	-0.124	-0.456	-0.001
103	A	103	SER	0	-0.016	0.013	3.351	-0.034	0.885	0.031	-0.285	-0.664	0.000
104	A	104	PRO	0	0.009	-0.004	2.347	-3.570	-5.090	7.935	-2.651	-3.764	-0.029
105	A	105	VAL	0	-0.044	-0.013	3.480	0.440	0.502	-0.003	0.181	-0.241	0.000
106	A	106	GLU	-1	-0.887	-0.960	3.806	-2.021	-1.727	0.004	-0.116	-0.182	-0.001
107	A	107	ASN	0	-0.003	-0.006	5.938	-0.013	-0.013	0.000	0.000	0.000	0.000
108	A	108	VAL	0	0.071	0.024	6.453	-0.242	-0.242	0.000	0.000	0.000	0.000
109	A	109	ASP	-1	-0.824	-0.875	7.596	-0.934	-0.934	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.952	-0.976	9.088	-1.117	-1.117	0.000	0.000	0.000	0.000
111	A	111	LEU	0	0.025	0.013	2.676	-0.410	0.080	0.602	-0.156	-0.936	0.001
112	A	112	ALA	0	0.006	-0.009	6.863	0.065	0.065	0.000	0.000	0.000	0.000
113	A	113	ALA	0	-0.010	0.010	9.206	0.153	0.153	0.000	0.000	0.000	0.000
114	A	114	TYR	0	-0.045	-0.045	7.581	0.199	0.199	0.000	0.000	0.000	0.000
115	A	115	LEU	0	0.026	0.002	4.713	0.106	0.167	-0.001	-0.001	-0.058	0.000
116	A	116	THR	0	-0.041	-0.027	9.312	0.212	0.212	0.000	0.000	0.000	0.000
117	A	117	GLN	0	-0.017	0.001	12.736	0.184	0.184	0.000	0.000	0.000	0.000
118	A	118	ILE	0	0.010	0.017	10.130	0.109	0.109	0.000	0.000	0.000	0.000
119	A	119	GLY	0	0.015	-0.021	12.520	0.109	0.109	0.000	0.000	0.000	0.000
120	A	120	GLN	0	-0.058	-0.043	13.842	0.078	0.078	0.000	0.000	0.000	0.000
121	A	121	SER	0	-0.019	-0.024	16.341	0.078	0.078	0.000	0.000	0.000	0.000
122	A	122	ALA	0	-0.048	-0.008	15.180	0.050	0.050	0.000	0.000	0.000	0.000
123	A	123	VAL	0	-0.072	-0.018	17.295	0.049	0.049	0.000	0.000	0.000	0.000
124	A	124	THR	0	0.006	-0.007	20.287	0.005	0.005	0.000	0.000	0.000	0.000
125	A	125	THR	0	-0.053	-0.024	23.501	0.012	0.012	0.000	0.000	0.000	0.000
126	A	126	ILE	0	-0.026	-0.012	23.306	-0.002	-0.002	0.000	0.000	0.000	0.000
127	A	127	ASP	-1	-0.926	-0.952	27.376	-0.122	-0.122	0.000	0.000	0.000	0.000
128	A	128	LEU	0	-0.051	-0.024	30.083	0.001	0.001	0.000	0.000	0.000	0.000
129	A	129	PRO	0	0.049	0.012	31.197	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	130	GLU	-1	-0.936	-0.955	33.604	-0.074	-0.074	0.000	0.000	0.000	0.000
131	A	131	LEU	0	0.005	-0.004	34.358	0.000	0.000	0.000	0.000	0.000	0.000
132	A	132	THR	0	-0.084	-0.037	38.732	0.006	0.006	0.000	0.000	0.000	0.000

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