FMO DATABASE

FMODB ID: K37Y3

Calculation Name: 3HFH-A-Xray320

Preferred Name:

Target Type:

Ligand Name: n-dimethyl-lysine

ligand 3-letter code: MLY

PDB ID: 3HFH

Chain ID: A

ChEMBL ID:

UniProt ID: O14776

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	171
LigandCharge	MLY=1
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1521964.681756
FMO2-HF: Nuclear repulsion	1448372.455511
FMO2-HF: Total energy	-73592.226245
FMO2-MP2: Total energy	-73807.001577

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:656:ACE )

Summations of interaction energy for fragment #1(A:656:ACE )

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.
4.101	-2.049	12.879	-4.499	-2.229	0.007

Interaction energy analysis for fragmet #1(A:656:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : -0.034

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	658	LEU	0	-0.032	0.001	3.795	1.010	1.996	0.012	-0.426	-0.572	0.000
4	A	659	GLY	0	0.017	0.001	5.347	0.251	0.295	0.000	-0.006	-0.037	0.000
5	A	660	SER	0	0.027	0.008	9.108	0.061	0.061	0.000	0.000	0.000	0.000
6	A	661	ALA	0	0.078	0.022	9.959	-0.062	-0.062	0.000	0.000	0.000	0.000
7	A	662	ARG	1	0.839	0.895	11.693	0.260	0.260	0.000	0.000	0.000	0.000
8	A	663	MET	0	0.014	0.011	9.239	0.023	0.023	0.000	0.000	0.000	0.000
9	A	664	MLY	1	0.835	0.913	6.358	0.429	0.429	0.000	0.000	0.000	0.000
10	A	665	GLN	0	0.044	0.012	8.433	0.156	0.156	0.000	0.000	0.000	0.000
11	A	666	PHE	0	0.003	0.013	11.372	0.082	0.082	0.000	0.000	0.000	0.000
12	A	667	MLY	1	0.944	0.998	2.013	1.545	-5.635	12.867	-4.067	-1.620	0.007
13	A	668	ASP	-1	-0.785	-0.885	8.095	-0.023	-0.023	0.000	0.000	0.000	0.000
14	A	669	MET	0	-0.026	0.004	10.097	0.040	0.040	0.000	0.000	0.000	0.000
15	A	670	LEU	0	-0.048	-0.026	10.365	0.017	0.017	0.000	0.000	0.000	0.000
16	A	671	LEU	0	0.007	-0.003	7.889	0.033	0.033	0.000	0.000	0.000	0.000
17	A	672	GLU	-1	-0.931	-0.958	12.247	0.012	0.012	0.000	0.000	0.000	0.000
18	A	673	ARG	1	0.849	0.918	14.907	-0.051	-0.051	0.000	0.000	0.000	0.000
19	A	674	GLY	0	-0.007	0.008	15.939	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	675	VAL	0	-0.025	-0.001	14.785	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	676	SER	0	-0.005	0.020	15.333	0.059	0.059	0.000	0.000	0.000	0.000
22	A	677	ALA	0	-0.022	-0.017	14.132	0.008	0.008	0.000	0.000	0.000	0.000
23	A	678	PHE	0	-0.049	-0.029	15.782	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	679	SER	0	-0.008	-0.016	19.221	-0.023	-0.023	0.000	0.000	0.000	0.000
25	A	680	THR	0	-0.002	0.021	19.761	0.008	0.008	0.000	0.000	0.000	0.000
26	A	681	TRP	0	0.068	0.032	15.874	0.000	0.000	0.000	0.000	0.000	0.000
27	A	682	GLU	-1	-0.868	-0.965	19.933	0.047	0.047	0.000	0.000	0.000	0.000
28	A	683	MLY	1	0.903	0.956	22.737	-0.080	-0.080	0.000	0.000	0.000	0.000
29	A	684	GLU	-1	-0.770	-0.888	18.488	0.135	0.135	0.000	0.000	0.000	0.000
30	A	685	LEU	0	0.012	0.023	20.517	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	686	HIS	0	-0.012	-0.013	21.478	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	687	MLY	1	0.878	0.948	19.658	-0.122	-0.122	0.000	0.000	0.000	0.000
33	A	688	ILE	0	-0.016	-0.031	16.587	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	689	VAL	0	-0.009	0.005	19.730	-0.015	-0.015	0.000	0.000	0.000	0.000
35	A	690	PHE	0	-0.004	0.013	22.289	-0.010	-0.010	0.000	0.000	0.000	0.000
36	A	691	ASP	-1	-0.757	-0.841	18.215	-0.020	-0.020	0.000	0.000	0.000	0.000
37	A	692	PRO	0	0.070	0.027	20.424	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	693	ARG	1	0.799	0.869	14.068	0.022	0.022	0.000	0.000	0.000	0.000
39	A	694	TYR	0	0.008	-0.005	16.831	-0.019	-0.019	0.000	0.000	0.000	0.000
40	A	695	LEU	0	-0.009	-0.017	18.557	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	696	LEU	0	-0.017	0.018	15.650	-0.011	-0.011	0.000	0.000	0.000	0.000
42	A	697	LEU	0	-0.022	0.005	12.590	-0.032	-0.032	0.000	0.000	0.000	0.000
43	A	698	ASN	0	0.047	0.038	17.164	0.029	0.029	0.000	0.000	0.000	0.000
44	A	699	PRO	0	0.059	0.000	17.942	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	700	MLY	1	1.010	1.016	17.416	0.085	0.085	0.000	0.000	0.000	0.000
46	A	701	GLU	-1	-0.773	-0.879	14.296	-0.181	-0.181	0.000	0.000	0.000	0.000
47	A	702	ARG	1	0.863	0.942	13.406	0.044	0.044	0.000	0.000	0.000	0.000
48	A	703	MLY	1	0.894	0.958	13.970	-0.019	-0.019	0.000	0.000	0.000	0.000
49	A	704	GLN	0	-0.033	-0.017	11.303	0.039	0.039	0.000	0.000	0.000	0.000
50	A	705	VAL	0	0.011	0.001	8.653	0.044	0.044	0.000	0.000	0.000	0.000
51	A	706	PHE	0	0.019	0.019	9.554	0.117	0.117	0.000	0.000	0.000	0.000
52	A	707	ASP	-1	-0.798	-0.917	11.807	0.178	0.178	0.000	0.000	0.000	0.000
53	A	708	GLN	0	-0.030	-0.008	6.233	-0.135	-0.135	0.000	0.000	0.000	0.000
54	A	709	TYR	0	-0.070	-0.083	7.972	0.237	0.237	0.000	0.000	0.000	0.000
55	A	710	VAL	0	0.012	0.009	8.925	0.074	0.074	0.000	0.000	0.000	0.000
56	A	711	MLY	1	0.928	0.967	10.043	-0.341	-0.341	0.000	0.000	0.000	0.000
57	A	712	THR	0	-0.026	-0.016	5.838	0.037	0.037	0.000	0.000	0.000	0.000
58	A	713	ARG	1	1.009	1.013	8.928	-0.366	-0.366	0.000	0.000	0.000	0.000
59	A	714	ALA	0	-0.004	0.000	10.947	-0.064	-0.064	0.000	0.000	0.000	0.000
60	A	715	GLU	-1	-0.972	-0.991	11.516	0.443	0.443	0.000	0.000	0.000	0.000
61	A	716	GLU	-1	-0.928	-0.969	7.559	1.369	1.369	0.000	0.000	0.000	0.000
62	A	717	GLU	-1	-0.869	-0.921	12.328	0.216	0.216	0.000	0.000	0.000	0.000
63	A	718	ARG	1	0.918	0.942	15.639	-0.318	-0.318	0.000	0.000	0.000	0.000
64	A	719	ARG	1	0.910	0.946	12.128	-0.493	-0.493	0.000	0.000	0.000	0.000
65	A	720	GLU	-1	-0.943	-0.946	15.382	0.281	0.281	0.000	0.000	0.000	0.000
66	A	721	MLY	1	0.913	0.952	17.030	-0.268	-0.268	0.000	0.000	0.000	0.000
67	A	722	MLY	1	0.992	0.987	20.157	-0.205	-0.205	0.000	0.000	0.000	0.000
68	A	723	ASN	0	-0.032	-0.030	17.189	0.012	0.012	0.000	0.000	0.000	0.000
69	A	724	MLY	1	1.029	1.035	20.451	-0.173	-0.173	0.000	0.000	0.000	0.000
70	A	725	ILE	0	-0.003	-0.004	22.490	-0.017	-0.017	0.000	0.000	0.000	0.000
71	A	726	MET	0	-0.062	-0.047	22.781	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	727	GLN	0	0.031	0.011	22.914	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	728	ALA	0	-0.001	0.009	24.986	-0.011	-0.011	0.000	0.000	0.000	0.000
74	A	729	MLY	1	0.879	0.944	27.913	-0.103	-0.103	0.000	0.000	0.000	0.000
75	A	730	GLU	-1	-0.874	-0.931	27.159	0.083	0.083	0.000	0.000	0.000	0.000
76	A	731	ASP	-1	-0.853	-0.915	27.390	0.100	0.100	0.000	0.000	0.000	0.000
77	A	732	PHE	0	-0.073	-0.044	30.374	-0.008	-0.008	0.000	0.000	0.000	0.000
78	A	733	MLY	1	0.899	0.936	31.718	-0.079	-0.079	0.000	0.000	0.000	0.000
79	A	734	MLY	1	0.937	0.983	28.710	-0.082	-0.082	0.000	0.000	0.000	0.000
80	A	735	MET	0	-0.124	-0.052	33.869	-0.004	-0.004	0.000	0.000	0.000	0.000
81	A	736	MET	0	-0.044	-0.007	36.197	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	737	NME	0	0.049	0.036	37.915	0.001	0.001	0.000	0.000	0.000	0.000
83	A	757	ACE	0	0.061	0.019	38.279	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	758	SER	0	-0.058	-0.046	32.740	0.002	0.002	0.000	0.000	0.000	0.000
85	A	759	ARG	1	1.046	1.021	30.986	-0.065	-0.065	0.000	0.000	0.000	0.000
86	A	760	PHE	0	0.005	0.000	32.906	0.003	0.003	0.000	0.000	0.000	0.000
87	A	761	MLY	1	0.943	0.963	33.681	-0.060	-0.060	0.000	0.000	0.000	0.000
88	A	762	ALA	0	0.015	0.019	29.470	0.002	0.002	0.000	0.000	0.000	0.000
89	A	763	ILE	0	0.010	0.028	30.595	0.006	0.006	0.000	0.000	0.000	0.000
90	A	764	GLU	-1	-0.865	-0.925	31.511	0.087	0.087	0.000	0.000	0.000	0.000
91	A	765	MLY	1	0.899	0.958	34.121	-0.066	-0.066	0.000	0.000	0.000	0.000
92	A	766	MET	0	0.080	0.031	37.787	0.001	0.001	0.000	0.000	0.000	0.000
93	A	767	MLY	1	0.971	0.973	39.323	-0.054	-0.054	0.000	0.000	0.000	0.000
94	A	768	ASP	-1	-0.816	-0.902	33.913	0.083	0.083	0.000	0.000	0.000	0.000
95	A	769	ARG	1	0.739	0.861	35.817	-0.067	-0.067	0.000	0.000	0.000	0.000
96	A	770	GLU	-1	-0.898	-0.974	37.424	0.047	0.047	0.000	0.000	0.000	0.000
97	A	771	ALA	0	-0.035	-0.003	38.116	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	772	LEU	0	0.014	0.000	32.943	0.002	0.002	0.000	0.000	0.000	0.000
99	A	773	PHE	0	0.028	0.022	37.515	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	774	ASN	0	0.022	0.007	40.173	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	775	GLU	-1	-0.962	-0.981	34.485	0.075	0.075	0.000	0.000	0.000	0.000
102	A	776	PHE	0	0.025	0.000	38.042	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	777	VAL	0	0.108	0.045	39.480	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	778	ALA	0	-0.063	-0.033	42.847	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	779	ALA	0	-0.035	-0.023	39.803	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	780	ALA	0	-0.025	-0.002	41.809	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	781	ARG	1	0.998	0.994	43.045	-0.037	-0.037	0.000	0.000	0.000	0.000
108	A	782	MLY	1	0.856	0.933	43.475	-0.042	-0.042	0.000	0.000	0.000	0.000
109	A	783	MLY	1	0.985	0.998	40.189	-0.042	-0.042	0.000	0.000	0.000	0.000
110	A	784	GLU	-1	-0.899	-0.950	44.333	0.033	0.033	0.000	0.000	0.000	0.000
111	A	785	MLY	1	0.825	0.914	47.968	-0.035	-0.035	0.000	0.000	0.000	0.000
112	A	786	GLU	-1	-0.889	-0.941	43.178	0.041	0.041	0.000	0.000	0.000	0.000
113	A	787	ASP	-1	-0.790	-0.894	44.817	0.036	0.036	0.000	0.000	0.000	0.000
114	A	788	SER	0	-0.038	-0.013	47.639	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	789	MLY	1	0.898	0.951	50.409	-0.027	-0.027	0.000	0.000	0.000	0.000
116	A	790	THR	0	0.026	0.007	46.525	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	791	ARG	1	0.980	0.980	47.201	-0.028	-0.028	0.000	0.000	0.000	0.000
118	A	792	GLY	0	0.045	0.026	51.122	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	793	GLU	-1	-0.940	-0.993	52.842	0.024	0.024	0.000	0.000	0.000	0.000
120	A	794	MLY	1	0.769	0.897	49.517	-0.023	-0.023	0.000	0.000	0.000	0.000
121	A	795	ILE	0	0.042	0.023	53.592	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	796	MLY	1	0.912	0.972	56.407	-0.018	-0.018	0.000	0.000	0.000	0.000
123	A	797	SER	0	0.015	-0.008	55.273	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	798	ASP	-1	-0.781	-0.874	53.762	0.019	0.019	0.000	0.000	0.000	0.000
125	A	799	PHE	0	-0.003	0.007	56.935	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	800	PHE	0	0.016	-0.010	60.105	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	801	GLU	-1	-0.906	-0.945	55.699	0.015	0.015	0.000	0.000	0.000	0.000
128	A	802	LEU	0	-0.051	-0.016	59.387	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	803	LEU	0	-0.017	-0.020	61.090	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	804	SER	0	-0.026	-0.005	61.125	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	805	ASN	0	-0.077	-0.030	59.519	0.000	0.000	0.000	0.000	0.000	0.000
132	A	806	HIS	0	-0.067	-0.053	63.244	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	807	HIS	0	-0.016	-0.009	66.991	0.000	0.000	0.000	0.000	0.000	0.000
134	A	808	LEU	0	-0.035	-0.023	67.633	0.000	0.000	0.000	0.000	0.000	0.000
135	A	809	ASP	-1	-0.839	-0.926	71.130	0.009	0.009	0.000	0.000	0.000	0.000
136	A	810	SER	0	0.072	0.017	73.475	0.000	0.000	0.000	0.000	0.000	0.000
137	A	811	GLN	0	-0.025	-0.007	75.905	0.000	0.000	0.000	0.000	0.000	0.000
138	A	812	SER	0	-0.052	-0.004	73.598	0.000	0.000	0.000	0.000	0.000	0.000
139	A	813	ARG	1	0.937	0.962	75.608	-0.008	-0.008	0.000	0.000	0.000	0.000
140	A	814	TRP	0	0.090	0.033	67.531	0.000	0.000	0.000	0.000	0.000	0.000
141	A	815	SER	0	-0.033	-0.017	73.514	0.000	0.000	0.000	0.000	0.000	0.000
142	A	816	MLY	1	0.977	0.986	75.023	-0.008	-0.008	0.000	0.000	0.000	0.000
143	A	817	VAL	0	-0.010	0.012	69.702	0.000	0.000	0.000	0.000	0.000	0.000
144	A	818	MLY	1	0.952	0.983	69.845	-0.011	-0.011	0.000	0.000	0.000	0.000
145	A	819	ASP	-1	-0.880	-0.951	69.390	0.010	0.010	0.000	0.000	0.000	0.000
146	A	820	MLY	1	0.857	0.948	68.729	-0.009	-0.009	0.000	0.000	0.000	0.000
147	A	821	VAL	0	-0.015	-0.009	64.867	0.000	0.000	0.000	0.000	0.000	0.000
148	A	822	GLU	-1	-0.934	-0.965	64.720	0.011	0.011	0.000	0.000	0.000	0.000
149	A	823	SER	0	-0.036	-0.023	63.650	0.000	0.000	0.000	0.000	0.000	0.000
150	A	824	ASP	-1	-0.805	-0.865	59.442	0.015	0.015	0.000	0.000	0.000	0.000
151	A	825	PRO	0	0.007	-0.025	56.437	0.000	0.000	0.000	0.000	0.000	0.000
152	A	826	ARG	1	0.788	0.883	55.669	-0.014	-0.014	0.000	0.000	0.000	0.000
153	A	827	TYR	0	0.034	0.021	58.331	0.000	0.000	0.000	0.000	0.000	0.000
154	A	828	MLY	1	0.906	0.945	58.871	-0.015	-0.015	0.000	0.000	0.000	0.000
155	A	829	ALA	0	-0.030	-0.003	56.776	0.000	0.000	0.000	0.000	0.000	0.000
156	A	830	VAL	0	0.012	0.019	58.550	0.001	0.001	0.000	0.000	0.000	0.000
157	A	831	ASP	-1	-0.915	-0.956	60.645	0.018	0.018	0.000	0.000	0.000	0.000
158	A	832	SER	0	0.049	0.025	62.542	-0.001	-0.001	0.000	0.000	0.000	0.000
159	A	833	SER	0	-0.036	-0.042	65.869	0.000	0.000	0.000	0.000	0.000	0.000
160	A	834	SER	0	0.022	0.003	68.661	0.000	0.000	0.000	0.000	0.000	0.000
161	A	835	MET	0	0.065	0.040	64.261	0.000	0.000	0.000	0.000	0.000	0.000
162	A	836	ARG	1	0.859	0.947	64.453	-0.014	-0.014	0.000	0.000	0.000	0.000
163	A	837	GLU	-1	-0.958	-0.974	66.805	0.012	0.012	0.000	0.000	0.000	0.000
164	A	838	ASP	-1	-0.856	-0.940	68.431	0.014	0.014	0.000	0.000	0.000	0.000
165	A	839	LEU	0	-0.083	-0.034	62.917	0.000	0.000	0.000	0.000	0.000	0.000
166	A	840	PHE	0	0.029	-0.001	66.637	0.000	0.000	0.000	0.000	0.000	0.000
167	A	841	MLY	1	0.936	0.962	68.665	-0.012	-0.012	0.000	0.000	0.000	0.000
168	A	842	GLN	0	0.035	0.008	65.339	0.000	0.000	0.000	0.000	0.000	0.000
169	A	843	TYR	0	-0.070	-0.038	64.007	0.000	0.000	0.000	0.000	0.000	0.000
170	A	844	ILE	0	-0.094	-0.037	67.559	0.000	0.000	0.000	0.000	0.000	0.000
171	A	845	GLU	-2	-1.927	-1.936	70.731	0.024	0.024	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:656:ACE )