FMO DATABASE

FMODB ID: 53M9Z

Calculation Name: 3HFH-A-Xray372

Preferred Name:

Target Type:

Ligand Name: n-dimethyl-lysine

Ligand 3-letter code: MLY

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3HFH

Chain ID: A

ChEMBL ID:

UniProt ID: O14776

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	168
LigandResidueName
LigandFragmentNumber	0
LigandCharge	MLY=1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1510740.992769
FMO2-HF: Nuclear repulsion	1437467.600699
FMO2-HF: Total energy	-73273.39207
FMO2-MP2: Total energy	-73487.110298

3D Structure Molmil

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:657:PRO)

Summations of interaction energy for fragment #1(A:657:PRO)

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.
-5.703	-3.765	-0.024	-0.795	-1.122	0.003

Interaction energy analysis for fragmet #1(A:657:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.021

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	659	GLY	0	0.022	0.006	3.820	-1.144	0.535	-0.025	-0.718	-0.938	0.003
4	A	660	SER	0	0.029	0.007	6.507	0.066	0.066	0.000	0.000	0.000	0.000
5	A	661	ALA	0	0.065	0.018	7.836	0.301	0.301	0.000	0.000	0.000	0.000
6	A	662	ARG	1	0.840	0.884	9.213	-0.015	-0.015	0.000	0.000	0.000	0.000
7	A	663	MET	0	0.013	0.012	8.595	-0.006	-0.006	0.000	0.000	0.000	0.000
8	A	664	MLY	1	0.810	0.896	5.818	-1.600	-1.600	0.000	0.000	0.000	0.000
9	A	665	GLN	0	0.053	0.019	7.942	-0.001	-0.001	0.000	0.000	0.000	0.000
10	A	666	PHE	0	0.021	0.014	11.559	-0.064	-0.064	0.000	0.000	0.000	0.000
11	A	667	MLY	1	0.992	0.982	4.063	-4.626	-4.367	0.001	-0.077	-0.184	0.000
12	A	668	ASP	-1	-0.800	-0.882	9.816	1.684	1.684	0.000	0.000	0.000	0.000
13	A	669	MET	0	-0.028	0.003	11.966	-0.160	-0.160	0.000	0.000	0.000	0.000
14	A	670	LEU	0	-0.028	-0.017	12.679	-0.100	-0.100	0.000	0.000	0.000	0.000
15	A	671	LEU	0	-0.014	-0.008	10.626	-0.067	-0.067	0.000	0.000	0.000	0.000
16	A	672	GLU	-1	-0.818	-0.868	14.900	0.532	0.532	0.000	0.000	0.000	0.000
17	A	673	ARG	1	0.814	0.913	17.403	-0.515	-0.515	0.000	0.000	0.000	0.000
18	A	674	GLY	0	0.001	0.013	18.561	-0.051	-0.051	0.000	0.000	0.000	0.000
19	A	675	VAL	0	-0.025	-0.005	17.383	-0.053	-0.053	0.000	0.000	0.000	0.000
20	A	676	SER	0	-0.003	0.004	18.096	0.048	0.048	0.000	0.000	0.000	0.000
21	A	677	ALA	0	-0.016	-0.013	16.931	0.020	0.020	0.000	0.000	0.000	0.000
22	A	678	PHE	0	-0.047	-0.033	18.518	-0.028	-0.028	0.000	0.000	0.000	0.000
23	A	679	SER	0	-0.012	-0.032	21.814	-0.025	-0.025	0.000	0.000	0.000	0.000
24	A	680	THR	0	-0.002	0.007	22.233	0.001	0.001	0.000	0.000	0.000	0.000
25	A	681	TRP	0	0.061	0.034	18.107	0.030	0.030	0.000	0.000	0.000	0.000
26	A	682	GLU	-1	-0.856	-0.951	22.155	0.167	0.167	0.000	0.000	0.000	0.000
27	A	683	MLY	1	0.909	0.959	25.106	-0.142	-0.142	0.000	0.000	0.000	0.000
28	A	684	GLU	-1	-0.732	-0.833	20.988	0.291	0.291	0.000	0.000	0.000	0.000
29	A	685	LEU	0	0.023	0.024	22.690	0.019	0.019	0.000	0.000	0.000	0.000
30	A	686	HIS	0	-0.033	-0.023	23.679	0.017	0.017	0.000	0.000	0.000	0.000
31	A	687	MLY	1	0.840	0.914	22.095	-0.289	-0.289	0.000	0.000	0.000	0.000
32	A	688	ILE	0	-0.015	-0.027	18.553	0.028	0.028	0.000	0.000	0.000	0.000
33	A	689	VAL	0	-0.018	-0.001	21.632	0.006	0.006	0.000	0.000	0.000	0.000
34	A	690	PHE	0	-0.008	0.015	24.083	-0.012	-0.012	0.000	0.000	0.000	0.000
35	A	691	ASP	-1	-0.731	-0.847	19.500	0.439	0.439	0.000	0.000	0.000	0.000
36	A	692	PRO	0	0.067	0.022	20.845	0.009	0.009	0.000	0.000	0.000	0.000
37	A	693	ARG	1	0.723	0.802	15.141	-0.608	-0.608	0.000	0.000	0.000	0.000
38	A	694	TYR	0	0.015	0.001	17.162	0.012	0.012	0.000	0.000	0.000	0.000
39	A	695	LEU	0	-0.013	-0.009	19.401	-0.023	-0.023	0.000	0.000	0.000	0.000
40	A	696	LEU	0	-0.018	0.016	15.016	-0.028	-0.028	0.000	0.000	0.000	0.000
41	A	697	LEU	0	-0.038	-0.006	13.048	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	698	ASN	0	0.041	0.025	17.226	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	699	PRO	0	0.076	0.012	18.701	0.029	0.029	0.000	0.000	0.000	0.000
44	A	700	MLY	1	0.990	1.011	17.224	0.052	0.052	0.000	0.000	0.000	0.000
45	A	701	GLU	-1	-0.775	-0.866	14.677	0.140	0.140	0.000	0.000	0.000	0.000
46	A	702	ARG	1	0.866	0.931	14.417	-0.184	-0.184	0.000	0.000	0.000	0.000
47	A	703	MLY	1	0.889	0.954	15.520	-0.052	-0.052	0.000	0.000	0.000	0.000
48	A	704	GLN	0	-0.026	-0.020	12.262	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	705	VAL	0	0.007	0.001	9.851	0.040	0.040	0.000	0.000	0.000	0.000
50	A	706	PHE	0	0.027	0.022	11.573	0.143	0.143	0.000	0.000	0.000	0.000
51	A	707	ASP	-1	-0.798	-0.914	14.067	0.213	0.213	0.000	0.000	0.000	0.000
52	A	708	GLN	0	-0.074	-0.040	7.850	-0.171	-0.171	0.000	0.000	0.000	0.000
53	A	709	TYR	0	-0.042	-0.045	10.588	0.119	0.119	0.000	0.000	0.000	0.000
54	A	710	VAL	0	-0.001	0.003	11.471	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	711	MLY	1	0.905	0.962	11.740	-0.022	-0.022	0.000	0.000	0.000	0.000
56	A	712	THR	0	-0.003	-0.005	8.246	-0.024	-0.024	0.000	0.000	0.000	0.000
57	A	713	ARG	1	0.931	0.973	11.379	-0.498	-0.498	0.000	0.000	0.000	0.000
58	A	714	ALA	0	-0.017	-0.004	13.689	-0.060	-0.060	0.000	0.000	0.000	0.000
59	A	715	GLU	-1	-0.953	-0.984	13.071	0.067	0.067	0.000	0.000	0.000	0.000
60	A	716	GLU	-1	-0.911	-0.962	9.489	0.813	0.813	0.000	0.000	0.000	0.000
61	A	717	GLU	-1	-0.780	-0.874	14.161	0.248	0.248	0.000	0.000	0.000	0.000
62	A	718	ARG	1	0.935	0.960	17.654	-0.177	-0.177	0.000	0.000	0.000	0.000
63	A	719	ARG	1	0.920	0.952	12.533	-0.130	-0.130	0.000	0.000	0.000	0.000
64	A	720	GLU	-1	-0.916	-0.942	16.939	0.221	0.221	0.000	0.000	0.000	0.000
65	A	721	MLY	1	0.876	0.931	18.442	-0.240	-0.240	0.000	0.000	0.000	0.000
66	A	722	MLY	1	0.970	0.984	21.610	-0.044	-0.044	0.000	0.000	0.000	0.000
67	A	723	ASN	0	-0.013	-0.024	18.333	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	724	MLY	1	1.029	1.033	21.502	-0.140	-0.140	0.000	0.000	0.000	0.000
69	A	725	ILE	0	0.005	-0.003	23.551	-0.009	-0.009	0.000	0.000	0.000	0.000
70	A	726	MET	0	-0.052	-0.040	23.856	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	727	GLN	0	-0.009	-0.009	23.639	-0.012	-0.012	0.000	0.000	0.000	0.000
72	A	728	ALA	0	0.014	0.016	25.745	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	729	MLY	1	0.874	0.942	28.763	-0.026	-0.026	0.000	0.000	0.000	0.000
74	A	730	GLU	-1	-0.803	-0.891	27.808	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	731	ASP	-1	-0.855	-0.912	27.971	0.032	0.032	0.000	0.000	0.000	0.000
76	A	732	PHE	0	-0.071	-0.042	30.905	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	733	MLY	1	0.844	0.897	32.287	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	734	MLY	1	0.930	0.983	28.720	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	735	MET	0	-0.132	-0.056	34.267	0.000	0.000	0.000	0.000	0.000	0.000
80	A	736	MET	0	-0.019	0.023	36.714	0.000	0.000	0.000	0.000	0.000	0.000
81	A	758	SER	0	0.029	0.000	33.155	0.000	0.000	0.000	0.000	0.000	0.000
82	A	759	ARG	1	0.990	0.989	31.610	-0.024	-0.024	0.000	0.000	0.000	0.000
83	A	760	PHE	0	0.052	0.017	33.586	0.001	0.001	0.000	0.000	0.000	0.000
84	A	761	MLY	1	0.945	0.952	34.970	-0.058	-0.058	0.000	0.000	0.000	0.000
85	A	762	ALA	0	0.007	0.015	30.530	0.003	0.003	0.000	0.000	0.000	0.000
86	A	763	ILE	0	-0.014	0.016	31.878	0.006	0.006	0.000	0.000	0.000	0.000
87	A	764	GLU	-1	-0.870	-0.929	32.993	0.085	0.085	0.000	0.000	0.000	0.000
88	A	765	MLY	1	0.927	0.958	35.614	-0.064	-0.064	0.000	0.000	0.000	0.000
89	A	766	MET	0	0.060	0.033	39.317	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	767	MLY	1	0.982	0.980	40.928	-0.040	-0.040	0.000	0.000	0.000	0.000
91	A	768	ASP	-1	-0.849	-0.914	35.727	0.050	0.050	0.000	0.000	0.000	0.000
92	A	769	ARG	1	0.778	0.879	37.006	-0.052	-0.052	0.000	0.000	0.000	0.000
93	A	770	GLU	-1	-0.876	-0.956	38.498	0.025	0.025	0.000	0.000	0.000	0.000
94	A	771	ALA	0	-0.041	-0.006	39.316	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	772	LEU	0	0.017	0.000	33.996	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	773	PHE	0	0.030	0.021	38.523	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	774	ASN	0	-0.019	-0.023	41.061	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	775	GLU	-1	-0.937	-0.966	35.320	0.012	0.012	0.000	0.000	0.000	0.000
99	A	776	PHE	0	0.045	0.010	38.138	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	777	VAL	0	0.096	0.039	40.232	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	778	ALA	0	-0.055	-0.027	43.695	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	779	ALA	0	-0.039	-0.028	40.537	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	780	ALA	0	-0.022	-0.001	42.398	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	781	ARG	1	0.998	0.998	43.641	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	782	MLY	1	0.854	0.934	44.194	0.002	0.002	0.000	0.000	0.000	0.000
106	A	783	MLY	1	0.955	0.987	40.945	0.016	0.016	0.000	0.000	0.000	0.000
107	A	784	GLU	-1	-0.890	-0.944	44.867	-0.006	-0.006	0.000	0.000	0.000	0.000
108	A	785	MLY	1	0.840	0.919	48.457	0.003	0.003	0.000	0.000	0.000	0.000
109	A	786	GLU	-1	-0.885	-0.941	43.534	-0.019	-0.019	0.000	0.000	0.000	0.000
110	A	787	ASP	-1	-0.780	-0.895	45.233	-0.018	-0.018	0.000	0.000	0.000	0.000
111	A	788	SER	0	-0.049	-0.016	47.982	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	789	MLY	1	0.824	0.902	50.794	0.014	0.014	0.000	0.000	0.000	0.000
113	A	790	THR	0	0.016	0.002	46.784	0.000	0.000	0.000	0.000	0.000	0.000
114	A	791	ARG	1	0.978	0.984	46.796	0.022	0.022	0.000	0.000	0.000	0.000
115	A	792	GLY	0	0.054	0.030	51.236	0.000	0.000	0.000	0.000	0.000	0.000
116	A	793	GLU	-1	-0.860	-0.938	53.471	-0.018	-0.018	0.000	0.000	0.000	0.000
117	A	794	MLY	1	0.804	0.901	49.495	0.026	0.026	0.000	0.000	0.000	0.000
118	A	795	ILE	0	0.051	0.025	53.463	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	796	MLY	1	0.914	0.978	56.252	0.016	0.016	0.000	0.000	0.000	0.000
120	A	797	SER	0	-0.005	-0.022	54.889	0.000	0.000	0.000	0.000	0.000	0.000
121	A	798	ASP	-1	-0.819	-0.877	53.558	-0.026	-0.026	0.000	0.000	0.000	0.000
122	A	799	PHE	0	0.008	0.009	56.453	0.000	0.000	0.000	0.000	0.000	0.000
123	A	800	PHE	0	-0.014	-0.022	59.734	0.000	0.000	0.000	0.000	0.000	0.000
124	A	801	GLU	-1	-0.863	-0.906	54.608	-0.028	-0.028	0.000	0.000	0.000	0.000
125	A	802	LEU	0	-0.025	-0.005	58.696	0.000	0.000	0.000	0.000	0.000	0.000
126	A	803	LEU	0	-0.008	-0.014	60.321	0.000	0.000	0.000	0.000	0.000	0.000
127	A	804	SER	0	-0.048	-0.023	60.313	0.000	0.000	0.000	0.000	0.000	0.000
128	A	805	ASN	0	-0.073	-0.027	58.396	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	806	HIS	0	-0.025	-0.017	62.200	0.000	0.000	0.000	0.000	0.000	0.000
130	A	807	HIS	0	-0.014	-0.007	65.964	0.000	0.000	0.000	0.000	0.000	0.000
131	A	808	LEU	0	-0.049	-0.029	66.979	0.001	0.001	0.000	0.000	0.000	0.000
132	A	809	ASP	-1	-0.793	-0.895	70.311	-0.016	-0.016	0.000	0.000	0.000	0.000
133	A	810	SER	0	0.063	0.018	72.770	0.000	0.000	0.000	0.000	0.000	0.000
134	A	811	GLN	0	-0.064	-0.030	75.354	0.001	0.001	0.000	0.000	0.000	0.000
135	A	812	SER	0	-0.048	-0.013	72.889	0.000	0.000	0.000	0.000	0.000	0.000
136	A	813	ARG	1	0.951	0.971	74.915	0.012	0.012	0.000	0.000	0.000	0.000
137	A	814	TRP	0	0.071	0.022	66.990	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	815	SER	0	-0.021	-0.012	72.911	0.000	0.000	0.000	0.000	0.000	0.000
139	A	816	MLY	1	0.974	0.988	74.311	0.014	0.014	0.000	0.000	0.000	0.000
140	A	817	VAL	0	-0.007	0.002	68.889	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	818	MLY	1	0.927	0.979	69.165	0.012	0.012	0.000	0.000	0.000	0.000
142	A	819	ASP	-1	-0.879	-0.949	68.622	-0.014	-0.014	0.000	0.000	0.000	0.000
143	A	820	MLY	1	0.807	0.913	68.046	0.018	0.018	0.000	0.000	0.000	0.000
144	A	821	VAL	0	-0.015	-0.012	64.046	-0.001	-0.001	0.000	0.000	0.000	0.000
145	A	822	GLU	-1	-0.836	-0.922	63.935	-0.014	-0.014	0.000	0.000	0.000	0.000
146	A	823	SER	0	-0.031	-0.020	62.633	0.000	0.000	0.000	0.000	0.000	0.000
147	A	824	ASP	-1	-0.795	-0.889	58.659	-0.023	-0.023	0.000	0.000	0.000	0.000
148	A	825	PRO	0	0.002	-0.025	55.606	0.001	0.001	0.000	0.000	0.000	0.000
149	A	826	ARG	1	0.768	0.876	54.680	0.026	0.026	0.000	0.000	0.000	0.000
150	A	827	TYR	0	-0.016	-0.006	57.740	0.001	0.001	0.000	0.000	0.000	0.000
151	A	828	MLY	1	0.887	0.943	58.092	0.019	0.019	0.000	0.000	0.000	0.000
152	A	829	ALA	0	-0.033	-0.001	56.518	0.001	0.001	0.000	0.000	0.000	0.000
153	A	830	VAL	0	0.009	0.017	58.251	0.001	0.001	0.000	0.000	0.000	0.000
154	A	831	ASP	-1	-0.857	-0.913	60.682	-0.010	-0.010	0.000	0.000	0.000	0.000
155	A	832	SER	0	0.012	-0.005	62.501	0.001	0.001	0.000	0.000	0.000	0.000
156	A	833	SER	0	-0.019	-0.021	65.891	-0.001	-0.001	0.000	0.000	0.000	0.000
157	A	834	SER	0	0.000	-0.001	68.522	0.000	0.000	0.000	0.000	0.000	0.000
158	A	835	MET	0	0.073	0.036	64.319	0.000	0.000	0.000	0.000	0.000	0.000
159	A	836	ARG	1	0.832	0.919	63.812	0.013	0.013	0.000	0.000	0.000	0.000
160	A	837	GLU	-1	-0.922	-0.957	66.606	-0.011	-0.011	0.000	0.000	0.000	0.000
161	A	838	ASP	-1	-0.807	-0.910	68.837	-0.011	-0.011	0.000	0.000	0.000	0.000
162	A	839	LEU	0	-0.048	-0.017	62.563	0.000	0.000	0.000	0.000	0.000	0.000
163	A	840	PHE	0	0.035	0.004	66.492	-0.001	-0.001	0.000	0.000	0.000	0.000
164	A	841	MLY	1	0.855	0.920	68.326	0.010	0.010	0.000	0.000	0.000	0.000
165	A	842	GLN	0	0.033	0.004	65.405	-0.001	-0.001	0.000	0.000	0.000	0.000
166	A	843	TYR	0	-0.063	-0.038	63.069	-0.001	-0.001	0.000	0.000	0.000	0.000
167	A	844	ILE	0	-0.054	-0.019	67.223	-0.001	-0.001	0.000	0.000	0.000	0.000
168	A	845	GLU	-1	-1.012	-0.979	70.494	-0.013	-0.013	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:657:PRO)