FMO DATABASE

FMODB ID: YYL62

Calculation Name: 3HFH-A-Xray372

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: 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:

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	168
LigandCharge	MLY=1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1513772.908371
FMO2-HF: Nuclear repulsion	1440498.524224
FMO2-HF: Total energy	-73274.384147
FMO2-MP2: Total energy	-73488.091199

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: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.
-5.426	-3.806	-0.008	-0.617	-0.997	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 : 0.012 / q_NPA : -0.018

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	0.052	0.020	3.856	-0.763	0.582	-0.010	-0.548	-0.788	0.003
4	A	660	SER	0	0.006	-0.007	6.129	0.172	0.172	0.000	0.000	0.000	0.000
5	A	661	ALA	0	0.049	0.022	7.478	0.381	0.381	0.000	0.000	0.000	0.000
6	A	662	ARG	1	0.841	0.891	8.811	-0.005	-0.005	0.000	0.000	0.000	0.000
7	A	663	MET	0	0.007	0.012	8.343	-0.013	-0.013	0.000	0.000	0.000	0.000
8	A	664	MLY	1	0.820	0.897	5.274	-1.614	-1.614	0.000	0.000	0.000	0.000
9	A	665	GLN	0	0.054	0.015	7.587	0.034	0.034	0.000	0.000	0.000	0.000
10	A	666	PHE	0	0.040	0.020	11.224	-0.079	-0.079	0.000	0.000	0.000	0.000
11	A	667	MLY	1	0.976	0.977	4.113	-4.744	-4.469	0.002	-0.069	-0.209	0.000
12	A	668	ASP	-1	-0.812	-0.888	9.362	1.751	1.751	0.000	0.000	0.000	0.000
13	A	669	MET	0	-0.020	0.009	11.572	-0.182	-0.182	0.000	0.000	0.000	0.000
14	A	670	LEU	0	-0.015	-0.008	12.228	-0.109	-0.109	0.000	0.000	0.000	0.000
15	A	671	LEU	0	-0.017	0.000	10.102	-0.075	-0.075	0.000	0.000	0.000	0.000
16	A	672	GLU	-1	-0.775	-0.854	14.492	0.485	0.485	0.000	0.000	0.000	0.000
17	A	673	ARG	1	0.760	0.876	16.897	-0.556	-0.556	0.000	0.000	0.000	0.000
18	A	674	GLY	0	0.011	0.015	18.218	-0.051	-0.051	0.000	0.000	0.000	0.000
19	A	675	VAL	0	-0.028	-0.008	16.756	-0.054	-0.054	0.000	0.000	0.000	0.000
20	A	676	SER	0	-0.005	0.002	17.698	0.047	0.047	0.000	0.000	0.000	0.000
21	A	677	ALA	0	-0.021	-0.014	16.236	0.014	0.014	0.000	0.000	0.000	0.000
22	A	678	PHE	0	-0.036	-0.026	18.032	-0.032	-0.032	0.000	0.000	0.000	0.000
23	A	679	SER	0	-0.012	-0.032	21.538	-0.028	-0.028	0.000	0.000	0.000	0.000
24	A	680	THR	0	-0.005	-0.008	22.435	-0.009	-0.009	0.000	0.000	0.000	0.000
25	A	681	TRP	0	0.017	0.022	17.922	0.030	0.030	0.000	0.000	0.000	0.000
26	A	682	GLU	-1	-0.838	-0.941	21.906	0.198	0.198	0.000	0.000	0.000	0.000
27	A	683	MLY	1	0.917	0.971	24.895	-0.166	-0.166	0.000	0.000	0.000	0.000
28	A	684	GLU	-1	-0.724	-0.828	20.459	0.328	0.328	0.000	0.000	0.000	0.000
29	A	685	LEU	0	0.034	0.026	22.473	0.021	0.021	0.000	0.000	0.000	0.000
30	A	686	HIS	0	-0.032	-0.031	23.451	0.015	0.015	0.000	0.000	0.000	0.000
31	A	687	MLY	1	0.834	0.916	21.698	-0.327	-0.327	0.000	0.000	0.000	0.000
32	A	688	ILE	0	-0.023	-0.026	18.225	0.031	0.031	0.000	0.000	0.000	0.000
33	A	689	VAL	0	-0.024	-0.010	21.161	0.007	0.007	0.000	0.000	0.000	0.000
34	A	690	PHE	0	-0.003	0.014	23.654	-0.014	-0.014	0.000	0.000	0.000	0.000
35	A	691	ASP	-1	-0.743	-0.842	18.999	0.474	0.474	0.000	0.000	0.000	0.000
36	A	692	PRO	0	0.050	0.005	20.409	0.009	0.009	0.000	0.000	0.000	0.000
37	A	693	ARG	1	0.712	0.794	14.680	-0.628	-0.628	0.000	0.000	0.000	0.000
38	A	694	TYR	0	0.026	0.007	16.717	0.012	0.012	0.000	0.000	0.000	0.000
39	A	695	LEU	0	-0.011	-0.016	18.896	-0.021	-0.021	0.000	0.000	0.000	0.000
40	A	696	LEU	0	-0.017	0.017	15.160	-0.030	-0.030	0.000	0.000	0.000	0.000
41	A	697	LEU	0	-0.040	-0.006	12.588	-0.012	-0.012	0.000	0.000	0.000	0.000
42	A	698	ASN	0	0.057	0.023	16.690	-0.010	-0.010	0.000	0.000	0.000	0.000
43	A	699	PRO	0	0.054	0.003	18.323	0.031	0.031	0.000	0.000	0.000	0.000
44	A	700	MLY	1	0.970	0.995	16.914	0.018	0.018	0.000	0.000	0.000	0.000
45	A	701	GLU	-1	-0.787	-0.869	14.245	0.175	0.175	0.000	0.000	0.000	0.000
46	A	702	ARG	1	0.889	0.959	14.019	-0.195	-0.195	0.000	0.000	0.000	0.000
47	A	703	MLY	1	0.891	0.949	15.238	-0.102	-0.102	0.000	0.000	0.000	0.000
48	A	704	GLN	0	-0.001	-0.008	12.310	-0.025	-0.025	0.000	0.000	0.000	0.000
49	A	705	VAL	0	-0.006	-0.004	9.408	0.052	0.052	0.000	0.000	0.000	0.000
50	A	706	PHE	0	0.018	0.014	11.351	0.146	0.146	0.000	0.000	0.000	0.000
51	A	707	ASP	-1	-0.784	-0.888	13.880	0.272	0.272	0.000	0.000	0.000	0.000
52	A	708	GLN	0	-0.048	-0.024	7.726	-0.192	-0.192	0.000	0.000	0.000	0.000
53	A	709	TYR	0	-0.039	-0.042	10.228	0.148	0.148	0.000	0.000	0.000	0.000
54	A	710	VAL	0	-0.002	-0.002	11.177	-0.032	-0.032	0.000	0.000	0.000	0.000
55	A	711	MLY	1	0.890	0.951	11.270	-0.085	-0.085	0.000	0.000	0.000	0.000
56	A	712	THR	0	-0.009	-0.001	7.869	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	713	ARG	1	0.892	0.928	10.971	-0.555	-0.555	0.000	0.000	0.000	0.000
58	A	714	ALA	0	-0.021	0.003	13.268	-0.075	-0.075	0.000	0.000	0.000	0.000
59	A	715	GLU	-1	-0.947	-0.989	12.446	0.102	0.102	0.000	0.000	0.000	0.000
60	A	716	GLU	-1	-0.914	-0.969	9.054	0.913	0.913	0.000	0.000	0.000	0.000
61	A	717	GLU	-1	-0.756	-0.844	13.583	0.253	0.253	0.000	0.000	0.000	0.000
62	A	718	ARG	1	0.944	0.974	17.042	-0.216	-0.216	0.000	0.000	0.000	0.000
63	A	719	ARG	1	0.924	0.959	12.004	-0.152	-0.152	0.000	0.000	0.000	0.000
64	A	720	GLU	-1	-0.908	-0.944	16.845	0.218	0.218	0.000	0.000	0.000	0.000
65	A	721	MLY	1	0.881	0.929	18.341	-0.255	-0.255	0.000	0.000	0.000	0.000
66	A	722	MLY	1	0.963	0.987	21.063	-0.055	-0.055	0.000	0.000	0.000	0.000
67	A	723	ASN	0	0.013	-0.018	17.959	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	724	MLY	1	1.011	1.021	21.178	-0.151	-0.151	0.000	0.000	0.000	0.000
69	A	725	ILE	0	-0.002	-0.003	23.092	-0.010	-0.010	0.000	0.000	0.000	0.000
70	A	726	MET	0	-0.037	-0.023	23.756	-0.009	-0.009	0.000	0.000	0.000	0.000
71	A	727	GLN	0	-0.015	-0.014	23.452	-0.011	-0.011	0.000	0.000	0.000	0.000
72	A	728	ALA	0	0.004	0.001	25.552	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	729	MLY	1	0.870	0.943	28.429	-0.030	-0.030	0.000	0.000	0.000	0.000
74	A	730	GLU	-1	-0.777	-0.872	27.871	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	731	ASP	-1	-0.845	-0.919	27.646	0.025	0.025	0.000	0.000	0.000	0.000
76	A	732	PHE	0	-0.051	-0.030	30.635	0.000	0.000	0.000	0.000	0.000	0.000
77	A	733	MLY	1	0.883	0.923	32.274	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	734	MLY	1	0.890	0.956	28.146	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	735	MET	0	-0.094	-0.033	34.102	0.002	0.002	0.000	0.000	0.000	0.000
80	A	736	MET	0	-0.041	0.020	36.855	0.000	0.000	0.000	0.000	0.000	0.000
81	A	758	SER	0	0.040	0.007	33.845	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	759	ARG	1	0.938	0.948	31.899	-0.019	-0.019	0.000	0.000	0.000	0.000
83	A	760	PHE	0	0.055	0.013	33.612	0.003	0.003	0.000	0.000	0.000	0.000
84	A	761	MLY	1	0.929	0.962	34.482	-0.056	-0.056	0.000	0.000	0.000	0.000
85	A	762	ALA	0	-0.012	0.009	29.967	0.005	0.005	0.000	0.000	0.000	0.000
86	A	763	ILE	0	-0.012	0.016	31.229	0.006	0.006	0.000	0.000	0.000	0.000
87	A	764	GLU	-1	-0.826	-0.920	33.498	0.077	0.077	0.000	0.000	0.000	0.000
88	A	765	MLY	1	0.878	0.936	35.244	-0.073	-0.073	0.000	0.000	0.000	0.000
89	A	766	MET	0	0.046	0.035	38.887	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	767	MLY	1	1.018	0.999	40.792	-0.043	-0.043	0.000	0.000	0.000	0.000
91	A	768	ASP	-1	-0.861	-0.919	35.845	0.052	0.052	0.000	0.000	0.000	0.000
92	A	769	ARG	1	0.856	0.900	36.686	-0.053	-0.053	0.000	0.000	0.000	0.000
93	A	770	GLU	-1	-0.888	-0.938	38.235	0.025	0.025	0.000	0.000	0.000	0.000
94	A	771	ALA	0	-0.023	-0.003	38.731	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	772	LEU	0	-0.022	-0.016	33.593	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	773	PHE	0	0.028	0.006	37.976	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	774	ASN	0	-0.023	-0.032	40.793	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	775	GLU	-1	-0.919	-0.948	35.402	0.014	0.014	0.000	0.000	0.000	0.000
99	A	776	PHE	0	0.047	0.016	37.807	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	777	VAL	0	0.024	0.011	40.055	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	778	ALA	0	-0.009	-0.005	43.412	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	779	ALA	0	-0.024	-0.016	40.094	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	780	ALA	0	-0.002	-0.002	42.078	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	781	ARG	1	0.865	0.903	43.472	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	782	MLY	1	0.880	0.950	43.931	0.000	0.000	0.000	0.000	0.000	0.000
106	A	783	MLY	1	0.933	0.974	41.021	0.016	0.016	0.000	0.000	0.000	0.000
107	A	784	GLU	-1	-0.789	-0.868	45.047	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	785	MLY	1	0.896	0.949	48.551	0.001	0.001	0.000	0.000	0.000	0.000
109	A	786	GLU	-1	-0.921	-0.944	43.130	-0.018	-0.018	0.000	0.000	0.000	0.000
110	A	787	ASP	-1	-0.816	-0.911	45.435	-0.018	-0.018	0.000	0.000	0.000	0.000
111	A	788	SER	0	-0.044	-0.039	48.034	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	789	MLY	1	0.837	0.916	51.054	0.013	0.013	0.000	0.000	0.000	0.000
113	A	790	THR	0	0.008	-0.014	46.984	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	791	ARG	1	0.957	0.974	47.037	0.021	0.021	0.000	0.000	0.000	0.000
115	A	792	GLY	0	0.051	0.031	51.290	0.000	0.000	0.000	0.000	0.000	0.000
116	A	793	GLU	-1	-0.834	-0.913	53.248	-0.016	-0.016	0.000	0.000	0.000	0.000
117	A	794	MLY	1	0.807	0.908	49.469	0.026	0.026	0.000	0.000	0.000	0.000
118	A	795	ILE	0	0.033	0.014	53.111	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	796	MLY	1	0.913	0.975	55.978	0.015	0.015	0.000	0.000	0.000	0.000
120	A	797	SER	0	-0.037	-0.035	54.573	0.000	0.000	0.000	0.000	0.000	0.000
121	A	798	ASP	-1	-0.841	-0.902	53.504	-0.025	-0.025	0.000	0.000	0.000	0.000
122	A	799	PHE	0	0.017	0.010	56.422	0.000	0.000	0.000	0.000	0.000	0.000
123	A	800	PHE	0	-0.001	-0.021	59.699	0.000	0.000	0.000	0.000	0.000	0.000
124	A	801	GLU	-1	-0.804	-0.850	55.308	-0.027	-0.027	0.000	0.000	0.000	0.000
125	A	802	LEU	0	-0.008	0.014	58.688	0.000	0.000	0.000	0.000	0.000	0.000
126	A	803	LEU	0	-0.031	-0.020	60.409	0.000	0.000	0.000	0.000	0.000	0.000
127	A	804	SER	0	-0.047	-0.038	60.077	0.000	0.000	0.000	0.000	0.000	0.000
128	A	805	ASN	0	-0.087	-0.042	58.469	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	806	HIS	0	-0.014	-0.006	62.197	0.000	0.000	0.000	0.000	0.000	0.000
130	A	807	HIS	0	0.007	0.007	66.077	0.001	0.001	0.000	0.000	0.000	0.000
131	A	808	LEU	0	-0.028	-0.024	67.052	0.001	0.001	0.000	0.000	0.000	0.000
132	A	809	ASP	-1	-0.784	-0.877	70.446	-0.016	-0.016	0.000	0.000	0.000	0.000
133	A	810	SER	0	0.058	0.022	72.969	0.000	0.000	0.000	0.000	0.000	0.000
134	A	811	GLN	0	-0.057	-0.027	75.507	0.001	0.001	0.000	0.000	0.000	0.000
135	A	812	SER	0	-0.061	-0.037	73.041	0.000	0.000	0.000	0.000	0.000	0.000
136	A	813	ARG	1	0.947	0.971	74.850	0.012	0.012	0.000	0.000	0.000	0.000
137	A	814	TRP	0	0.105	0.038	66.867	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	815	SER	0	-0.019	-0.022	72.923	0.000	0.000	0.000	0.000	0.000	0.000
139	A	816	MLY	1	0.944	0.989	74.684	0.015	0.015	0.000	0.000	0.000	0.000
140	A	817	VAL	0	-0.018	-0.014	68.840	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	818	MLY	1	0.932	0.984	68.831	0.012	0.012	0.000	0.000	0.000	0.000
142	A	819	ASP	-1	-0.875	-0.947	68.351	-0.015	-0.015	0.000	0.000	0.000	0.000
143	A	820	MLY	1	0.792	0.918	68.235	0.018	0.018	0.000	0.000	0.000	0.000
144	A	821	VAL	0	-0.012	-0.011	64.017	-0.001	-0.001	0.000	0.000	0.000	0.000
145	A	822	GLU	-1	-0.804	-0.893	63.647	-0.014	-0.014	0.000	0.000	0.000	0.000
146	A	823	SER	0	-0.021	-0.013	62.688	0.000	0.000	0.000	0.000	0.000	0.000
147	A	824	ASP	-1	-0.799	-0.893	58.380	-0.024	-0.024	0.000	0.000	0.000	0.000
148	A	825	PRO	0	-0.036	-0.039	55.326	0.001	0.001	0.000	0.000	0.000	0.000
149	A	826	ARG	1	0.746	0.841	54.556	0.026	0.026	0.000	0.000	0.000	0.000
150	A	827	TYR	0	-0.023	-0.022	57.808	0.001	0.001	0.000	0.000	0.000	0.000
151	A	828	MLY	1	0.873	0.932	58.101	0.020	0.020	0.000	0.000	0.000	0.000
152	A	829	ALA	0	-0.030	-0.004	56.279	0.001	0.001	0.000	0.000	0.000	0.000
153	A	830	VAL	0	-0.002	0.021	58.050	0.001	0.001	0.000	0.000	0.000	0.000
154	A	831	ASP	-1	-0.816	-0.887	60.794	-0.010	-0.010	0.000	0.000	0.000	0.000
155	A	832	SER	0	-0.022	-0.028	62.409	0.000	0.000	0.000	0.000	0.000	0.000
156	A	833	SER	0	-0.021	-0.039	65.771	0.000	0.000	0.000	0.000	0.000	0.000
157	A	834	SER	0	0.006	0.013	68.269	0.000	0.000	0.000	0.000	0.000	0.000
158	A	835	MET	0	0.066	0.036	64.052	0.000	0.000	0.000	0.000	0.000	0.000
159	A	836	ARG	1	0.836	0.912	63.938	0.013	0.013	0.000	0.000	0.000	0.000
160	A	837	GLU	-1	-0.893	-0.939	66.639	-0.011	-0.011	0.000	0.000	0.000	0.000
161	A	838	ASP	-1	-0.812	-0.911	68.897	-0.010	-0.010	0.000	0.000	0.000	0.000
162	A	839	LEU	0	-0.057	-0.025	62.474	0.000	0.000	0.000	0.000	0.000	0.000
163	A	840	PHE	0	0.030	0.001	66.325	-0.001	-0.001	0.000	0.000	0.000	0.000
164	A	841	MLY	1	0.801	0.891	68.429	0.010	0.010	0.000	0.000	0.000	0.000
165	A	842	GLN	0	0.056	0.023	65.395	-0.001	-0.001	0.000	0.000	0.000	0.000
166	A	843	TYR	0	-0.032	-0.020	63.139	-0.001	-0.001	0.000	0.000	0.000	0.000
167	A	844	ILE	0	-0.063	-0.018	67.192	-0.001	-0.001	0.000	0.000	0.000	0.000
168	A	845	GLU	-1	-1.039	-1.004	69.594	-0.012	-0.012	0.000	0.000	0.000	0.000

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