FMO DATABASE

FMODB ID: 437NN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1509985.923055
FMO2-HF: Nuclear repulsion	1436715.732186
FMO2-HF: Total energy	-73270.190869
FMO2-MP2: Total energy	-73483.983778

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.
-3.154	-1.094	-0.013	-0.868	-1.179	0.004

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 : 0.028 / q_NPA : -0.010

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	0.024	0.004	3.820	-0.276	1.431	-0.020	-0.750	-0.936	0.003
4	A	660	SER	0	0.031	0.011	6.507	0.300	0.300	0.000	0.000	0.000	0.000
5	A	661	ALA	0	0.075	0.021	7.899	0.220	0.220	0.000	0.000	0.000	0.000
6	A	662	ARG	1	0.842	0.895	9.264	0.148	0.148	0.000	0.000	0.000	0.000
7	A	663	MET	0	0.017	0.013	8.740	-0.027	-0.027	0.000	0.000	0.000	0.000
8	A	664	MLY	1	0.819	0.906	6.070	-1.980	-1.980	0.000	0.000	0.000	0.000
9	A	665	GLN	0	0.051	0.014	8.040	0.024	0.024	0.000	0.000	0.000	0.000
10	A	666	PHE	0	0.006	0.014	11.655	-0.047	-0.047	0.000	0.000	0.000	0.000
11	A	667	MLY	1	0.983	0.977	3.448	-3.560	-3.207	0.007	-0.118	-0.243	0.001
12	A	668	ASP	-1	-0.783	-0.884	9.768	1.749	1.749	0.000	0.000	0.000	0.000
13	A	669	MET	0	-0.025	0.004	11.752	-0.123	-0.123	0.000	0.000	0.000	0.000
14	A	670	LEU	0	-0.042	-0.025	11.975	-0.080	-0.080	0.000	0.000	0.000	0.000
15	A	671	LEU	0	0.003	-0.004	10.512	-0.052	-0.052	0.000	0.000	0.000	0.000
16	A	672	GLU	-1	-0.931	-0.958	14.528	0.596	0.596	0.000	0.000	0.000	0.000
17	A	673	ARG	1	0.851	0.919	17.177	-0.402	-0.402	0.000	0.000	0.000	0.000
18	A	674	GLY	0	-0.006	0.011	18.184	-0.048	-0.048	0.000	0.000	0.000	0.000
19	A	675	VAL	0	-0.018	0.000	16.790	-0.052	-0.052	0.000	0.000	0.000	0.000
20	A	676	SER	0	-0.009	0.018	17.557	0.035	0.035	0.000	0.000	0.000	0.000
21	A	677	ALA	0	-0.023	-0.017	16.517	0.005	0.005	0.000	0.000	0.000	0.000
22	A	678	PHE	0	-0.046	-0.028	18.097	-0.036	-0.036	0.000	0.000	0.000	0.000
23	A	679	SER	0	-0.005	-0.014	21.376	-0.008	-0.008	0.000	0.000	0.000	0.000
24	A	680	THR	0	-0.004	0.022	21.770	-0.008	-0.008	0.000	0.000	0.000	0.000
25	A	681	TRP	0	0.066	0.031	17.267	0.024	0.024	0.000	0.000	0.000	0.000
26	A	682	GLU	-1	-0.864	-0.965	21.588	0.048	0.048	0.000	0.000	0.000	0.000
27	A	683	MLY	1	0.905	0.957	24.525	-0.056	-0.056	0.000	0.000	0.000	0.000
28	A	684	GLU	-1	-0.745	-0.874	20.510	0.186	0.186	0.000	0.000	0.000	0.000
29	A	685	LEU	0	0.007	0.022	22.019	0.021	0.021	0.000	0.000	0.000	0.000
30	A	686	HIS	0	-0.009	-0.011	23.021	0.021	0.021	0.000	0.000	0.000	0.000
31	A	687	MLY	1	0.846	0.929	21.437	-0.194	-0.194	0.000	0.000	0.000	0.000
32	A	688	ILE	0	-0.018	-0.031	18.046	0.028	0.028	0.000	0.000	0.000	0.000
33	A	689	VAL	0	-0.004	0.006	21.113	0.009	0.009	0.000	0.000	0.000	0.000
34	A	690	PHE	0	-0.010	0.010	23.544	-0.008	-0.008	0.000	0.000	0.000	0.000
35	A	691	ASP	-1	-0.756	-0.839	19.495	0.377	0.377	0.000	0.000	0.000	0.000
36	A	692	PRO	0	0.072	0.027	20.809	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	693	ARG	1	0.800	0.869	15.051	-0.557	-0.557	0.000	0.000	0.000	0.000
38	A	694	TYR	0	0.005	-0.006	17.246	-0.017	-0.017	0.000	0.000	0.000	0.000
39	A	695	LEU	0	-0.009	-0.018	19.214	-0.036	-0.036	0.000	0.000	0.000	0.000
40	A	696	LEU	0	-0.015	0.019	14.880	-0.023	-0.023	0.000	0.000	0.000	0.000
41	A	697	LEU	0	-0.022	0.005	12.920	-0.026	-0.026	0.000	0.000	0.000	0.000
42	A	698	ASN	0	0.046	0.038	17.183	0.006	0.006	0.000	0.000	0.000	0.000
43	A	699	PRO	0	0.059	0.000	18.200	0.004	0.004	0.000	0.000	0.000	0.000
44	A	700	MLY	1	1.006	1.013	17.404	0.231	0.231	0.000	0.000	0.000	0.000
45	A	701	GLU	-1	-0.771	-0.878	14.221	-0.111	-0.111	0.000	0.000	0.000	0.000
46	A	702	ARG	1	0.864	0.943	13.840	-0.087	-0.087	0.000	0.000	0.000	0.000
47	A	703	MLY	1	0.891	0.957	14.920	0.164	0.164	0.000	0.000	0.000	0.000
48	A	704	GLN	0	-0.031	-0.017	11.209	0.038	0.038	0.000	0.000	0.000	0.000
49	A	705	VAL	0	0.013	0.001	9.206	-0.030	-0.030	0.000	0.000	0.000	0.000
50	A	706	PHE	0	0.014	0.018	11.000	0.102	0.102	0.000	0.000	0.000	0.000
51	A	707	ASP	-1	-0.795	-0.916	13.567	-0.046	-0.046	0.000	0.000	0.000	0.000
52	A	708	GLN	0	-0.029	-0.008	7.428	-0.011	-0.011	0.000	0.000	0.000	0.000
53	A	709	TYR	0	-0.068	-0.081	10.113	0.088	0.088	0.000	0.000	0.000	0.000
54	A	710	VAL	0	0.010	0.008	10.983	0.046	0.046	0.000	0.000	0.000	0.000
55	A	711	MLY	1	0.928	0.967	11.450	0.342	0.342	0.000	0.000	0.000	0.000
56	A	712	THR	0	-0.023	-0.015	8.250	-0.061	-0.061	0.000	0.000	0.000	0.000
57	A	713	ARG	1	1.011	1.014	11.177	-0.334	-0.334	0.000	0.000	0.000	0.000
58	A	714	ALA	0	-0.006	-0.001	13.402	-0.013	-0.013	0.000	0.000	0.000	0.000
59	A	715	GLU	-1	-0.972	-0.991	12.840	-0.147	-0.147	0.000	0.000	0.000	0.000
60	A	716	GLU	-1	-0.927	-0.968	9.589	0.645	0.645	0.000	0.000	0.000	0.000
61	A	717	GLU	-1	-0.868	-0.921	14.175	0.189	0.189	0.000	0.000	0.000	0.000
62	A	718	ARG	1	0.917	0.941	17.682	-0.046	-0.046	0.000	0.000	0.000	0.000
63	A	719	ARG	1	0.911	0.946	13.281	-0.080	-0.080	0.000	0.000	0.000	0.000
64	A	720	GLU	-1	-0.943	-0.946	17.005	0.236	0.236	0.000	0.000	0.000	0.000
65	A	721	MLY	1	0.911	0.951	18.465	-0.164	-0.164	0.000	0.000	0.000	0.000
66	A	722	MLY	1	0.992	0.987	21.485	0.003	0.003	0.000	0.000	0.000	0.000
67	A	723	ASN	0	-0.031	-0.032	18.169	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	724	MLY	1	1.029	1.036	21.531	-0.133	-0.133	0.000	0.000	0.000	0.000
69	A	725	ILE	0	-0.005	-0.004	23.568	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	726	MET	0	-0.062	-0.045	23.557	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	727	GLN	0	0.029	0.010	23.654	-0.012	-0.012	0.000	0.000	0.000	0.000
72	A	728	ALA	0	-0.002	0.010	25.764	0.000	0.000	0.000	0.000	0.000	0.000
73	A	729	MLY	1	0.899	0.955	28.777	-0.019	-0.019	0.000	0.000	0.000	0.000
74	A	730	GLU	-1	-0.873	-0.933	27.640	0.009	0.009	0.000	0.000	0.000	0.000
75	A	731	ASP	-1	-0.854	-0.915	27.871	0.059	0.059	0.000	0.000	0.000	0.000
76	A	732	PHE	0	-0.069	-0.040	30.916	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	733	MLY	1	0.908	0.939	32.213	-0.010	-0.010	0.000	0.000	0.000	0.000
78	A	734	MLY	1	0.924	0.974	28.897	-0.025	-0.025	0.000	0.000	0.000	0.000
79	A	735	MET	0	-0.103	-0.042	34.281	0.002	0.002	0.000	0.000	0.000	0.000
80	A	736	MET	0	-0.016	0.024	36.607	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	758	SER	0	0.027	-0.004	33.107	0.000	0.000	0.000	0.000	0.000	0.000
82	A	759	ARG	1	0.993	0.988	31.509	-0.047	-0.047	0.000	0.000	0.000	0.000
83	A	760	PHE	0	0.031	0.010	33.584	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	761	MLY	1	0.942	0.958	34.781	-0.074	-0.074	0.000	0.000	0.000	0.000
85	A	762	ALA	0	0.015	0.019	30.503	0.002	0.002	0.000	0.000	0.000	0.000
86	A	763	ILE	0	0.010	0.030	31.797	0.004	0.004	0.000	0.000	0.000	0.000
87	A	764	GLU	-1	-0.865	-0.925	33.312	0.081	0.081	0.000	0.000	0.000	0.000
88	A	765	MLY	1	0.900	0.958	35.621	-0.058	-0.058	0.000	0.000	0.000	0.000
89	A	766	MET	0	0.084	0.034	39.326	0.001	0.001	0.000	0.000	0.000	0.000
90	A	767	MLY	1	0.971	0.973	40.851	-0.030	-0.030	0.000	0.000	0.000	0.000
91	A	768	ASP	-1	-0.818	-0.903	35.377	0.039	0.039	0.000	0.000	0.000	0.000
92	A	769	ARG	1	0.737	0.859	37.107	-0.055	-0.055	0.000	0.000	0.000	0.000
93	A	770	GLU	-1	-0.898	-0.974	38.516	0.025	0.025	0.000	0.000	0.000	0.000
94	A	771	ALA	0	-0.036	-0.005	39.369	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	772	LEU	0	0.019	0.004	34.027	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	773	PHE	0	0.027	0.021	38.551	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	774	ASN	0	0.019	0.004	41.084	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	775	GLU	-1	-0.975	-0.987	35.422	0.010	0.010	0.000	0.000	0.000	0.000
99	A	776	PHE	0	0.027	0.001	38.741	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	777	VAL	0	0.111	0.046	40.263	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	778	ALA	0	-0.066	-0.034	43.724	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	779	ALA	0	-0.038	-0.024	40.574	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	780	ALA	0	-0.023	-0.001	42.430	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	781	ARG	1	1.001	0.996	43.675	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	782	MLY	1	0.853	0.931	44.110	0.006	0.006	0.000	0.000	0.000	0.000
106	A	783	MLY	1	1.021	1.018	40.815	0.009	0.009	0.000	0.000	0.000	0.000
107	A	784	GLU	-1	-0.894	-0.945	44.801	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	785	MLY	1	0.825	0.912	48.411	0.005	0.005	0.000	0.000	0.000	0.000
109	A	786	GLU	-1	-0.894	-0.943	43.380	-0.020	-0.020	0.000	0.000	0.000	0.000
110	A	787	ASP	-1	-0.816	-0.908	45.093	-0.014	-0.014	0.000	0.000	0.000	0.000
111	A	788	SER	0	-0.041	-0.016	47.885	0.000	0.000	0.000	0.000	0.000	0.000
112	A	789	MLY	1	0.894	0.950	50.637	0.015	0.015	0.000	0.000	0.000	0.000
113	A	790	THR	0	0.027	0.007	46.602	0.000	0.000	0.000	0.000	0.000	0.000
114	A	791	ARG	1	0.981	0.981	46.887	0.016	0.016	0.000	0.000	0.000	0.000
115	A	792	GLY	0	0.046	0.027	51.149	0.000	0.000	0.000	0.000	0.000	0.000
116	A	793	GLU	-1	-0.947	-0.997	52.883	-0.020	-0.020	0.000	0.000	0.000	0.000
117	A	794	MLY	1	0.772	0.898	49.127	0.021	0.021	0.000	0.000	0.000	0.000
118	A	795	ILE	0	0.047	0.026	53.408	0.000	0.000	0.000	0.000	0.000	0.000
119	A	796	MLY	1	0.932	0.982	56.206	0.016	0.016	0.000	0.000	0.000	0.000
120	A	797	SER	0	0.011	-0.010	54.945	0.000	0.000	0.000	0.000	0.000	0.000
121	A	798	ASP	-1	-0.780	-0.874	53.258	-0.022	-0.022	0.000	0.000	0.000	0.000
122	A	799	PHE	0	0.004	0.010	56.374	0.000	0.000	0.000	0.000	0.000	0.000
123	A	800	PHE	0	0.002	-0.017	59.603	0.000	0.000	0.000	0.000	0.000	0.000
124	A	801	GLU	-1	-0.905	-0.945	54.676	-0.025	-0.025	0.000	0.000	0.000	0.000
125	A	802	LEU	0	-0.056	-0.017	58.590	0.000	0.000	0.000	0.000	0.000	0.000
126	A	803	LEU	0	-0.007	-0.017	60.223	0.000	0.000	0.000	0.000	0.000	0.000
127	A	804	SER	0	-0.041	-0.012	60.177	0.000	0.000	0.000	0.000	0.000	0.000
128	A	805	ASN	0	-0.074	-0.029	58.334	0.000	0.000	0.000	0.000	0.000	0.000
129	A	806	HIS	0	-0.041	-0.034	62.071	0.000	0.000	0.000	0.000	0.000	0.000
130	A	807	HIS	0	-0.014	-0.007	65.837	0.000	0.000	0.000	0.000	0.000	0.000
131	A	808	LEU	0	-0.031	-0.022	66.780	0.001	0.001	0.000	0.000	0.000	0.000
132	A	809	ASP	-1	-0.837	-0.925	70.189	-0.016	-0.016	0.000	0.000	0.000	0.000
133	A	810	SER	0	0.041	-0.001	72.649	0.000	0.000	0.000	0.000	0.000	0.000
134	A	811	GLN	0	-0.009	0.002	75.244	0.001	0.001	0.000	0.000	0.000	0.000
135	A	812	SER	0	-0.048	-0.003	72.807	0.000	0.000	0.000	0.000	0.000	0.000
136	A	813	ARG	1	0.937	0.963	74.809	0.010	0.010	0.000	0.000	0.000	0.000
137	A	814	TRP	0	0.092	0.034	66.951	0.000	0.000	0.000	0.000	0.000	0.000
138	A	815	SER	0	-0.028	-0.016	72.836	0.000	0.000	0.000	0.000	0.000	0.000
139	A	816	MLY	1	0.982	0.989	74.234	0.012	0.012	0.000	0.000	0.000	0.000
140	A	817	VAL	0	-0.009	0.012	68.830	0.000	0.000	0.000	0.000	0.000	0.000
141	A	818	MLY	1	0.951	0.984	69.120	0.008	0.008	0.000	0.000	0.000	0.000
142	A	819	ASP	-1	-0.869	-0.946	68.547	-0.010	-0.010	0.000	0.000	0.000	0.000
143	A	820	MLY	1	0.831	0.932	67.620	0.015	0.015	0.000	0.000	0.000	0.000
144	A	821	VAL	0	-0.024	-0.017	63.990	-0.001	-0.001	0.000	0.000	0.000	0.000
145	A	822	GLU	-1	-0.925	-0.961	63.860	-0.010	-0.010	0.000	0.000	0.000	0.000
146	A	823	SER	0	-0.033	-0.022	62.542	0.000	0.000	0.000	0.000	0.000	0.000
147	A	824	ASP	-1	-0.808	-0.865	58.542	-0.017	-0.017	0.000	0.000	0.000	0.000
148	A	825	PRO	0	0.010	-0.024	55.609	0.001	0.001	0.000	0.000	0.000	0.000
149	A	826	ARG	1	0.789	0.884	54.862	0.021	0.021	0.000	0.000	0.000	0.000
150	A	827	TYR	0	0.030	0.019	57.674	0.000	0.000	0.000	0.000	0.000	0.000
151	A	828	MLY	1	0.909	0.947	58.102	0.011	0.011	0.000	0.000	0.000	0.000
152	A	829	ALA	0	-0.029	-0.003	56.461	0.001	0.001	0.000	0.000	0.000	0.000
153	A	830	VAL	0	0.014	0.019	58.218	0.000	0.000	0.000	0.000	0.000	0.000
154	A	831	ASP	-1	-0.916	-0.957	60.653	-0.006	-0.006	0.000	0.000	0.000	0.000
155	A	832	SER	0	0.052	0.027	62.491	0.001	0.001	0.000	0.000	0.000	0.000
156	A	833	SER	0	-0.033	-0.040	65.879	-0.001	-0.001	0.000	0.000	0.000	0.000
157	A	834	SER	0	0.019	0.002	68.497	0.000	0.000	0.000	0.000	0.000	0.000
158	A	835	MET	0	0.071	0.043	64.463	0.000	0.000	0.000	0.000	0.000	0.000
159	A	836	ARG	1	0.866	0.950	64.135	0.008	0.008	0.000	0.000	0.000	0.000
160	A	837	GLU	-1	-0.963	-0.974	66.561	-0.009	-0.009	0.000	0.000	0.000	0.000
161	A	838	ASP	-1	-0.861	-0.943	68.415	-0.010	-0.010	0.000	0.000	0.000	0.000
162	A	839	LEU	0	-0.074	-0.030	62.735	-0.001	-0.001	0.000	0.000	0.000	0.000
163	A	840	PHE	0	0.028	0.001	66.432	-0.001	-0.001	0.000	0.000	0.000	0.000
164	A	841	MLY	1	0.946	0.966	68.252	0.009	0.009	0.000	0.000	0.000	0.000
165	A	842	GLN	0	0.017	-0.002	65.283	-0.001	-0.001	0.000	0.000	0.000	0.000
166	A	843	TYR	0	-0.063	-0.034	63.358	-0.001	-0.001	0.000	0.000	0.000	0.000
167	A	844	ILE	0	-0.060	-0.012	67.133	-0.001	-0.001	0.000	0.000	0.000	0.000
168	A	845	GLU	-1	-1.009	-0.984	70.415	-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)