FMO DATABASE

FMODB ID: V55R1

Calculation Name: 4DOW-A-Xray372

Preferred Name:

Target Type:

Ligand Name: n-dimethyl-lysine

ligand 3-letter code: MLY

PDB ID: 4DOW

Chain ID: A

ChEMBL ID:

UniProt ID: P62806

Base Structure: X-ray

Registration Date: 2023-06-21

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	157
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1558591.284112
FMO2-HF: Nuclear repulsion	1495361.797919
FMO2-HF: Total energy	-63229.486193
FMO2-MP2: Total energy	-63415.452851

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:13:THR)

Summations of interaction energy for fragment #1(A:13:THR)

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.
-5.792	0.718	0.808	-3.312	-4.005	-0.009

Interaction energy analysis for fragmet #1(A:13:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.048 / q_NPA : 0.030

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	15	SER	0	-0.041	-0.029	3.804	0.251	3.200	-0.027	-1.510	-1.411	0.008
4	A	16	TRP	0	-0.011	-0.021	5.575	-0.366	-0.366	0.000	0.000	0.000	0.000
5	A	17	VAL	0	0.038	0.028	9.295	-0.053	-0.053	0.000	0.000	0.000	0.000
6	A	18	GLY	0	-0.019	-0.006	11.505	0.032	0.032	0.000	0.000	0.000	0.000
7	A	19	ARG	1	0.950	0.960	14.349	0.071	0.071	0.000	0.000	0.000	0.000
8	A	20	PRO	0	0.008	0.013	16.354	-0.024	-0.024	0.000	0.000	0.000	0.000
9	A	21	LEU	0	-0.032	-0.028	17.714	-0.023	-0.023	0.000	0.000	0.000	0.000
10	A	22	PRO	0	-0.013	-0.013	20.613	0.021	0.021	0.000	0.000	0.000	0.000
11	A	23	ASN	0	-0.051	-0.021	22.219	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	24	ARG	1	0.896	0.943	21.655	-0.058	-0.058	0.000	0.000	0.000	0.000
13	A	25	LYS	1	0.942	0.974	22.287	-0.095	-0.095	0.000	0.000	0.000	0.000
14	A	26	GLN	0	0.072	0.035	23.333	0.010	0.010	0.000	0.000	0.000	0.000
15	A	27	PHE	0	-0.001	-0.003	21.365	0.009	0.009	0.000	0.000	0.000	0.000
16	A	28	GLN	0	0.022	0.026	18.481	0.024	0.024	0.000	0.000	0.000	0.000
17	A	29	GLN	0	-0.038	-0.010	16.002	0.003	0.003	0.000	0.000	0.000	0.000
18	A	30	MET	0	0.043	0.046	16.448	0.027	0.027	0.000	0.000	0.000	0.000
19	A	31	TYR	0	0.008	0.021	13.857	-0.017	-0.017	0.000	0.000	0.000	0.000
20	A	32	ARG	1	0.968	0.978	15.855	0.215	0.215	0.000	0.000	0.000	0.000
21	A	33	GLU	-1	-0.863	-0.947	12.519	-0.443	-0.443	0.000	0.000	0.000	0.000
22	A	34	ILE	0	-0.026	-0.009	7.388	0.172	0.172	0.000	0.000	0.000	0.000
23	A	35	CYS	0	0.003	0.014	6.911	-0.283	-0.283	0.000	0.000	0.000	0.000
24	A	36	MET	0	0.001	0.000	4.110	-0.055	0.098	0.000	-0.048	-0.105	0.000
25	A	37	LYS	1	0.953	0.987	2.587	2.147	3.432	0.381	-0.514	-1.151	-0.002
26	A	38	ILE	0	0.037	0.029	2.676	-4.488	-2.483	0.455	-1.232	-1.229	-0.015
27	A	39	ASN	0	-0.049	-0.043	5.403	0.174	0.174	0.000	0.000	0.000	0.000
28	A	40	ASP	-1	-0.832	-0.913	7.670	-0.557	-0.557	0.000	0.000	0.000	0.000
29	A	41	GLY	0	-0.097	-0.056	8.184	0.052	0.052	0.000	0.000	0.000	0.000
30	A	42	SER	0	0.017	-0.004	8.331	-0.089	-0.089	0.000	0.000	0.000	0.000
31	A	43	GLU	-1	-0.927	-0.961	6.501	-1.871	-1.871	0.000	0.000	0.000	0.000
32	A	44	ILE	0	-0.007	0.001	7.505	0.435	0.435	0.000	0.000	0.000	0.000
33	A	45	HIS	0	-0.033	-0.018	8.636	-0.264	-0.264	0.000	0.000	0.000	0.000
34	A	46	ILE	0	-0.012	-0.005	8.848	0.104	0.104	0.000	0.000	0.000	0.000
35	A	47	LYS	1	0.876	0.930	12.165	0.548	0.548	0.000	0.000	0.000	0.000
36	A	48	VAL	0	0.022	0.003	15.449	0.009	0.009	0.000	0.000	0.000	0.000
37	A	49	GLY	0	-0.062	-0.029	17.660	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	50	GLN	0	-0.007	0.017	15.145	-0.047	-0.047	0.000	0.000	0.000	0.000
39	A	51	PHE	0	0.029	0.011	16.834	0.040	0.040	0.000	0.000	0.000	0.000
40	A	52	VAL	0	0.006	0.005	11.658	-0.077	-0.077	0.000	0.000	0.000	0.000
41	A	53	LEU	0	0.006	0.004	12.869	0.103	0.103	0.000	0.000	0.000	0.000
42	A	54	ILE	0	0.001	-0.005	11.775	-0.080	-0.080	0.000	0.000	0.000	0.000
43	A	55	GLN	0	-0.013	-0.023	11.235	-0.030	-0.030	0.000	0.000	0.000	0.000
44	A	56	GLY	0	0.020	0.015	13.090	0.047	0.047	0.000	0.000	0.000	0.000
45	A	57	GLU	-1	-0.897	-0.961	16.104	0.104	0.104	0.000	0.000	0.000	0.000
46	A	58	ASP	-1	-0.888	-0.942	16.747	0.136	0.136	0.000	0.000	0.000	0.000
47	A	59	ASN	0	-0.060	-0.026	18.271	-0.018	-0.018	0.000	0.000	0.000	0.000
48	A	60	LYS	1	0.902	0.956	19.966	-0.050	-0.050	0.000	0.000	0.000	0.000
49	A	61	LYS	1	0.927	0.963	18.962	0.057	0.057	0.000	0.000	0.000	0.000
50	A	62	PRO	0	0.052	0.037	14.695	0.020	0.020	0.000	0.000	0.000	0.000
51	A	63	TYR	0	0.049	0.036	16.550	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	64	VAL	0	0.009	0.006	16.493	-0.039	-0.039	0.000	0.000	0.000	0.000
53	A	65	ALA	0	0.011	0.005	16.626	0.037	0.037	0.000	0.000	0.000	0.000
54	A	66	LYS	1	0.972	0.994	17.254	0.056	0.056	0.000	0.000	0.000	0.000
55	A	67	LEU	0	0.001	0.006	12.794	0.045	0.045	0.000	0.000	0.000	0.000
56	A	68	ILE	0	-0.043	-0.034	17.169	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	69	GLU	-1	-0.870	-0.954	17.772	0.105	0.105	0.000	0.000	0.000	0.000
58	A	70	LEU	0	0.009	0.019	11.495	0.005	0.005	0.000	0.000	0.000	0.000
59	A	71	PHE	0	-0.018	-0.031	13.688	-0.010	-0.010	0.000	0.000	0.000	0.000
60	A	72	GLN	0	0.081	0.069	11.363	0.163	0.163	0.000	0.000	0.000	0.000
61	A	73	ASN	0	-0.023	-0.037	13.952	-0.143	-0.143	0.000	0.000	0.000	0.000
62	A	74	GLY	0	-0.005	-0.021	15.688	0.063	0.063	0.000	0.000	0.000	0.000
63	A	75	ALA	0	-0.045	-0.020	17.773	-0.015	-0.015	0.000	0.000	0.000	0.000
64	A	76	GLU	-1	-0.817	-0.902	15.159	0.532	0.532	0.000	0.000	0.000	0.000
65	A	77	VAL	0	-0.019	0.011	16.335	0.018	0.018	0.000	0.000	0.000	0.000
66	A	78	PRO	0	0.043	-0.018	12.328	-0.038	-0.038	0.000	0.000	0.000	0.000
67	A	79	PRO	0	-0.006	0.011	12.536	0.020	0.020	0.000	0.000	0.000	0.000
68	A	80	LYS	1	0.945	0.985	8.443	-1.433	-1.433	0.000	0.000	0.000	0.000
69	A	81	LYS	1	0.865	0.954	5.614	-2.768	-2.768	0.000	0.000	0.000	0.000
70	A	82	CYM	-1	-0.817	-0.844	9.909	0.581	0.581	0.000	0.000	0.000	0.000
71	A	83	ALA	0	0.019	0.001	12.287	-0.085	-0.085	0.000	0.000	0.000	0.000
72	A	84	ARG	1	0.874	0.956	14.115	-0.108	-0.108	0.000	0.000	0.000	0.000
73	A	85	VAL	0	-0.015	-0.013	15.959	-0.042	-0.042	0.000	0.000	0.000	0.000
74	A	86	GLN	0	-0.048	-0.027	18.848	0.025	0.025	0.000	0.000	0.000	0.000
75	A	87	TRP	0	0.023	-0.003	17.220	-0.034	-0.034	0.000	0.000	0.000	0.000
76	A	88	PHE	0	0.022	0.007	21.004	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	89	VAL	0	0.015	0.026	22.576	0.007	0.007	0.000	0.000	0.000	0.000
78	A	90	ARG	1	0.929	0.941	18.758	0.103	0.103	0.000	0.000	0.000	0.000
79	A	91	PHE	0	0.105	0.043	25.317	0.011	0.011	0.000	0.000	0.000	0.000
80	A	92	LEU	0	-0.078	-0.054	26.855	0.007	0.007	0.000	0.000	0.000	0.000
81	A	93	GLU	-1	-0.923	-0.960	23.414	0.011	0.011	0.000	0.000	0.000	0.000
82	A	94	ILE	0	-0.023	0.013	27.390	0.006	0.006	0.000	0.000	0.000	0.000
83	A	95	PRO	0	0.024	0.013	30.814	0.000	0.000	0.000	0.000	0.000	0.000
84	A	96	VAL	0	0.105	0.027	33.575	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	97	SER	0	-0.057	-0.028	35.507	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	98	LYS	1	0.843	0.917	35.742	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	99	ARG	1	0.902	0.969	31.287	0.004	0.004	0.000	0.000	0.000	0.000
88	A	100	HIS	0	0.001	0.000	36.181	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	101	LEU	0	-0.024	-0.005	38.193	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	102	LEU	0	-0.034	0.009	33.739	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	103	GLY	0	0.001	0.001	37.703	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	104	ARG	1	0.775	0.834	33.541	0.049	0.049	0.000	0.000	0.000	0.000
93	A	105	SER	0	-0.004	0.000	35.077	0.003	0.003	0.000	0.000	0.000	0.000
94	A	106	PRO	0	-0.049	-0.006	31.008	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	107	PRO	0	0.059	0.031	29.958	0.002	0.002	0.000	0.000	0.000	0.000
96	A	108	ALA	0	-0.017	-0.025	26.030	0.000	0.000	0.000	0.000	0.000	0.000
97	A	109	GLN	0	-0.020	-0.021	24.453	0.008	0.008	0.000	0.000	0.000	0.000
98	A	110	GLU	-1	-0.775	-0.827	25.595	-0.071	-0.071	0.000	0.000	0.000	0.000
99	A	111	ILE	0	-0.103	-0.043	22.261	0.007	0.007	0.000	0.000	0.000	0.000
100	A	112	PHE	0	0.029	-0.012	26.121	0.001	0.001	0.000	0.000	0.000	0.000
101	A	113	TRP	0	0.016	0.015	25.452	-0.005	-0.005	0.000	0.000	0.000	0.000
102	A	114	TYR	0	-0.043	-0.034	25.488	0.006	0.006	0.000	0.000	0.000	0.000
103	A	115	ASP	-1	-0.935	-0.965	27.247	-0.006	-0.006	0.000	0.000	0.000	0.000
104	A	116	CYS	0	-0.096	-0.048	28.708	0.005	0.005	0.000	0.000	0.000	0.000
105	A	117	SER	0	-0.014	-0.011	27.841	0.000	0.000	0.000	0.000	0.000	0.000
106	A	118	ASP	-1	-0.726	-0.846	27.909	0.046	0.046	0.000	0.000	0.000	0.000
107	A	119	TRP	0	-0.029	-0.008	23.671	0.014	0.014	0.000	0.000	0.000	0.000
108	A	120	ASP	-1	-0.836	-0.927	20.501	0.149	0.149	0.000	0.000	0.000	0.000
109	A	121	ASN	0	0.005	0.007	20.355	0.015	0.015	0.000	0.000	0.000	0.000
110	A	122	LYS	1	0.795	0.846	14.772	-0.432	-0.432	0.000	0.000	0.000	0.000
111	A	123	ILE	0	0.005	0.012	12.422	0.006	0.006	0.000	0.000	0.000	0.000
112	A	124	ASN	0	0.071	0.028	9.846	0.002	0.002	0.000	0.000	0.000	0.000
113	A	125	VAL	0	-0.001	-0.008	5.964	-0.049	-0.049	0.000	0.000	0.000	0.000
114	A	126	GLU	-1	-0.948	-0.974	4.456	2.684	2.802	-0.001	-0.008	-0.109	0.000
115	A	127	THR	0	-0.051	-0.026	6.518	-0.164	-0.164	0.000	0.000	0.000	0.000
116	A	128	ILE	0	-0.066	-0.022	7.745	-0.057	-0.057	0.000	0.000	0.000	0.000
117	A	129	ILE	0	0.014	0.009	7.009	-0.238	-0.238	0.000	0.000	0.000	0.000
118	A	130	GLY	0	0.030	0.000	8.027	-0.337	-0.337	0.000	0.000	0.000	0.000
119	A	131	PRO	0	-0.042	-0.015	9.667	0.188	0.188	0.000	0.000	0.000	0.000
120	A	132	VAL	0	0.024	0.013	12.824	0.016	0.016	0.000	0.000	0.000	0.000
121	A	133	GLN	0	-0.003	-0.001	16.222	0.003	0.003	0.000	0.000	0.000	0.000
122	A	134	VAL	0	-0.002	-0.009	19.577	0.018	0.018	0.000	0.000	0.000	0.000
123	A	135	VAL	0	-0.002	-0.010	22.033	-0.004	-0.004	0.000	0.000	0.000	0.000
124	A	136	ALA	0	-0.036	-0.011	25.643	0.009	0.009	0.000	0.000	0.000	0.000
125	A	137	LEU	0	-0.034	-0.004	28.655	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	138	ALA	0	0.030	-0.001	31.861	0.005	0.005	0.000	0.000	0.000	0.000
127	A	139	PRO	0	-0.024	-0.030	35.293	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	140	GLU	-1	-0.928	-0.972	36.761	-0.057	-0.057	0.000	0.000	0.000	0.000
129	A	141	GLU	-1	-0.833	-0.880	34.267	-0.088	-0.088	0.000	0.000	0.000	0.000
130	A	142	VAL	0	-0.007	-0.018	35.582	0.003	0.003	0.000	0.000	0.000	0.000
131	A	143	ILE	0	-0.022	-0.020	29.046	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	144	PRO	0	0.065	0.028	30.298	0.006	0.006	0.000	0.000	0.000	0.000
133	A	145	VAL	0	-0.090	-0.043	29.317	-0.007	-0.007	0.000	0.000	0.000	0.000
134	A	146	ASP	-1	-0.859	-0.900	30.598	-0.104	-0.104	0.000	0.000	0.000	0.000
135	A	147	GLN	0	-0.033	-0.039	29.657	-0.009	-0.009	0.000	0.000	0.000	0.000
136	A	148	LYS	1	0.896	0.946	23.267	0.210	0.210	0.000	0.000	0.000	0.000
137	A	149	SER	0	-0.012	-0.022	24.111	-0.010	-0.010	0.000	0.000	0.000	0.000
138	A	150	GLU	-1	-0.934	-0.955	23.982	-0.175	-0.175	0.000	0.000	0.000	0.000
139	A	151	GLU	-1	-0.905	-0.945	17.813	-0.307	-0.307	0.000	0.000	0.000	0.000
140	A	152	THR	0	-0.097	-0.038	20.165	-0.026	-0.026	0.000	0.000	0.000	0.000
141	A	153	LEU	0	-0.014	0.007	19.765	0.022	0.022	0.000	0.000	0.000	0.000
142	A	154	PHE	0	0.046	0.012	23.394	-0.008	-0.008	0.000	0.000	0.000	0.000
143	A	155	VAL	0	-0.033	-0.020	26.096	0.009	0.009	0.000	0.000	0.000	0.000
144	A	156	LYS	1	0.875	0.954	27.925	0.066	0.066	0.000	0.000	0.000	0.000
145	A	157	LEU	0	-0.013	-0.006	31.102	0.004	0.004	0.000	0.000	0.000	0.000
146	A	158	SER	0	-0.014	-0.014	30.089	-0.004	-0.004	0.000	0.000	0.000	0.000
147	A	159	TRP	0	-0.002	0.007	29.818	0.003	0.003	0.000	0.000	0.000	0.000
148	A	160	ASN	0	0.123	0.069	30.713	0.003	0.003	0.000	0.000	0.000	0.000
149	A	161	LYS	1	0.827	0.905	30.654	-0.026	-0.026	0.000	0.000	0.000	0.000
150	A	162	LYS	1	0.832	0.910	33.869	-0.009	-0.009	0.000	0.000	0.000	0.000
151	A	163	ASP	-1	-0.754	-0.898	36.697	-0.012	-0.012	0.000	0.000	0.000	0.000
152	A	164	PHE	0	-0.034	-0.033	32.048	0.000	0.000	0.000	0.000	0.000	0.000
153	A	165	ALA	0	0.009	0.016	34.780	0.002	0.002	0.000	0.000	0.000	0.000
154	A	166	PRO	0	0.041	0.002	34.662	-0.004	-0.004	0.000	0.000	0.000	0.000
155	A	167	LEU	0	0.027	0.018	29.050	0.003	0.003	0.000	0.000	0.000	0.000
156	A	168	PRO	0	-0.026	-0.005	30.717	0.001	0.001	0.000	0.000	0.000	0.000
157	A	169	PRO	0	-0.001	0.013	30.312	-0.007	-0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:13:THR)