FMO DATABASE

FMODB ID: K3J93

Calculation Name: 2VGY-A-Xray372

Preferred Name:

Target Type:

Ligand Name: n-dimethyl-lysine

ligand 3-letter code: MLY

PDB ID: 2VGY

Chain ID: A

ChEMBL ID:

UniProt ID: O87496

Base Structure: X-ray

Registration Date: 2023-06-19

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	132
LigandCharge	MLY=1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1176641.786126
FMO2-HF: Nuclear repulsion	1122586.067292
FMO2-HF: Total energy	-54055.718834
FMO2-MP2: Total energy	-54211.073589

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:29:ASN)

Summations of interaction energy for fragment #1(A:29:ASN)

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.
-16.87	-7.896	4.731	-6.32	-7.382	-0.035

Interaction energy analysis for fragmet #1(A:29:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / q_NPA : -0.017

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	31	ILE	0	-0.067	-0.034	2.971	-4.394	-0.723	0.056	-1.857	-1.870	0.003
4	A	32	SER	0	-0.037	-0.026	4.837	-1.076	-1.076	0.000	0.000	0.000	0.000
5	A	33	SER	0	0.037	0.038	6.329	0.885	0.885	0.000	0.000	0.000	0.000
6	A	34	ASP	-1	-0.889	-0.944	7.758	1.326	1.326	0.000	0.000	0.000	0.000
7	A	35	THR	0	0.041	-0.002	9.561	-0.229	-0.229	0.000	0.000	0.000	0.000
8	A	36	LEU	0	0.028	0.011	4.797	-0.674	-0.550	-0.001	-0.002	-0.120	0.000
9	A	37	GLU	-1	-0.785	-0.889	9.357	0.332	0.332	0.000	0.000	0.000	0.000
10	A	38	GLN	0	-0.051	-0.022	12.457	-0.171	-0.171	0.000	0.000	0.000	0.000
11	A	39	LEU	0	-0.019	-0.012	9.267	-0.104	-0.104	0.000	0.000	0.000	0.000
12	A	40	TYR	0	0.037	0.021	12.296	-0.129	-0.129	0.000	0.000	0.000	0.000
13	A	41	SER	0	-0.030	-0.016	13.942	-0.081	-0.081	0.000	0.000	0.000	0.000
14	A	42	LEU	0	-0.029	-0.007	16.182	-0.035	-0.035	0.000	0.000	0.000	0.000
15	A	43	ALA	0	0.028	0.002	15.251	-0.025	-0.025	0.000	0.000	0.000	0.000
16	A	44	PHE	0	-0.005	0.001	17.283	-0.031	-0.031	0.000	0.000	0.000	0.000
17	A	45	ASN	0	0.021	-0.006	19.381	-0.024	-0.024	0.000	0.000	0.000	0.000
18	A	46	GLN	0	-0.020	-0.013	18.785	-0.022	-0.022	0.000	0.000	0.000	0.000
19	A	47	TYR	0	0.006	0.006	20.987	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	48	GLN	0	-0.027	-0.011	22.774	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	49	SER	0	-0.107	-0.050	25.070	0.008	0.008	0.000	0.000	0.000	0.000
22	A	50	GLY	0	0.012	0.015	26.231	0.004	0.004	0.000	0.000	0.000	0.000
23	A	51	MLY	1	0.914	0.964	23.519	0.014	0.014	0.000	0.000	0.000	0.000
24	A	52	TYR	0	0.046	0.004	22.628	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	53	GLU	-1	-0.875	-0.942	21.364	-0.180	-0.180	0.000	0.000	0.000	0.000
26	A	54	ASP	-1	-0.958	-0.983	20.105	-0.110	-0.110	0.000	0.000	0.000	0.000
27	A	55	ALA	0	0.028	0.007	18.130	-0.013	-0.013	0.000	0.000	0.000	0.000
28	A	56	HIS	0	0.032	0.027	16.734	-0.058	-0.058	0.000	0.000	0.000	0.000
29	A	57	MLY	1	0.905	0.959	15.820	0.098	0.098	0.000	0.000	0.000	0.000
30	A	58	VAL	0	-0.026	-0.004	13.178	-0.056	-0.056	0.000	0.000	0.000	0.000
31	A	59	PHE	0	0.038	-0.001	11.932	-0.026	-0.026	0.000	0.000	0.000	0.000
32	A	60	GLN	0	0.031	0.015	11.552	-0.062	-0.062	0.000	0.000	0.000	0.000
33	A	61	ALA	0	-0.009	-0.005	9.793	-0.190	-0.190	0.000	0.000	0.000	0.000
34	A	62	LEU	0	-0.016	-0.003	7.637	-0.208	-0.208	0.000	0.000	0.000	0.000
35	A	63	CYS	0	-0.060	-0.024	6.943	-0.148	-0.148	0.000	0.000	0.000	0.000
36	A	64	VAL	0	-0.048	-0.012	5.155	-0.451	-0.451	0.000	0.000	0.000	0.000
37	A	65	LEU	0	-0.098	-0.049	2.890	-2.035	-1.395	0.105	-0.187	-0.558	0.000
38	A	66	ASP	-1	-0.790	-0.913	2.292	-8.459	-4.486	4.568	-4.172	-4.369	-0.038
39	A	67	HIS	0	-0.036	0.000	3.783	-0.234	0.103	0.002	-0.077	-0.261	0.000
40	A	68	TYR	0	-0.018	-0.036	3.603	0.421	0.650	0.001	-0.025	-0.204	0.000
41	A	69	ASP	-1	-0.775	-0.865	6.433	0.436	0.436	0.000	0.000	0.000	0.000
42	A	70	SER	0	0.004	-0.003	8.109	0.081	0.081	0.000	0.000	0.000	0.000
43	A	71	ARG	1	0.770	0.858	9.764	-0.116	-0.116	0.000	0.000	0.000	0.000
44	A	72	PHE	0	0.010	-0.004	7.171	0.102	0.102	0.000	0.000	0.000	0.000
45	A	73	PHE	0	0.023	0.016	8.890	0.107	0.107	0.000	0.000	0.000	0.000
46	A	74	LEU	0	-0.040	-0.009	13.757	0.080	0.080	0.000	0.000	0.000	0.000
47	A	75	GLY	0	0.007	0.002	15.629	0.052	0.052	0.000	0.000	0.000	0.000
48	A	76	LEU	0	-0.005	-0.008	14.169	0.044	0.044	0.000	0.000	0.000	0.000
49	A	77	GLY	0	0.033	0.003	16.981	0.032	0.032	0.000	0.000	0.000	0.000
50	A	78	ALA	0	0.024	0.023	19.392	0.038	0.038	0.000	0.000	0.000	0.000
51	A	79	CYS	0	-0.070	-0.031	19.295	0.043	0.043	0.000	0.000	0.000	0.000
52	A	80	ARG	1	0.898	0.943	17.838	0.522	0.522	0.000	0.000	0.000	0.000
53	A	81	GLN	0	0.043	0.023	22.823	0.000	0.000	0.000	0.000	0.000	0.000
54	A	82	ALA	0	-0.071	-0.027	24.839	0.020	0.020	0.000	0.000	0.000	0.000
55	A	83	MET	0	-0.081	-0.030	22.192	0.023	0.023	0.000	0.000	0.000	0.000
56	A	84	GLY	0	0.010	0.012	27.204	0.005	0.005	0.000	0.000	0.000	0.000
57	A	85	GLN	0	-0.035	-0.022	23.565	-0.020	-0.020	0.000	0.000	0.000	0.000
58	A	86	TYR	0	0.055	-0.004	25.175	-0.026	-0.026	0.000	0.000	0.000	0.000
59	A	87	ASP	-1	-0.820	-0.907	25.492	-0.288	-0.288	0.000	0.000	0.000	0.000
60	A	88	LEU	0	-0.036	-0.023	21.520	-0.035	-0.035	0.000	0.000	0.000	0.000
61	A	89	ALA	0	-0.019	-0.008	20.817	-0.049	-0.049	0.000	0.000	0.000	0.000
62	A	90	ILE	0	0.011	-0.008	20.920	-0.028	-0.028	0.000	0.000	0.000	0.000
63	A	91	HIS	0	-0.001	0.021	16.952	0.034	0.034	0.000	0.000	0.000	0.000
64	A	92	SER	0	-0.020	-0.017	16.658	-0.043	-0.043	0.000	0.000	0.000	0.000
65	A	93	TYR	0	-0.068	-0.060	16.356	-0.054	-0.054	0.000	0.000	0.000	0.000
66	A	94	GLU	-1	-0.909	-0.954	18.264	-0.466	-0.466	0.000	0.000	0.000	0.000
67	A	95	GLU	-1	-0.911	-0.964	13.454	-1.078	-1.078	0.000	0.000	0.000	0.000
68	A	96	GLY	0	0.003	-0.015	13.106	-0.121	-0.121	0.000	0.000	0.000	0.000
69	A	97	ALA	0	-0.003	0.000	14.196	0.002	0.002	0.000	0.000	0.000	0.000
70	A	98	VAL	0	-0.047	-0.024	13.069	0.037	0.037	0.000	0.000	0.000	0.000
71	A	99	MET	0	-0.072	-0.013	9.402	-0.105	-0.105	0.000	0.000	0.000	0.000
72	A	100	ASP	-1	-0.884	-0.955	12.118	-0.390	-0.390	0.000	0.000	0.000	0.000
73	A	101	ILE	0	0.005	0.008	14.943	0.072	0.072	0.000	0.000	0.000	0.000
74	A	102	MLY	1	0.905	0.954	17.948	0.354	0.354	0.000	0.000	0.000	0.000
75	A	103	GLU	-1	-0.852	-0.912	17.752	-0.208	-0.208	0.000	0.000	0.000	0.000
76	A	104	PRO	0	0.012	-0.004	19.689	-0.016	-0.016	0.000	0.000	0.000	0.000
77	A	105	ARG	1	0.857	0.917	19.055	0.211	0.211	0.000	0.000	0.000	0.000
78	A	106	PHE	0	0.009	0.034	14.880	0.006	0.006	0.000	0.000	0.000	0.000
79	A	107	PRO	0	0.046	0.017	20.733	0.005	0.005	0.000	0.000	0.000	0.000
80	A	108	PHE	0	-0.015	-0.005	24.003	0.024	0.024	0.000	0.000	0.000	0.000
81	A	109	HIS	1	0.845	0.911	21.757	0.246	0.246	0.000	0.000	0.000	0.000
82	A	110	ALA	0	0.083	0.048	23.157	0.009	0.009	0.000	0.000	0.000	0.000
83	A	111	ALA	0	0.038	0.026	24.991	0.011	0.011	0.000	0.000	0.000	0.000
84	A	112	GLU	-1	-0.824	-0.898	27.414	-0.166	-0.166	0.000	0.000	0.000	0.000
85	A	113	CYS	0	-0.060	-0.020	25.969	0.009	0.009	0.000	0.000	0.000	0.000
86	A	114	LEU	0	0.049	0.027	27.876	0.011	0.011	0.000	0.000	0.000	0.000
87	A	115	LEU	0	-0.028	-0.017	30.434	0.015	0.015	0.000	0.000	0.000	0.000
88	A	116	GLN	0	-0.088	-0.032	31.389	0.016	0.016	0.000	0.000	0.000	0.000
89	A	117	MLY	1	0.866	0.960	28.515	0.247	0.247	0.000	0.000	0.000	0.000
90	A	118	GLY	0	-0.050	-0.016	33.499	0.005	0.005	0.000	0.000	0.000	0.000
91	A	119	GLU	-1	-0.893	-0.951	31.697	-0.213	-0.213	0.000	0.000	0.000	0.000
92	A	120	LEU	0	0.007	-0.029	33.713	-0.005	-0.005	0.000	0.000	0.000	0.000
93	A	121	ALA	0	0.010	0.017	35.198	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	122	GLU	-1	-0.882	-0.945	30.493	-0.237	-0.237	0.000	0.000	0.000	0.000
95	A	123	ALA	0	-0.015	-0.010	30.559	-0.011	-0.011	0.000	0.000	0.000	0.000
96	A	124	GLU	-1	-0.851	-0.939	31.212	-0.145	-0.145	0.000	0.000	0.000	0.000
97	A	125	SER	0	0.002	0.010	30.744	0.002	0.002	0.000	0.000	0.000	0.000
98	A	126	GLY	0	0.028	0.025	27.628	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	127	LEU	0	-0.035	-0.036	27.949	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	128	PHE	0	0.002	-0.005	30.340	0.009	0.009	0.000	0.000	0.000	0.000
101	A	129	LEU	0	0.048	0.045	24.149	0.002	0.002	0.000	0.000	0.000	0.000
102	A	130	ALA	0	0.009	-0.005	25.862	0.000	0.000	0.000	0.000	0.000	0.000
103	A	131	GLN	0	-0.010	-0.013	26.881	0.007	0.007	0.000	0.000	0.000	0.000
104	A	132	GLU	-1	-0.944	-0.978	28.689	-0.184	-0.184	0.000	0.000	0.000	0.000
105	A	133	LEU	0	-0.070	-0.025	22.233	0.006	0.006	0.000	0.000	0.000	0.000
106	A	134	ILE	0	-0.088	-0.037	25.627	0.010	0.010	0.000	0.000	0.000	0.000
107	A	135	ALA	0	0.019	0.006	27.551	0.014	0.014	0.000	0.000	0.000	0.000
108	A	136	ASN	0	-0.048	-0.030	30.267	0.008	0.008	0.000	0.000	0.000	0.000
109	A	137	MLY	1	0.913	0.983	22.500	0.161	0.161	0.000	0.000	0.000	0.000
110	A	138	PRO	0	0.030	-0.006	30.001	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	139	GLU	-1	-0.901	-0.948	24.967	-0.088	-0.088	0.000	0.000	0.000	0.000
112	A	140	PHE	0	-0.004	-0.006	22.470	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	141	MLY	1	0.922	0.966	28.453	0.045	0.045	0.000	0.000	0.000	0.000
114	A	142	GLU	-1	-0.866	-0.950	30.710	-0.066	-0.066	0.000	0.000	0.000	0.000
115	A	143	LEU	0	-0.041	-0.010	25.570	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	144	SER	0	0.019	0.010	29.733	-0.009	-0.009	0.000	0.000	0.000	0.000
117	A	145	THR	0	0.040	0.031	32.028	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	146	ARG	1	0.866	0.917	30.428	0.136	0.136	0.000	0.000	0.000	0.000
119	A	147	VAL	0	0.038	0.020	29.750	-0.003	-0.003	0.000	0.000	0.000	0.000
120	A	148	SER	0	-0.019	-0.026	32.756	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	149	SER	0	-0.048	-0.016	36.180	0.003	0.003	0.000	0.000	0.000	0.000
122	A	150	MET	0	-0.027	-0.011	30.958	0.001	0.001	0.000	0.000	0.000	0.000
123	A	151	LEU	0	0.031	0.021	34.109	0.000	0.000	0.000	0.000	0.000	0.000
124	A	152	GLU	-1	-0.844	-0.924	36.980	-0.089	-0.089	0.000	0.000	0.000	0.000
125	A	153	ALA	0	-0.030	-0.011	38.645	0.004	0.004	0.000	0.000	0.000	0.000
126	A	154	ILE	0	-0.023	-0.020	35.063	0.003	0.003	0.000	0.000	0.000	0.000
127	A	155	MLY	1	0.834	0.926	39.636	0.093	0.093	0.000	0.000	0.000	0.000
128	A	156	LEU	0	-0.025	-0.012	41.962	0.004	0.004	0.000	0.000	0.000	0.000
129	A	157	MLY	1	0.903	0.965	40.727	0.114	0.114	0.000	0.000	0.000	0.000
130	A	158	MLY	1	0.825	0.923	40.015	0.123	0.123	0.000	0.000	0.000	0.000
131	A	159	GLU	-1	-0.917	-0.962	44.069	-0.095	-0.095	0.000	0.000	0.000	0.000
132	A	160	MET	0	-0.050	-0.007	46.969	0.005	0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:29:ASN)