FMO DATABASE

FMODB ID: 4359N

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	OptHSide
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	-1176576.960497
FMO2-HF: Nuclear repulsion	1122520.050207
FMO2-HF: Total energy	-54056.91029
FMO2-MP2: Total energy	-54212.259236

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.
-25.103	-16.246	6.008	-6.8	-8.064	-0.04

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 : -0.040 / q_NPA : -0.023

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	-0.074	-0.036	3.143	-4.973	-1.255	0.027	-1.890	-1.855	0.004
4	A	32	SER	0	-0.035	-0.021	4.820	-1.009	-1.009	0.000	0.000	0.000	0.000
5	A	33	SER	0	0.021	0.015	6.399	1.079	1.079	0.000	0.000	0.000	0.000
6	A	34	ASP	-1	-0.861	-0.920	8.187	0.546	0.546	0.000	0.000	0.000	0.000
7	A	35	THR	0	0.021	-0.011	9.590	-0.199	-0.199	0.000	0.000	0.000	0.000
8	A	36	LEU	0	0.026	0.015	5.336	-0.301	-0.301	0.000	0.000	0.000	0.000
9	A	37	GLU	-1	-0.774	-0.856	9.391	-0.455	-0.455	0.000	0.000	0.000	0.000
10	A	38	GLN	0	-0.035	-0.016	12.956	-0.077	-0.077	0.000	0.000	0.000	0.000
11	A	39	LEU	0	-0.004	-0.006	9.365	-0.020	-0.020	0.000	0.000	0.000	0.000
12	A	40	TYR	0	0.034	0.021	12.313	-0.043	-0.043	0.000	0.000	0.000	0.000
13	A	41	SER	0	-0.044	-0.019	13.940	0.035	0.035	0.000	0.000	0.000	0.000
14	A	42	LEU	0	-0.031	-0.016	16.195	0.031	0.031	0.000	0.000	0.000	0.000
15	A	43	ALA	0	0.036	0.010	15.216	0.032	0.032	0.000	0.000	0.000	0.000
16	A	44	PHE	0	-0.004	-0.003	17.274	0.029	0.029	0.000	0.000	0.000	0.000
17	A	45	ASN	0	0.023	-0.005	19.382	0.034	0.034	0.000	0.000	0.000	0.000
18	A	46	GLN	0	-0.017	-0.003	18.658	-0.013	-0.013	0.000	0.000	0.000	0.000
19	A	47	TYR	0	0.001	-0.001	20.939	0.027	0.027	0.000	0.000	0.000	0.000
20	A	48	GLN	0	-0.027	-0.010	22.771	0.042	0.042	0.000	0.000	0.000	0.000
21	A	49	SER	0	-0.114	-0.057	25.059	0.036	0.036	0.000	0.000	0.000	0.000
22	A	50	GLY	0	0.011	0.014	26.208	0.019	0.019	0.000	0.000	0.000	0.000
23	A	51	MLY	1	0.915	0.967	23.696	0.260	0.260	0.000	0.000	0.000	0.000
24	A	52	TYR	0	0.054	0.007	22.615	-0.033	-0.033	0.000	0.000	0.000	0.000
25	A	53	GLU	-1	-0.821	-0.927	21.354	-0.483	-0.483	0.000	0.000	0.000	0.000
26	A	54	ASP	-1	-0.936	-0.972	20.091	-0.448	-0.448	0.000	0.000	0.000	0.000
27	A	55	ALA	0	0.017	0.003	18.110	-0.063	-0.063	0.000	0.000	0.000	0.000
28	A	56	HIS	0	0.037	0.031	16.724	-0.103	-0.103	0.000	0.000	0.000	0.000
29	A	57	MLY	1	0.831	0.930	15.809	0.360	0.360	0.000	0.000	0.000	0.000
30	A	58	VAL	0	-0.020	-0.005	13.171	-0.137	-0.137	0.000	0.000	0.000	0.000
31	A	59	PHE	0	0.040	0.003	11.918	-0.167	-0.167	0.000	0.000	0.000	0.000
32	A	60	GLN	0	0.021	0.015	11.553	-0.187	-0.187	0.000	0.000	0.000	0.000
33	A	61	ALA	0	-0.005	-0.003	9.769	-0.299	-0.299	0.000	0.000	0.000	0.000
34	A	62	LEU	0	-0.020	-0.004	7.619	-0.490	-0.490	0.000	0.000	0.000	0.000
35	A	63	CYS	0	-0.065	-0.027	6.953	-0.703	-0.703	0.000	0.000	0.000	0.000
36	A	64	VAL	0	-0.050	-0.017	5.188	-0.516	-0.516	0.000	0.000	0.000	0.000
37	A	65	LEU	0	-0.083	-0.037	2.860	-2.819	-2.037	0.118	-0.222	-0.678	0.000
38	A	66	ASP	-1	-0.790	-0.924	2.324	-16.427	-12.662	5.840	-4.741	-4.864	-0.043
39	A	67	HIS	0	-0.043	0.003	3.400	0.486	0.767	0.020	0.103	-0.404	-0.001
40	A	68	TYR	0	-0.015	-0.024	3.499	1.665	1.976	0.003	-0.050	-0.263	0.000
41	A	69	ASP	-1	-0.784	-0.858	6.283	-0.301	-0.301	0.000	0.000	0.000	0.000
42	A	70	SER	0	0.018	0.002	7.777	0.038	0.038	0.000	0.000	0.000	0.000
43	A	71	ARG	1	0.753	0.812	9.256	0.928	0.928	0.000	0.000	0.000	0.000
44	A	72	PHE	0	0.015	-0.008	6.793	0.364	0.364	0.000	0.000	0.000	0.000
45	A	73	PHE	0	0.038	0.025	8.419	0.183	0.183	0.000	0.000	0.000	0.000
46	A	74	LEU	0	-0.034	-0.011	13.288	0.180	0.180	0.000	0.000	0.000	0.000
47	A	75	GLY	0	0.006	0.003	15.180	0.112	0.112	0.000	0.000	0.000	0.000
48	A	76	LEU	0	0.002	-0.002	13.550	0.107	0.107	0.000	0.000	0.000	0.000
49	A	77	GLY	0	0.029	0.004	16.382	0.087	0.087	0.000	0.000	0.000	0.000
50	A	78	ALA	0	0.029	0.024	18.737	0.085	0.085	0.000	0.000	0.000	0.000
51	A	79	CYS	0	-0.075	-0.037	19.123	0.078	0.078	0.000	0.000	0.000	0.000
52	A	80	ARG	1	0.889	0.946	17.036	0.979	0.979	0.000	0.000	0.000	0.000
53	A	81	GLN	0	0.030	0.017	22.272	0.016	0.016	0.000	0.000	0.000	0.000
54	A	82	ALA	0	-0.072	-0.025	24.271	0.042	0.042	0.000	0.000	0.000	0.000
55	A	83	MET	0	-0.086	-0.034	22.188	0.040	0.040	0.000	0.000	0.000	0.000
56	A	84	GLY	0	0.016	0.015	26.981	0.016	0.016	0.000	0.000	0.000	0.000
57	A	85	GLN	0	-0.037	-0.024	23.242	-0.028	-0.028	0.000	0.000	0.000	0.000
58	A	86	TYR	0	0.042	-0.010	24.229	-0.050	-0.050	0.000	0.000	0.000	0.000
59	A	87	ASP	-1	-0.814	-0.911	24.660	-0.448	-0.448	0.000	0.000	0.000	0.000
60	A	88	LEU	0	-0.010	-0.007	20.733	-0.043	-0.043	0.000	0.000	0.000	0.000
61	A	89	ALA	0	-0.023	-0.009	19.872	-0.085	-0.085	0.000	0.000	0.000	0.000
62	A	90	ILE	0	0.012	-0.005	20.232	-0.049	-0.049	0.000	0.000	0.000	0.000
63	A	91	HIS	0	-0.037	-0.001	15.727	0.079	0.079	0.000	0.000	0.000	0.000
64	A	92	SER	0	-0.019	-0.012	15.686	-0.048	-0.048	0.000	0.000	0.000	0.000
65	A	93	TYR	0	-0.085	-0.076	15.800	-0.098	-0.098	0.000	0.000	0.000	0.000
66	A	94	GLU	-1	-0.923	-0.954	17.976	-0.618	-0.618	0.000	0.000	0.000	0.000
67	A	95	GLU	-1	-0.866	-0.946	12.794	-1.447	-1.447	0.000	0.000	0.000	0.000
68	A	96	GLY	0	0.006	-0.013	12.910	-0.137	-0.137	0.000	0.000	0.000	0.000
69	A	97	ALA	0	-0.008	-0.003	13.993	0.027	0.027	0.000	0.000	0.000	0.000
70	A	98	VAL	0	-0.047	-0.025	13.172	0.082	0.082	0.000	0.000	0.000	0.000
71	A	99	MET	0	-0.068	-0.015	9.343	0.020	0.020	0.000	0.000	0.000	0.000
72	A	100	ASP	-1	-0.885	-0.958	12.075	-0.541	-0.541	0.000	0.000	0.000	0.000
73	A	101	ILE	0	0.000	0.008	14.851	0.063	0.063	0.000	0.000	0.000	0.000
74	A	102	MLY	1	0.909	0.953	17.966	0.356	0.356	0.000	0.000	0.000	0.000
75	A	103	GLU	-1	-0.793	-0.839	17.323	-0.432	-0.432	0.000	0.000	0.000	0.000
76	A	104	PRO	0	0.025	0.004	19.497	-0.023	-0.023	0.000	0.000	0.000	0.000
77	A	105	ARG	1	0.797	0.838	19.142	0.437	0.437	0.000	0.000	0.000	0.000
78	A	106	PHE	0	0.009	0.030	14.536	0.000	0.000	0.000	0.000	0.000	0.000
79	A	107	PRO	0	0.030	0.015	20.484	0.004	0.004	0.000	0.000	0.000	0.000
80	A	108	PHE	0	-0.014	0.000	23.799	0.032	0.032	0.000	0.000	0.000	0.000
81	A	109	HIS	1	0.867	0.910	21.418	0.491	0.491	0.000	0.000	0.000	0.000
82	A	110	ALA	0	0.071	0.044	22.771	0.011	0.011	0.000	0.000	0.000	0.000
83	A	111	ALA	0	0.041	0.028	24.612	0.020	0.020	0.000	0.000	0.000	0.000
84	A	112	GLU	-1	-0.824	-0.881	27.017	-0.333	-0.333	0.000	0.000	0.000	0.000
85	A	113	CYS	0	-0.061	-0.024	25.497	0.008	0.008	0.000	0.000	0.000	0.000
86	A	114	LEU	0	0.061	0.033	27.311	0.016	0.016	0.000	0.000	0.000	0.000
87	A	115	LEU	0	-0.037	-0.018	29.872	0.025	0.025	0.000	0.000	0.000	0.000
88	A	116	GLN	0	-0.083	-0.030	30.702	0.022	0.022	0.000	0.000	0.000	0.000
89	A	117	MLY	1	0.779	0.896	27.497	0.381	0.381	0.000	0.000	0.000	0.000
90	A	118	GLY	0	-0.043	-0.015	32.740	0.012	0.012	0.000	0.000	0.000	0.000
91	A	119	GLU	-1	-0.819	-0.893	30.966	-0.317	-0.317	0.000	0.000	0.000	0.000
92	A	120	LEU	0	0.016	-0.020	33.232	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	121	ALA	0	0.009	0.015	34.886	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	122	GLU	-1	-0.890	-0.950	29.906	-0.329	-0.329	0.000	0.000	0.000	0.000
95	A	123	ALA	0	-0.011	-0.005	30.251	-0.015	-0.015	0.000	0.000	0.000	0.000
96	A	124	GLU	-1	-0.816	-0.902	31.012	-0.205	-0.205	0.000	0.000	0.000	0.000
97	A	125	SER	0	0.000	0.007	30.635	0.007	0.007	0.000	0.000	0.000	0.000
98	A	126	GLY	0	0.030	0.026	27.480	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	127	LEU	0	-0.020	-0.029	27.774	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	128	PHE	0	-0.002	-0.009	30.139	0.010	0.010	0.000	0.000	0.000	0.000
101	A	129	LEU	0	0.044	0.041	24.004	0.005	0.005	0.000	0.000	0.000	0.000
102	A	130	ALA	0	0.019	-0.001	25.682	0.002	0.002	0.000	0.000	0.000	0.000
103	A	131	GLN	0	-0.010	-0.014	26.695	0.011	0.011	0.000	0.000	0.000	0.000
104	A	132	GLU	-1	-0.958	-0.979	28.650	-0.223	-0.223	0.000	0.000	0.000	0.000
105	A	133	LEU	0	-0.068	-0.026	22.131	0.012	0.012	0.000	0.000	0.000	0.000
106	A	134	ILE	0	-0.086	-0.036	25.478	0.008	0.008	0.000	0.000	0.000	0.000
107	A	135	ALA	0	0.015	0.003	27.362	0.019	0.019	0.000	0.000	0.000	0.000
108	A	136	ASN	0	-0.055	-0.034	30.122	0.009	0.009	0.000	0.000	0.000	0.000
109	A	137	MLY	1	0.893	0.961	22.337	0.241	0.241	0.000	0.000	0.000	0.000
110	A	138	PRO	0	0.033	-0.007	29.790	-0.012	-0.012	0.000	0.000	0.000	0.000
111	A	139	GLU	-1	-0.876	-0.923	24.380	-0.197	-0.197	0.000	0.000	0.000	0.000
112	A	140	PHE	0	0.018	0.004	22.031	-0.012	-0.012	0.000	0.000	0.000	0.000
113	A	141	MLY	1	0.890	0.941	28.153	0.135	0.135	0.000	0.000	0.000	0.000
114	A	142	GLU	-1	-0.844	-0.924	30.295	-0.156	-0.156	0.000	0.000	0.000	0.000
115	A	143	LEU	0	-0.026	-0.008	25.201	-0.003	-0.003	0.000	0.000	0.000	0.000
116	A	144	SER	0	0.028	0.016	29.402	-0.008	-0.008	0.000	0.000	0.000	0.000
117	A	145	THR	0	0.006	0.012	31.744	0.005	0.005	0.000	0.000	0.000	0.000
118	A	146	ARG	1	0.844	0.901	30.265	0.283	0.283	0.000	0.000	0.000	0.000
119	A	147	VAL	0	0.043	0.020	29.468	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	148	SER	0	-0.016	-0.019	32.477	0.006	0.006	0.000	0.000	0.000	0.000
121	A	149	SER	0	-0.072	-0.019	35.856	0.005	0.005	0.000	0.000	0.000	0.000
122	A	150	MET	0	-0.006	-0.005	30.239	0.003	0.003	0.000	0.000	0.000	0.000
123	A	151	LEU	0	0.032	0.022	33.832	0.002	0.002	0.000	0.000	0.000	0.000
124	A	152	GLU	-1	-0.797	-0.880	36.738	-0.138	-0.138	0.000	0.000	0.000	0.000
125	A	153	ALA	0	-0.044	-0.017	38.357	0.007	0.007	0.000	0.000	0.000	0.000
126	A	154	ILE	0	-0.032	-0.023	34.736	0.005	0.005	0.000	0.000	0.000	0.000
127	A	155	MLY	1	0.808	0.897	39.395	0.144	0.144	0.000	0.000	0.000	0.000
128	A	156	LEU	0	-0.020	-0.013	41.745	0.008	0.008	0.000	0.000	0.000	0.000
129	A	157	MLY	1	0.906	0.963	40.256	0.186	0.186	0.000	0.000	0.000	0.000
130	A	158	MLY	1	0.776	0.884	39.657	0.178	0.178	0.000	0.000	0.000	0.000
131	A	159	GLU	-1	-0.911	-0.967	43.820	-0.137	-0.137	0.000	0.000	0.000	0.000
132	A	160	MET	0	-0.048	-0.010	46.779	0.008	0.008	0.000	0.000	0.000	0.000

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