FMO DATABASE

FMODB ID: 5342Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1179647.33718
FMO2-HF: Nuclear repulsion	1125590.302374
FMO2-HF: Total energy	-54057.034806
FMO2-MP2: Total energy	-54212.369232

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.
-43.849	-41.625	19.959	-10.911	-11.272	-0.093

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 : -0.045 / q_NPA : -0.049

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	-0.061	-0.029	3.058	-5.133	-1.845	0.071	-1.623	-1.735	0.005
4	A	32	SER	0	-0.070	-0.036	4.169	-0.646	-0.215	-0.001	-0.174	-0.256	0.000
5	A	33	SER	0	0.009	-0.014	5.915	0.896	0.896	0.000	0.000	0.000	0.000
6	A	34	ASP	-1	-0.855	-0.915	7.801	-1.310	-1.310	0.000	0.000	0.000	0.000
7	A	35	THR	0	-0.009	-0.007	9.225	-0.096	-0.096	0.000	0.000	0.000	0.000
8	A	36	LEU	0	0.041	0.028	4.503	-0.018	0.095	-0.001	-0.010	-0.102	0.000
9	A	37	GLU	-1	-0.756	-0.853	8.845	-1.738	-1.738	0.000	0.000	0.000	0.000
10	A	38	GLN	0	-0.038	-0.016	12.011	0.151	0.151	0.000	0.000	0.000	0.000
11	A	39	LEU	0	0.014	0.006	9.017	0.163	0.163	0.000	0.000	0.000	0.000
12	A	40	TYR	0	0.033	0.021	11.292	0.120	0.120	0.000	0.000	0.000	0.000
13	A	41	SER	0	-0.025	-0.010	13.057	0.207	0.207	0.000	0.000	0.000	0.000
14	A	42	LEU	0	-0.038	-0.014	15.725	0.131	0.131	0.000	0.000	0.000	0.000
15	A	43	ALA	0	0.050	0.024	14.547	0.122	0.122	0.000	0.000	0.000	0.000
16	A	44	PHE	0	0.015	0.003	16.567	0.131	0.131	0.000	0.000	0.000	0.000
17	A	45	ASN	0	-0.004	-0.016	18.522	0.149	0.149	0.000	0.000	0.000	0.000
18	A	46	GLN	0	-0.018	-0.004	18.097	0.006	0.006	0.000	0.000	0.000	0.000
19	A	47	TYR	0	-0.008	-0.008	19.961	0.072	0.072	0.000	0.000	0.000	0.000
20	A	48	GLN	0	-0.026	-0.016	21.880	0.104	0.104	0.000	0.000	0.000	0.000
21	A	49	SER	0	-0.110	-0.054	24.282	0.069	0.069	0.000	0.000	0.000	0.000
22	A	50	GLY	0	0.014	0.008	25.643	0.032	0.032	0.000	0.000	0.000	0.000
23	A	51	MLY	1	0.910	0.968	23.277	0.555	0.555	0.000	0.000	0.000	0.000
24	A	52	TYR	0	0.037	0.005	21.976	-0.063	-0.063	0.000	0.000	0.000	0.000
25	A	53	GLU	-1	-0.805	-0.918	20.888	-0.723	-0.723	0.000	0.000	0.000	0.000
26	A	54	ASP	-1	-0.934	-0.977	19.844	-0.791	-0.791	0.000	0.000	0.000	0.000
27	A	55	ALA	0	0.017	0.006	17.770	-0.117	-0.117	0.000	0.000	0.000	0.000
28	A	56	HIS	0	0.042	0.039	16.238	-0.130	-0.130	0.000	0.000	0.000	0.000
29	A	57	MLY	1	0.823	0.928	15.516	0.594	0.594	0.000	0.000	0.000	0.000
30	A	58	VAL	0	-0.010	0.000	12.878	-0.204	-0.204	0.000	0.000	0.000	0.000
31	A	59	PHE	0	0.031	-0.001	11.774	-0.340	-0.340	0.000	0.000	0.000	0.000
32	A	60	GLN	0	0.021	0.016	10.953	-0.279	-0.279	0.000	0.000	0.000	0.000
33	A	61	ALA	0	-0.011	-0.007	9.840	-0.281	-0.281	0.000	0.000	0.000	0.000
34	A	62	LEU	0	-0.018	-0.005	7.436	-0.817	-0.817	0.000	0.000	0.000	0.000
35	A	63	CYS	0	-0.055	-0.020	6.149	-1.397	-1.397	0.000	0.000	0.000	0.000
36	A	64	VAL	0	-0.047	-0.016	5.569	0.229	0.229	0.000	0.000	0.000	0.000
37	A	65	LEU	0	-0.070	-0.025	3.190	-2.215	-1.031	0.033	-0.519	-0.698	-0.001
38	A	66	ASP	-1	-0.806	-0.922	1.848	-37.370	-39.866	19.771	-9.193	-8.083	-0.096
39	A	67	HIS	0	-0.028	0.005	2.969	2.977	2.529	0.087	0.617	-0.256	-0.001
40	A	68	TYR	0	0.010	-0.018	4.333	1.928	2.080	-0.001	-0.009	-0.142	0.000
41	A	69	ASP	-1	-0.799	-0.867	6.217	-1.844	-1.844	0.000	0.000	0.000	0.000
42	A	70	SER	0	0.032	0.008	7.762	0.094	0.094	0.000	0.000	0.000	0.000
43	A	71	ARG	1	0.735	0.802	8.687	2.421	2.421	0.000	0.000	0.000	0.000
44	A	72	PHE	0	0.010	-0.003	5.949	0.555	0.555	0.000	0.000	0.000	0.000
45	A	73	PHE	0	0.058	0.032	8.656	0.249	0.249	0.000	0.000	0.000	0.000
46	A	74	LEU	0	-0.027	-0.003	12.916	0.245	0.245	0.000	0.000	0.000	0.000
47	A	75	GLY	0	0.018	0.006	14.706	0.161	0.161	0.000	0.000	0.000	0.000
48	A	76	LEU	0	0.002	0.003	13.156	0.154	0.154	0.000	0.000	0.000	0.000
49	A	77	GLY	0	0.032	0.010	15.846	0.138	0.138	0.000	0.000	0.000	0.000
50	A	78	ALA	0	0.014	0.011	18.539	0.112	0.112	0.000	0.000	0.000	0.000
51	A	79	CYS	0	-0.084	-0.045	18.262	0.092	0.092	0.000	0.000	0.000	0.000
52	A	80	ARG	1	0.865	0.926	16.479	1.182	1.182	0.000	0.000	0.000	0.000
53	A	81	GLN	0	0.008	-0.002	21.906	0.034	0.034	0.000	0.000	0.000	0.000
54	A	82	ALA	0	-0.070	-0.027	23.811	0.055	0.055	0.000	0.000	0.000	0.000
55	A	83	MET	0	-0.075	-0.025	21.652	0.039	0.039	0.000	0.000	0.000	0.000
56	A	84	GLY	0	0.026	0.019	26.353	0.024	0.024	0.000	0.000	0.000	0.000
57	A	85	GLN	0	-0.023	-0.010	22.794	-0.026	-0.026	0.000	0.000	0.000	0.000
58	A	86	TYR	0	0.012	-0.031	24.078	-0.058	-0.058	0.000	0.000	0.000	0.000
59	A	87	ASP	-1	-0.803	-0.907	24.693	-0.471	-0.471	0.000	0.000	0.000	0.000
60	A	88	LEU	0	0.015	0.005	20.795	-0.032	-0.032	0.000	0.000	0.000	0.000
61	A	89	ALA	0	-0.034	-0.009	19.865	-0.105	-0.105	0.000	0.000	0.000	0.000
62	A	90	ILE	0	-0.012	-0.010	20.206	-0.059	-0.059	0.000	0.000	0.000	0.000
63	A	91	HIS	0	-0.024	0.002	16.186	0.067	0.067	0.000	0.000	0.000	0.000
64	A	92	SER	0	-0.008	-0.039	15.300	-0.035	-0.035	0.000	0.000	0.000	0.000
65	A	93	TYR	0	-0.093	-0.068	15.962	-0.127	-0.127	0.000	0.000	0.000	0.000
66	A	94	GLU	-1	-0.915	-0.957	18.196	-0.563	-0.563	0.000	0.000	0.000	0.000
67	A	95	GLU	-1	-0.828	-0.903	13.297	-1.409	-1.409	0.000	0.000	0.000	0.000
68	A	96	GLY	0	0.021	-0.010	13.380	-0.093	-0.093	0.000	0.000	0.000	0.000
69	A	97	ALA	0	-0.034	-0.019	14.447	0.019	0.019	0.000	0.000	0.000	0.000
70	A	98	VAL	0	-0.050	-0.028	13.818	0.109	0.109	0.000	0.000	0.000	0.000
71	A	99	MET	0	-0.069	-0.005	10.117	0.118	0.118	0.000	0.000	0.000	0.000
72	A	100	ASP	-1	-0.901	-0.962	12.474	-0.602	-0.602	0.000	0.000	0.000	0.000
73	A	101	ILE	0	0.003	0.000	15.108	0.033	0.033	0.000	0.000	0.000	0.000
74	A	102	MLY	1	0.903	0.950	18.026	0.337	0.337	0.000	0.000	0.000	0.000
75	A	103	GLU	-1	-0.781	-0.837	17.336	-0.670	-0.670	0.000	0.000	0.000	0.000
76	A	104	PRO	0	0.019	0.004	19.536	-0.015	-0.015	0.000	0.000	0.000	0.000
77	A	105	ARG	1	0.785	0.843	19.037	0.683	0.683	0.000	0.000	0.000	0.000
78	A	106	PHE	0	0.018	0.035	14.693	-0.016	-0.016	0.000	0.000	0.000	0.000
79	A	107	PRO	0	0.011	0.016	20.794	0.011	0.011	0.000	0.000	0.000	0.000
80	A	108	PHE	0	0.015	0.004	24.179	0.034	0.034	0.000	0.000	0.000	0.000
81	A	109	HIS	1	0.869	0.915	21.358	0.665	0.665	0.000	0.000	0.000	0.000
82	A	110	ALA	0	0.062	0.040	23.174	0.009	0.009	0.000	0.000	0.000	0.000
83	A	111	ALA	0	0.039	0.025	24.820	0.027	0.027	0.000	0.000	0.000	0.000
84	A	112	GLU	-1	-0.820	-0.868	26.946	-0.455	-0.455	0.000	0.000	0.000	0.000
85	A	113	CYS	0	-0.056	-0.020	25.293	0.004	0.004	0.000	0.000	0.000	0.000
86	A	114	LEU	0	0.053	0.031	27.835	0.019	0.019	0.000	0.000	0.000	0.000
87	A	115	LEU	0	-0.057	-0.040	30.123	0.029	0.029	0.000	0.000	0.000	0.000
88	A	116	GLN	0	-0.078	-0.025	30.351	0.018	0.018	0.000	0.000	0.000	0.000
89	A	117	MLY	1	0.771	0.894	27.845	0.395	0.395	0.000	0.000	0.000	0.000
90	A	118	GLY	0	-0.004	0.007	33.022	0.019	0.019	0.000	0.000	0.000	0.000
91	A	119	GLU	-1	-0.803	-0.881	31.063	-0.328	-0.328	0.000	0.000	0.000	0.000
92	A	120	LEU	0	-0.009	-0.029	33.556	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	121	ALA	0	0.026	0.020	35.347	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	122	GLU	-1	-0.903	-0.938	30.490	-0.309	-0.309	0.000	0.000	0.000	0.000
95	A	123	ALA	0	0.007	0.000	30.576	-0.016	-0.016	0.000	0.000	0.000	0.000
96	A	124	GLU	-1	-0.823	-0.903	31.478	-0.216	-0.216	0.000	0.000	0.000	0.000
97	A	125	SER	0	-0.017	-0.013	31.421	0.007	0.007	0.000	0.000	0.000	0.000
98	A	126	GLY	0	0.012	0.012	27.979	-0.004	-0.004	0.000	0.000	0.000	0.000
99	A	127	LEU	0	-0.018	-0.028	28.068	-0.018	-0.018	0.000	0.000	0.000	0.000
100	A	128	PHE	0	0.005	-0.002	30.470	0.005	0.005	0.000	0.000	0.000	0.000
101	A	129	LEU	0	0.046	0.037	24.545	0.000	0.000	0.000	0.000	0.000	0.000
102	A	130	ALA	0	-0.011	-0.012	26.120	-0.009	-0.009	0.000	0.000	0.000	0.000
103	A	131	GLN	0	-0.010	-0.022	27.154	0.006	0.006	0.000	0.000	0.000	0.000
104	A	132	GLU	-1	-0.958	-0.978	28.857	-0.218	-0.218	0.000	0.000	0.000	0.000
105	A	133	LEU	0	-0.038	-0.017	22.441	0.013	0.013	0.000	0.000	0.000	0.000
106	A	134	ILE	0	-0.051	-0.025	25.530	-0.006	-0.006	0.000	0.000	0.000	0.000
107	A	135	ALA	0	0.006	0.009	27.471	0.013	0.013	0.000	0.000	0.000	0.000
108	A	136	ASN	0	-0.052	-0.031	29.882	0.009	0.009	0.000	0.000	0.000	0.000
109	A	137	MLY	1	0.853	0.932	22.353	0.334	0.334	0.000	0.000	0.000	0.000
110	A	138	PRO	0	0.023	-0.012	29.534	-0.019	-0.019	0.000	0.000	0.000	0.000
111	A	139	GLU	-1	-0.860	-0.914	23.781	-0.340	-0.340	0.000	0.000	0.000	0.000
112	A	140	PHE	0	0.043	0.016	21.830	-0.027	-0.027	0.000	0.000	0.000	0.000
113	A	141	MLY	1	0.877	0.938	27.834	0.254	0.254	0.000	0.000	0.000	0.000
114	A	142	GLU	-1	-0.815	-0.896	29.984	-0.264	-0.264	0.000	0.000	0.000	0.000
115	A	143	LEU	0	-0.023	-0.004	25.090	0.002	0.002	0.000	0.000	0.000	0.000
116	A	144	SER	0	0.066	0.030	29.261	0.003	0.003	0.000	0.000	0.000	0.000
117	A	145	THR	0	-0.042	-0.004	31.598	0.018	0.018	0.000	0.000	0.000	0.000
118	A	146	ARG	1	0.824	0.889	30.009	0.400	0.400	0.000	0.000	0.000	0.000
119	A	147	VAL	0	0.030	0.008	29.215	0.002	0.002	0.000	0.000	0.000	0.000
120	A	148	SER	0	0.006	-0.017	32.226	0.013	0.013	0.000	0.000	0.000	0.000
121	A	149	SER	0	-0.071	-0.022	35.767	0.009	0.009	0.000	0.000	0.000	0.000
122	A	150	MET	0	-0.010	-0.005	30.235	0.001	0.001	0.000	0.000	0.000	0.000
123	A	151	LEU	0	0.023	0.021	33.781	0.006	0.006	0.000	0.000	0.000	0.000
124	A	152	GLU	-1	-0.802	-0.881	36.655	-0.164	-0.164	0.000	0.000	0.000	0.000
125	A	153	ALA	0	-0.045	-0.024	38.259	0.009	0.009	0.000	0.000	0.000	0.000
126	A	154	ILE	0	-0.040	-0.012	34.739	0.005	0.005	0.000	0.000	0.000	0.000
127	A	155	MLY	1	0.803	0.891	39.402	0.172	0.172	0.000	0.000	0.000	0.000
128	A	156	LEU	0	-0.023	-0.020	41.849	0.010	0.010	0.000	0.000	0.000	0.000
129	A	157	MLY	1	0.902	0.963	40.324	0.217	0.217	0.000	0.000	0.000	0.000
130	A	158	MLY	1	0.791	0.888	39.788	0.189	0.189	0.000	0.000	0.000	0.000
131	A	159	GLU	-1	-0.886	-0.957	43.999	-0.147	-0.147	0.000	0.000	0.000	0.000
132	A	160	MET	0	-0.059	-0.018	46.949	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)