FMO DATABASE

FMODB ID: VQGM1

Calculation Name: 2ZPM-A-Xray372

Preferred Name:

Target Type:

Ligand Name: n-dimethyl-lysine

ligand 3-letter code: MLY

PDB ID: 2ZPM

Chain ID: A

ChEMBL ID:

UniProt ID: P0AEH1

Base Structure: X-ray

Registration Date: 2023-09-23

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	86
LigandCharge	MLY=1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-544350.040431
FMO2-HF: Nuclear repulsion	512576.594303
FMO2-HF: Total energy	-31773.446128
FMO2-MP2: Total energy	-31868.046783

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:224:PRO)

Summations of interaction energy for fragment #1(A:224: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.
-12.267	-2.241	5.642	-5.179	-10.487	-0.033

Interaction energy analysis for fragmet #1(A:224:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / q_NPA : -0.028

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

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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	226	LEU	0	-0.008	-0.001	3.850	0.098	1.644	-0.014	-0.647	-0.884	0.001
4	A	227	GLU	-1	-0.793	-0.855	6.433	1.303	1.303	0.000	0.000	0.000	0.000
5	A	228	ASN	0	-0.027	-0.041	9.114	-0.168	-0.168	0.000	0.000	0.000	0.000
6	A	229	VAL	0	-0.028	-0.009	10.853	-0.036	-0.036	0.000	0.000	0.000	0.000
7	A	230	GLN	0	-0.026	-0.018	13.185	-0.014	-0.014	0.000	0.000	0.000	0.000
8	A	231	PRO	0	0.054	0.029	16.395	-0.042	-0.042	0.000	0.000	0.000	0.000
9	A	232	ASN	0	-0.024	-0.024	19.417	0.005	0.005	0.000	0.000	0.000	0.000
10	A	233	SER	0	-0.001	0.005	16.157	-0.015	-0.015	0.000	0.000	0.000	0.000
11	A	234	ALA	0	0.056	0.022	15.377	-0.020	-0.020	0.000	0.000	0.000	0.000
12	A	235	ALA	0	0.018	0.005	12.085	-0.047	-0.047	0.000	0.000	0.000	0.000
13	A	236	SER	0	-0.029	-0.006	13.775	-0.028	-0.028	0.000	0.000	0.000	0.000
14	A	237	MLY	1	0.776	0.873	16.541	0.129	0.129	0.000	0.000	0.000	0.000
15	A	238	ALA	0	-0.017	-0.001	13.601	0.000	0.000	0.000	0.000	0.000	0.000
16	A	239	GLY	0	0.016	0.022	14.459	-0.052	-0.052	0.000	0.000	0.000	0.000
17	A	240	LEU	0	-0.029	-0.010	8.665	-0.046	-0.046	0.000	0.000	0.000	0.000
18	A	241	GLN	0	-0.038	-0.038	10.905	0.109	0.109	0.000	0.000	0.000	0.000
19	A	242	ALA	0	0.013	0.009	10.348	-0.131	-0.131	0.000	0.000	0.000	0.000
20	A	243	GLY	0	-0.001	-0.002	8.944	0.023	0.023	0.000	0.000	0.000	0.000
21	A	244	ASP	-1	-0.749	-0.827	7.169	-0.932	-0.932	0.000	0.000	0.000	0.000
22	A	245	ARG	1	0.807	0.887	2.891	0.201	1.536	0.165	-0.410	-1.091	-0.001
23	A	246	ILE	0	0.016	0.000	2.690	-0.444	0.975	0.453	-0.569	-1.303	-0.001
24	A	247	VAL	0	-0.003	0.002	2.527	-4.280	-2.315	1.312	-1.401	-1.875	-0.019
25	A	248	MLY	1	0.894	0.937	5.272	1.010	1.097	-0.001	-0.001	-0.085	0.000
26	A	249	VAL	0	0.033	0.017	6.476	-0.009	-0.009	0.000	0.000	0.000	0.000
27	A	250	ASP	-1	-0.795	-0.890	9.181	-0.428	-0.428	0.000	0.000	0.000	0.000
28	A	251	GLY	0	0.035	0.020	12.317	0.069	0.069	0.000	0.000	0.000	0.000
29	A	252	GLN	0	-0.062	-0.038	10.642	0.041	0.041	0.000	0.000	0.000	0.000
30	A	253	PRO	0	0.004	-0.013	7.529	-0.153	-0.153	0.000	0.000	0.000	0.000
31	A	254	LEU	0	-0.021	0.008	2.316	-0.313	0.033	2.038	-0.608	-1.776	-0.002
32	A	255	THR	0	-0.023	-0.022	2.757	-2.948	-1.495	0.430	-0.707	-1.176	-0.009
33	A	256	GLN	0	0.014	0.002	4.749	0.364	0.477	-0.001	-0.013	-0.099	0.000
34	A	257	TRP	0	0.052	0.024	2.238	-2.053	-0.380	1.260	-0.803	-2.130	-0.002
35	A	258	VAL	0	0.046	0.014	4.455	-0.343	-0.254	0.000	-0.020	-0.068	0.000
36	A	259	THR	0	0.040	0.015	6.882	0.014	0.014	0.000	0.000	0.000	0.000
37	A	260	PHE	0	0.054	0.032	4.956	-0.047	-0.047	0.000	0.000	0.000	0.000
38	A	261	VAL	0	-0.013	-0.003	6.828	0.037	0.037	0.000	0.000	0.000	0.000
39	A	262	MET	0	0.015	0.016	9.075	0.026	0.026	0.000	0.000	0.000	0.000
40	A	263	LEU	0	0.004	0.009	9.007	0.003	0.003	0.000	0.000	0.000	0.000
41	A	264	VAL	0	-0.009	-0.005	9.866	0.015	0.015	0.000	0.000	0.000	0.000
42	A	265	ARG	1	0.869	0.938	12.265	-0.077	-0.077	0.000	0.000	0.000	0.000
43	A	266	ASP	-1	-0.830	-0.942	14.860	-0.034	-0.034	0.000	0.000	0.000	0.000
44	A	267	ASN	0	-0.049	-0.021	14.603	-0.009	-0.009	0.000	0.000	0.000	0.000
45	A	268	PRO	0	0.008	-0.002	17.045	-0.024	-0.024	0.000	0.000	0.000	0.000
46	A	269	GLY	0	-0.017	-0.006	18.810	0.007	0.007	0.000	0.000	0.000	0.000
47	A	270	MLY	1	0.840	0.931	15.376	0.343	0.343	0.000	0.000	0.000	0.000
48	A	271	SER	0	-0.001	-0.020	16.596	-0.014	-0.014	0.000	0.000	0.000	0.000
49	A	272	LEU	0	-0.031	0.003	11.045	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	273	ALA	0	0.023	0.009	13.499	-0.013	-0.013	0.000	0.000	0.000	0.000
51	A	274	LEU	0	-0.042	-0.032	7.859	-0.088	-0.088	0.000	0.000	0.000	0.000
52	A	275	GLU	-1	-0.841	-0.885	8.610	-0.649	-0.649	0.000	0.000	0.000	0.000
53	A	276	ILE	0	-0.047	-0.026	6.666	-0.494	-0.494	0.000	0.000	0.000	0.000
54	A	277	GLU	-1	-0.821	-0.887	6.918	-1.214	-1.214	0.000	0.000	0.000	0.000
55	A	278	ARG	1	0.802	0.847	8.340	0.467	0.467	0.000	0.000	0.000	0.000
56	A	279	GLN	0	-0.008	-0.015	11.189	0.102	0.102	0.000	0.000	0.000	0.000
57	A	280	GLY	0	0.011	0.016	11.635	0.066	0.066	0.000	0.000	0.000	0.000
58	A	281	SER	0	-0.002	0.012	12.954	0.010	0.010	0.000	0.000	0.000	0.000
59	A	282	PRO	0	-0.021	-0.006	11.431	-0.116	-0.116	0.000	0.000	0.000	0.000
60	A	283	LEU	0	-0.008	-0.018	11.334	0.134	0.134	0.000	0.000	0.000	0.000
61	A	284	SER	0	0.009	-0.010	11.232	-0.129	-0.129	0.000	0.000	0.000	0.000
62	A	285	LEU	0	-0.038	-0.018	10.628	0.064	0.064	0.000	0.000	0.000	0.000
63	A	286	THR	0	-0.049	-0.036	13.403	0.005	0.005	0.000	0.000	0.000	0.000
64	A	287	LEU	0	-0.003	0.010	10.368	0.023	0.023	0.000	0.000	0.000	0.000
65	A	288	ILE	0	0.024	0.016	14.094	0.001	0.001	0.000	0.000	0.000	0.000
66	A	289	PRO	0	-0.029	-0.003	13.437	0.029	0.029	0.000	0.000	0.000	0.000
67	A	290	GLU	-1	-0.764	-0.860	15.955	-0.111	-0.111	0.000	0.000	0.000	0.000
68	A	291	SER	0	0.013	-0.007	18.501	0.010	0.010	0.000	0.000	0.000	0.000
69	A	292	MLY	1	0.904	0.957	18.183	-0.029	-0.029	0.000	0.000	0.000	0.000
70	A	293	PRO	0	0.041	0.001	22.017	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	294	GLY	0	-0.016	0.018	22.025	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	295	ASN	0	-0.003	-0.017	22.837	0.000	0.000	0.000	0.000	0.000	0.000
73	A	296	GLY	0	0.014	0.022	25.778	0.002	0.002	0.000	0.000	0.000	0.000
74	A	297	MLY	1	0.899	0.955	20.367	0.030	0.030	0.000	0.000	0.000	0.000
75	A	298	ALA	0	-0.002	0.010	23.271	0.009	0.009	0.000	0.000	0.000	0.000
76	A	299	ILE	0	-0.037	-0.025	17.342	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	300	GLY	0	0.021	0.016	16.584	0.001	0.001	0.000	0.000	0.000	0.000
78	A	301	PHE	0	-0.033	-0.039	14.774	0.027	0.027	0.000	0.000	0.000	0.000
79	A	302	VAL	0	0.035	-0.004	10.587	-0.022	-0.022	0.000	0.000	0.000	0.000
80	A	303	GLY	0	0.029	0.019	13.980	-0.032	-0.032	0.000	0.000	0.000	0.000
81	A	304	ILE	0	-0.010	0.004	7.586	-0.023	-0.023	0.000	0.000	0.000	0.000
82	A	305	GLU	-1	-0.838	-0.892	10.464	0.275	0.275	0.000	0.000	0.000	0.000
83	A	306	PRO	0	-0.018	-0.036	6.306	-0.043	-0.043	0.000	0.000	0.000	0.000
84	A	307	MLY	1	0.837	0.914	5.029	-1.729	-1.729	0.000	0.000	0.000	0.000
85	A	308	VAL	0	0.009	0.001	6.886	-0.075	-0.075	0.000	0.000	0.000	0.000
86	A	309	ILE	0	-0.035	-0.011	9.414	0.161	0.161	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:224:PRO)