FMO DATABASE

FMODB ID: YVG32

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

Total energy (hartree)

FMO2-HF: Electronic energy	-543808.758532
FMO2-HF: Nuclear repulsion	512035.588235
FMO2-HF: Total energy	-31773.170296
FMO2-MP2: Total energy	-31867.793738

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.
-9.669	-0.18	4.209	-4.569	-9.128	-0.017

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 : 0.016 / q_NPA : -0.014

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	-0.019	-0.009	3.592	0.799	2.726	-0.019	-0.770	-1.139	0.001
4	A	227	GLU	-1	-0.768	-0.858	6.132	0.988	0.988	0.000	0.000	0.000	0.000
5	A	228	ASN	0	0.000	-0.014	8.796	-0.153	-0.153	0.000	0.000	0.000	0.000
6	A	229	VAL	0	-0.029	-0.004	10.590	-0.011	-0.011	0.000	0.000	0.000	0.000
7	A	230	GLN	0	-0.068	-0.028	12.861	0.005	0.005	0.000	0.000	0.000	0.000
8	A	231	PRO	0	0.076	0.044	16.109	-0.044	-0.044	0.000	0.000	0.000	0.000
9	A	232	ASN	0	-0.046	-0.036	19.147	0.008	0.008	0.000	0.000	0.000	0.000
10	A	233	SER	0	0.003	-0.002	15.744	0.000	0.000	0.000	0.000	0.000	0.000
11	A	234	ALA	0	0.061	0.028	14.884	-0.026	-0.026	0.000	0.000	0.000	0.000
12	A	235	ALA	0	0.012	-0.006	11.500	-0.054	-0.054	0.000	0.000	0.000	0.000
13	A	236	SER	0	-0.034	-0.010	13.133	-0.048	-0.048	0.000	0.000	0.000	0.000
14	A	237	MLY	1	0.812	0.890	15.898	0.154	0.154	0.000	0.000	0.000	0.000
15	A	238	ALA	0	-0.022	-0.001	13.064	0.001	0.001	0.000	0.000	0.000	0.000
16	A	239	GLY	0	0.010	0.017	14.493	-0.052	-0.052	0.000	0.000	0.000	0.000
17	A	240	LEU	0	-0.031	-0.006	8.253	-0.062	-0.062	0.000	0.000	0.000	0.000
18	A	241	GLN	0	-0.046	-0.037	10.836	0.146	0.146	0.000	0.000	0.000	0.000
19	A	242	ALA	0	0.030	0.006	10.193	-0.205	-0.205	0.000	0.000	0.000	0.000
20	A	243	GLY	0	-0.009	-0.003	8.278	0.029	0.029	0.000	0.000	0.000	0.000
21	A	244	ASP	-1	-0.757	-0.823	7.598	-1.363	-1.363	0.000	0.000	0.000	0.000
22	A	245	ARG	1	0.930	0.967	2.800	0.080	1.378	0.201	-0.389	-1.109	0.000
23	A	246	ILE	0	-0.007	-0.014	2.367	-0.288	1.312	0.657	-0.761	-1.496	-0.001
24	A	247	VAL	0	0.001	0.007	2.845	-3.196	-1.457	0.524	-0.951	-1.311	-0.010
25	A	248	MLY	1	0.899	0.942	5.264	1.073	1.146	-0.001	0.000	-0.071	0.000
26	A	249	VAL	0	0.010	0.009	6.564	-0.056	-0.056	0.000	0.000	0.000	0.000
27	A	250	ASP	-1	-0.826	-0.924	9.250	-0.415	-0.415	0.000	0.000	0.000	0.000
28	A	251	GLY	0	-0.011	0.001	12.316	0.075	0.075	0.000	0.000	0.000	0.000
29	A	252	GLN	0	-0.007	-0.003	10.816	0.051	0.051	0.000	0.000	0.000	0.000
30	A	253	PRO	0	-0.036	-0.031	7.572	-0.176	-0.176	0.000	0.000	0.000	0.000
31	A	254	LEU	0	0.002	0.012	2.455	-0.376	0.277	1.122	-0.452	-1.324	-0.002
32	A	255	THR	0	-0.012	-0.015	3.465	-1.657	-0.956	0.018	-0.339	-0.380	-0.002
33	A	256	GLN	0	-0.008	-0.008	5.412	0.600	0.600	0.000	0.000	0.000	0.000
34	A	257	TRP	0	0.062	0.031	2.231	-1.721	-0.303	1.707	-0.887	-2.238	-0.003
35	A	258	VAL	0	0.052	0.012	4.056	-0.485	-0.405	0.000	-0.020	-0.060	0.000
36	A	259	THR	0	0.044	0.014	7.133	-0.067	-0.067	0.000	0.000	0.000	0.000
37	A	260	PHE	0	0.040	0.029	5.182	-0.157	-0.157	0.000	0.000	0.000	0.000
38	A	261	VAL	0	-0.020	-0.003	7.044	-0.022	-0.022	0.000	0.000	0.000	0.000
39	A	262	MET	0	0.001	-0.002	9.082	-0.025	-0.025	0.000	0.000	0.000	0.000
40	A	263	LEU	0	0.018	0.019	9.201	-0.027	-0.027	0.000	0.000	0.000	0.000
41	A	264	VAL	0	0.000	-0.001	9.950	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	265	ARG	1	0.867	0.946	12.506	-0.205	-0.205	0.000	0.000	0.000	0.000
43	A	266	ASP	-1	-0.864	-0.947	14.909	0.024	0.024	0.000	0.000	0.000	0.000
44	A	267	ASN	0	-0.078	-0.040	15.083	-0.015	-0.015	0.000	0.000	0.000	0.000
45	A	268	PRO	0	0.006	-0.001	17.171	-0.031	-0.031	0.000	0.000	0.000	0.000
46	A	269	GLY	0	-0.028	-0.010	18.781	0.008	0.008	0.000	0.000	0.000	0.000
47	A	270	MLY	1	0.891	0.973	15.870	0.294	0.294	0.000	0.000	0.000	0.000
48	A	271	SER	0	-0.023	-0.026	16.665	-0.020	-0.020	0.000	0.000	0.000	0.000
49	A	272	LEU	0	-0.046	-0.020	11.280	0.008	0.008	0.000	0.000	0.000	0.000
50	A	273	ALA	0	0.031	0.023	13.167	-0.028	-0.028	0.000	0.000	0.000	0.000
51	A	274	LEU	0	-0.033	-0.025	7.646	-0.085	-0.085	0.000	0.000	0.000	0.000
52	A	275	GLU	-1	-0.831	-0.883	9.054	-0.700	-0.700	0.000	0.000	0.000	0.000
53	A	276	ILE	0	-0.041	-0.032	6.952	-0.505	-0.505	0.000	0.000	0.000	0.000
54	A	277	GLU	-1	-0.917	-0.962	7.103	-1.309	-1.309	0.000	0.000	0.000	0.000
55	A	278	ARG	1	0.813	0.848	8.295	0.560	0.560	0.000	0.000	0.000	0.000
56	A	279	GLN	0	-0.018	-0.016	11.099	0.149	0.149	0.000	0.000	0.000	0.000
57	A	280	GLY	0	0.010	0.012	11.427	0.096	0.096	0.000	0.000	0.000	0.000
58	A	281	SER	0	0.003	0.006	12.692	0.058	0.058	0.000	0.000	0.000	0.000
59	A	282	PRO	0	-0.024	0.001	11.523	-0.142	-0.142	0.000	0.000	0.000	0.000
60	A	283	LEU	0	-0.020	-0.024	11.642	0.143	0.143	0.000	0.000	0.000	0.000
61	A	284	SER	0	0.011	-0.013	11.860	-0.126	-0.126	0.000	0.000	0.000	0.000
62	A	285	LEU	0	-0.057	-0.016	10.801	0.065	0.065	0.000	0.000	0.000	0.000
63	A	286	THR	0	-0.020	-0.017	13.234	-0.010	-0.010	0.000	0.000	0.000	0.000
64	A	287	LEU	0	0.001	0.006	9.938	0.027	0.027	0.000	0.000	0.000	0.000
65	A	288	ILE	0	0.014	0.008	13.580	0.011	0.011	0.000	0.000	0.000	0.000
66	A	289	PRO	0	-0.039	-0.002	13.347	0.027	0.027	0.000	0.000	0.000	0.000
67	A	290	GLU	-1	-0.746	-0.853	15.806	-0.140	-0.140	0.000	0.000	0.000	0.000
68	A	291	SER	0	0.011	-0.020	18.315	0.005	0.005	0.000	0.000	0.000	0.000
69	A	292	MLY	1	0.907	0.969	18.199	-0.049	-0.049	0.000	0.000	0.000	0.000
70	A	293	PRO	0	0.070	0.022	22.045	0.000	0.000	0.000	0.000	0.000	0.000
71	A	294	GLY	0	-0.024	0.009	22.086	0.001	0.001	0.000	0.000	0.000	0.000
72	A	295	ASN	0	-0.025	-0.034	22.995	-0.009	-0.009	0.000	0.000	0.000	0.000
73	A	296	GLY	0	0.052	0.031	25.740	0.006	0.006	0.000	0.000	0.000	0.000
74	A	297	MLY	1	0.952	0.975	21.202	-0.018	-0.018	0.000	0.000	0.000	0.000
75	A	298	ALA	0	-0.017	0.009	23.139	0.010	0.010	0.000	0.000	0.000	0.000
76	A	299	ILE	0	-0.043	-0.026	17.428	0.005	0.005	0.000	0.000	0.000	0.000
77	A	300	GLY	0	0.031	0.019	16.481	-0.009	-0.009	0.000	0.000	0.000	0.000
78	A	301	PHE	0	-0.038	-0.042	15.061	0.044	0.044	0.000	0.000	0.000	0.000
79	A	302	VAL	0	0.052	0.003	10.303	-0.021	-0.021	0.000	0.000	0.000	0.000
80	A	303	GLY	0	0.017	0.017	13.683	-0.045	-0.045	0.000	0.000	0.000	0.000
81	A	304	ILE	0	-0.012	0.005	7.230	-0.034	-0.034	0.000	0.000	0.000	0.000
82	A	305	GLU	-1	-0.850	-0.911	10.163	0.264	0.264	0.000	0.000	0.000	0.000
83	A	306	PRO	0	-0.024	-0.041	6.186	-0.090	-0.090	0.000	0.000	0.000	0.000
84	A	307	MLY	1	0.854	0.930	5.032	-1.440	-1.440	0.000	0.000	0.000	0.000
85	A	308	VAL	0	-0.023	-0.016	6.641	0.073	0.073	0.000	0.000	0.000	0.000
86	A	309	ILE	0	-0.033	-0.008	9.142	0.168	0.168	0.000	0.000	0.000	0.000

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