FMO DATABASE

FMODB ID: 5JVMZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-543199.677539
FMO2-HF: Nuclear repulsion	511426.912532
FMO2-HF: Total energy	-31772.765007
FMO2-MP2: Total energy	-31867.414273

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.
-11.465	-2.031	6.934	-5.453	-10.913	-0.021

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 : 0.015 / q_NPA : -0.007

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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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	-0.024	-0.010	3.463	0.289	2.507	-0.024	-0.893	-1.300	0.002
4	A	227	GLU	-1	-0.865	-0.927	6.145	0.413	0.413	0.000	0.000	0.000	0.000
5	A	228	ASN	0	-0.013	-0.019	8.830	-0.120	-0.120	0.000	0.000	0.000	0.000
6	A	229	VAL	0	-0.014	0.004	10.588	-0.015	-0.015	0.000	0.000	0.000	0.000
7	A	230	GLN	0	-0.013	-0.002	12.852	0.022	0.022	0.000	0.000	0.000	0.000
8	A	231	PRO	0	0.070	0.042	16.096	-0.039	-0.039	0.000	0.000	0.000	0.000
9	A	232	ASN	0	-0.035	-0.031	19.131	0.009	0.009	0.000	0.000	0.000	0.000
10	A	233	SER	0	0.006	0.005	15.710	0.003	0.003	0.000	0.000	0.000	0.000
11	A	234	ALA	0	0.049	0.017	14.923	-0.026	-0.026	0.000	0.000	0.000	0.000
12	A	235	ALA	0	0.018	-0.003	11.500	-0.050	-0.050	0.000	0.000	0.000	0.000
13	A	236	SER	0	-0.036	-0.008	13.146	-0.049	-0.049	0.000	0.000	0.000	0.000
14	A	237	MLY	1	0.837	0.895	15.909	0.179	0.179	0.000	0.000	0.000	0.000
15	A	238	ALA	0	-0.020	0.001	13.054	0.005	0.005	0.000	0.000	0.000	0.000
16	A	239	GLY	0	0.003	0.012	14.529	-0.048	-0.048	0.000	0.000	0.000	0.000
17	A	240	LEU	0	-0.043	-0.014	8.264	-0.071	-0.071	0.000	0.000	0.000	0.000
18	A	241	GLN	0	-0.041	-0.029	10.880	0.152	0.152	0.000	0.000	0.000	0.000
19	A	242	ALA	0	0.041	0.010	10.193	-0.227	-0.227	0.000	0.000	0.000	0.000
20	A	243	GLY	0	-0.017	-0.006	8.181	0.053	0.053	0.000	0.000	0.000	0.000
21	A	244	ASP	-1	-0.762	-0.844	7.670	-1.449	-1.449	0.000	0.000	0.000	0.000
22	A	245	ARG	1	0.942	0.974	2.446	-0.358	0.246	2.711	-0.816	-2.499	0.000
23	A	246	ILE	0	0.009	-0.005	2.335	-0.764	1.189	0.846	-0.998	-1.801	-0.003
24	A	247	VAL	0	-0.002	0.006	2.812	-3.407	-1.622	0.862	-1.093	-1.554	-0.012
25	A	248	MLY	1	0.902	0.944	5.241	1.055	1.126	-0.001	0.000	-0.069	0.000
26	A	249	VAL	0	0.005	0.002	6.582	-0.083	-0.083	0.000	0.000	0.000	0.000
27	A	250	ASP	-1	-0.826	-0.919	9.308	-0.352	-0.352	0.000	0.000	0.000	0.000
28	A	251	GLY	0	-0.019	-0.003	12.325	0.075	0.075	0.000	0.000	0.000	0.000
29	A	252	GLN	0	-0.017	-0.007	10.838	0.050	0.050	0.000	0.000	0.000	0.000
30	A	253	PRO	0	-0.042	-0.035	7.564	-0.176	-0.176	0.000	0.000	0.000	0.000
31	A	254	LEU	0	0.009	0.016	2.501	-0.278	0.352	0.937	-0.401	-1.166	-0.002
32	A	255	THR	0	-0.017	-0.020	3.747	-1.127	-0.726	0.004	-0.156	-0.250	-0.001
33	A	256	GLN	0	-0.002	-0.001	5.818	0.617	0.617	0.000	0.000	0.000	0.000
34	A	257	TRP	0	0.061	0.025	2.465	-2.083	-0.478	1.600	-1.070	-2.135	-0.005
35	A	258	VAL	0	0.051	0.014	4.265	-0.645	-0.600	0.000	-0.018	-0.027	0.000
36	A	259	THR	0	0.042	0.016	7.209	-0.144	-0.144	0.000	0.000	0.000	0.000
37	A	260	PHE	0	0.034	0.024	5.334	-0.227	-0.227	0.000	0.000	0.000	0.000
38	A	261	VAL	0	-0.026	-0.003	7.317	-0.079	-0.079	0.000	0.000	0.000	0.000
39	A	262	MET	0	-0.002	-0.008	9.411	-0.057	-0.057	0.000	0.000	0.000	0.000
40	A	263	LEU	0	0.016	0.022	9.274	-0.043	-0.043	0.000	0.000	0.000	0.000
41	A	264	VAL	0	0.006	0.000	9.945	-0.024	-0.024	0.000	0.000	0.000	0.000
42	A	265	ARG	1	0.878	0.948	12.519	-0.252	-0.252	0.000	0.000	0.000	0.000
43	A	266	ASP	-1	-0.854	-0.938	15.161	0.068	0.068	0.000	0.000	0.000	0.000
44	A	267	ASN	0	-0.103	-0.052	15.010	-0.011	-0.011	0.000	0.000	0.000	0.000
45	A	268	PRO	0	0.005	0.002	17.196	-0.035	-0.035	0.000	0.000	0.000	0.000
46	A	269	GLY	0	-0.026	-0.015	18.800	0.009	0.009	0.000	0.000	0.000	0.000
47	A	270	MLY	1	0.934	0.982	16.874	0.211	0.211	0.000	0.000	0.000	0.000
48	A	271	SER	0	-0.019	-0.023	16.702	-0.023	-0.023	0.000	0.000	0.000	0.000
49	A	272	LEU	0	-0.043	-0.017	11.123	0.013	0.013	0.000	0.000	0.000	0.000
50	A	273	ALA	0	0.029	0.025	13.217	-0.038	-0.038	0.000	0.000	0.000	0.000
51	A	274	LEU	0	-0.034	-0.027	7.722	-0.072	-0.072	0.000	0.000	0.000	0.000
52	A	275	GLU	-1	-0.844	-0.895	9.103	-0.687	-0.687	0.000	0.000	0.000	0.000
53	A	276	ILE	0	-0.035	-0.033	6.769	-0.494	-0.494	0.000	0.000	0.000	0.000
54	A	277	GLU	-1	-0.942	-0.973	6.691	-1.154	-1.154	0.000	0.000	0.000	0.000
55	A	278	ARG	1	0.833	0.873	7.814	0.586	0.586	0.000	0.000	0.000	0.000
56	A	279	GLN	0	-0.022	-0.018	10.614	0.166	0.166	0.000	0.000	0.000	0.000
57	A	280	GLY	0	0.005	0.010	11.023	0.103	0.103	0.000	0.000	0.000	0.000
58	A	281	SER	0	0.008	0.003	12.338	0.067	0.067	0.000	0.000	0.000	0.000
59	A	282	PRO	0	-0.017	0.009	11.197	-0.148	-0.148	0.000	0.000	0.000	0.000
60	A	283	LEU	0	-0.024	-0.027	11.302	0.139	0.139	0.000	0.000	0.000	0.000
61	A	284	SER	0	0.015	0.001	11.542	-0.119	-0.119	0.000	0.000	0.000	0.000
62	A	285	LEU	0	-0.048	-0.013	10.708	0.058	0.058	0.000	0.000	0.000	0.000
63	A	286	THR	0	-0.019	-0.014	13.288	0.000	0.000	0.000	0.000	0.000	0.000
64	A	287	LEU	0	0.001	0.004	9.850	0.020	0.020	0.000	0.000	0.000	0.000
65	A	288	ILE	0	0.010	0.007	13.618	0.019	0.019	0.000	0.000	0.000	0.000
66	A	289	PRO	0	-0.044	-0.003	13.365	0.021	0.021	0.000	0.000	0.000	0.000
67	A	290	GLU	-1	-0.768	-0.863	15.825	-0.157	-0.157	0.000	0.000	0.000	0.000
68	A	291	SER	0	0.014	-0.011	18.323	0.012	0.012	0.000	0.000	0.000	0.000
69	A	292	MLY	1	0.904	0.962	18.436	-0.031	-0.031	0.000	0.000	0.000	0.000
70	A	293	PRO	0	0.066	0.021	22.019	0.003	0.003	0.000	0.000	0.000	0.000
71	A	294	GLY	0	-0.020	0.011	22.043	0.003	0.003	0.000	0.000	0.000	0.000
72	A	295	ASN	0	-0.021	-0.032	22.950	-0.012	-0.012	0.000	0.000	0.000	0.000
73	A	296	GLY	0	0.051	0.032	25.699	0.008	0.008	0.000	0.000	0.000	0.000
74	A	297	MLY	1	0.948	0.971	22.192	-0.044	-0.044	0.000	0.000	0.000	0.000
75	A	298	ALA	0	-0.015	0.009	23.329	0.010	0.010	0.000	0.000	0.000	0.000
76	A	299	ILE	0	-0.046	-0.025	17.377	0.008	0.008	0.000	0.000	0.000	0.000
77	A	300	GLY	0	0.034	0.024	16.491	-0.014	-0.014	0.000	0.000	0.000	0.000
78	A	301	PHE	0	-0.051	-0.050	15.054	0.044	0.044	0.000	0.000	0.000	0.000
79	A	302	VAL	0	0.060	0.006	10.314	-0.019	-0.019	0.000	0.000	0.000	0.000
80	A	303	GLY	0	0.021	0.021	13.684	-0.049	-0.049	0.000	0.000	0.000	0.000
81	A	304	ILE	0	-0.013	0.004	7.170	-0.041	-0.041	0.000	0.000	0.000	0.000
82	A	305	GLU	-1	-0.918	-0.947	10.166	0.176	0.176	0.000	0.000	0.000	0.000
83	A	306	PRO	0	-0.022	-0.044	6.201	-0.140	-0.140	0.000	0.000	0.000	0.000
84	A	307	MLY	1	0.959	1.003	4.751	-1.020	-0.898	-0.001	-0.008	-0.112	0.000
85	A	308	VAL	0	-0.007	-0.002	6.692	0.225	0.225	0.000	0.000	0.000	0.000
86	A	309	ILE	0	-0.038	-0.008	9.167	0.145	0.145	0.000	0.000	0.000	0.000

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