FMO DATABASE

FMODB ID: 2N2NR

Calculation Name: 5X5L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5X5L

Chain ID: A

ChEMBL ID:

UniProt ID: E1A0Z5

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	100
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-810913.880266
FMO2-HF: Nuclear repulsion	769340.090952
FMO2-HF: Total energy	-41573.789315
FMO2-MP2: Total energy	-41693.587421

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:141:LYS)

Summations of interaction energy for fragment #1(A:141:LYS)

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.
-226.973	-225.962	41.949	-19.681	-23.284	-0.215

Interaction energy analysis for fragmet #1(A:141:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.819 / q_NPA : 0.898

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	143	TYR	0	-0.027	-0.056	3.874	-0.186	1.690	-0.023	-0.972	-0.881	0.002
4	A	144	LYS	1	0.881	0.939	6.999	20.772	20.772	0.000	0.000	0.000	0.000
5	A	145	ASN	0	0.011	0.001	10.466	-0.518	-0.518	0.000	0.000	0.000	0.000
6	A	146	ILE	0	0.023	0.018	6.163	0.701	0.701	0.000	0.000	0.000	0.000
7	A	147	GLU	-1	-0.795	-0.879	3.850	-27.077	-26.704	0.001	-0.061	-0.313	0.000
8	A	148	ILE	0	-0.041	-0.019	2.320	0.559	2.880	1.449	-0.793	-2.978	-0.002
9	A	149	ASP	-1	-0.763	-0.869	2.237	-40.717	-38.512	3.074	-2.509	-2.770	-0.035
10	A	150	THR	0	-0.036	-0.047	3.122	-4.173	-3.588	0.044	-0.121	-0.509	-0.001
11	A	151	ASP	-1	-0.972	-0.947	5.835	-30.838	-30.838	0.000	0.000	0.000	0.000
12	A	152	THR	0	0.005	-0.002	9.131	2.299	2.299	0.000	0.000	0.000	0.000
13	A	153	HIS	0	-0.018	-0.008	8.079	2.028	2.028	0.000	0.000	0.000	0.000
14	A	154	SER	0	-0.028	-0.011	7.976	1.645	1.645	0.000	0.000	0.000	0.000
15	A	155	VAL	0	-0.022	-0.023	6.608	-4.638	-4.638	0.000	0.000	0.000	0.000
16	A	156	TYR	0	-0.026	-0.025	6.760	4.173	4.173	0.000	0.000	0.000	0.000
17	A	157	ILE	0	-0.004	0.005	8.803	-1.952	-1.952	0.000	0.000	0.000	0.000
18	A	158	HIS	0	0.019	-0.003	7.712	2.407	2.407	0.000	0.000	0.000	0.000
19	A	159	SER	0	-0.009	-0.012	12.566	1.451	1.451	0.000	0.000	0.000	0.000
20	A	160	GLU	-1	-0.851	-0.916	14.309	-17.007	-17.007	0.000	0.000	0.000	0.000
21	A	161	ASN	0	-0.069	-0.026	15.753	0.852	0.852	0.000	0.000	0.000	0.000
22	A	162	LYS	1	0.868	0.917	15.190	14.787	14.787	0.000	0.000	0.000	0.000
23	A	163	LYS	1	0.834	0.916	7.186	21.863	21.863	0.000	0.000	0.000	0.000
24	A	164	ILE	0	-0.022	0.001	12.611	1.002	1.002	0.000	0.000	0.000	0.000
25	A	165	LEU	0	0.007	0.003	11.427	-1.414	-1.414	0.000	0.000	0.000	0.000
26	A	166	LEU	0	0.012	0.002	11.564	1.128	1.128	0.000	0.000	0.000	0.000
27	A	167	ASN	0	-0.001	0.008	13.341	-1.388	-1.388	0.000	0.000	0.000	0.000
28	A	168	LEU	0	-0.010	-0.004	9.260	0.691	0.691	0.000	0.000	0.000	0.000
29	A	169	THR	0	-0.039	-0.042	13.336	0.770	0.770	0.000	0.000	0.000	0.000
30	A	170	LEU	0	0.044	0.017	10.953	-1.824	-1.824	0.000	0.000	0.000	0.000
31	A	171	THR	0	0.030	0.006	11.134	-2.268	-2.268	0.000	0.000	0.000	0.000
32	A	172	GLU	-1	-0.762	-0.845	10.918	-22.209	-22.209	0.000	0.000	0.000	0.000
33	A	173	TYR	0	-0.004	-0.010	5.516	-4.348	-4.348	0.000	0.000	0.000	0.000
34	A	174	LYS	1	0.826	0.918	6.687	20.048	20.048	0.000	0.000	0.000	0.000
35	A	175	ILE	0	-0.008	-0.010	6.294	-4.535	-4.535	0.000	0.000	0.000	0.000
36	A	176	ILE	0	0.000	-0.005	5.685	-2.496	-2.496	0.000	0.000	0.000	0.000
37	A	177	SER	0	0.026	0.004	2.558	-19.568	-17.387	1.227	-1.383	-2.025	-0.013
38	A	178	PHE	0	0.012	0.018	1.756	-34.238	-38.468	12.616	-4.727	-3.660	-0.051
39	A	179	MET	0	-0.040	-0.024	4.181	2.315	2.420	-0.001	-0.002	-0.103	0.000
40	A	180	ILE	0	-0.039	-0.020	2.214	4.610	3.854	3.637	-0.667	-2.215	-0.002
41	A	181	ASP	-1	-0.806	-0.888	1.968	-138.337	-142.118	19.923	-8.409	-7.732	-0.113
42	A	182	GLN	0	-0.070	-0.042	3.980	10.387	10.519	0.002	-0.037	-0.098	0.000
43	A	183	PRO	0	0.049	0.031	6.689	3.601	3.601	0.000	0.000	0.000	0.000
44	A	184	HIS	0	0.012	-0.007	8.830	1.319	1.319	0.000	0.000	0.000	0.000
45	A	185	LYS	1	0.760	0.879	10.499	28.298	28.298	0.000	0.000	0.000	0.000
46	A	186	VAL	0	-0.038	-0.026	12.381	-0.571	-0.571	0.000	0.000	0.000	0.000
47	A	187	PHE	0	0.032	0.025	7.676	0.701	0.701	0.000	0.000	0.000	0.000
48	A	188	THR	0	0.002	-0.034	12.992	1.028	1.028	0.000	0.000	0.000	0.000
49	A	189	ARG	1	0.805	0.880	14.651	14.906	14.906	0.000	0.000	0.000	0.000
50	A	190	GLY	0	0.087	0.046	15.911	-0.672	-0.672	0.000	0.000	0.000	0.000
51	A	191	GLU	-1	-0.762	-0.833	12.134	-23.519	-23.519	0.000	0.000	0.000	0.000
52	A	192	LEU	0	0.019	-0.001	10.088	-1.621	-1.621	0.000	0.000	0.000	0.000
53	A	193	MET	0	-0.004	-0.002	12.282	-0.905	-0.905	0.000	0.000	0.000	0.000
54	A	194	ASN	0	0.008	-0.002	14.316	-0.214	-0.214	0.000	0.000	0.000	0.000
55	A	195	HIS	0	-0.012	0.013	8.963	-0.487	-0.487	0.000	0.000	0.000	0.000
56	A	196	CYS	0	-0.056	-0.026	9.160	-2.527	-2.527	0.000	0.000	0.000	0.000
57	A	197	MET	0	-0.077	-0.030	11.008	0.735	0.735	0.000	0.000	0.000	0.000
58	A	198	ASN	0	-0.017	-0.009	14.767	-0.303	-0.303	0.000	0.000	0.000	0.000
59	A	199	ASP	-1	-0.826	-0.884	17.213	-17.511	-17.511	0.000	0.000	0.000	0.000
60	A	200	SER	0	-0.066	-0.036	17.828	-0.120	-0.120	0.000	0.000	0.000	0.000
61	A	201	ASP	-1	-0.879	-0.947	19.202	-14.290	-14.290	0.000	0.000	0.000	0.000
62	A	202	ALA	0	-0.027	-0.029	20.544	0.590	0.590	0.000	0.000	0.000	0.000
63	A	203	LEU	0	0.015	-0.002	22.429	0.001	0.001	0.000	0.000	0.000	0.000
64	A	204	GLU	-1	-0.800	-0.925	20.038	-15.949	-15.949	0.000	0.000	0.000	0.000
65	A	205	ARG	1	0.874	0.922	20.018	12.747	12.747	0.000	0.000	0.000	0.000
66	A	206	THR	0	0.028	0.012	19.546	0.049	0.049	0.000	0.000	0.000	0.000
67	A	207	VAL	0	0.071	0.051	14.796	-0.577	-0.577	0.000	0.000	0.000	0.000
68	A	208	ASP	-1	-0.784	-0.837	16.745	-16.258	-16.258	0.000	0.000	0.000	0.000
69	A	209	SER	0	-0.082	-0.047	18.849	-0.111	-0.111	0.000	0.000	0.000	0.000
70	A	210	HIS	0	-0.017	-0.011	14.709	0.072	0.072	0.000	0.000	0.000	0.000
71	A	211	VAL	0	0.039	0.016	13.190	-0.740	-0.740	0.000	0.000	0.000	0.000
72	A	212	SER	0	-0.047	-0.017	15.099	-0.118	-0.118	0.000	0.000	0.000	0.000
73	A	213	LYS	1	0.946	0.971	17.130	15.706	15.706	0.000	0.000	0.000	0.000
74	A	214	LEU	0	0.019	0.017	9.764	0.267	0.267	0.000	0.000	0.000	0.000
75	A	215	ARG	1	0.882	0.944	13.999	17.613	17.613	0.000	0.000	0.000	0.000
76	A	216	LYS	1	0.877	0.947	15.484	14.591	14.591	0.000	0.000	0.000	0.000
77	A	217	LYS	1	0.855	0.900	14.740	19.492	19.492	0.000	0.000	0.000	0.000
78	A	218	LEU	0	-0.010	0.007	10.731	-0.447	-0.447	0.000	0.000	0.000	0.000
79	A	219	GLU	-1	-0.896	-0.966	14.890	-14.765	-14.765	0.000	0.000	0.000	0.000
80	A	220	GLU	-1	-0.960	-0.967	18.462	-15.002	-15.002	0.000	0.000	0.000	0.000
81	A	221	GLN	0	-0.043	-0.022	15.755	0.719	0.719	0.000	0.000	0.000	0.000
82	A	222	GLY	0	-0.007	-0.004	17.165	-0.221	-0.221	0.000	0.000	0.000	0.000
83	A	223	ILE	0	-0.063	-0.027	12.375	0.174	0.174	0.000	0.000	0.000	0.000
84	A	224	PHE	0	0.048	0.011	16.191	-0.467	-0.467	0.000	0.000	0.000	0.000
85	A	225	GLN	0	-0.074	-0.051	17.046	-0.655	-0.655	0.000	0.000	0.000	0.000
86	A	226	MET	0	0.052	0.049	11.279	-0.674	-0.674	0.000	0.000	0.000	0.000
87	A	227	LEU	0	-0.023	-0.019	10.465	1.090	1.090	0.000	0.000	0.000	0.000
88	A	228	ILE	0	0.009	0.031	14.009	1.473	1.473	0.000	0.000	0.000	0.000
89	A	229	ASN	0	0.020	0.001	16.690	-0.901	-0.901	0.000	0.000	0.000	0.000
90	A	230	VAL	0	-0.020	-0.005	17.697	0.612	0.612	0.000	0.000	0.000	0.000
91	A	231	ARG	1	0.964	0.960	20.192	11.196	11.196	0.000	0.000	0.000	0.000
92	A	232	GLY	0	0.015	0.012	23.309	0.344	0.344	0.000	0.000	0.000	0.000
93	A	233	VAL	0	-0.005	0.008	18.395	0.096	0.096	0.000	0.000	0.000	0.000
94	A	234	GLY	0	0.009	-0.014	16.770	-0.364	-0.364	0.000	0.000	0.000	0.000
95	A	235	TYR	0	-0.071	-0.050	13.864	1.238	1.238	0.000	0.000	0.000	0.000
96	A	236	ARG	1	0.950	1.003	12.650	17.223	17.223	0.000	0.000	0.000	0.000
97	A	237	LEU	0	0.006	0.016	7.772	1.258	1.258	0.000	0.000	0.000	0.000
98	A	238	ASP	-1	-0.708	-0.845	10.995	-19.774	-19.774	0.000	0.000	0.000	0.000
99	A	239	ASN	0	-0.068	-0.057	13.156	0.235	0.235	0.000	0.000	0.000	0.000
100	A	240	PRO	0	0.029	0.039	15.894	0.659	0.659	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:141:LYS)