FMO DATABASE

FMODB ID: MN3NZ

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-806503.942842
FMO2-HF: Nuclear repulsion	764932.43796
FMO2-HF: Total energy	-41571.504882
FMO2-MP2: Total energy	-41691.39423

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.
-211.682	-205.023	32.072	-18.496	-20.236	-0.173

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 : 0.893 / q_NPA : 0.952

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	-0.031	-0.068	3.823	-0.136	2.240	-0.025	-1.244	-1.107	0.006
4	A	144	LYS	1	0.862	0.919	6.750	21.290	21.290	0.000	0.000	0.000	0.000
5	A	145	ASN	0	0.073	0.043	10.148	0.520	0.520	0.000	0.000	0.000	0.000
6	A	146	ILE	0	0.017	0.012	6.035	1.087	1.087	0.000	0.000	0.000	0.000
7	A	147	GLU	-1	-0.902	-0.952	3.700	-32.047	-31.693	0.001	-0.065	-0.291	0.000
8	A	148	ILE	0	-0.029	-0.017	2.660	2.153	4.142	0.418	-0.509	-1.899	-0.001
9	A	149	ASP	-1	-0.833	-0.911	2.304	-44.256	-41.344	2.552	-2.586	-2.879	-0.036
10	A	150	THR	0	-0.038	-0.049	3.105	-2.012	-1.259	0.079	-0.171	-0.660	-0.001
11	A	151	ASP	-1	-0.998	-0.984	5.799	-27.663	-27.663	0.000	0.000	0.000	0.000
12	A	152	THR	0	0.050	0.029	8.462	1.661	1.661	0.000	0.000	0.000	0.000
13	A	153	HIS	0	-0.058	-0.029	8.545	1.382	1.382	0.000	0.000	0.000	0.000
14	A	154	SER	0	-0.047	-0.007	8.269	2.498	2.498	0.000	0.000	0.000	0.000
15	A	155	VAL	0	0.002	-0.006	7.011	-3.942	-3.942	0.000	0.000	0.000	0.000
16	A	156	TYR	0	0.019	-0.009	7.353	4.216	4.216	0.000	0.000	0.000	0.000
17	A	157	ILE	0	-0.002	-0.002	9.208	-1.891	-1.891	0.000	0.000	0.000	0.000
18	A	158	HIS	0	-0.008	0.002	7.283	2.813	2.813	0.000	0.000	0.000	0.000
19	A	159	SER	0	-0.005	-0.013	12.464	1.570	1.570	0.000	0.000	0.000	0.000
20	A	160	GLU	-1	-0.887	-0.940	14.258	-17.438	-17.438	0.000	0.000	0.000	0.000
21	A	161	ASN	0	-0.082	-0.032	15.366	0.931	0.931	0.000	0.000	0.000	0.000
22	A	162	LYS	1	0.864	0.915	15.380	15.031	15.031	0.000	0.000	0.000	0.000
23	A	163	LYS	1	0.928	0.983	8.342	20.694	20.694	0.000	0.000	0.000	0.000
24	A	164	ILE	0	-0.005	-0.001	13.052	0.724	0.724	0.000	0.000	0.000	0.000
25	A	165	LEU	0	-0.002	0.007	11.446	-1.511	-1.511	0.000	0.000	0.000	0.000
26	A	166	LEU	0	-0.005	-0.005	11.367	1.261	1.261	0.000	0.000	0.000	0.000
27	A	167	ASN	0	-0.008	0.006	13.724	-1.220	-1.220	0.000	0.000	0.000	0.000
28	A	168	LEU	0	-0.008	-0.007	9.724	0.590	0.590	0.000	0.000	0.000	0.000
29	A	169	THR	0	0.017	0.012	13.813	0.753	0.753	0.000	0.000	0.000	0.000
30	A	170	LEU	0	0.050	0.020	11.121	-1.936	-1.936	0.000	0.000	0.000	0.000
31	A	171	THR	0	0.033	-0.004	11.061	-2.223	-2.223	0.000	0.000	0.000	0.000
32	A	172	GLU	-1	-0.825	-0.904	10.878	-21.890	-21.890	0.000	0.000	0.000	0.000
33	A	173	TYR	0	0.044	0.024	5.688	-3.329	-3.329	0.000	0.000	0.000	0.000
34	A	174	LYS	1	0.941	0.972	6.814	19.802	19.802	0.000	0.000	0.000	0.000
35	A	175	ILE	0	0.009	-0.001	6.194	-4.764	-4.764	0.000	0.000	0.000	0.000
36	A	176	ILE	0	0.005	0.001	6.066	-2.375	-2.375	0.000	0.000	0.000	0.000
37	A	177	SER	0	0.008	-0.001	2.512	-19.263	-17.208	1.002	-1.294	-1.763	-0.013
38	A	178	PHE	0	0.013	0.030	1.657	-37.206	-44.555	17.560	-6.495	-3.715	-0.058
39	A	179	MET	0	-0.043	-0.032	4.252	1.767	1.877	-0.001	-0.003	-0.106	0.000
40	A	180	ILE	0	-0.044	-0.017	2.012	5.142	2.346	6.947	-1.234	-2.917	-0.003
41	A	181	ASP	-1	-0.850	-0.916	2.257	-115.113	-108.959	3.538	-4.880	-4.812	-0.067
42	A	182	GLN	0	-0.052	-0.032	4.014	7.834	7.935	0.001	-0.015	-0.087	0.000
43	A	183	PRO	0	0.047	0.030	6.984	2.514	2.514	0.000	0.000	0.000	0.000
44	A	184	HIS	0	0.001	-0.015	8.751	1.418	1.418	0.000	0.000	0.000	0.000
45	A	185	LYS	1	0.783	0.916	10.759	27.511	27.511	0.000	0.000	0.000	0.000
46	A	186	VAL	0	-0.027	-0.027	12.485	-0.560	-0.560	0.000	0.000	0.000	0.000
47	A	187	PHE	0	0.035	0.022	7.945	0.974	0.974	0.000	0.000	0.000	0.000
48	A	188	THR	0	0.024	0.006	13.251	1.149	1.149	0.000	0.000	0.000	0.000
49	A	189	ARG	1	0.851	0.886	14.753	14.420	14.420	0.000	0.000	0.000	0.000
50	A	190	GLY	0	0.089	0.045	16.207	-0.486	-0.486	0.000	0.000	0.000	0.000
51	A	191	GLU	-1	-0.830	-0.907	12.321	-23.044	-23.044	0.000	0.000	0.000	0.000
52	A	192	LEU	0	0.025	-0.011	10.198	-1.485	-1.485	0.000	0.000	0.000	0.000
53	A	193	MET	0	-0.028	-0.017	12.416	-0.880	-0.880	0.000	0.000	0.000	0.000
54	A	194	ASN	0	0.020	0.002	14.545	0.185	0.185	0.000	0.000	0.000	0.000
55	A	195	HIS	0	-0.031	0.007	8.940	-0.621	-0.621	0.000	0.000	0.000	0.000
56	A	196	CYS	0	-0.061	-0.028	9.132	-3.274	-3.274	0.000	0.000	0.000	0.000
57	A	197	MET	0	-0.085	-0.032	11.011	0.494	0.494	0.000	0.000	0.000	0.000
58	A	198	ASN	0	-0.095	0.582	14.761	-0.161	-0.161	0.000	0.000	0.000	0.000
59	A	199	ASP	-1	-0.447	-1.036	16.211	-18.939	-18.939	0.000	0.000	0.000	0.000
60	A	200	SER	0	-0.347	-0.511	17.055	1.282	1.282	0.000	0.000	0.000	0.000
61	A	201	ASP	-1	-0.911	-0.923	19.139	-13.918	-13.918	0.000	0.000	0.000	0.000
62	A	202	ALA	0	-0.079	-0.026	20.909	0.637	0.637	0.000	0.000	0.000	0.000
63	A	203	LEU	0	0.006	-0.012	22.674	0.029	0.029	0.000	0.000	0.000	0.000
64	A	204	GLU	-1	-0.846	-0.945	20.469	-15.251	-15.251	0.000	0.000	0.000	0.000
65	A	205	ARG	1	0.847	0.908	20.343	12.410	12.410	0.000	0.000	0.000	0.000
66	A	206	THR	0	0.041	0.023	19.411	0.004	0.004	0.000	0.000	0.000	0.000
67	A	207	VAL	0	0.054	0.044	15.090	-0.588	-0.588	0.000	0.000	0.000	0.000
68	A	208	ASP	-1	-0.737	-0.848	16.780	-16.042	-16.042	0.000	0.000	0.000	0.000
69	A	209	SER	0	-0.086	-0.042	18.673	-0.065	-0.065	0.000	0.000	0.000	0.000
70	A	210	HIS	0	0.019	-0.001	14.792	0.031	0.031	0.000	0.000	0.000	0.000
71	A	211	VAL	0	0.032	0.027	13.431	-0.795	-0.795	0.000	0.000	0.000	0.000
72	A	212	SER	0	-0.064	-0.030	15.348	-0.155	-0.155	0.000	0.000	0.000	0.000
73	A	213	LYS	1	0.962	0.974	17.720	15.071	15.071	0.000	0.000	0.000	0.000
74	A	214	LEU	0	0.032	0.031	10.338	0.251	0.251	0.000	0.000	0.000	0.000
75	A	215	ARG	1	0.896	0.938	14.715	17.238	17.238	0.000	0.000	0.000	0.000
76	A	216	LYS	1	0.902	0.950	16.147	14.096	14.096	0.000	0.000	0.000	0.000
77	A	217	LYS	1	0.867	0.913	15.389	19.147	19.147	0.000	0.000	0.000	0.000
78	A	218	LEU	0	-0.003	0.000	11.104	-0.196	-0.196	0.000	0.000	0.000	0.000
79	A	219	GLU	-1	-0.912	-0.967	15.250	-14.694	-14.694	0.000	0.000	0.000	0.000
80	A	220	GLU	-1	-1.006	-0.995	18.816	-14.598	-14.598	0.000	0.000	0.000	0.000
81	A	221	GLN	0	-0.037	-0.008	15.772	0.706	0.706	0.000	0.000	0.000	0.000
82	A	222	GLY	0	-0.023	-0.014	17.341	-0.286	-0.286	0.000	0.000	0.000	0.000
83	A	223	ILE	0	-0.052	-0.013	12.645	-0.153	-0.153	0.000	0.000	0.000	0.000
84	A	224	PHE	0	0.050	0.015	16.592	-0.189	-0.189	0.000	0.000	0.000	0.000
85	A	225	GLN	0	-0.102	-0.069	17.432	-0.595	-0.595	0.000	0.000	0.000	0.000
86	A	226	MET	0	0.121	0.085	11.153	-1.228	-1.228	0.000	0.000	0.000	0.000
87	A	227	LEU	0	-0.045	-0.026	11.395	1.059	1.059	0.000	0.000	0.000	0.000
88	A	228	ILE	0	0.021	0.045	14.557	1.452	1.452	0.000	0.000	0.000	0.000
89	A	229	ASN	0	0.004	-0.022	16.821	-0.882	-0.882	0.000	0.000	0.000	0.000
90	A	230	VAL	0	-0.023	0.000	17.554	0.582	0.582	0.000	0.000	0.000	0.000
91	A	231	ARG	1	0.972	0.961	20.373	11.300	11.300	0.000	0.000	0.000	0.000
92	A	232	GLY	0	-0.001	0.000	23.468	0.257	0.257	0.000	0.000	0.000	0.000
93	A	233	VAL	0	0.004	0.021	19.239	0.117	0.117	0.000	0.000	0.000	0.000
94	A	234	GLY	0	-0.008	-0.023	17.178	-0.379	-0.379	0.000	0.000	0.000	0.000
95	A	235	TYR	0	-0.055	-0.020	14.056	1.220	1.220	0.000	0.000	0.000	0.000
96	A	236	ARG	1	0.961	1.000	13.034	16.798	16.798	0.000	0.000	0.000	0.000
97	A	237	LEU	0	0.007	0.031	8.281	1.392	1.392	0.000	0.000	0.000	0.000
98	A	238	ASP	-1	-0.726	-0.843	11.468	-19.883	-19.883	0.000	0.000	0.000	0.000
99	A	239	ASN	0	-0.070	-0.028	13.551	-0.132	-0.132	0.000	0.000	0.000	0.000
100	A	240	PRO	0	0.028	0.015	16.483	0.549	0.549	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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