FMO DATABASE

FMODB ID: 179ZZ

Calculation Name: 1BII-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1BII

Chain ID: B

ChEMBL ID:

UniProt ID: P01887

Base Structure: X-ray

Registration Date: 2023-06-26

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	98
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-778178.447036
FMO2-HF: Nuclear repulsion	736194.743516
FMO2-HF: Total energy	-41983.70352
FMO2-MP2: Total energy	-42102.616659

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(B:301:ILE)

Summations of interaction energy for fragment #1(B:301:ILE)

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.
-1.41	2.108	0.182	-1.594	-2.106	-0.002

Interaction energy analysis for fragmet #1(B:301:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : -0.003

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	B	303	LYS	1	0.838	0.924	3.858	-0.795	1.079	-0.020	-0.963	-0.891	0.001
4	B	304	THR	0	0.052	0.025	6.845	-0.386	-0.386	0.000	0.000	0.000	0.000
5	B	305	PRO	0	-0.018	0.011	10.531	0.061	0.061	0.000	0.000	0.000	0.000
6	B	306	GLN	0	-0.033	-0.012	12.622	-0.051	-0.051	0.000	0.000	0.000	0.000
7	B	307	ILE	0	-0.009	-0.020	15.387	-0.031	-0.031	0.000	0.000	0.000	0.000
8	B	308	GLN	0	-0.001	0.003	18.606	0.007	0.007	0.000	0.000	0.000	0.000
9	B	309	VAL	0	-0.004	-0.013	21.937	-0.011	-0.011	0.000	0.000	0.000	0.000
10	B	310	TYR	0	0.025	0.016	23.228	0.000	0.000	0.000	0.000	0.000	0.000
11	B	311	SER	0	0.006	0.004	28.095	-0.004	-0.004	0.000	0.000	0.000	0.000
12	B	312	ARG	1	0.835	0.919	28.034	-0.017	-0.017	0.000	0.000	0.000	0.000
13	B	313	HIS	0	0.042	0.032	31.321	0.004	0.004	0.000	0.000	0.000	0.000
14	B	314	PRO	0	0.067	0.023	34.599	0.001	0.001	0.000	0.000	0.000	0.000
15	B	315	PRO	0	-0.002	0.007	35.020	-0.004	-0.004	0.000	0.000	0.000	0.000
16	B	316	GLU	-1	-0.807	-0.882	37.026	0.021	0.021	0.000	0.000	0.000	0.000
17	B	317	ASN	0	-0.049	-0.043	40.321	-0.001	-0.001	0.000	0.000	0.000	0.000
18	B	318	GLY	0	-0.033	-0.011	41.862	-0.001	-0.001	0.000	0.000	0.000	0.000
19	B	319	LYS	1	0.801	0.881	40.662	-0.021	-0.021	0.000	0.000	0.000	0.000
20	B	320	PRO	0	-0.014	-0.011	39.318	0.001	0.001	0.000	0.000	0.000	0.000
21	B	321	ASN	0	-0.010	-0.006	34.282	0.002	0.002	0.000	0.000	0.000	0.000
22	B	322	ILE	0	-0.008	-0.012	29.951	-0.003	-0.003	0.000	0.000	0.000	0.000
23	B	323	LEU	0	0.007	0.022	28.356	0.005	0.005	0.000	0.000	0.000	0.000
24	B	324	ASN	0	0.006	-0.024	25.328	-0.009	-0.009	0.000	0.000	0.000	0.000
25	B	325	CYS	0	-0.082	-0.038	21.795	-0.003	-0.003	0.000	0.000	0.000	0.000
26	B	326	TYR	0	0.011	0.026	18.344	-0.003	-0.003	0.000	0.000	0.000	0.000
27	B	327	VAL	0	-0.004	-0.009	14.536	0.014	0.014	0.000	0.000	0.000	0.000
28	B	328	THR	0	0.033	0.003	13.872	-0.001	-0.001	0.000	0.000	0.000	0.000
29	B	329	GLN	0	0.042	0.002	10.644	0.167	0.167	0.000	0.000	0.000	0.000
30	B	330	PHE	0	0.002	0.022	8.753	0.229	0.229	0.000	0.000	0.000	0.000
31	B	331	HIS	0	-0.015	-0.022	3.005	-1.218	0.426	0.202	-0.631	-1.215	-0.003
32	B	332	PRO	0	0.042	0.023	5.661	-0.021	-0.021	0.000	0.000	0.000	0.000
33	B	333	PRO	0	0.023	0.006	6.565	0.261	0.261	0.000	0.000	0.000	0.000
34	B	334	HIS	0	-0.015	0.012	9.654	0.105	0.105	0.000	0.000	0.000	0.000
35	B	335	ILE	0	0.017	0.002	11.649	0.005	0.005	0.000	0.000	0.000	0.000
36	B	336	GLU	-1	-0.823	-0.875	14.355	-0.064	-0.064	0.000	0.000	0.000	0.000
37	B	337	ILE	0	0.031	0.005	17.111	0.014	0.014	0.000	0.000	0.000	0.000
38	B	338	GLN	0	-0.071	-0.059	20.374	0.003	0.003	0.000	0.000	0.000	0.000
39	B	339	MET	0	0.045	0.046	24.004	0.006	0.006	0.000	0.000	0.000	0.000
40	B	340	LEU	0	-0.051	-0.027	26.191	-0.007	-0.007	0.000	0.000	0.000	0.000
41	B	341	LYS	1	0.880	0.926	29.307	-0.002	-0.002	0.000	0.000	0.000	0.000
42	B	342	ASN	0	-0.023	-0.023	32.984	-0.001	-0.001	0.000	0.000	0.000	0.000
43	B	343	GLY	0	0.029	0.026	31.076	-0.002	-0.002	0.000	0.000	0.000	0.000
44	B	344	LYS	1	0.926	0.967	30.596	0.007	0.007	0.000	0.000	0.000	0.000
45	B	345	LYS	1	0.900	0.956	24.436	0.050	0.050	0.000	0.000	0.000	0.000
46	B	346	ILE	0	-0.001	0.003	29.499	-0.001	-0.001	0.000	0.000	0.000	0.000
47	B	347	PRO	0	-0.016	-0.019	29.601	-0.003	-0.003	0.000	0.000	0.000	0.000
48	B	348	LYS	1	0.818	0.909	30.461	0.004	0.004	0.000	0.000	0.000	0.000
49	B	349	VAL	0	-0.029	-0.002	25.223	0.005	0.005	0.000	0.000	0.000	0.000
50	B	350	GLU	-1	-0.848	-0.904	26.743	-0.016	-0.016	0.000	0.000	0.000	0.000
51	B	351	MET	0	-0.033	-0.033	19.124	0.008	0.008	0.000	0.000	0.000	0.000
52	B	352	SER	0	-0.023	-0.031	22.286	-0.007	-0.007	0.000	0.000	0.000	0.000
53	B	353	ASP	-1	-0.841	-0.917	19.873	0.015	0.015	0.000	0.000	0.000	0.000
54	B	354	MET	0	-0.018	-0.005	15.669	0.005	0.005	0.000	0.000	0.000	0.000
55	B	355	SER	0	-0.004	0.008	14.980	-0.022	-0.022	0.000	0.000	0.000	0.000
56	B	356	PHE	0	0.006	0.010	10.675	-0.007	-0.007	0.000	0.000	0.000	0.000
57	B	357	SER	0	0.015	0.017	11.640	-0.010	-0.010	0.000	0.000	0.000	0.000
58	B	358	LYS	1	0.924	0.941	12.295	-0.154	-0.154	0.000	0.000	0.000	0.000
59	B	359	ASP	-1	-0.765	-0.848	9.947	0.660	0.660	0.000	0.000	0.000	0.000
60	B	360	TRP	0	-0.029	-0.017	7.257	0.135	0.135	0.000	0.000	0.000	0.000
61	B	361	SER	0	-0.093	-0.042	7.453	-0.141	-0.141	0.000	0.000	0.000	0.000
62	B	362	PHE	0	0.045	-0.003	7.308	-0.097	-0.097	0.000	0.000	0.000	0.000
63	B	363	TYR	0	-0.078	-0.045	10.578	0.069	0.069	0.000	0.000	0.000	0.000
64	B	364	ILE	0	-0.017	-0.006	14.102	-0.040	-0.040	0.000	0.000	0.000	0.000
65	B	365	LEU	0	-0.009	0.002	17.191	0.022	0.022	0.000	0.000	0.000	0.000
66	B	366	ALA	0	0.036	0.029	20.862	-0.012	-0.012	0.000	0.000	0.000	0.000
67	B	367	HIS	0	-0.003	-0.006	22.905	0.015	0.015	0.000	0.000	0.000	0.000
68	B	368	THR	0	-0.016	-0.036	26.647	-0.007	-0.007	0.000	0.000	0.000	0.000
69	B	369	GLU	-1	-0.824	-0.900	30.129	0.002	0.002	0.000	0.000	0.000	0.000
70	B	370	PHE	0	-0.070	-0.043	33.430	-0.001	-0.001	0.000	0.000	0.000	0.000
71	B	371	THR	0	0.034	0.023	35.484	0.001	0.001	0.000	0.000	0.000	0.000
72	B	372	PRO	0	-0.016	0.018	36.196	-0.001	-0.001	0.000	0.000	0.000	0.000
73	B	373	THR	0	0.037	-0.014	38.010	-0.001	-0.001	0.000	0.000	0.000	0.000
74	B	374	GLU	-1	-0.767	-0.864	39.223	0.026	0.026	0.000	0.000	0.000	0.000
75	B	375	THR	0	-0.012	-0.004	41.127	0.001	0.001	0.000	0.000	0.000	0.000
76	B	376	ASP	-1	-0.855	-0.886	36.758	0.008	0.008	0.000	0.000	0.000	0.000
77	B	377	THR	0	0.010	0.011	32.238	0.003	0.003	0.000	0.000	0.000	0.000
78	B	378	TYR	0	0.018	0.000	30.918	-0.005	-0.005	0.000	0.000	0.000	0.000
79	B	379	ALA	0	-0.005	-0.004	27.224	0.005	0.005	0.000	0.000	0.000	0.000
80	B	381	ARG	1	0.917	0.959	21.699	0.025	0.025	0.000	0.000	0.000	0.000
81	B	382	VAL	0	0.015	0.008	15.936	-0.011	-0.011	0.000	0.000	0.000	0.000
82	B	383	LYS	1	0.888	0.927	16.021	0.099	0.099	0.000	0.000	0.000	0.000
83	B	384	HIS	0	0.050	0.021	8.231	0.077	0.077	0.000	0.000	0.000	0.000
84	B	385	ASP	-1	-0.818	-0.914	8.341	-0.432	-0.432	0.000	0.000	0.000	0.000
85	B	386	SER	0	-0.062	-0.032	7.331	0.002	0.002	0.000	0.000	0.000	0.000
86	B	387	MET	0	-0.077	-0.038	8.459	0.116	0.116	0.000	0.000	0.000	0.000
87	B	388	ALA	0	0.016	0.011	12.058	-0.033	-0.033	0.000	0.000	0.000	0.000
88	B	389	GLU	-1	-0.928	-0.956	14.229	-0.025	-0.025	0.000	0.000	0.000	0.000
89	B	390	PRO	0	-0.068	-0.037	16.525	0.010	0.010	0.000	0.000	0.000	0.000
90	B	391	LYS	1	0.989	0.999	17.326	-0.087	-0.087	0.000	0.000	0.000	0.000
91	B	392	THR	0	-0.009	-0.013	18.989	-0.007	-0.007	0.000	0.000	0.000	0.000
92	B	393	VAL	0	-0.029	-0.019	21.308	0.014	0.014	0.000	0.000	0.000	0.000
93	B	394	TYR	0	0.030	0.000	24.182	-0.009	-0.009	0.000	0.000	0.000	0.000
94	B	395	TRP	0	-0.015	-0.022	27.471	0.003	0.003	0.000	0.000	0.000	0.000
95	B	396	ASP	-1	-0.844	-0.913	28.911	0.056	0.056	0.000	0.000	0.000	0.000
96	B	397	ARG	1	0.803	0.885	30.337	-0.029	-0.029	0.000	0.000	0.000	0.000
97	B	398	ASP	-1	-0.902	-0.952	33.050	0.046	0.046	0.000	0.000	0.000	0.000
98	B	399	MET	0	-0.101	-0.037	26.605	0.009	0.009	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:301:ILE)