FMO DATABASE

FMODB ID: 6674Z

Calculation Name: 2BW3-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2BW3

Chain ID: B

ChEMBL ID:

UniProt ID: Q25438

Base Structure: X-ray

Registration Date: 2023-03-13

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	84
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-456238.988396
FMO2-HF: Nuclear repulsion	422790.608747
FMO2-HF: Total energy	-33448.37965
FMO2-MP2: Total energy	-33543.179454

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:76:SER)

Summations of interaction energy for fragment #1(B:76:SER)

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.
-0.773	1.011	-0.012	-0.906	-0.866	0.004

Interaction energy analysis for fragmet #1(B:76:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : 0.005

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	78	MET	0	0.002	0.009	3.883	-0.034	1.621	-0.011	-0.896	-0.748	0.004
4	B	79	GLN	0	-0.024	-0.017	4.968	0.493	0.622	-0.001	-0.010	-0.118	0.000
5	B	80	SER	0	0.008	-0.008	8.405	-0.135	-0.135	0.000	0.000	0.000	0.000
6	B	81	ARG	1	0.920	0.957	10.722	-0.032	-0.032	0.000	0.000	0.000	0.000
7	B	82	GLU	-1	-0.882	-0.928	8.459	-1.109	-1.109	0.000	0.000	0.000	0.000
8	B	83	LEU	0	-0.011	-0.009	5.239	0.219	0.219	0.000	0.000	0.000	0.000
9	B	84	LYS	1	0.960	0.971	8.993	0.083	0.083	0.000	0.000	0.000	0.000
10	B	85	THR	0	0.032	0.027	11.279	-0.021	-0.021	0.000	0.000	0.000	0.000
11	B	86	VAL	0	0.014	0.009	12.838	0.057	0.057	0.000	0.000	0.000	0.000
12	B	87	SER	0	0.010	-0.029	15.813	-0.038	-0.038	0.000	0.000	0.000	0.000
13	B	88	ALA	0	0.018	-0.005	18.321	-0.017	-0.017	0.000	0.000	0.000	0.000
14	B	89	ASP	-1	-0.800	-0.883	20.202	-0.164	-0.164	0.000	0.000	0.000	0.000
15	B	90	CYS	0	-0.005	0.010	18.264	0.007	0.007	0.000	0.000	0.000	0.000
16	B	91	LYS	1	0.915	0.962	14.207	0.415	0.415	0.000	0.000	0.000	0.000
17	B	92	LYS	1	0.872	0.921	17.633	0.126	0.126	0.000	0.000	0.000	0.000
18	B	93	GLU	-1	-0.830	-0.904	21.062	-0.065	-0.065	0.000	0.000	0.000	0.000
19	B	94	ALA	0	0.012	0.005	16.644	0.018	0.018	0.000	0.000	0.000	0.000
20	B	95	ILE	0	0.007	0.005	17.530	0.018	0.018	0.000	0.000	0.000	0.000
21	B	96	GLU	-1	-0.864	-0.912	19.488	-0.090	-0.090	0.000	0.000	0.000	0.000
22	B	97	LYS	1	0.874	0.925	20.748	0.071	0.071	0.000	0.000	0.000	0.000
23	B	98	CYS	0	-0.033	-0.015	17.785	0.020	0.020	0.000	0.000	0.000	0.000
24	B	99	ALA	0	0.006	0.001	20.449	0.012	0.012	0.000	0.000	0.000	0.000
25	B	100	GLN	0	-0.017	-0.023	23.370	0.016	0.016	0.000	0.000	0.000	0.000
26	B	101	TRP	0	-0.040	-0.022	19.030	0.008	0.008	0.000	0.000	0.000	0.000
27	B	102	VAL	0	-0.019	-0.014	21.373	0.005	0.005	0.000	0.000	0.000	0.000
28	B	103	VAL	0	0.011	0.012	24.380	0.003	0.003	0.000	0.000	0.000	0.000
29	B	104	ARG	1	0.917	0.951	27.858	0.013	0.013	0.000	0.000	0.000	0.000
30	B	105	ASP	-1	-0.809	-0.878	26.112	0.039	0.039	0.000	0.000	0.000	0.000
31	B	106	CYS	0	-0.066	-0.020	28.286	0.005	0.005	0.000	0.000	0.000	0.000
32	B	107	ARG	1	0.808	0.899	23.252	-0.022	-0.022	0.000	0.000	0.000	0.000
33	B	108	PRO	0	0.028	0.018	22.067	-0.011	-0.011	0.000	0.000	0.000	0.000
34	B	109	PHE	0	0.072	0.011	20.697	0.008	0.008	0.000	0.000	0.000	0.000
35	B	110	SER	0	0.014	0.011	17.719	-0.007	-0.007	0.000	0.000	0.000	0.000
36	B	111	ALA	0	0.010	0.020	16.830	0.019	0.019	0.000	0.000	0.000	0.000
37	B	112	VAL	0	0.005	-0.004	14.809	0.035	0.035	0.000	0.000	0.000	0.000
38	B	113	SER	0	-0.077	-0.046	12.277	0.009	0.009	0.000	0.000	0.000	0.000
39	B	114	GLY	0	0.026	0.022	12.133	0.044	0.044	0.000	0.000	0.000	0.000
40	B	115	SER	0	0.027	0.001	10.076	-0.018	-0.018	0.000	0.000	0.000	0.000
41	B	116	GLY	0	0.054	0.023	11.205	0.054	0.054	0.000	0.000	0.000	0.000
42	B	117	PHE	0	0.023	0.020	13.855	-0.015	-0.015	0.000	0.000	0.000	0.000
43	B	118	ILE	0	0.029	0.009	8.086	0.006	0.006	0.000	0.000	0.000	0.000
44	B	119	ASP	-1	-0.849	-0.920	9.536	1.026	1.026	0.000	0.000	0.000	0.000
45	B	120	MET	0	-0.014	0.005	12.021	-0.051	-0.051	0.000	0.000	0.000	0.000
46	B	121	ILE	0	0.003	0.001	12.911	-0.038	-0.038	0.000	0.000	0.000	0.000
47	B	122	LYS	1	0.823	0.899	6.745	-1.509	-1.509	0.000	0.000	0.000	0.000
48	B	123	PHE	0	-0.022	0.001	12.537	-0.035	-0.035	0.000	0.000	0.000	0.000
49	B	124	PHE	0	0.060	0.010	15.776	-0.025	-0.025	0.000	0.000	0.000	0.000
50	B	125	ILE	0	-0.018	-0.001	12.564	-0.034	-0.034	0.000	0.000	0.000	0.000
51	B	126	LYS	1	0.797	0.882	15.204	-0.234	-0.234	0.000	0.000	0.000	0.000
52	B	127	VAL	0	0.014	0.007	16.746	-0.016	-0.016	0.000	0.000	0.000	0.000
53	B	128	GLY	0	0.046	0.023	19.463	-0.012	-0.012	0.000	0.000	0.000	0.000
54	B	129	ALA	0	-0.082	-0.048	17.596	-0.016	-0.016	0.000	0.000	0.000	0.000
55	B	130	GLU	-1	-0.895	-0.922	19.585	0.171	0.171	0.000	0.000	0.000	0.000
56	B	131	TYR	0	-0.047	-0.022	22.153	-0.006	-0.006	0.000	0.000	0.000	0.000
57	B	132	GLY	0	-0.024	0.000	23.500	-0.008	-0.008	0.000	0.000	0.000	0.000
58	B	133	ASP	-1	-0.912	-0.967	24.451	-0.007	-0.007	0.000	0.000	0.000	0.000
59	B	134	HIS	0	-0.067	-0.028	25.775	0.006	0.006	0.000	0.000	0.000	0.000
60	B	135	VAL	0	-0.010	0.000	24.406	0.005	0.005	0.000	0.000	0.000	0.000
61	B	136	ASN	0	0.018	0.007	27.491	-0.003	-0.003	0.000	0.000	0.000	0.000
62	B	137	VAL	0	0.036	0.011	25.110	0.010	0.010	0.000	0.000	0.000	0.000
63	B	138	GLU	-1	-0.939	-0.986	27.431	0.045	0.045	0.000	0.000	0.000	0.000
64	B	139	GLU	-1	-1.027	-1.006	30.219	0.077	0.077	0.000	0.000	0.000	0.000
65	B	140	LEU	0	0.020	0.028	23.587	0.008	0.008	0.000	0.000	0.000	0.000
66	B	141	LEU	0	-0.045	-0.015	23.585	0.016	0.016	0.000	0.000	0.000	0.000
67	B	142	PRO	0	-0.019	0.002	25.707	-0.007	-0.007	0.000	0.000	0.000	0.000
68	B	143	SER	0	0.075	0.034	28.547	0.000	0.000	0.000	0.000	0.000	0.000
69	B	144	PRO	0	0.062	0.011	29.495	0.007	0.007	0.000	0.000	0.000	0.000
70	B	145	ILE	0	0.004	0.003	30.473	0.006	0.006	0.000	0.000	0.000	0.000
71	B	146	THR	0	-0.014	-0.016	30.317	0.002	0.002	0.000	0.000	0.000	0.000
72	B	147	LEU	0	0.040	0.024	23.972	0.008	0.008	0.000	0.000	0.000	0.000
73	B	148	SER	0	0.037	0.015	27.684	0.007	0.007	0.000	0.000	0.000	0.000
74	B	149	ARG	1	0.910	0.964	29.771	-0.072	-0.072	0.000	0.000	0.000	0.000
75	B	150	LYS	1	0.873	0.931	24.504	-0.181	-0.181	0.000	0.000	0.000	0.000
76	B	151	VAL	0	0.018	0.002	24.404	0.010	0.010	0.000	0.000	0.000	0.000
77	B	152	THR	0	-0.037	-0.030	26.733	0.001	0.001	0.000	0.000	0.000	0.000
78	B	153	SER	0	-0.001	-0.012	28.460	-0.003	-0.003	0.000	0.000	0.000	0.000
79	B	154	ASP	-1	-0.805	-0.873	24.372	0.188	0.188	0.000	0.000	0.000	0.000
80	B	155	ALA	0	0.011	0.011	26.265	0.011	0.011	0.000	0.000	0.000	0.000
81	B	156	LYS	1	0.884	0.923	27.911	-0.107	-0.107	0.000	0.000	0.000	0.000
82	B	157	GLU	-1	-0.901	-0.948	26.897	0.159	0.159	0.000	0.000	0.000	0.000
83	B	158	LYS	1	0.799	0.920	24.310	-0.190	-0.190	0.000	0.000	0.000	0.000
84	B	159	ALA	0	-0.016	-0.002	29.465	-0.007	-0.007	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:76:SER)