FMO DATABASE

FMODB ID: Z2QYN

Calculation Name: 2BW3-B-Xray308

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	84
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-455167.385899
FMO2-HF: Nuclear repulsion	421720.306347
FMO2-HF: Total energy	-33447.079551
FMO2-MP2: Total energy	-33541.923483

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.
1.005	2.131	-0.01	-0.493	-0.624	0

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 : -0.026 / q_NPA : -0.027

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].
3	B	78	MET	0	0.012	0.017	3.813	2.729	3.855	-0.010	-0.493	-0.624
4	B	79	GLN	0	-0.026	-0.011	5.774	0.213	0.213	0.000	0.000	0.000
5	B	80	SER	0	0.027	0.002	8.440	-0.295	-0.295	0.000	0.000	0.000
6	B	81	ARG	1	0.919	0.959	11.355	-0.756	-0.756	0.000	0.000	0.000
7	B	82	GLU	-1	-0.912	-0.950	9.167	-0.297	-0.297	0.000	0.000	0.000
8	B	83	LEU	0	-0.010	-0.005	5.213	0.120	0.120	0.000	0.000	0.000
9	B	84	LYS	1	0.976	0.975	9.478	-0.468	-0.468	0.000	0.000	0.000
10	B	85	THR	0	0.019	0.029	11.610	-0.105	-0.105	0.000	0.000	0.000
11	B	86	VAL	0	-0.031	-0.016	13.057	0.069	0.069	0.000	0.000	0.000
12	B	87	SER	0	0.049	0.022	15.973	-0.055	-0.055	0.000	0.000	0.000
13	B	88	ALA	0	0.021	-0.012	18.528	-0.028	-0.028	0.000	0.000	0.000
14	B	89	ASP	-1	-0.858	-0.929	20.229	-0.144	-0.144	0.000	0.000	0.000
15	B	90	CYS	0	-0.010	0.005	17.982	0.000	0.000	0.000	0.000	0.000
16	B	91	LYS	1	0.975	0.971	14.483	0.454	0.454	0.000	0.000	0.000
17	B	92	LYS	1	0.926	0.974	17.761	0.139	0.139	0.000	0.000	0.000
18	B	93	GLU	-1	-0.863	-0.926	21.132	-0.061	-0.061	0.000	0.000	0.000
19	B	94	ALA	0	-0.011	-0.004	16.785	0.013	0.013	0.000	0.000	0.000
20	B	95	ILE	0	-0.019	-0.010	18.208	-0.007	-0.007	0.000	0.000	0.000
21	B	96	GLU	-1	-0.918	-0.965	19.895	-0.124	-0.124	0.000	0.000	0.000
22	B	97	LYS	1	0.960	0.976	20.993	0.053	0.053	0.000	0.000	0.000
23	B	98	CYS	0	-0.014	-0.008	17.788	0.016	0.016	0.000	0.000	0.000
24	B	99	ALA	0	-0.003	0.005	20.362	0.003	0.003	0.000	0.000	0.000
25	B	100	GLN	0	-0.016	-0.027	22.991	0.027	0.027	0.000	0.000	0.000
26	B	101	TRP	0	-0.014	0.007	17.957	0.004	0.004	0.000	0.000	0.000
27	B	102	VAL	0	-0.035	-0.021	21.181	0.009	0.009	0.000	0.000	0.000
28	B	103	VAL	0	-0.004	0.002	24.105	0.008	0.008	0.000	0.000	0.000
29	B	104	ARG	1	0.897	0.944	27.550	0.047	0.047	0.000	0.000	0.000
30	B	105	ASP	-1	-0.883	-0.934	25.824	-0.021	-0.021	0.000	0.000	0.000
31	B	106	CYS	0	-0.085	-0.033	27.765	0.002	0.002	0.000	0.000	0.000
32	B	107	ARG	1	0.916	0.968	22.264	0.054	0.054	0.000	0.000	0.000
33	B	108	PRO	0	0.027	0.013	20.872	-0.012	-0.012	0.000	0.000	0.000
34	B	109	PHE	0	0.096	0.023	19.868	-0.005	-0.005	0.000	0.000	0.000
35	B	110	SER	0	0.001	-0.006	17.037	-0.022	-0.022	0.000	0.000	0.000
36	B	111	ALA	0	0.021	0.019	16.226	-0.018	-0.018	0.000	0.000	0.000
37	B	112	VAL	0	-0.006	0.000	14.459	0.030	0.030	0.000	0.000	0.000
38	B	113	SER	0	-0.079	-0.032	11.540	-0.057	-0.057	0.000	0.000	0.000
39	B	114	GLY	0	0.006	0.011	11.178	-0.055	-0.055	0.000	0.000	0.000
40	B	115	SER	0	0.058	0.009	9.935	-0.006	-0.006	0.000	0.000	0.000
41	B	116	GLY	0	0.045	0.026	10.910	0.146	0.146	0.000	0.000	0.000
42	B	117	PHE	0	0.005	0.003	13.039	0.069	0.069	0.000	0.000	0.000
43	B	118	ILE	0	0.031	0.002	7.465	0.055	0.055	0.000	0.000	0.000
44	B	119	ASP	-1	-0.907	-0.948	9.690	1.236	1.236	0.000	0.000	0.000
45	B	120	MET	0	-0.039	-0.012	11.595	0.045	0.045	0.000	0.000	0.000
46	B	121	ILE	0	-0.003	-0.005	12.675	0.005	0.005	0.000	0.000	0.000
47	B	122	LYS	1	0.924	0.957	5.476	-2.022	-2.022	0.000	0.000	0.000
48	B	123	PHE	0	-0.011	0.005	12.263	0.047	0.047	0.000	0.000	0.000
49	B	124	PHE	0	0.058	0.009	15.249	-0.019	-0.019	0.000	0.000	0.000
50	B	125	ILE	0	-0.003	0.010	12.844	-0.033	-0.033	0.000	0.000	0.000
51	B	126	LYS	1	0.895	0.958	14.798	-0.587	-0.587	0.000	0.000	0.000
52	B	127	VAL	0	-0.011	0.001	16.490	-0.027	-0.027	0.000	0.000	0.000
53	B	128	GLY	0	0.053	0.030	19.504	-0.023	-0.023	0.000	0.000	0.000
54	B	129	ALA	0	-0.097	-0.056	17.547	-0.019	-0.019	0.000	0.000	0.000
55	B	130	GLU	-1	-0.988	-0.988	19.650	0.433	0.433	0.000	0.000	0.000
56	B	131	TYR	0	-0.033	-0.022	22.071	-0.029	-0.029	0.000	0.000	0.000
57	B	132	GLY	0	-0.028	-0.001	23.554	-0.025	-0.025	0.000	0.000	0.000
58	B	133	ASP	-1	-0.992	-1.008	24.680	0.080	0.080	0.000	0.000	0.000
59	B	134	HIS	0	0.009	0.001	25.681	-0.002	-0.002	0.000	0.000	0.000
60	B	135	VAL	0	0.014	0.018	24.396	0.005	0.005	0.000	0.000	0.000
61	B	136	ASN	0	0.003	0.001	27.560	-0.018	-0.018	0.000	0.000	0.000
62	B	137	VAL	0	0.031	-0.003	25.102	0.013	0.013	0.000	0.000	0.000
63	B	138	GLU	-1	-0.946	-0.979	27.488	0.075	0.075	0.000	0.000	0.000
64	B	139	GLU	-1	-1.022	-1.010	30.005	0.150	0.150	0.000	0.000	0.000
65	B	140	LEU	0	0.016	0.030	23.193	0.012	0.012	0.000	0.000	0.000
66	B	141	LEU	0	-0.073	-0.029	23.178	0.016	0.016	0.000	0.000	0.000
67	B	142	PRO	0	0.013	0.022	25.291	-0.010	-0.010	0.000	0.000	0.000
68	B	143	SER	0	0.071	0.025	28.252	-0.010	-0.010	0.000	0.000	0.000
69	B	144	PRO	0	0.073	0.010	29.067	0.008	0.008	0.000	0.000	0.000
70	B	145	ILE	0	-0.012	-0.007	30.147	0.006	0.006	0.000	0.000	0.000
71	B	146	THR	0	-0.010	-0.010	29.909	0.004	0.004	0.000	0.000	0.000
72	B	147	LEU	0	0.040	0.027	24.021	0.012	0.012	0.000	0.000	0.000
73	B	148	SER	0	0.000	-0.001	27.790	0.008	0.008	0.000	0.000	0.000
74	B	149	ARG	1	0.940	0.959	29.801	-0.081	-0.081	0.000	0.000	0.000
75	B	150	LYS	1	0.927	0.992	24.520	-0.244	-0.244	0.000	0.000	0.000
76	B	151	VAL	0	0.030	0.009	24.387	0.011	0.011	0.000	0.000	0.000
77	B	152	THR	0	-0.022	-0.013	26.740	-0.002	-0.002	0.000	0.000	0.000
78	B	153	SER	0	-0.018	-0.017	29.011	-0.003	-0.003	0.000	0.000	0.000
79	B	154	ASP	-1	-0.844	-0.923	23.983	0.244	0.244	0.000	0.000	0.000
80	B	155	ALA	0	-0.064	-0.041	26.767	0.007	0.007	0.000	0.000	0.000
81	B	156	LYS	1	0.903	0.926	27.911	-0.100	-0.100	0.000	0.000	0.000
82	B	157	GLU	-1	-0.925	-0.943	26.926	0.201	0.201	0.000	0.000	0.000
83	B	158	LYS	1	0.779	0.908	24.384	-0.206	-0.206	0.000	0.000	0.000
84	B	159	ALA	-1	-0.928	-0.948	29.528	0.123	0.123	0.000	0.000	0.000

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