FMO DATABASE

FMODB ID: 7GNKK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-455273.416743
FMO2-HF: Nuclear repulsion	421825.733285
FMO2-HF: Total energy	-33447.683458
FMO2-MP2: Total energy	-33542.5278

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.
0.817	1.963	-0.014	-0.491	-0.64	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 : -0.029 / q_NPA : -0.028

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	3.814	2.683	3.829	-0.014	-0.491	-0.640
4	B	79	GLN	0	-0.027	-0.012	5.774	0.178	0.178	0.000	0.000	0.000
5	B	80	SER	0	0.025	0.001	8.440	-0.285	-0.285	0.000	0.000	0.000
6	B	81	ARG	1	0.921	0.959	11.358	-0.762	-0.762	0.000	0.000	0.000
7	B	82	GLU	-1	-0.912	-0.950	9.169	-0.284	-0.284	0.000	0.000	0.000
8	B	83	LEU	0	-0.012	-0.005	5.213	0.118	0.118	0.000	0.000	0.000
9	B	84	LYS	1	0.977	0.975	9.478	-0.467	-0.467	0.000	0.000	0.000
10	B	85	THR	0	0.018	0.029	11.618	-0.098	-0.098	0.000	0.000	0.000
11	B	86	VAL	0	-0.032	-0.016	13.064	0.066	0.066	0.000	0.000	0.000
12	B	87	SER	0	0.051	0.022	15.978	-0.054	-0.054	0.000	0.000	0.000
13	B	88	ALA	0	0.021	-0.012	18.530	-0.027	-0.027	0.000	0.000	0.000
14	B	89	ASP	-1	-0.857	-0.929	20.230	-0.142	-0.142	0.000	0.000	0.000
15	B	90	CYS	0	-0.011	0.004	17.990	0.000	0.000	0.000	0.000	0.000
16	B	91	LYS	1	0.974	0.971	14.481	0.452	0.452	0.000	0.000	0.000
17	B	92	LYS	1	0.927	0.975	17.760	0.137	0.137	0.000	0.000	0.000
18	B	93	GLU	-1	-0.863	-0.926	21.129	-0.061	-0.061	0.000	0.000	0.000
19	B	94	ALA	0	-0.012	-0.004	16.788	0.013	0.013	0.000	0.000	0.000
20	B	95	ILE	0	-0.018	-0.010	18.202	-0.007	-0.007	0.000	0.000	0.000
21	B	96	GLU	-1	-0.921	-0.965	19.900	-0.125	-0.125	0.000	0.000	0.000
22	B	97	LYS	1	0.962	0.976	20.992	0.050	0.050	0.000	0.000	0.000
23	B	98	CYS	0	-0.015	-0.009	17.788	0.016	0.016	0.000	0.000	0.000
24	B	99	ALA	0	-0.002	0.005	20.363	0.003	0.003	0.000	0.000	0.000
25	B	100	GLN	0	-0.015	-0.027	22.994	0.026	0.026	0.000	0.000	0.000
26	B	101	TRP	0	-0.015	0.007	17.955	0.004	0.004	0.000	0.000	0.000
27	B	102	VAL	0	-0.035	-0.022	21.182	0.009	0.009	0.000	0.000	0.000
28	B	103	VAL	0	-0.006	0.001	24.105	0.007	0.007	0.000	0.000	0.000
29	B	104	ARG	1	0.903	0.946	27.550	0.046	0.046	0.000	0.000	0.000
30	B	105	ASP	-1	-0.886	-0.935	25.821	-0.021	-0.021	0.000	0.000	0.000
31	B	106	CYS	0	-0.084	-0.033	27.765	0.003	0.003	0.000	0.000	0.000
32	B	107	ARG	1	0.911	0.967	22.262	0.054	0.054	0.000	0.000	0.000
33	B	108	PRO	0	0.026	0.013	20.872	-0.011	-0.011	0.000	0.000	0.000
34	B	109	PHE	0	0.101	0.025	19.873	-0.004	-0.004	0.000	0.000	0.000
35	B	110	SER	0	0.001	-0.006	17.040	-0.021	-0.021	0.000	0.000	0.000
36	B	111	ALA	0	0.019	0.017	16.227	-0.020	-0.020	0.000	0.000	0.000
37	B	112	VAL	0	-0.005	0.000	14.460	0.030	0.030	0.000	0.000	0.000
38	B	113	SER	0	-0.079	-0.031	11.541	-0.054	-0.054	0.000	0.000	0.000
39	B	114	GLY	0	0.007	0.011	11.177	-0.058	-0.058	0.000	0.000	0.000
40	B	115	SER	0	0.058	0.009	9.927	-0.008	-0.008	0.000	0.000	0.000
41	B	116	GLY	0	0.042	0.024	10.902	0.142	0.142	0.000	0.000	0.000
42	B	117	PHE	0	0.005	0.004	13.035	0.070	0.070	0.000	0.000	0.000
43	B	118	ILE	0	0.034	0.003	7.457	0.056	0.056	0.000	0.000	0.000
44	B	119	ASP	-1	-0.910	-0.950	9.690	1.221	1.221	0.000	0.000	0.000
45	B	120	MET	0	-0.041	-0.013	11.581	0.049	0.049	0.000	0.000	0.000
46	B	121	ILE	0	0.001	-0.004	12.667	0.008	0.008	0.000	0.000	0.000
47	B	122	LYS	1	0.923	0.957	5.462	-2.011	-2.011	0.000	0.000	0.000
48	B	123	PHE	0	-0.014	0.004	12.260	0.048	0.048	0.000	0.000	0.000
49	B	124	PHE	0	0.060	0.008	15.246	-0.015	-0.015	0.000	0.000	0.000
50	B	125	ILE	0	-0.001	0.011	12.844	-0.032	-0.032	0.000	0.000	0.000
51	B	126	LYS	1	0.892	0.957	14.795	-0.591	-0.591	0.000	0.000	0.000
52	B	127	VAL	0	-0.012	0.001	16.487	-0.025	-0.025	0.000	0.000	0.000
53	B	128	GLY	0	0.055	0.031	19.501	-0.022	-0.022	0.000	0.000	0.000
54	B	129	ALA	0	-0.095	-0.055	17.545	-0.019	-0.019	0.000	0.000	0.000
55	B	130	GLU	-1	-0.990	-0.989	19.648	0.436	0.436	0.000	0.000	0.000
56	B	131	TYR	0	-0.032	-0.021	22.068	-0.028	-0.028	0.000	0.000	0.000
57	B	132	GLY	0	-0.028	-0.001	23.552	-0.025	-0.025	0.000	0.000	0.000
58	B	133	ASP	-1	-0.991	-1.007	24.678	0.082	0.082	0.000	0.000	0.000
59	B	134	HIS	0	0.009	0.001	25.679	-0.002	-0.002	0.000	0.000	0.000
60	B	135	VAL	0	0.013	0.018	24.393	0.005	0.005	0.000	0.000	0.000
61	B	136	ASN	0	0.004	0.002	27.557	-0.018	-0.018	0.000	0.000	0.000
62	B	137	VAL	0	0.031	-0.003	25.092	0.013	0.013	0.000	0.000	0.000
63	B	138	GLU	-1	-0.945	-0.979	27.478	0.076	0.076	0.000	0.000	0.000
64	B	139	GLU	-1	-1.022	-1.010	30.002	0.151	0.151	0.000	0.000	0.000
65	B	140	LEU	0	0.016	0.030	23.190	0.012	0.012	0.000	0.000	0.000
66	B	141	LEU	0	-0.072	-0.029	23.167	0.016	0.016	0.000	0.000	0.000
67	B	142	PRO	0	0.010	0.021	25.279	-0.010	-0.010	0.000	0.000	0.000
68	B	143	SER	0	0.073	0.027	28.241	-0.010	-0.010	0.000	0.000	0.000
69	B	144	PRO	0	0.076	0.011	29.056	0.008	0.008	0.000	0.000	0.000
70	B	145	ILE	0	-0.012	-0.007	30.136	0.006	0.006	0.000	0.000	0.000
71	B	146	THR	0	-0.010	-0.010	29.895	0.003	0.003	0.000	0.000	0.000
72	B	147	LEU	0	0.040	0.028	24.009	0.012	0.012	0.000	0.000	0.000
73	B	148	SER	0	0.002	0.000	27.790	0.009	0.009	0.000	0.000	0.000
74	B	149	ARG	1	0.939	0.958	29.789	-0.081	-0.081	0.000	0.000	0.000
75	B	150	LYS	1	0.929	0.993	24.520	-0.244	-0.244	0.000	0.000	0.000
76	B	151	VAL	0	0.035	0.011	24.387	0.011	0.011	0.000	0.000	0.000
77	B	152	THR	0	-0.021	-0.012	26.740	-0.001	-0.001	0.000	0.000	0.000
78	B	153	SER	0	-0.014	-0.016	29.017	-0.003	-0.003	0.000	0.000	0.000
79	B	154	ASP	-1	-0.845	-0.922	23.983	0.243	0.243	0.000	0.000	0.000
80	B	155	ALA	0	-0.056	-0.036	26.767	0.008	0.008	0.000	0.000	0.000
81	B	156	LYS	1	0.907	0.929	27.911	-0.099	-0.099	0.000	0.000	0.000
82	B	157	GLU	-1	-0.914	-0.937	26.925	0.200	0.200	0.000	0.000	0.000
83	B	158	LYS	1	0.821	0.932	24.385	-0.207	-0.207	0.000	0.000	0.000
84	B	159	ALA	0	-0.009	0.005	29.528	-0.011	-0.011	0.000	0.000	0.000

Top

Graph

Manual

About

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