FMO DATABASE

FMODB ID: 17G5Z

Calculation Name: 3BEY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BEY

Chain ID: A

ChEMBL ID:

UniProt ID: O27018

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	OptHSide
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	88
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-497359.811275
FMO2-HF: Nuclear repulsion	463156.292458
FMO2-HF: Total energy	-34203.518817
FMO2-MP2: Total energy	-34301.495599

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:7:ARG)

Summations of interaction energy for fragment #1(A:7:ARG)

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.
-108.81	-106.307	11.074	-6.637	-6.938	-0.039

Interaction energy analysis for fragmet #1(A:7:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.959 / q_NPA : 0.962

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	9	LEU	0	0.009	-0.006	3.798	1.249	3.378	0.014	-0.926	-1.216	0.004
4	A	10	GLU	-1	-0.916	-0.963	1.670	-56.174	-56.503	11.016	-5.552	-5.135	-0.040
5	A	11	GLU	-1	-0.937	-0.950	3.312	-29.142	-28.439	0.044	-0.159	-0.587	-0.003
6	A	12	LEU	0	-0.083	-0.045	6.267	3.529	3.529	0.000	0.000	0.000	0.000
7	A	13	PRO	0	0.047	0.014	8.266	0.324	0.324	0.000	0.000	0.000	0.000
8	A	14	GLU	-1	-0.888	-0.938	9.193	-15.154	-15.154	0.000	0.000	0.000	0.000
9	A	15	VAL	0	0.010	-0.005	10.165	0.344	0.344	0.000	0.000	0.000	0.000
10	A	16	ALA	0	0.005	0.022	7.192	0.320	0.320	0.000	0.000	0.000	0.000
11	A	17	GLU	-1	-0.850	-0.916	9.135	-17.275	-17.275	0.000	0.000	0.000	0.000
12	A	18	SER	0	-0.048	-0.021	11.607	0.864	0.864	0.000	0.000	0.000	0.000
13	A	19	PHE	0	-0.030	-0.025	9.867	0.387	0.387	0.000	0.000	0.000	0.000
14	A	20	LYN	0	0.037	0.050	10.471	-0.181	-0.181	0.000	0.000	0.000	0.000
15	A	21	ASN	0	-0.033	-0.038	12.660	1.169	1.169	0.000	0.000	0.000	0.000
16	A	22	PHE	0	-0.040	-0.014	16.004	0.672	0.672	0.000	0.000	0.000	0.000
17	A	23	ARG	1	0.899	0.917	9.565	21.282	21.282	0.000	0.000	0.000	0.000
18	A	24	GLU	-1	-0.855	-0.937	16.334	-14.592	-14.592	0.000	0.000	0.000	0.000
19	A	25	ALA	0	-0.008	0.007	17.921	0.655	0.655	0.000	0.000	0.000	0.000
20	A	26	VAL	0	-0.054	-0.034	19.091	0.532	0.532	0.000	0.000	0.000	0.000
21	A	27	ARG	1	0.834	0.916	16.509	15.970	15.970	0.000	0.000	0.000	0.000
22	A	28	SER	0	-0.044	-0.013	20.956	0.463	0.463	0.000	0.000	0.000	0.000
23	A	29	GLU	-1	-0.824	-0.899	23.273	-9.473	-9.473	0.000	0.000	0.000	0.000
24	A	30	GLY	0	0.003	-0.003	26.000	-0.026	-0.026	0.000	0.000	0.000	0.000
25	A	31	LYS	1	0.788	0.879	29.459	9.804	9.804	0.000	0.000	0.000	0.000
26	A	32	LEU	0	-0.011	0.008	27.482	0.204	0.204	0.000	0.000	0.000	0.000
27	A	33	THR	0	-0.021	-0.048	28.501	-0.296	-0.296	0.000	0.000	0.000	0.000
28	A	34	GLU	-1	-0.832	-0.941	22.700	-12.733	-12.733	0.000	0.000	0.000	0.000
29	A	35	ARG	1	0.892	0.925	25.527	9.407	9.407	0.000	0.000	0.000	0.000
30	A	36	GLU	-1	-0.834	-0.890	27.249	-9.684	-9.684	0.000	0.000	0.000	0.000
31	A	37	LYS	1	0.843	0.927	23.313	11.395	11.395	0.000	0.000	0.000	0.000
32	A	38	LEU	0	0.009	0.028	21.356	-0.464	-0.464	0.000	0.000	0.000	0.000
33	A	39	LEU	0	-0.003	0.000	22.752	-0.395	-0.395	0.000	0.000	0.000	0.000
34	A	40	ILE	0	-0.003	-0.001	23.654	-0.051	-0.051	0.000	0.000	0.000	0.000
35	A	41	SER	0	0.008	-0.001	19.088	-0.276	-0.276	0.000	0.000	0.000	0.000
36	A	42	VAL	0	0.007	0.029	20.113	-0.628	-0.628	0.000	0.000	0.000	0.000
37	A	43	ALA	0	0.032	0.021	21.656	-0.182	-0.182	0.000	0.000	0.000	0.000
38	A	44	CYS	0	-0.023	-0.024	21.155	0.135	0.135	0.000	0.000	0.000	0.000
39	A	45	SER	0	-0.041	-0.028	17.752	-0.574	-0.574	0.000	0.000	0.000	0.000
40	A	46	VAL	0	0.021	0.008	19.279	-0.306	-0.306	0.000	0.000	0.000	0.000
41	A	47	ALA	0	-0.024	-0.007	21.703	0.169	0.169	0.000	0.000	0.000	0.000
42	A	48	VAL	0	-0.063	-0.023	18.094	0.357	0.357	0.000	0.000	0.000	0.000
43	A	49	ARG	1	0.841	0.912	17.701	14.882	14.882	0.000	0.000	0.000	0.000
44	A	50	CYS	0	0.039	0.033	12.016	-1.653	-1.653	0.000	0.000	0.000	0.000
45	A	51	ASP	-1	-0.829	-0.921	14.317	-17.043	-17.043	0.000	0.000	0.000	0.000
46	A	52	ALA	0	-0.033	-0.019	10.032	-0.095	-0.095	0.000	0.000	0.000	0.000
47	A	54	THR	0	0.020	-0.009	14.112	0.767	0.767	0.000	0.000	0.000	0.000
48	A	55	ARG	1	0.931	0.973	11.735	21.916	21.916	0.000	0.000	0.000	0.000
49	A	56	ARG	1	0.835	0.914	12.172	21.215	21.215	0.000	0.000	0.000	0.000
50	A	57	HIS	0	0.008	-0.012	14.597	0.281	0.281	0.000	0.000	0.000	0.000
51	A	58	ALA	0	0.007	0.007	17.747	0.801	0.801	0.000	0.000	0.000	0.000
52	A	59	GLU	-1	-0.862	-0.929	13.872	-20.284	-20.284	0.000	0.000	0.000	0.000
53	A	60	GLU	-1	-0.761	-0.858	15.269	-17.703	-17.703	0.000	0.000	0.000	0.000
54	A	61	ALA	0	-0.020	-0.015	19.421	0.673	0.673	0.000	0.000	0.000	0.000
55	A	62	LEU	0	-0.034	-0.019	20.939	0.552	0.552	0.000	0.000	0.000	0.000
56	A	63	GLU	-1	-1.022	-0.986	19.178	-15.632	-15.632	0.000	0.000	0.000	0.000
57	A	64	ALA	0	-0.014	-0.015	23.107	0.190	0.190	0.000	0.000	0.000	0.000
58	A	65	GLY	0	-0.062	-0.027	25.612	0.467	0.467	0.000	0.000	0.000	0.000
59	A	66	ILE	0	-0.064	-0.019	25.327	0.371	0.371	0.000	0.000	0.000	0.000
60	A	67	THR	0	0.026	-0.023	26.730	-0.252	-0.252	0.000	0.000	0.000	0.000
61	A	68	GLU	-1	-0.892	-0.960	25.100	-11.650	-11.650	0.000	0.000	0.000	0.000
62	A	69	GLY	0	-0.014	-0.007	27.283	-0.037	-0.037	0.000	0.000	0.000	0.000
63	A	70	GLU	-1	-0.777	-0.858	29.504	-9.851	-9.851	0.000	0.000	0.000	0.000
64	A	71	LEU	0	0.005	0.000	22.974	-0.067	-0.067	0.000	0.000	0.000	0.000
65	A	72	ALA	0	-0.024	-0.003	26.688	-0.166	-0.166	0.000	0.000	0.000	0.000
66	A	73	GLU	-1	-0.894	-0.939	28.369	-9.088	-9.088	0.000	0.000	0.000	0.000
67	A	74	ALA	0	-0.009	-0.003	26.753	0.098	0.098	0.000	0.000	0.000	0.000
68	A	75	ALA	0	-0.041	-0.032	25.426	-0.078	-0.078	0.000	0.000	0.000	0.000
69	A	76	ALA	0	0.004	-0.001	26.859	0.025	0.025	0.000	0.000	0.000	0.000
70	A	77	VAL	0	0.032	0.017	30.095	0.164	0.164	0.000	0.000	0.000	0.000
71	A	78	ALA	0	0.002	0.005	25.818	0.125	0.125	0.000	0.000	0.000	0.000
72	A	79	ALA	0	-0.022	-0.018	27.921	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	80	LEU	0	0.010	0.013	29.446	0.215	0.215	0.000	0.000	0.000	0.000
74	A	81	ILE	0	0.022	0.015	29.498	0.244	0.244	0.000	0.000	0.000	0.000
75	A	82	ARG	1	0.876	0.950	24.021	11.945	11.945	0.000	0.000	0.000	0.000
76	A	83	ALA	0	-0.003	0.007	29.754	0.112	0.112	0.000	0.000	0.000	0.000
77	A	84	GLY	0	0.010	-0.003	33.203	0.251	0.251	0.000	0.000	0.000	0.000
78	A	85	SER	0	-0.035	-0.045	30.974	0.145	0.145	0.000	0.000	0.000	0.000
79	A	86	ALA	0	0.007	0.006	32.697	0.145	0.145	0.000	0.000	0.000	0.000
80	A	87	MET	0	-0.003	-0.013	34.274	0.222	0.222	0.000	0.000	0.000	0.000
81	A	88	ASN	0	-0.023	-0.001	36.231	0.371	0.371	0.000	0.000	0.000	0.000
82	A	89	THR	0	-0.015	-0.003	34.659	0.135	0.135	0.000	0.000	0.000	0.000
83	A	90	ALA	0	0.000	0.000	37.262	0.152	0.152	0.000	0.000	0.000	0.000
84	A	91	SER	0	-0.035	-0.015	39.679	0.230	0.230	0.000	0.000	0.000	0.000
85	A	92	ALA	0	0.003	-0.006	40.337	0.193	0.193	0.000	0.000	0.000	0.000
86	A	93	ILE	0	-0.059	-0.014	41.652	0.045	0.045	0.000	0.000	0.000	0.000
87	A	94	PHE	0	-0.067	-0.026	43.908	0.185	0.185	0.000	0.000	0.000	0.000
88	A	95	ARG	1	0.985	0.996	46.642	6.055	6.055	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:7:ARG)