FMO DATABASE

FMODB ID: J3J99

Calculation Name: 4HBO-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4HBO

Chain ID: B

ChEMBL ID:

UniProt ID: P08563

Base Structure: X-ray

Registration Date: 2023-06-20

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	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	76
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-465177.660583
FMO2-HF: Nuclear repulsion	434492.052414
FMO2-HF: Total energy	-30685.608169
FMO2-MP2: Total energy	-30774.758203

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:26:ALA)

Summations of interaction energy for fragment #1(B:26:ALA)

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.
-1.491	1.322	1.174	-1.384	-2.604	-0.005

Interaction energy analysis for fragmet #1(B:26:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : -0.002

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	28	VAL	0	-0.001	-0.006	3.855	0.874	1.976	-0.016	-0.507	-0.579	0.001
4	B	29	THR	0	0.007	0.009	6.722	-0.327	-0.327	0.000	0.000	0.000	0.000
5	B	30	SER	0	-0.028	-0.030	10.478	0.036	0.036	0.000	0.000	0.000	0.000
6	B	31	TRP	0	0.007	-0.003	13.668	-0.004	-0.004	0.000	0.000	0.000	0.000
7	B	32	LEU	0	-0.025	-0.009	17.364	-0.016	-0.016	0.000	0.000	0.000	0.000
8	B	33	TRP	0	-0.007	0.006	20.232	0.001	0.001	0.000	0.000	0.000	0.000
9	B	34	SER	0	-0.004	0.007	23.850	-0.004	-0.004	0.000	0.000	0.000	0.000
10	B	35	GLU	-1	-0.772	-0.849	27.413	0.010	0.010	0.000	0.000	0.000	0.000
11	B	36	GLY	0	0.025	0.021	31.116	-0.005	-0.005	0.000	0.000	0.000	0.000
12	B	37	GLU	-1	-0.902	-0.960	33.358	-0.003	-0.003	0.000	0.000	0.000	0.000
13	B	38	GLY	0	-0.020	-0.009	32.851	-0.004	-0.004	0.000	0.000	0.000	0.000
14	B	39	ALA	0	-0.047	-0.002	29.328	-0.006	-0.006	0.000	0.000	0.000	0.000
15	B	40	VAL	0	-0.030	-0.027	25.107	0.000	0.000	0.000	0.000	0.000	0.000
16	B	41	PHE	0	0.009	-0.016	21.015	0.000	0.000	0.000	0.000	0.000	0.000
17	B	42	TYR	0	0.016	0.005	18.827	-0.007	-0.007	0.000	0.000	0.000	0.000
18	B	43	ARG	1	0.809	0.868	11.977	-0.103	-0.103	0.000	0.000	0.000	0.000
19	B	44	VAL	0	-0.010	0.004	12.274	-0.019	-0.019	0.000	0.000	0.000	0.000
20	B	45	ASP	-1	-0.782	-0.865	8.642	0.215	0.215	0.000	0.000	0.000	0.000
21	B	46	LEU	0	-0.009	0.006	6.653	-0.071	-0.071	0.000	0.000	0.000	0.000
22	B	47	HIS	0	-0.026	-0.037	4.260	-0.167	-0.113	-0.001	-0.031	-0.022	0.000
23	B	48	PHE	0	0.019	0.023	2.309	-1.343	0.314	1.191	-0.846	-2.003	-0.006
24	B	68	TYR	0	0.008	-0.003	17.993	-0.013	-0.013	0.000	0.000	0.000	0.000
25	B	69	ASN	0	-0.034	-0.046	17.672	0.034	0.034	0.000	0.000	0.000	0.000
26	B	70	PRO	0	-0.009	0.016	15.372	-0.025	-0.025	0.000	0.000	0.000	0.000
27	B	71	CYS	0	0.000	0.003	14.108	-0.072	-0.072	0.000	0.000	0.000	0.000
28	B	72	GLY	0	0.020	0.008	15.786	0.038	0.038	0.000	0.000	0.000	0.000
29	B	73	PRO	0	-0.046	-0.044	17.349	-0.019	-0.019	0.000	0.000	0.000	0.000
30	B	74	GLU	-1	-0.852	-0.909	18.962	-0.220	-0.220	0.000	0.000	0.000	0.000
31	B	75	PRO	0	-0.031	0.001	18.155	0.020	0.020	0.000	0.000	0.000	0.000
32	B	76	PRO	0	0.030	0.001	21.062	-0.001	-0.001	0.000	0.000	0.000	0.000
33	B	77	ALA	0	0.099	0.047	23.398	-0.002	-0.002	0.000	0.000	0.000	0.000
34	B	78	HIS	0	-0.002	-0.009	23.998	-0.012	-0.012	0.000	0.000	0.000	0.000
35	B	79	VAL	0	0.025	0.010	20.358	0.002	0.002	0.000	0.000	0.000	0.000
36	B	80	VAL	0	-0.008	0.011	18.422	-0.007	-0.007	0.000	0.000	0.000	0.000
37	B	81	ARG	1	0.952	0.984	19.920	0.083	0.083	0.000	0.000	0.000	0.000
38	B	82	ALA	0	-0.007	0.003	22.474	0.006	0.006	0.000	0.000	0.000	0.000
39	B	83	TYR	0	0.046	0.021	12.307	0.037	0.037	0.000	0.000	0.000	0.000
40	B	84	ASN	0	-0.024	-0.017	15.974	-0.027	-0.027	0.000	0.000	0.000	0.000
41	B	85	GLN	0	-0.019	0.010	18.390	0.008	0.008	0.000	0.000	0.000	0.000
42	B	86	PRO	0	0.025	0.020	20.784	0.001	0.001	0.000	0.000	0.000	0.000
43	B	87	ALA	0	-0.027	-0.022	21.990	0.011	0.011	0.000	0.000	0.000	0.000
44	B	88	GLY	0	0.016	0.004	22.091	0.000	0.000	0.000	0.000	0.000	0.000
45	B	89	ASP	-1	-0.866	-0.904	23.726	-0.006	-0.006	0.000	0.000	0.000	0.000
46	B	90	VAL	0	-0.035	-0.026	21.618	-0.004	-0.004	0.000	0.000	0.000	0.000
47	B	91	ARG	1	0.778	0.877	24.245	0.010	0.010	0.000	0.000	0.000	0.000
48	B	92	GLY	0	0.050	0.032	24.023	0.005	0.005	0.000	0.000	0.000	0.000
49	B	93	VAL	0	-0.009	-0.008	19.365	-0.004	-0.004	0.000	0.000	0.000	0.000
50	B	94	TRP	0	0.058	0.038	18.012	0.021	0.021	0.000	0.000	0.000	0.000
51	B	95	GLY	0	0.000	-0.006	18.776	0.024	0.024	0.000	0.000	0.000	0.000
52	B	96	LYS	1	0.880	0.931	18.163	-0.220	-0.220	0.000	0.000	0.000	0.000
53	B	97	GLY	0	0.015	-0.008	17.252	0.033	0.033	0.000	0.000	0.000	0.000
54	B	98	GLU	-1	-0.845	-0.873	13.035	0.665	0.665	0.000	0.000	0.000	0.000
55	B	99	ARG	1	0.859	0.911	13.295	-0.596	-0.596	0.000	0.000	0.000	0.000
56	B	100	THR	0	0.010	-0.037	14.069	-0.025	-0.025	0.000	0.000	0.000	0.000
57	B	101	TYR	0	-0.031	-0.007	12.957	0.044	0.044	0.000	0.000	0.000	0.000
58	B	102	ALA	0	0.018	0.012	16.348	0.001	0.001	0.000	0.000	0.000	0.000
59	B	103	GLU	-1	-0.925	-0.965	18.878	0.043	0.043	0.000	0.000	0.000	0.000
60	B	104	GLN	0	0.014	0.003	19.894	-0.018	-0.018	0.000	0.000	0.000	0.000
61	B	105	ASP	-1	-0.802	-0.876	23.550	-0.006	-0.006	0.000	0.000	0.000	0.000
62	B	106	PHE	0	0.011	0.002	22.006	-0.003	-0.003	0.000	0.000	0.000	0.000
63	B	107	ARG	1	0.927	0.946	27.723	0.028	0.028	0.000	0.000	0.000	0.000
64	B	108	VAL	0	0.010	0.008	25.118	-0.006	-0.006	0.000	0.000	0.000	0.000
65	B	109	GLY	0	-0.017	0.003	28.500	0.001	0.001	0.000	0.000	0.000	0.000
66	B	110	GLY	0	0.017	-0.001	31.681	0.004	0.004	0.000	0.000	0.000	0.000
67	B	111	THR	0	-0.008	0.011	28.840	0.003	0.003	0.000	0.000	0.000	0.000
68	B	112	ARG	1	0.767	0.845	29.080	-0.003	-0.003	0.000	0.000	0.000	0.000
69	B	113	TRP	0	-0.013	-0.021	23.642	-0.001	-0.001	0.000	0.000	0.000	0.000
70	B	114	HIS	0	0.019	-0.003	24.228	0.002	0.002	0.000	0.000	0.000	0.000
71	B	115	ARG	1	0.764	0.858	17.602	0.096	0.096	0.000	0.000	0.000	0.000
72	B	116	LEU	0	0.007	0.012	17.678	0.008	0.008	0.000	0.000	0.000	0.000
73	B	117	LEU	0	0.058	0.015	13.756	0.007	0.007	0.000	0.000	0.000	0.000
74	B	118	ARG	1	0.872	0.945	9.534	-0.454	-0.454	0.000	0.000	0.000	0.000
75	B	119	MET	0	0.031	0.014	12.593	-0.062	-0.062	0.000	0.000	0.000	0.000
76	B	120	PRO	0	0.005	0.044	11.372	0.023	0.023	0.000	0.000	0.000	0.000

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Overview

Highlights

Manual

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Interactive mode: IFIE and PIEDA for fragment #1(B:26:ALA)