FMO DATABASE

FMODB ID: VR451

Calculation Name: 1HBX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1HBX

Chain ID: A

ChEMBL ID:

UniProt ID: P28324

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	87
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-519659.808274
FMO2-HF: Nuclear repulsion	484999.439135
FMO2-HF: Total energy	-34660.369139
FMO2-MP2: Total energy	-34760.240111

3D Structure Molmil

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:137:GLY)

Summations of interaction energy for fragment #1(A:137:GLY)

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.
-0.3	0.506	-0.008	-0.387	-0.412	0.001

Interaction energy analysis for fragmet #1(A:137:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.071 / 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

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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	139	LYS	1	1.015	1.004	3.873	1.472	2.278	-0.008	-0.387	-0.412	0.001
4	A	140	THR	0	0.035	0.005	6.142	0.077	0.077	0.000	0.000	0.000	0.000
5	A	141	ARG	1	1.031	1.022	6.916	-0.480	-0.480	0.000	0.000	0.000	0.000
6	A	142	GLY	0	0.020	0.024	8.155	0.001	0.001	0.000	0.000	0.000	0.000
7	A	143	ARG	1	0.951	0.963	11.121	-0.319	-0.319	0.000	0.000	0.000	0.000
8	A	144	VAL	0	0.007	0.013	12.047	0.041	0.041	0.000	0.000	0.000	0.000
9	A	145	LYS	1	0.947	0.982	14.355	-0.381	-0.381	0.000	0.000	0.000	0.000
10	A	146	ILE	0	-0.005	-0.002	17.502	0.012	0.012	0.000	0.000	0.000	0.000
11	A	147	LYS	1	0.848	0.900	20.433	-0.185	-0.185	0.000	0.000	0.000	0.000
12	A	148	MET	0	-0.016	-0.019	23.653	0.000	0.000	0.000	0.000	0.000	0.000
13	A	149	GLU	-1	-0.766	-0.856	26.213	0.165	0.165	0.000	0.000	0.000	0.000
14	A	150	PHE	0	0.046	0.024	27.799	0.007	0.007	0.000	0.000	0.000	0.000
15	A	151	ILE	0	-0.054	-0.030	23.806	0.016	0.016	0.000	0.000	0.000	0.000
16	A	152	ASP	-1	-0.792	-0.888	26.913	0.120	0.120	0.000	0.000	0.000	0.000
17	A	153	ASN	0	-0.020	-0.014	22.476	-0.014	-0.014	0.000	0.000	0.000	0.000
18	A	154	LYS	1	1.009	0.991	25.663	-0.066	-0.066	0.000	0.000	0.000	0.000
19	A	155	LEU	0	0.079	0.054	22.262	0.000	0.000	0.000	0.000	0.000	0.000
20	A	156	ARG	1	0.982	0.987	19.309	-0.235	-0.235	0.000	0.000	0.000	0.000
21	A	157	ARG	1	0.836	0.910	22.863	-0.094	-0.094	0.000	0.000	0.000	0.000
22	A	158	TYR	0	0.081	0.042	26.173	0.002	0.002	0.000	0.000	0.000	0.000
23	A	159	THR	0	-0.022	-0.012	20.949	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	160	THR	0	-0.075	-0.064	23.046	0.009	0.009	0.000	0.000	0.000	0.000
25	A	161	PHE	0	0.015	0.010	24.319	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	162	SER	0	0.016	0.001	26.164	-0.009	-0.009	0.000	0.000	0.000	0.000
27	A	163	LYS	1	0.907	0.958	19.791	-0.163	-0.163	0.000	0.000	0.000	0.000
28	A	164	ARG	1	0.956	0.970	24.205	-0.174	-0.174	0.000	0.000	0.000	0.000
29	A	165	LYS	1	0.907	0.991	27.269	-0.073	-0.073	0.000	0.000	0.000	0.000
30	A	166	THR	0	-0.011	-0.013	27.592	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	167	GLY	0	-0.016	-0.006	27.798	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	168	ILE	0	-0.014	-0.016	28.625	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	169	MET	0	0.041	0.023	31.744	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	170	LYS	1	0.877	0.934	28.948	-0.064	-0.064	0.000	0.000	0.000	0.000
35	A	171	LYS	1	0.861	0.909	28.577	-0.087	-0.087	0.000	0.000	0.000	0.000
36	A	172	ALA	0	0.019	0.027	33.349	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	173	TYR	0	0.037	0.036	35.332	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	174	GLU	-1	-0.789	-0.874	31.267	0.065	0.065	0.000	0.000	0.000	0.000
39	A	175	LEU	0	0.009	0.014	35.954	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	176	SER	0	0.009	0.000	37.962	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	177	THR	0	-0.063	-0.040	38.760	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	178	LEU	0	-0.042	-0.018	35.842	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	179	THR	0	-0.013	-0.015	39.694	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	180	GLY	0	0.039	0.037	42.609	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	181	THR	0	-0.046	-0.039	42.571	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	182	GLN	0	-0.024	-0.014	44.460	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	183	VAL	0	0.042	0.013	39.699	0.002	0.002	0.000	0.000	0.000	0.000
48	A	184	LEU	0	-0.001	-0.004	42.572	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	185	LEU	0	-0.032	-0.009	35.356	0.004	0.004	0.000	0.000	0.000	0.000
50	A	186	LEU	0	0.033	0.015	39.534	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	187	VAL	0	-0.040	-0.028	33.619	0.005	0.005	0.000	0.000	0.000	0.000
52	A	188	ALA	0	0.074	0.046	37.078	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	189	SER	0	-0.056	-0.036	34.511	0.005	0.005	0.000	0.000	0.000	0.000
54	A	190	GLU	-1	-0.787	-0.873	32.431	0.085	0.085	0.000	0.000	0.000	0.000
55	A	191	THR	0	-0.094	-0.065	34.167	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	192	GLY	0	0.083	0.058	37.076	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	193	HIS	0	0.015	0.016	37.422	0.000	0.000	0.000	0.000	0.000	0.000
58	A	194	VAL	0	0.041	0.020	38.353	0.005	0.005	0.000	0.000	0.000	0.000
59	A	195	TYR	0	0.029	0.008	34.439	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	196	THR	0	-0.013	-0.019	38.159	0.002	0.002	0.000	0.000	0.000	0.000
61	A	197	PHE	0	0.035	0.009	38.626	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	198	ALA	0	0.013	0.008	40.586	0.002	0.002	0.000	0.000	0.000	0.000
63	A	199	THR	0	0.036	0.031	43.469	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	200	ARG	1	0.993	0.985	45.489	-0.023	-0.023	0.000	0.000	0.000	0.000
65	A	201	LYS	1	0.942	0.961	49.075	-0.028	-0.028	0.000	0.000	0.000	0.000
66	A	202	LEU	0	0.025	0.014	46.008	0.000	0.000	0.000	0.000	0.000	0.000
67	A	203	GLN	0	0.035	0.029	45.701	0.002	0.002	0.000	0.000	0.000	0.000
68	A	204	PRO	0	0.017	0.018	48.604	0.000	0.000	0.000	0.000	0.000	0.000
69	A	205	MET	0	-0.005	0.012	47.966	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	206	ILE	0	0.014	0.001	44.647	0.001	0.001	0.000	0.000	0.000	0.000
71	A	207	THR	0	-0.031	-0.019	47.986	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	208	SER	0	-0.013	-0.020	50.613	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	209	GLU	-1	-0.783	-0.885	53.103	0.024	0.024	0.000	0.000	0.000	0.000
74	A	210	THR	0	0.023	0.009	54.733	0.001	0.001	0.000	0.000	0.000	0.000
75	A	211	GLY	0	0.017	0.024	51.613	0.001	0.001	0.000	0.000	0.000	0.000
76	A	212	LYS	1	0.830	0.893	49.490	-0.023	-0.023	0.000	0.000	0.000	0.000
77	A	213	ALA	0	0.039	0.028	50.655	0.001	0.001	0.000	0.000	0.000	0.000
78	A	214	LEU	0	0.015	0.025	50.572	0.001	0.001	0.000	0.000	0.000	0.000
79	A	215	ILE	0	0.015	0.003	45.553	0.002	0.002	0.000	0.000	0.000	0.000
80	A	216	GLN	0	-0.036	-0.028	47.044	0.003	0.003	0.000	0.000	0.000	0.000
81	A	217	THR	0	0.004	-0.003	48.949	0.000	0.000	0.000	0.000	0.000	0.000
82	A	218	CYS	0	-0.084	-0.048	46.790	0.001	0.001	0.000	0.000	0.000	0.000
83	A	219	LEU	0	-0.070	-0.049	42.235	0.002	0.002	0.000	0.000	0.000	0.000
84	A	220	ASN	0	-0.064	-0.032	45.031	0.001	0.001	0.000	0.000	0.000	0.000
85	A	221	SER	0	-0.003	0.017	47.128	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	222	PRO	0	-0.042	-0.010	46.694	0.001	0.001	0.000	0.000	0.000	0.000
87	A	223	ASP	-1	-0.967	-0.983	42.442	0.054	0.054	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:137:GLY)