FMO DATABASE

FMODB ID: 49ZKN

Calculation Name: 5HLZ-D-Xray372

Preferred Name: Inhibin beta A chain

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5HLZ

Chain ID: D

ChEMBL ID: CHEMBL3588735

UniProt ID: P08476

Base Structure: X-ray

Registration Date: 2023-09-19

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	78
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-499587.247333
FMO2-HF: Nuclear repulsion	464177.520689
FMO2-HF: Total energy	-35409.726644
FMO2-MP2: Total energy	-35503.092818

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(D:311:GLY)

Summations of interaction energy for fragment #1(D:311: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.
-1.348	1.215	3.443	-2.559	-3.447	-0.02

Interaction energy analysis for fragmet #1(D:311:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : 0.015

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	D	313	GLU	-1	-0.895	-0.949	3.857	-0.510	0.550	-0.013	-0.502	-0.545	0.001
4	D	314	CYS	0	-0.031	0.001	6.409	0.460	0.460	0.000	0.000	0.000	0.000
5	D	315	ASP	-1	-0.801	-0.895	10.163	-0.262	-0.262	0.000	0.000	0.000	0.000
6	D	316	GLY	0	-0.031	-0.014	13.039	0.035	0.035	0.000	0.000	0.000	0.000
7	D	317	LYS	1	0.858	0.912	15.559	0.225	0.225	0.000	0.000	0.000	0.000
8	D	318	VAL	0	-0.035	-0.007	10.183	0.037	0.037	0.000	0.000	0.000	0.000
9	D	319	ASN	0	-0.006	-0.013	13.550	0.035	0.035	0.000	0.000	0.000	0.000
10	D	320	ILE	0	0.003	0.014	9.480	0.023	0.023	0.000	0.000	0.000	0.000
11	D	321	CYS	0	-0.062	-0.002	9.252	0.024	0.024	0.000	0.000	0.000	0.000
12	D	323	LYS	1	0.880	0.919	5.036	0.438	0.438	0.000	0.000	0.000	0.000
13	D	324	LYS	1	0.852	0.909	7.760	-0.402	-0.402	0.000	0.000	0.000	0.000
14	D	325	GLN	0	0.048	0.017	9.633	0.059	0.059	0.000	0.000	0.000	0.000
15	D	326	PHE	0	-0.010	0.002	11.975	-0.036	-0.036	0.000	0.000	0.000	0.000
16	D	327	PHE	0	-0.013	-0.009	15.710	0.015	0.015	0.000	0.000	0.000	0.000
17	D	328	VAL	0	0.013	0.005	17.882	0.003	0.003	0.000	0.000	0.000	0.000
18	D	329	SER	0	-0.007	-0.028	21.073	0.001	0.001	0.000	0.000	0.000	0.000
19	D	330	PHE	0	0.032	0.004	22.716	0.005	0.005	0.000	0.000	0.000	0.000
20	D	331	LYS	1	0.925	0.970	26.477	0.033	0.033	0.000	0.000	0.000	0.000
21	D	332	ASP	-1	-0.855	-0.897	26.377	-0.023	-0.023	0.000	0.000	0.000	0.000
22	D	333	ILE	0	-0.030	-0.013	24.727	0.003	0.003	0.000	0.000	0.000	0.000
23	D	334	GLY	0	-0.020	0.005	28.253	0.004	0.004	0.000	0.000	0.000	0.000
24	D	335	TRP	0	0.022	-0.005	25.224	0.005	0.005	0.000	0.000	0.000	0.000
25	D	336	ASN	0	-0.062	-0.032	29.701	0.000	0.000	0.000	0.000	0.000	0.000
26	D	337	ASP	-1	-0.884	-0.936	30.745	0.006	0.006	0.000	0.000	0.000	0.000
27	D	338	TRP	0	0.014	0.011	28.413	0.000	0.000	0.000	0.000	0.000	0.000
28	D	339	ILE	0	-0.035	-0.018	26.057	0.001	0.001	0.000	0.000	0.000	0.000
29	D	340	ILE	0	-0.019	0.000	29.608	-0.005	-0.005	0.000	0.000	0.000	0.000
30	D	341	ALA	0	-0.027	-0.008	26.720	-0.007	-0.007	0.000	0.000	0.000	0.000
31	D	342	PRO	0	0.007	0.000	21.500	0.005	0.005	0.000	0.000	0.000	0.000
32	D	343	SER	0	0.012	-0.024	24.273	0.003	0.003	0.000	0.000	0.000	0.000
33	D	344	GLY	0	0.008	0.000	22.156	-0.002	-0.002	0.000	0.000	0.000	0.000
34	D	345	TYR	0	-0.052	-0.029	16.330	-0.006	-0.006	0.000	0.000	0.000	0.000
35	D	346	HIS	0	0.018	0.000	13.643	-0.018	-0.018	0.000	0.000	0.000	0.000
36	D	347	ALA	0	0.027	0.031	14.522	0.029	0.029	0.000	0.000	0.000	0.000
37	D	348	ASN	0	-0.062	-0.044	9.398	-0.033	-0.033	0.000	0.000	0.000	0.000
38	D	349	TYR	0	-0.072	-0.051	11.460	0.036	0.036	0.000	0.000	0.000	0.000
39	D	350	CYS	0	-0.077	-0.031	3.833	-0.630	-0.559	-0.001	-0.017	-0.053	0.000
40	D	351	GLU	-1	-0.780	-0.859	10.722	0.139	0.139	0.000	0.000	0.000	0.000
41	D	352	GLY	0	0.055	0.021	11.505	0.042	0.042	0.000	0.000	0.000	0.000
42	D	353	GLU	-1	-0.962	-0.967	13.618	0.302	0.302	0.000	0.000	0.000	0.000
43	D	354	CYS	0	-0.080	-0.030	6.757	-0.608	-0.608	0.000	0.000	0.000	0.000
44	D	389	SER	0	-0.003	-0.016	13.980	0.034	0.034	0.000	0.000	0.000	0.000
45	D	390	CYS	0	-0.042	-0.031	13.986	-0.076	-0.076	0.000	0.000	0.000	0.000
46	D	392	VAL	0	0.042	0.033	11.206	-0.083	-0.083	0.000	0.000	0.000	0.000
47	D	393	PRO	0	0.032	-0.007	8.649	0.341	0.341	0.000	0.000	0.000	0.000
48	D	394	THR	0	-0.012	-0.006	4.810	-0.286	-0.286	0.000	0.000	0.000	0.000
49	D	395	LYS	1	0.804	0.897	5.730	0.018	0.018	0.000	0.000	0.000	0.000
50	D	396	LEU	0	0.017	0.011	8.176	0.008	0.008	0.000	0.000	0.000	0.000
51	D	397	ARG	1	0.907	0.940	11.259	-0.004	-0.004	0.000	0.000	0.000	0.000
52	D	398	PRO	0	-0.016	-0.018	13.495	0.007	0.007	0.000	0.000	0.000	0.000
53	D	399	MET	0	-0.033	-0.003	16.847	-0.015	-0.015	0.000	0.000	0.000	0.000
54	D	400	SER	0	-0.043	-0.031	19.230	0.004	0.004	0.000	0.000	0.000	0.000
55	D	401	MET	0	-0.048	-0.026	22.698	-0.002	-0.002	0.000	0.000	0.000	0.000
56	D	402	LEU	0	-0.011	-0.014	25.170	0.001	0.001	0.000	0.000	0.000	0.000
57	D	403	TYR	0	-0.073	-0.051	28.699	0.000	0.000	0.000	0.000	0.000	0.000
58	D	404	TYR	0	0.018	0.012	31.109	0.000	0.000	0.000	0.000	0.000	0.000
59	D	405	ASP	-1	-0.864	-0.913	33.183	0.037	0.037	0.000	0.000	0.000	0.000
60	D	406	ASP	-1	-0.762	-0.879	34.893	0.018	0.018	0.000	0.000	0.000	0.000
61	D	407	GLY	0	-0.032	-0.003	38.462	-0.002	-0.002	0.000	0.000	0.000	0.000
62	D	408	GLN	0	-0.087	-0.050	40.718	-0.002	-0.002	0.000	0.000	0.000	0.000
63	D	409	ASN	0	-0.082	-0.047	37.903	0.000	0.000	0.000	0.000	0.000	0.000
64	D	410	ILE	0	0.010	0.011	33.917	0.001	0.001	0.000	0.000	0.000	0.000
65	D	411	ILE	0	-0.012	-0.007	30.548	0.001	0.001	0.000	0.000	0.000	0.000
66	D	412	LYS	1	0.826	0.907	25.787	-0.014	-0.014	0.000	0.000	0.000	0.000
67	D	413	LYS	1	0.892	0.935	26.411	-0.040	-0.040	0.000	0.000	0.000	0.000
68	D	414	ASP	-1	-0.770	-0.864	23.253	0.013	0.013	0.000	0.000	0.000	0.000
69	D	415	ILE	0	0.008	0.022	20.446	0.007	0.007	0.000	0.000	0.000	0.000
70	D	416	GLN	0	0.042	0.001	18.996	0.014	0.014	0.000	0.000	0.000	0.000
71	D	417	ASN	0	-0.029	-0.034	15.044	0.011	0.011	0.000	0.000	0.000	0.000
72	D	418	MET	0	0.037	0.042	15.378	0.031	0.031	0.000	0.000	0.000	0.000
73	D	419	ILE	0	0.003	0.010	11.640	-0.011	-0.011	0.000	0.000	0.000	0.000
74	D	420	VAL	0	0.033	0.024	7.879	0.021	0.021	0.000	0.000	0.000	0.000
75	D	421	GLU	-1	-0.858	-0.913	6.867	-0.229	-0.229	0.000	0.000	0.000	0.000
76	D	422	GLU	-1	-0.843	-0.936	2.519	-2.875	-1.429	3.458	-2.028	-2.875	-0.021
77	D	424	GLY	0	0.074	0.036	4.606	2.190	2.176	-0.001	-0.012	0.026	0.000
78	D	426	SER	0	0.035	0.017	9.372	0.108	0.108	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:311:GLY)