FMO DATABASE

FMODB ID: R92K8

Calculation Name: 5HLZ-F-Xray372

Preferred Name: Inhibin beta A chain

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5HLZ

Chain ID: F

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	82
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-531385.336206
FMO2-HF: Nuclear repulsion	494550.81329
FMO2-HF: Total energy	-36834.522916
FMO2-MP2: Total energy	-36932.219147

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(F:311:GLY)

Summations of interaction energy for fragment #1(F: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.
-9.708	-7.515	6.754	-4.447	-4.499	-0.043

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : 0.004

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	F	313	GLU	-1	-0.857	-0.925	3.860	-1.093	-0.091	-0.009	-0.449	-0.543	0.001
4	F	314	CYS	0	-0.031	-0.019	5.823	0.266	0.266	0.000	0.000	0.000	0.000
5	F	315	ASP	-1	-0.815	-0.906	10.260	-0.462	-0.462	0.000	0.000	0.000	0.000
6	F	316	GLY	0	0.001	0.004	12.833	0.087	0.087	0.000	0.000	0.000	0.000
7	F	317	LYS	1	0.801	0.899	14.323	0.448	0.448	0.000	0.000	0.000	0.000
8	F	318	VAL	0	-0.033	-0.015	10.838	0.024	0.024	0.000	0.000	0.000	0.000
9	F	319	ASN	0	0.027	0.010	13.598	-0.004	-0.004	0.000	0.000	0.000	0.000
10	F	320	ILE	0	-0.003	0.008	8.528	0.064	0.064	0.000	0.000	0.000	0.000
11	F	321	CYS	0	-0.057	0.007	7.673	-0.130	-0.130	0.000	0.000	0.000	0.000
12	F	323	LYS	1	0.859	0.908	4.179	1.925	2.030	-0.001	-0.014	-0.090	0.000
13	F	324	LYS	1	0.902	0.954	7.697	0.030	0.030	0.000	0.000	0.000	0.000
14	F	325	GLN	0	0.055	0.025	8.693	0.001	0.001	0.000	0.000	0.000	0.000
15	F	326	PHE	0	-0.009	0.001	11.878	0.007	0.007	0.000	0.000	0.000	0.000
16	F	327	PHE	0	-0.009	-0.003	15.625	0.015	0.015	0.000	0.000	0.000	0.000
17	F	328	VAL	0	0.008	0.002	17.783	0.015	0.015	0.000	0.000	0.000	0.000
18	F	329	SER	0	-0.006	-0.029	20.959	0.002	0.002	0.000	0.000	0.000	0.000
19	F	330	PHE	0	0.037	0.003	22.624	0.007	0.007	0.000	0.000	0.000	0.000
20	F	331	LYS	1	0.924	0.969	26.382	0.120	0.120	0.000	0.000	0.000	0.000
21	F	332	ASP	-1	-0.852	-0.896	26.321	-0.130	-0.130	0.000	0.000	0.000	0.000
22	F	333	ILE	0	-0.033	-0.014	24.596	0.003	0.003	0.000	0.000	0.000	0.000
23	F	334	GLY	0	-0.017	0.007	28.137	0.008	0.008	0.000	0.000	0.000	0.000
24	F	335	TRP	0	0.018	-0.005	25.095	0.004	0.004	0.000	0.000	0.000	0.000
25	F	336	ASN	0	-0.064	-0.033	29.723	-0.001	-0.001	0.000	0.000	0.000	0.000
26	F	337	ASP	-1	-0.882	-0.936	30.713	-0.060	-0.060	0.000	0.000	0.000	0.000
27	F	338	TRP	0	0.017	0.011	28.135	0.003	0.003	0.000	0.000	0.000	0.000
28	F	339	ILE	0	-0.038	-0.018	25.895	0.002	0.002	0.000	0.000	0.000	0.000
29	F	340	ILE	0	-0.017	0.001	29.513	-0.006	-0.006	0.000	0.000	0.000	0.000
30	F	341	ALA	0	-0.021	-0.008	26.668	-0.008	-0.008	0.000	0.000	0.000	0.000
31	F	342	PRO	0	0.010	0.003	21.547	0.008	0.008	0.000	0.000	0.000	0.000
32	F	343	SER	0	0.011	-0.022	24.380	0.007	0.007	0.000	0.000	0.000	0.000
33	F	344	GLY	0	0.006	-0.001	22.132	0.001	0.001	0.000	0.000	0.000	0.000
34	F	345	TYR	0	-0.044	-0.027	16.105	-0.009	-0.009	0.000	0.000	0.000	0.000
35	F	346	HIS	0	0.016	0.000	13.573	-0.043	-0.043	0.000	0.000	0.000	0.000
36	F	347	ALA	0	0.034	0.033	14.334	0.014	0.014	0.000	0.000	0.000	0.000
37	F	348	ASN	0	-0.062	-0.047	8.981	-0.010	-0.010	0.000	0.000	0.000	0.000
38	F	349	TYR	0	-0.046	-0.017	11.283	0.064	0.064	0.000	0.000	0.000	0.000
39	F	350	CYS	0	-0.073	-0.026	3.398	-0.485	-0.328	0.011	-0.078	-0.089	0.000
40	F	351	GLU	-1	-0.890	-0.945	10.036	0.011	0.011	0.000	0.000	0.000	0.000
41	F	352	GLY	0	0.048	0.015	11.265	-0.099	-0.099	0.000	0.000	0.000	0.000
42	F	353	GLU	-1	-0.948	-0.960	12.106	0.205	0.205	0.000	0.000	0.000	0.000
43	F	354	CYS	0	-0.094	-0.050	4.978	-0.362	-0.359	-0.002	-0.002	0.000	0.000
44	F	355	PRO	0	0.030	0.019	13.040	-0.035	-0.035	0.000	0.000	0.000	0.000
45	F	356	SER	0	-0.035	-0.026	15.863	0.037	0.037	0.000	0.000	0.000	0.000
46	F	387	LEU	0	0.064	0.040	17.362	-0.005	-0.005	0.000	0.000	0.000	0.000
47	F	388	LYS	1	0.928	0.955	16.566	-0.255	-0.255	0.000	0.000	0.000	0.000
48	F	389	SER	0	0.020	0.031	11.194	0.042	0.042	0.000	0.000	0.000	0.000
49	F	390	CYS	0	-0.043	-0.052	12.659	-0.095	-0.095	0.000	0.000	0.000	0.000
50	F	392	VAL	0	0.032	0.021	9.794	-0.075	-0.075	0.000	0.000	0.000	0.000
51	F	393	PRO	0	0.031	0.000	8.002	0.211	0.211	0.000	0.000	0.000	0.000
52	F	394	THR	0	-0.013	-0.012	4.922	-0.210	-0.210	0.000	0.000	0.000	0.000
53	F	395	LYS	1	0.814	0.903	5.474	0.911	0.911	0.000	0.000	0.000	0.000
54	F	396	LEU	0	0.008	0.009	8.249	-0.122	-0.122	0.000	0.000	0.000	0.000
55	F	397	ARG	1	0.901	0.936	11.253	0.354	0.354	0.000	0.000	0.000	0.000
56	F	398	PRO	0	-0.014	-0.015	13.376	0.002	0.002	0.000	0.000	0.000	0.000
57	F	399	MET	0	-0.057	-0.009	16.758	-0.034	-0.034	0.000	0.000	0.000	0.000
58	F	400	SER	0	-0.021	0.007	19.094	0.015	0.015	0.000	0.000	0.000	0.000
59	F	401	MET	0	-0.036	-0.028	22.770	-0.013	-0.013	0.000	0.000	0.000	0.000
60	F	402	LEU	0	-0.004	-0.013	25.180	0.009	0.009	0.000	0.000	0.000	0.000
61	F	403	TYR	0	-0.078	-0.054	28.689	-0.006	-0.006	0.000	0.000	0.000	0.000
62	F	404	TYR	0	0.021	0.015	31.060	0.005	0.005	0.000	0.000	0.000	0.000
63	F	405	ASP	-1	-0.874	-0.920	33.144	-0.022	-0.022	0.000	0.000	0.000	0.000
64	F	406	ASP	-1	-0.784	-0.903	34.774	-0.021	-0.021	0.000	0.000	0.000	0.000
65	F	407	GLY	0	-0.041	-0.011	38.243	-0.003	-0.003	0.000	0.000	0.000	0.000
66	F	408	GLN	0	-0.090	-0.053	40.630	0.000	0.000	0.000	0.000	0.000	0.000
67	F	409	ASN	0	-0.026	-0.001	37.587	-0.001	-0.001	0.000	0.000	0.000	0.000
68	F	410	ILE	0	0.013	0.011	34.038	-0.002	-0.002	0.000	0.000	0.000	0.000
69	F	411	ILE	0	-0.024	-0.011	30.566	0.004	0.004	0.000	0.000	0.000	0.000
70	F	412	LYS	1	0.814	0.901	25.852	0.048	0.048	0.000	0.000	0.000	0.000
71	F	413	LYS	1	0.889	0.934	26.372	0.025	0.025	0.000	0.000	0.000	0.000
72	F	414	ASP	-1	-0.782	-0.891	23.360	-0.061	-0.061	0.000	0.000	0.000	0.000
73	F	415	ILE	0	0.003	0.020	20.298	0.015	0.015	0.000	0.000	0.000	0.000
74	F	416	GLN	0	0.047	0.002	18.921	0.001	0.001	0.000	0.000	0.000	0.000
75	F	417	ASN	0	-0.030	-0.036	14.968	0.007	0.007	0.000	0.000	0.000	0.000
76	F	418	MET	0	0.026	0.040	15.251	0.011	0.011	0.000	0.000	0.000	0.000
77	F	419	ILE	0	0.011	0.014	11.409	-0.024	-0.024	0.000	0.000	0.000	0.000
78	F	420	VAL	0	0.036	0.021	7.682	0.043	0.043	0.000	0.000	0.000	0.000
79	F	421	GLU	-1	-0.844	-0.899	6.921	-0.715	-0.715	0.000	0.000	0.000	0.000
80	F	422	GLU	-1	-0.838	-0.936	2.004	-9.733	-9.946	6.398	-3.102	-3.082	-0.036
81	F	424	GLY	0	0.074	0.029	2.870	-0.646	0.493	0.357	-0.802	-0.695	-0.008
82	F	426	SER	0	0.050	0.022	8.215	0.191	0.191	0.000	0.000	0.000	0.000

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