FMO DATABASE

FMODB ID: QY64Y

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	OptH
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	-498009.691271
FMO2-HF: Nuclear repulsion	462600.884234
FMO2-HF: Total energy	-35408.807037
FMO2-MP2: Total energy	-35502.122768

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.
-1.996	0.915	0.289	-1.541	-1.659	-0.005

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 : 0.018 / 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

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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	-0.941	-0.980	3.801	-1.606	-0.345	-0.018	-0.596	-0.648	0.002
4	D	314	CYS	0	-0.058	0.009	5.833	0.835	0.835	0.000	0.000	0.000	0.000
5	D	315	ASP	-1	-0.819	-0.908	9.869	-0.465	-0.465	0.000	0.000	0.000	0.000
6	D	316	GLY	0	-0.042	-0.039	12.931	0.053	0.053	0.000	0.000	0.000	0.000
7	D	317	LYS	1	0.955	0.977	15.791	0.130	0.130	0.000	0.000	0.000	0.000
8	D	318	VAL	0	-0.035	0.001	10.596	0.073	0.073	0.000	0.000	0.000	0.000
9	D	319	ASN	0	0.000	-0.010	13.569	-0.005	-0.005	0.000	0.000	0.000	0.000
10	D	320	ILE	0	-0.001	0.012	8.857	0.032	0.032	0.000	0.000	0.000	0.000
11	D	321	CYS	0	-0.052	-0.001	8.528	-0.100	-0.100	0.000	0.000	0.000	0.000
12	D	323	LYS	1	0.910	0.951	5.927	0.954	0.954	0.000	0.000	0.000	0.000
13	D	324	LYS	1	0.911	0.947	7.909	-0.177	-0.177	0.000	0.000	0.000	0.000
14	D	325	GLN	0	-0.002	-0.011	10.289	-0.101	-0.101	0.000	0.000	0.000	0.000
15	D	326	PHE	0	-0.013	0.004	12.698	-0.009	-0.009	0.000	0.000	0.000	0.000
16	D	327	PHE	0	-0.012	-0.005	16.451	0.012	0.012	0.000	0.000	0.000	0.000
17	D	328	VAL	0	0.029	0.017	18.292	0.010	0.010	0.000	0.000	0.000	0.000
18	D	329	SER	0	0.020	0.008	21.526	0.001	0.001	0.000	0.000	0.000	0.000
19	D	330	PHE	0	0.063	0.015	23.548	0.006	0.006	0.000	0.000	0.000	0.000
20	D	331	LYS	1	0.918	0.956	27.164	0.081	0.081	0.000	0.000	0.000	0.000
21	D	332	ASP	-1	-0.915	-0.943	27.129	-0.078	-0.078	0.000	0.000	0.000	0.000
22	D	333	ILE	0	-0.057	-0.028	25.465	0.004	0.004	0.000	0.000	0.000	0.000
23	D	334	GLY	0	-0.007	0.009	29.046	0.006	0.006	0.000	0.000	0.000	0.000
24	D	335	TRP	0	0.001	-0.015	26.135	0.004	0.004	0.000	0.000	0.000	0.000
25	D	336	ASN	0	-0.051	-0.027	30.373	0.001	0.001	0.000	0.000	0.000	0.000
26	D	337	ASP	-1	-0.868	-0.928	31.323	-0.035	-0.035	0.000	0.000	0.000	0.000
27	D	338	TRP	0	0.006	0.004	29.073	0.001	0.001	0.000	0.000	0.000	0.000
28	D	339	ILE	0	-0.035	0.002	26.702	0.001	0.001	0.000	0.000	0.000	0.000
29	D	340	ILE	0	-0.026	-0.006	30.350	-0.005	-0.005	0.000	0.000	0.000	0.000
30	D	341	ALA	0	-0.024	-0.004	27.439	-0.008	-0.008	0.000	0.000	0.000	0.000
31	D	342	PRO	0	-0.018	-0.007	22.414	0.006	0.006	0.000	0.000	0.000	0.000
32	D	343	SER	0	0.026	-0.007	24.342	0.007	0.007	0.000	0.000	0.000	0.000
33	D	344	GLY	0	0.047	0.004	22.553	0.005	0.005	0.000	0.000	0.000	0.000
34	D	345	TYR	0	-0.035	-0.024	16.976	-0.007	-0.007	0.000	0.000	0.000	0.000
35	D	346	HIS	0	-0.017	-0.014	14.308	-0.011	-0.011	0.000	0.000	0.000	0.000
36	D	347	ALA	0	0.030	0.022	14.918	0.011	0.011	0.000	0.000	0.000	0.000
37	D	348	ASN	0	0.003	0.008	10.283	-0.019	-0.019	0.000	0.000	0.000	0.000
38	D	349	TYR	0	-0.009	-0.006	11.982	0.036	0.036	0.000	0.000	0.000	0.000
39	D	350	CYS	0	-0.068	-0.006	4.148	-0.159	-0.120	-0.002	-0.010	-0.026	0.000
40	D	351	GLU	-1	-0.872	-0.941	10.460	0.046	0.046	0.000	0.000	0.000	0.000
41	D	352	GLY	0	0.029	-0.001	11.148	0.019	0.019	0.000	0.000	0.000	0.000
42	D	353	GLU	-1	-0.957	-0.964	12.978	0.277	0.277	0.000	0.000	0.000	0.000
43	D	354	CYS	0	-0.102	-0.029	5.910	-0.612	-0.612	0.000	0.000	0.000	0.000
44	D	389	SER	0	-0.017	-0.025	13.529	0.027	0.027	0.000	0.000	0.000	0.000
45	D	390	CYS	0	0.006	-0.026	13.857	-0.071	-0.071	0.000	0.000	0.000	0.000
46	D	392	VAL	0	0.017	0.009	10.632	-0.121	-0.121	0.000	0.000	0.000	0.000
47	D	393	PRO	0	0.057	-0.017	8.554	0.188	0.188	0.000	0.000	0.000	0.000
48	D	394	THR	0	-0.025	-0.007	5.731	0.158	0.158	0.000	0.000	0.000	0.000
49	D	395	LYS	1	0.881	0.957	6.908	0.255	0.255	0.000	0.000	0.000	0.000
50	D	396	LEU	0	0.014	0.009	8.442	-0.066	-0.066	0.000	0.000	0.000	0.000
51	D	397	ARG	1	0.960	0.978	11.609	0.203	0.203	0.000	0.000	0.000	0.000
52	D	398	PRO	0	-0.020	-0.017	13.936	0.003	0.003	0.000	0.000	0.000	0.000
53	D	399	MET	0	-0.035	-0.009	17.736	-0.022	-0.022	0.000	0.000	0.000	0.000
54	D	400	SER	0	-0.047	-0.053	19.859	0.012	0.012	0.000	0.000	0.000	0.000
55	D	401	MET	0	-0.059	-0.026	23.576	-0.007	-0.007	0.000	0.000	0.000	0.000
56	D	402	LEU	0	-0.030	-0.028	25.889	0.005	0.005	0.000	0.000	0.000	0.000
57	D	403	TYR	0	-0.027	-0.015	28.920	-0.002	-0.002	0.000	0.000	0.000	0.000
58	D	404	TYR	0	0.006	-0.007	31.525	0.003	0.003	0.000	0.000	0.000	0.000
59	D	405	ASP	-1	-0.976	-0.990	34.484	-0.006	-0.006	0.000	0.000	0.000	0.000
60	D	406	ASP	-1	-0.836	-0.908	35.715	-0.008	-0.008	0.000	0.000	0.000	0.000
61	D	407	GLY	0	-0.046	-0.027	38.985	-0.003	-0.003	0.000	0.000	0.000	0.000
62	D	408	GLN	0	-0.045	-0.030	41.600	-0.001	-0.001	0.000	0.000	0.000	0.000
63	D	409	ASN	0	-0.014	0.000	38.184	0.001	0.001	0.000	0.000	0.000	0.000
64	D	410	ILE	0	0.010	0.007	34.200	-0.001	-0.001	0.000	0.000	0.000	0.000
65	D	411	ILE	0	-0.010	0.003	30.862	0.002	0.002	0.000	0.000	0.000	0.000
66	D	412	LYS	1	0.951	0.979	26.848	0.039	0.039	0.000	0.000	0.000	0.000
67	D	413	LYS	1	0.942	0.970	26.910	0.002	0.002	0.000	0.000	0.000	0.000
68	D	414	ASP	-1	-0.809	-0.881	23.613	-0.043	-0.043	0.000	0.000	0.000	0.000
69	D	415	ILE	0	-0.035	-0.006	20.712	0.011	0.011	0.000	0.000	0.000	0.000
70	D	416	GLN	0	0.034	0.008	19.108	-0.005	-0.005	0.000	0.000	0.000	0.000
71	D	417	ASN	0	-0.008	-0.031	15.224	-0.003	-0.003	0.000	0.000	0.000	0.000
72	D	418	MET	0	0.019	0.033	16.168	0.014	0.014	0.000	0.000	0.000	0.000
73	D	419	ILE	0	-0.009	-0.001	12.380	-0.012	-0.012	0.000	0.000	0.000	0.000
74	D	420	VAL	0	0.026	0.015	8.560	0.023	0.023	0.000	0.000	0.000	0.000
75	D	421	GLU	-1	-0.953	-0.984	7.315	-0.440	-0.440	0.000	0.000	0.000	0.000
76	D	422	GLU	-1	-0.923	-0.980	3.083	-2.203	-0.728	0.307	-0.842	-0.940	-0.007
77	D	424	GLY	0	0.079	0.045	3.890	0.756	0.892	0.002	-0.093	-0.045	0.000
78	D	426	SER	0	0.038	0.026	9.427	0.102	0.102	0.000	0.000	0.000	0.000

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