FMO DATABASE

FMODB ID: MVY2Z

Calculation Name: 5HLZ-H-Xray372

Preferred Name: Inhibin beta A chain

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5HLZ

Chain ID: H

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	80
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-510591.315886
FMO2-HF: Nuclear repulsion	474539.114184
FMO2-HF: Total energy	-36052.201702
FMO2-MP2: Total energy	-36147.386857

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(H:311:GLY)

Summations of interaction energy for fragment #1(H: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.
-2.068	1.043	0.457	-1.683	-1.884	-0.007

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : 0.006

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	H	313	GLU	-1	-0.946	-0.986	3.798	-1.573	-0.310	-0.018	-0.601	-0.643	0.002
4	H	314	CYS	0	-0.084	-0.026	5.974	0.834	0.834	0.000	0.000	0.000	0.000
5	H	315	ASP	-1	-0.843	-0.918	9.926	-0.454	-0.454	0.000	0.000	0.000	0.000
6	H	316	GLY	0	-0.041	-0.030	12.797	0.044	0.044	0.000	0.000	0.000	0.000
7	H	317	LYS	1	0.904	0.960	15.836	0.123	0.123	0.000	0.000	0.000	0.000
8	H	318	VAL	0	0.045	0.029	10.510	0.004	0.004	0.000	0.000	0.000	0.000
9	H	319	ASN	0	-0.017	-0.022	13.457	-0.013	-0.013	0.000	0.000	0.000	0.000
10	H	320	ILE	0	0.012	0.023	8.791	0.039	0.039	0.000	0.000	0.000	0.000
11	H	321	CYS	0	-0.045	-0.001	8.719	-0.072	-0.072	0.000	0.000	0.000	0.000
12	H	323	LYS	1	0.905	0.952	5.512	0.918	0.918	0.000	0.000	0.000	0.000
13	H	324	LYS	1	0.894	0.954	7.690	-0.259	-0.259	0.000	0.000	0.000	0.000
14	H	325	GLN	0	0.003	-0.008	9.768	-0.097	-0.097	0.000	0.000	0.000	0.000
15	H	326	PHE	0	-0.012	0.001	12.265	-0.013	-0.013	0.000	0.000	0.000	0.000
16	H	327	PHE	0	-0.007	-0.003	16.032	0.014	0.014	0.000	0.000	0.000	0.000
17	H	328	VAL	0	0.023	0.016	18.006	0.009	0.009	0.000	0.000	0.000	0.000
18	H	329	SER	0	0.025	0.012	21.252	0.001	0.001	0.000	0.000	0.000	0.000
19	H	330	PHE	0	0.065	0.015	23.261	0.006	0.006	0.000	0.000	0.000	0.000
20	H	331	LYS	1	0.913	0.947	26.850	0.070	0.070	0.000	0.000	0.000	0.000
21	H	332	ASP	-1	-0.913	-0.941	26.797	-0.070	-0.070	0.000	0.000	0.000	0.000
22	H	333	ILE	0	-0.061	-0.029	25.208	0.004	0.004	0.000	0.000	0.000	0.000
23	H	334	GLY	0	-0.004	0.010	28.758	0.006	0.006	0.000	0.000	0.000	0.000
24	H	335	TRP	0	0.003	-0.011	25.929	0.004	0.004	0.000	0.000	0.000	0.000
25	H	336	ASN	0	-0.050	-0.025	30.044	0.001	0.001	0.000	0.000	0.000	0.000
26	H	337	ASP	-1	-0.872	-0.931	31.061	-0.029	-0.029	0.000	0.000	0.000	0.000
27	H	338	TRP	0	0.012	0.007	28.934	0.001	0.001	0.000	0.000	0.000	0.000
28	H	339	ILE	0	-0.031	0.002	26.420	0.001	0.001	0.000	0.000	0.000	0.000
29	H	340	ILE	0	-0.033	-0.006	30.085	-0.005	-0.005	0.000	0.000	0.000	0.000
30	H	341	ALA	0	-0.028	-0.004	27.391	-0.007	-0.007	0.000	0.000	0.000	0.000
31	H	342	PRO	0	-0.004	-0.004	22.223	0.005	0.005	0.000	0.000	0.000	0.000
32	H	343	SER	0	0.026	-0.007	24.494	0.007	0.007	0.000	0.000	0.000	0.000
33	H	344	GLY	0	0.038	0.001	22.342	0.004	0.004	0.000	0.000	0.000	0.000
34	H	345	TYR	0	-0.042	-0.028	16.859	-0.007	-0.007	0.000	0.000	0.000	0.000
35	H	346	HIS	0	-0.009	-0.013	14.059	-0.011	-0.011	0.000	0.000	0.000	0.000
36	H	347	ALA	0	0.024	0.021	14.780	0.015	0.015	0.000	0.000	0.000	0.000
37	H	348	ASN	0	0.002	0.007	10.072	-0.024	-0.024	0.000	0.000	0.000	0.000
38	H	349	TYR	0	0.012	0.000	11.809	0.047	0.047	0.000	0.000	0.000	0.000
39	H	350	CYS	0	-0.063	0.000	4.227	-0.203	-0.169	-0.002	-0.006	-0.026	0.000
40	H	351	GLU	-1	-0.892	-0.939	10.547	0.178	0.178	0.000	0.000	0.000	0.000
41	H	352	GLY	0	0.023	-0.007	11.274	-0.028	-0.028	0.000	0.000	0.000	0.000
42	H	353	GLU	-1	-0.932	-0.952	12.216	0.274	0.274	0.000	0.000	0.000	0.000
43	H	354	CYS	0	-0.148	-0.065	6.466	-0.516	-0.516	0.000	0.000	0.000	0.000
44	H	355	PRO	0	0.025	0.015	13.978	-0.070	-0.070	0.000	0.000	0.000	0.000
45	H	356	SER	0	-0.004	0.010	16.386	0.045	0.045	0.000	0.000	0.000	0.000
46	H	389	SER	0	0.002	-0.016	13.466	0.016	0.016	0.000	0.000	0.000	0.000
47	H	390	CYS	0	0.013	-0.014	14.243	-0.070	-0.070	0.000	0.000	0.000	0.000
48	H	392	VAL	0	0.031	0.019	11.001	-0.113	-0.113	0.000	0.000	0.000	0.000
49	H	393	PRO	0	0.037	-0.023	8.675	0.193	0.193	0.000	0.000	0.000	0.000
50	H	394	THR	0	-0.099	-0.049	6.199	0.115	0.115	0.000	0.000	0.000	0.000
51	H	395	LYS	1	0.915	0.972	7.083	0.180	0.180	0.000	0.000	0.000	0.000
52	H	396	LEU	0	0.013	0.005	8.669	-0.046	-0.046	0.000	0.000	0.000	0.000
53	H	397	ARG	1	0.960	0.979	11.662	0.160	0.160	0.000	0.000	0.000	0.000
54	H	398	PRO	0	-0.027	-0.019	13.896	0.004	0.004	0.000	0.000	0.000	0.000
55	H	399	MET	0	-0.028	-0.010	17.637	-0.021	-0.021	0.000	0.000	0.000	0.000
56	H	400	SER	0	-0.025	0.012	19.770	0.012	0.012	0.000	0.000	0.000	0.000
57	H	401	MET	0	-0.026	-0.016	23.478	-0.006	-0.006	0.000	0.000	0.000	0.000
58	H	402	LEU	0	-0.019	-0.023	25.745	0.004	0.004	0.000	0.000	0.000	0.000
59	H	403	TYR	0	-0.028	-0.016	28.783	-0.002	-0.002	0.000	0.000	0.000	0.000
60	H	404	TYR	0	-0.001	-0.007	31.289	0.002	0.002	0.000	0.000	0.000	0.000
61	H	405	ASP	-1	-0.976	-0.989	34.151	0.000	0.000	0.000	0.000	0.000	0.000
62	H	406	ASP	-1	-0.836	-0.909	35.552	-0.005	-0.005	0.000	0.000	0.000	0.000
63	H	407	GLY	0	-0.043	-0.027	38.731	-0.003	-0.003	0.000	0.000	0.000	0.000
64	H	408	GLN	0	-0.045	-0.029	41.321	-0.001	-0.001	0.000	0.000	0.000	0.000
65	H	409	ASN	0	-0.012	0.000	38.069	0.000	0.000	0.000	0.000	0.000	0.000
66	H	410	ILE	0	0.009	0.005	34.016	-0.001	-0.001	0.000	0.000	0.000	0.000
67	H	411	ILE	0	-0.011	0.001	30.782	0.002	0.002	0.000	0.000	0.000	0.000
68	H	412	LYS	1	0.946	0.979	26.837	0.032	0.032	0.000	0.000	0.000	0.000
69	H	413	LYS	1	0.942	0.974	26.885	-0.006	-0.006	0.000	0.000	0.000	0.000
70	H	414	ASP	-1	-0.867	-0.954	23.688	-0.033	-0.033	0.000	0.000	0.000	0.000
71	H	415	ILE	0	-0.043	-0.016	20.869	0.009	0.009	0.000	0.000	0.000	0.000
72	H	416	GLN	0	0.034	0.011	19.149	-0.004	-0.004	0.000	0.000	0.000	0.000
73	H	417	ASN	0	-0.003	-0.027	15.278	-0.003	-0.003	0.000	0.000	0.000	0.000
74	H	418	MET	0	0.017	0.029	16.172	0.005	0.005	0.000	0.000	0.000	0.000
75	H	419	ILE	0	0.008	0.013	12.034	-0.011	-0.011	0.000	0.000	0.000	0.000
76	H	420	VAL	0	0.027	0.015	8.407	0.021	0.021	0.000	0.000	0.000	0.000
77	H	421	GLU	-1	-0.932	-0.974	7.062	-0.368	-0.368	0.000	0.000	0.000	0.000
78	H	422	GLU	-1	-0.896	-0.962	3.064	-2.457	-0.661	0.478	-1.055	-1.219	-0.009
79	H	424	GLY	0	0.095	0.050	4.321	1.083	1.101	-0.001	-0.021	0.004	0.000
80	H	426	SER	0	0.021	0.011	9.655	0.041	0.041	0.000	0.000	0.000	0.000

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