FMO DATABASE

FMODB ID: Z68GN

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	OptHSide
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	-529828.405594
FMO2-HF: Nuclear repulsion	492994.237967
FMO2-HF: Total energy	-36834.167627
FMO2-MP2: Total energy	-36931.807918

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.
-5.439	-1.428	1.077	-2.535	-2.554	-0.018

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 : 0.010 / 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	F	313	GLU	-1	-0.861	-0.947	3.801	-1.754	-0.592	-0.013	-0.515	-0.634	0.002
4	F	314	CYS	0	-0.081	-0.026	5.691	0.625	0.625	0.000	0.000	0.000	0.000
5	F	315	ASP	-1	-0.856	-0.932	10.071	-0.567	-0.567	0.000	0.000	0.000	0.000
6	F	316	GLY	0	-0.017	-0.015	12.886	0.070	0.070	0.000	0.000	0.000	0.000
7	F	317	LYS	1	0.924	0.970	15.968	0.169	0.169	0.000	0.000	0.000	0.000
8	F	318	VAL	0	-0.006	0.011	10.297	0.000	0.000	0.000	0.000	0.000	0.000
9	F	319	ASN	0	0.008	-0.010	13.194	-0.004	-0.004	0.000	0.000	0.000	0.000
10	F	320	ILE	0	0.001	0.017	8.401	0.055	0.055	0.000	0.000	0.000	0.000
11	F	321	CYS	0	-0.049	-0.009	7.859	-0.137	-0.137	0.000	0.000	0.000	0.000
12	F	323	LYS	1	0.842	0.919	4.772	1.832	1.909	-0.001	-0.005	-0.071	0.000
13	F	324	LYS	1	0.889	0.941	7.916	-0.013	-0.013	0.000	0.000	0.000	0.000
14	F	325	GLN	0	0.043	0.014	9.333	-0.055	-0.055	0.000	0.000	0.000	0.000
15	F	326	PHE	0	-0.017	0.003	12.471	0.010	0.010	0.000	0.000	0.000	0.000
16	F	327	PHE	0	0.001	0.003	16.217	0.014	0.014	0.000	0.000	0.000	0.000
17	F	328	VAL	0	0.017	0.012	17.999	0.017	0.017	0.000	0.000	0.000	0.000
18	F	329	SER	0	-0.017	-0.042	21.322	-0.006	-0.006	0.000	0.000	0.000	0.000
19	F	330	PHE	0	0.039	0.001	23.163	0.008	0.008	0.000	0.000	0.000	0.000
20	F	331	LYS	1	0.941	0.968	26.850	0.119	0.119	0.000	0.000	0.000	0.000
21	F	332	ASP	-1	-0.877	-0.894	26.771	-0.130	-0.130	0.000	0.000	0.000	0.000
22	F	333	ILE	0	-0.043	-0.021	25.324	0.004	0.004	0.000	0.000	0.000	0.000
23	F	334	GLY	0	0.004	0.015	28.887	0.008	0.008	0.000	0.000	0.000	0.000
24	F	335	TRP	0	-0.003	-0.018	25.713	0.003	0.003	0.000	0.000	0.000	0.000
25	F	336	ASN	0	-0.063	-0.034	30.120	-0.002	-0.002	0.000	0.000	0.000	0.000
26	F	337	ASP	-1	-0.876	-0.932	31.008	-0.066	-0.066	0.000	0.000	0.000	0.000
27	F	338	TRP	0	0.030	0.012	28.657	0.002	0.002	0.000	0.000	0.000	0.000
28	F	339	ILE	0	-0.042	0.002	26.498	0.001	0.001	0.000	0.000	0.000	0.000
29	F	340	ILE	0	-0.034	-0.005	30.031	-0.005	-0.005	0.000	0.000	0.000	0.000
30	F	341	ALA	0	-0.018	0.001	27.075	-0.008	-0.008	0.000	0.000	0.000	0.000
31	F	342	PRO	0	-0.011	-0.006	21.956	0.006	0.006	0.000	0.000	0.000	0.000
32	F	343	SER	0	0.050	-0.001	24.098	0.007	0.007	0.000	0.000	0.000	0.000
33	F	344	GLY	0	0.007	-0.010	22.147	0.007	0.007	0.000	0.000	0.000	0.000
34	F	345	TYR	0	-0.031	-0.017	16.721	-0.010	-0.010	0.000	0.000	0.000	0.000
35	F	346	HIS	0	0.000	-0.008	13.996	-0.027	-0.027	0.000	0.000	0.000	0.000
36	F	347	ALA	0	0.026	0.021	14.804	0.004	0.004	0.000	0.000	0.000	0.000
37	F	348	ASN	0	-0.021	0.001	9.791	0.000	0.000	0.000	0.000	0.000	0.000
38	F	349	TYR	0	-0.012	-0.012	12.106	0.054	0.054	0.000	0.000	0.000	0.000
39	F	350	CYS	0	-0.053	-0.012	4.250	-0.039	-0.011	-0.002	-0.017	-0.009	0.000
40	F	351	GLU	-1	-0.904	-0.941	10.288	0.050	0.050	0.000	0.000	0.000	0.000
41	F	352	GLY	0	0.050	-0.002	10.756	-0.061	-0.061	0.000	0.000	0.000	0.000
42	F	353	GLU	-1	-0.938	-0.953	11.784	0.210	0.210	0.000	0.000	0.000	0.000
43	F	354	CYS	0	-0.138	-0.052	5.253	-0.418	-0.423	-0.002	0.000	0.006	0.000
44	F	355	PRO	0	0.031	0.019	13.211	-0.058	-0.058	0.000	0.000	0.000	0.000
45	F	356	SER	0	-0.040	-0.021	16.049	0.050	0.050	0.000	0.000	0.000	0.000
46	F	387	LEU	0	0.049	0.033	17.835	-0.006	-0.006	0.000	0.000	0.000	0.000
47	F	388	LYS	1	0.943	0.957	16.922	-0.269	-0.269	0.000	0.000	0.000	0.000
48	F	389	SER	0	-0.006	0.012	11.584	0.016	0.016	0.000	0.000	0.000	0.000
49	F	390	CYS	0	-0.003	-0.033	13.451	-0.060	-0.060	0.000	0.000	0.000	0.000
50	F	392	VAL	0	0.031	0.021	10.238	-0.113	-0.113	0.000	0.000	0.000	0.000
51	F	393	PRO	0	0.040	-0.010	8.343	0.157	0.157	0.000	0.000	0.000	0.000
52	F	394	THR	0	-0.044	-0.023	5.419	-0.093	-0.093	0.000	0.000	0.000	0.000
53	F	395	LYS	1	0.820	0.907	6.458	0.770	0.770	0.000	0.000	0.000	0.000
54	F	396	LEU	0	0.010	0.000	8.771	-0.092	-0.092	0.000	0.000	0.000	0.000
55	F	397	ARG	1	0.906	0.943	11.621	0.391	0.391	0.000	0.000	0.000	0.000
56	F	398	PRO	0	-0.020	-0.016	13.825	0.004	0.004	0.000	0.000	0.000	0.000
57	F	399	MET	0	-0.045	-0.009	17.469	-0.029	-0.029	0.000	0.000	0.000	0.000
58	F	400	SER	0	-0.013	0.006	19.568	0.017	0.017	0.000	0.000	0.000	0.000
59	F	401	MET	0	-0.045	-0.021	23.288	-0.011	-0.011	0.000	0.000	0.000	0.000
60	F	402	LEU	0	-0.016	-0.020	25.636	0.008	0.008	0.000	0.000	0.000	0.000
61	F	403	TYR	0	-0.059	-0.034	28.899	-0.005	-0.005	0.000	0.000	0.000	0.000
62	F	404	TYR	0	0.018	0.002	31.234	0.005	0.005	0.000	0.000	0.000	0.000
63	F	405	ASP	-1	-0.896	-0.952	34.029	-0.035	-0.035	0.000	0.000	0.000	0.000
64	F	406	ASP	-1	-0.849	-0.913	35.633	-0.028	-0.028	0.000	0.000	0.000	0.000
65	F	407	GLY	0	-0.040	-0.028	38.794	-0.004	-0.004	0.000	0.000	0.000	0.000
66	F	408	GLN	0	-0.058	-0.039	41.388	0.000	0.000	0.000	0.000	0.000	0.000
67	F	409	ASN	0	-0.001	0.013	38.047	0.001	0.001	0.000	0.000	0.000	0.000
68	F	410	ILE	0	0.011	0.004	33.892	-0.003	-0.003	0.000	0.000	0.000	0.000
69	F	411	ILE	0	-0.025	-0.005	30.620	0.003	0.003	0.000	0.000	0.000	0.000
70	F	412	LYS	1	0.846	0.916	26.360	0.068	0.068	0.000	0.000	0.000	0.000
71	F	413	LYS	1	0.913	0.954	26.752	0.042	0.042	0.000	0.000	0.000	0.000
72	F	414	ASP	-1	-0.814	-0.910	23.592	-0.084	-0.084	0.000	0.000	0.000	0.000
73	F	415	ILE	0	-0.011	0.005	20.712	0.013	0.013	0.000	0.000	0.000	0.000
74	F	416	GLN	0	0.030	0.007	19.162	-0.007	-0.007	0.000	0.000	0.000	0.000
75	F	417	ASN	0	-0.014	-0.031	15.407	0.002	0.002	0.000	0.000	0.000	0.000
76	F	418	MET	0	0.016	0.033	16.381	0.010	0.010	0.000	0.000	0.000	0.000
77	F	419	ILE	0	0.013	0.009	11.944	-0.011	-0.011	0.000	0.000	0.000	0.000
78	F	420	VAL	0	0.021	0.010	8.714	0.028	0.028	0.000	0.000	0.000	0.000
79	F	421	GLU	-1	-0.855	-0.906	7.203	-0.693	-0.693	0.000	0.000	0.000	0.000
80	F	422	GLU	-1	-0.837	-0.932	2.627	-5.483	-3.211	1.075	-1.709	-1.639	-0.018
81	F	424	GLY	0	0.084	0.042	3.515	-0.061	0.416	0.020	-0.289	-0.207	-0.002
82	F	426	SER	0	0.043	0.016	8.748	0.148	0.148	0.000	0.000	0.000	0.000

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