FMO DATABASE

FMODB ID: V5LZ1

Calculation Name: 5HLZ-B-Xray372

Preferred Name: Inhibin beta A chain

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5HLZ

Chain ID: B

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	-529858.23901
FMO2-HF: Nuclear repulsion	493023.588353
FMO2-HF: Total energy	-36834.650657
FMO2-MP2: Total energy	-36932.348996

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(B:311:GLY)

Summations of interaction energy for fragment #1(B: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.
-4.31	-1.832	3.711	-2.419	-3.769	-0.025

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : 0.014

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	B	313	GLU	-1	-0.867	-0.927	3.854	-0.732	0.226	-0.008	-0.430	-0.519	0.002
4	B	314	CYS	0	-0.042	-0.022	6.208	0.529	0.529	0.000	0.000	0.000	0.000
5	B	315	ASP	-1	-0.811	-0.903	9.967	-0.220	-0.220	0.000	0.000	0.000	0.000
6	B	316	GLY	0	-0.029	-0.012	12.429	0.028	0.028	0.000	0.000	0.000	0.000
7	B	317	LYS	1	0.789	0.895	14.909	0.200	0.200	0.000	0.000	0.000	0.000
8	B	318	VAL	0	-0.002	-0.001	10.682	-0.014	-0.014	0.000	0.000	0.000	0.000
9	B	319	ASN	0	0.005	-0.004	13.624	0.017	0.017	0.000	0.000	0.000	0.000
10	B	320	ILE	0	-0.013	0.007	9.212	0.010	0.010	0.000	0.000	0.000	0.000
11	B	321	CYS	0	-0.041	0.004	9.047	0.037	0.037	0.000	0.000	0.000	0.000
12	B	323	LYS	1	0.853	0.898	4.207	0.562	0.679	-0.001	-0.012	-0.105	0.000
13	B	324	LYS	1	0.831	0.904	7.095	-0.351	-0.351	0.000	0.000	0.000	0.000
14	B	325	GLN	0	0.043	0.026	8.820	0.062	0.062	0.000	0.000	0.000	0.000
15	B	326	PHE	0	0.014	0.008	11.851	-0.036	-0.036	0.000	0.000	0.000	0.000
16	B	327	PHE	0	-0.021	-0.005	15.506	0.017	0.017	0.000	0.000	0.000	0.000
17	B	328	VAL	0	0.011	0.001	17.671	0.003	0.003	0.000	0.000	0.000	0.000
18	B	329	SER	0	-0.009	-0.031	20.811	0.002	0.002	0.000	0.000	0.000	0.000
19	B	330	PHE	0	0.039	0.004	22.696	0.005	0.005	0.000	0.000	0.000	0.000
20	B	331	LYS	1	0.923	0.968	26.313	0.038	0.038	0.000	0.000	0.000	0.000
21	B	332	ASP	-1	-0.853	-0.896	26.101	-0.030	-0.030	0.000	0.000	0.000	0.000
22	B	333	ILE	0	-0.034	-0.015	24.460	0.003	0.003	0.000	0.000	0.000	0.000
23	B	334	GLY	0	-0.016	0.008	28.024	0.004	0.004	0.000	0.000	0.000	0.000
24	B	335	TRP	0	0.017	-0.006	25.111	0.005	0.005	0.000	0.000	0.000	0.000
25	B	336	ASN	0	-0.063	-0.033	29.635	0.000	0.000	0.000	0.000	0.000	0.000
26	B	337	ASP	-1	-0.882	-0.935	30.645	0.000	0.000	0.000	0.000	0.000	0.000
27	B	338	TRP	0	0.016	0.012	28.216	0.000	0.000	0.000	0.000	0.000	0.000
28	B	339	ILE	0	-0.038	-0.018	25.948	0.001	0.001	0.000	0.000	0.000	0.000
29	B	340	ILE	0	-0.019	0.000	29.548	-0.005	-0.005	0.000	0.000	0.000	0.000
30	B	341	ALA	0	-0.021	-0.008	26.663	-0.007	-0.007	0.000	0.000	0.000	0.000
31	B	342	PRO	0	0.011	0.004	21.573	0.005	0.005	0.000	0.000	0.000	0.000
32	B	343	SER	0	0.008	-0.023	24.249	0.003	0.003	0.000	0.000	0.000	0.000
33	B	344	GLY	0	0.009	-0.001	22.071	-0.001	-0.001	0.000	0.000	0.000	0.000
34	B	345	TYR	0	-0.039	-0.021	16.239	-0.007	-0.007	0.000	0.000	0.000	0.000
35	B	346	HIS	0	-0.004	-0.004	13.608	-0.019	-0.019	0.000	0.000	0.000	0.000
36	B	347	ALA	0	0.034	0.030	14.611	0.025	0.025	0.000	0.000	0.000	0.000
37	B	348	ASN	0	-0.059	-0.044	9.476	-0.022	-0.022	0.000	0.000	0.000	0.000
38	B	349	TYR	0	-0.073	-0.056	11.263	0.022	0.022	0.000	0.000	0.000	0.000
39	B	350	CYS	0	-0.041	0.003	3.823	-0.735	-0.658	-0.001	-0.017	-0.059	0.000
40	B	351	GLU	-1	-0.745	-0.846	10.353	0.076	0.076	0.000	0.000	0.000	0.000
41	B	352	GLY	0	0.058	0.025	10.867	0.067	0.067	0.000	0.000	0.000	0.000
42	B	353	GLU	-1	-0.893	-0.934	13.041	0.432	0.432	0.000	0.000	0.000	0.000
43	B	354	CYS	0	-0.079	-0.058	6.809	-0.510	-0.510	0.000	0.000	0.000	0.000
44	B	355	PRO	0	0.045	0.029	13.881	-0.068	-0.068	0.000	0.000	0.000	0.000
45	B	356	SER	0	-0.023	-0.001	16.677	-0.026	-0.026	0.000	0.000	0.000	0.000
46	B	387	LEU	0	-0.002	-0.004	18.631	-0.003	-0.003	0.000	0.000	0.000	0.000
47	B	388	LYS	1	0.904	0.935	19.310	-0.267	-0.267	0.000	0.000	0.000	0.000
48	B	389	SER	0	0.017	-0.010	13.700	0.072	0.072	0.000	0.000	0.000	0.000
49	B	390	CYS	0	-0.019	-0.014	14.228	-0.063	-0.063	0.000	0.000	0.000	0.000
50	B	392	VAL	0	0.024	0.023	11.142	-0.094	-0.094	0.000	0.000	0.000	0.000
51	B	393	PRO	0	0.072	0.003	8.454	0.335	0.335	0.000	0.000	0.000	0.000
52	B	394	THR	0	-0.023	-0.006	4.824	-0.372	-0.372	0.000	0.000	0.000	0.000
53	B	395	LYS	1	0.801	0.898	5.692	0.234	0.234	0.000	0.000	0.000	0.000
54	B	396	LEU	0	0.016	0.011	8.148	0.013	0.013	0.000	0.000	0.000	0.000
55	B	397	ARG	1	0.909	0.941	11.188	0.049	0.049	0.000	0.000	0.000	0.000
56	B	398	PRO	0	-0.011	-0.016	13.465	0.011	0.011	0.000	0.000	0.000	0.000
57	B	399	MET	0	-0.053	-0.005	16.797	-0.016	-0.016	0.000	0.000	0.000	0.000
58	B	400	SER	0	-0.016	0.009	19.146	0.006	0.006	0.000	0.000	0.000	0.000
59	B	401	MET	0	-0.033	-0.028	22.820	-0.003	-0.003	0.000	0.000	0.000	0.000
60	B	402	LEU	0	0.000	-0.010	25.284	0.002	0.002	0.000	0.000	0.000	0.000
61	B	403	TYR	0	-0.074	-0.050	28.715	-0.001	-0.001	0.000	0.000	0.000	0.000
62	B	404	TYR	0	0.017	0.011	31.117	0.000	0.000	0.000	0.000	0.000	0.000
63	B	405	ASP	-1	-0.864	-0.914	33.231	0.027	0.027	0.000	0.000	0.000	0.000
64	B	406	ASP	-1	-0.763	-0.880	34.907	0.013	0.013	0.000	0.000	0.000	0.000
65	B	407	GLY	0	-0.033	-0.003	38.455	-0.002	-0.002	0.000	0.000	0.000	0.000
66	B	408	GLN	0	-0.085	-0.049	40.688	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	409	ASN	0	-0.083	-0.048	37.911	0.000	0.000	0.000	0.000	0.000	0.000
68	B	410	ILE	0	0.011	0.011	34.036	0.001	0.001	0.000	0.000	0.000	0.000
69	B	411	ILE	0	-0.013	-0.009	30.653	0.001	0.001	0.000	0.000	0.000	0.000
70	B	412	LYS	1	0.814	0.901	25.930	0.001	0.001	0.000	0.000	0.000	0.000
71	B	413	LYS	1	0.891	0.936	26.642	-0.028	-0.028	0.000	0.000	0.000	0.000
72	B	414	ASP	-1	-0.790	-0.888	23.566	-0.003	-0.003	0.000	0.000	0.000	0.000
73	B	415	ILE	0	-0.006	0.008	20.915	0.007	0.007	0.000	0.000	0.000	0.000
74	B	416	GLN	0	0.035	-0.001	18.800	0.009	0.009	0.000	0.000	0.000	0.000
75	B	417	ASN	0	-0.021	-0.031	14.971	0.003	0.003	0.000	0.000	0.000	0.000
76	B	418	MET	0	0.043	0.039	15.397	0.025	0.025	0.000	0.000	0.000	0.000
77	B	419	ILE	0	-0.013	0.010	11.394	-0.006	-0.006	0.000	0.000	0.000	0.000
78	B	420	VAL	0	0.034	0.021	7.770	0.014	0.014	0.000	0.000	0.000	0.000
79	B	421	GLU	-1	-0.853	-0.911	6.788	-0.306	-0.306	0.000	0.000	0.000	0.000
80	B	422	GLU	-1	-0.853	-0.942	2.182	-6.097	-4.823	3.722	-1.947	-3.048	-0.027
81	B	424	GLY	0	0.034	0.017	4.634	2.752	2.804	-0.001	-0.013	-0.038	0.000
82	B	426	SER	0	0.022	0.031	9.976	0.007	0.007	0.000	0.000	0.000	0.000

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