FMO DATABASE

FMODB ID: YZ872

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	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	-527918.176071
FMO2-HF: Nuclear repulsion	491083.91169
FMO2-HF: Total energy	-36834.264382
FMO2-MP2: Total energy	-36931.889142

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.
-2.765	0.493	0.396	-1.7	-1.953	-0.008

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 : 0.018 / q_NPA : 0.003

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	-0.897	-0.964	3.805	-1.678	-0.439	-0.015	-0.566	-0.658	0.002
4	B	314	CYS	0	-0.069	-0.015	5.840	0.585	0.585	0.000	0.000	0.000	0.000
5	B	315	ASP	-1	-0.883	-0.946	10.092	-0.537	-0.537	0.000	0.000	0.000	0.000
6	B	316	GLY	0	-0.027	-0.020	12.914	0.065	0.065	0.000	0.000	0.000	0.000
7	B	317	LYS	1	0.909	0.967	15.932	0.180	0.180	0.000	0.000	0.000	0.000
8	B	318	VAL	0	0.040	0.014	10.680	0.001	0.001	0.000	0.000	0.000	0.000
9	B	319	ASN	0	-0.009	-0.010	13.463	-0.007	-0.007	0.000	0.000	0.000	0.000
10	B	320	ILE	0	0.000	0.014	8.593	0.048	0.048	0.000	0.000	0.000	0.000
11	B	321	CYS	0	-0.049	-0.010	8.194	-0.136	-0.136	0.000	0.000	0.000	0.000
12	B	323	LYS	1	0.861	0.930	5.366	1.542	1.542	0.000	0.000	0.000	0.000
13	B	324	LYS	1	0.879	0.941	8.126	-0.024	-0.024	0.000	0.000	0.000	0.000
14	B	325	GLN	0	0.040	0.019	9.869	-0.010	-0.010	0.000	0.000	0.000	0.000
15	B	326	PHE	0	-0.009	0.002	12.945	-0.011	-0.011	0.000	0.000	0.000	0.000
16	B	327	PHE	0	-0.020	-0.003	16.635	0.014	0.014	0.000	0.000	0.000	0.000
17	B	328	VAL	0	0.016	0.009	18.468	0.014	0.014	0.000	0.000	0.000	0.000
18	B	329	SER	0	-0.010	-0.040	21.758	-0.004	-0.004	0.000	0.000	0.000	0.000
19	B	330	PHE	0	0.040	0.003	23.637	0.006	0.006	0.000	0.000	0.000	0.000
20	B	331	LYS	1	0.940	0.965	27.324	0.103	0.103	0.000	0.000	0.000	0.000
21	B	332	ASP	-1	-0.876	-0.894	27.167	-0.113	-0.113	0.000	0.000	0.000	0.000
22	B	333	ILE	0	-0.046	-0.022	25.777	0.003	0.003	0.000	0.000	0.000	0.000
23	B	334	GLY	0	0.004	0.015	29.361	0.007	0.007	0.000	0.000	0.000	0.000
24	B	335	TRP	0	0.000	-0.016	26.239	0.003	0.003	0.000	0.000	0.000	0.000
25	B	336	ASN	0	-0.065	-0.033	30.533	-0.001	-0.001	0.000	0.000	0.000	0.000
26	B	337	ASP	-1	-0.876	-0.934	31.426	-0.055	-0.055	0.000	0.000	0.000	0.000
27	B	338	TRP	0	0.028	0.012	29.210	0.001	0.001	0.000	0.000	0.000	0.000
28	B	339	ILE	0	-0.042	-0.001	26.986	0.001	0.001	0.000	0.000	0.000	0.000
29	B	340	ILE	0	-0.035	-0.005	30.470	-0.005	-0.005	0.000	0.000	0.000	0.000
30	B	341	ALA	0	-0.018	0.001	27.400	-0.007	-0.007	0.000	0.000	0.000	0.000
31	B	342	PRO	0	-0.009	-0.006	22.370	0.006	0.006	0.000	0.000	0.000	0.000
32	B	343	SER	0	0.051	0.000	24.435	0.006	0.006	0.000	0.000	0.000	0.000
33	B	344	GLY	0	0.007	-0.013	22.635	0.006	0.006	0.000	0.000	0.000	0.000
34	B	345	TYR	0	-0.035	-0.020	17.233	-0.009	-0.009	0.000	0.000	0.000	0.000
35	B	346	HIS	0	-0.006	-0.010	14.548	-0.024	-0.024	0.000	0.000	0.000	0.000
36	B	347	ALA	0	0.019	0.017	15.447	0.006	0.006	0.000	0.000	0.000	0.000
37	B	348	ASN	0	-0.024	-0.006	10.408	-0.006	-0.006	0.000	0.000	0.000	0.000
38	B	349	TYR	0	-0.060	-0.054	12.442	0.038	0.038	0.000	0.000	0.000	0.000
39	B	350	CYS	0	-0.020	0.004	4.277	-0.077	-0.057	-0.002	-0.009	-0.008	0.000
40	B	351	GLU	-1	-0.787	-0.859	10.664	-0.066	-0.066	0.000	0.000	0.000	0.000
41	B	352	GLY	0	0.043	-0.004	10.831	-0.035	-0.035	0.000	0.000	0.000	0.000
42	B	353	GLU	-1	-0.918	-0.945	12.218	0.262	0.262	0.000	0.000	0.000	0.000
43	B	354	CYS	0	-0.086	-0.040	5.730	-0.349	-0.349	0.000	0.000	0.000	0.000
44	B	355	PRO	0	0.047	0.027	13.299	-0.066	-0.066	0.000	0.000	0.000	0.000
45	B	356	SER	0	-0.021	-0.003	16.129	-0.011	-0.011	0.000	0.000	0.000	0.000
46	B	387	LEU	0	-0.018	-0.013	18.432	-0.005	-0.005	0.000	0.000	0.000	0.000
47	B	388	LYS	1	0.928	0.950	18.540	-0.230	-0.230	0.000	0.000	0.000	0.000
48	B	389	SER	0	0.003	-0.005	12.564	0.029	0.029	0.000	0.000	0.000	0.000
49	B	390	CYS	0	0.025	-0.008	13.925	-0.041	-0.041	0.000	0.000	0.000	0.000
50	B	392	VAL	0	0.014	0.016	10.475	-0.107	-0.107	0.000	0.000	0.000	0.000
51	B	393	PRO	0	0.058	-0.002	8.427	0.138	0.138	0.000	0.000	0.000	0.000
52	B	394	THR	0	-0.056	-0.040	5.228	-0.100	-0.100	0.000	0.000	0.000	0.000
53	B	395	LYS	1	0.816	0.906	6.577	0.514	0.514	0.000	0.000	0.000	0.000
54	B	396	LEU	0	0.010	-0.001	8.814	-0.084	-0.084	0.000	0.000	0.000	0.000
55	B	397	ARG	1	0.911	0.942	11.857	0.310	0.310	0.000	0.000	0.000	0.000
56	B	398	PRO	0	-0.024	-0.016	14.156	0.000	0.000	0.000	0.000	0.000	0.000
57	B	399	MET	0	-0.042	-0.004	17.824	-0.025	-0.025	0.000	0.000	0.000	0.000
58	B	400	SER	0	-0.019	0.002	19.956	0.014	0.014	0.000	0.000	0.000	0.000
59	B	401	MET	0	-0.046	-0.023	23.655	-0.010	-0.010	0.000	0.000	0.000	0.000
60	B	402	LEU	0	-0.019	-0.022	26.050	0.007	0.007	0.000	0.000	0.000	0.000
61	B	403	TYR	0	-0.055	-0.031	29.431	-0.004	-0.004	0.000	0.000	0.000	0.000
62	B	404	TYR	0	0.030	0.010	31.741	0.004	0.004	0.000	0.000	0.000	0.000
63	B	405	ASP	-1	-0.902	-0.950	34.592	-0.026	-0.026	0.000	0.000	0.000	0.000
64	B	406	ASP	-1	-0.849	-0.916	36.174	-0.022	-0.022	0.000	0.000	0.000	0.000
65	B	407	GLY	0	-0.040	-0.027	39.349	-0.003	-0.003	0.000	0.000	0.000	0.000
66	B	408	GLN	0	-0.056	-0.038	41.947	0.000	0.000	0.000	0.000	0.000	0.000
67	B	409	ASN	0	-0.010	0.009	38.656	0.001	0.001	0.000	0.000	0.000	0.000
68	B	410	ILE	0	0.014	0.004	34.329	-0.002	-0.002	0.000	0.000	0.000	0.000
69	B	411	ILE	0	-0.023	-0.007	31.115	0.003	0.003	0.000	0.000	0.000	0.000
70	B	412	LYS	1	0.843	0.914	26.690	0.054	0.054	0.000	0.000	0.000	0.000
71	B	413	LYS	1	0.913	0.954	27.293	0.031	0.031	0.000	0.000	0.000	0.000
72	B	414	ASP	-1	-0.812	-0.910	23.972	-0.066	-0.066	0.000	0.000	0.000	0.000
73	B	415	ILE	0	-0.013	0.005	21.402	0.011	0.011	0.000	0.000	0.000	0.000
74	B	416	GLN	0	0.033	0.008	19.564	-0.004	-0.004	0.000	0.000	0.000	0.000
75	B	417	ASN	0	-0.014	-0.028	15.703	0.002	0.002	0.000	0.000	0.000	0.000
76	B	418	MET	0	0.030	0.030	16.646	0.005	0.005	0.000	0.000	0.000	0.000
77	B	419	ILE	0	0.005	0.011	12.419	-0.009	-0.009	0.000	0.000	0.000	0.000
78	B	420	VAL	0	0.023	0.013	8.936	0.028	0.028	0.000	0.000	0.000	0.000
79	B	421	GLU	-1	-0.856	-0.910	7.381	-0.544	-0.544	0.000	0.000	0.000	0.000
80	B	422	GLU	-1	-0.853	-0.934	2.889	-2.604	-0.988	0.403	-0.938	-1.081	-0.009
81	B	424	GLY	0	0.042	0.036	3.593	0.271	0.654	0.010	-0.187	-0.206	-0.001
82	B	426	SER	0	0.022	0.028	9.271	0.033	0.033	0.000	0.000	0.000	0.000

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