FMO DATABASE

FMODB ID: R5L58

Calculation Name: 3BHP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BHP

Chain ID: A

ChEMBL ID:

UniProt ID: O31818

Base Structure: X-ray

Registration Date: 2023-03-14

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	52
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-241412.805039
FMO2-HF: Nuclear repulsion	220820.457633
FMO2-HF: Total energy	-20592.347406
FMO2-MP2: Total energy	-20651.972752

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(A:1:MET)

Summations of interaction energy for fragment #1(A:1:MET)

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.
-12.161	-6.018	7.427	-4.871	-8.697	-0.015

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.008

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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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	A	3	SER	0	0.022	0.003	2.926	-3.576	-1.233	0.226	-1.274	-1.296	-0.003
4	A	4	ASN	0	0.111	0.033	4.646	-0.771	-0.606	-0.001	-0.010	-0.153	0.000
5	A	5	ALA	0	0.032	0.025	6.100	0.260	0.260	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.911	0.953	7.235	0.810	0.810	0.000	0.000	0.000	0.000
7	A	7	ILE	0	0.006	0.019	2.366	0.281	-0.165	2.219	-0.296	-1.477	0.000
8	A	8	ALA	0	0.015	0.005	6.527	0.306	0.306	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.849	0.909	9.690	0.542	0.542	0.000	0.000	0.000	0.000
10	A	10	ILE	0	0.003	0.003	7.068	0.156	0.156	0.000	0.000	0.000	0.000
11	A	11	ASN	0	0.004	-0.012	7.814	0.233	0.233	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.908	-0.950	11.221	-0.409	-0.409	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.021	-0.012	14.030	0.075	0.075	0.000	0.000	0.000	0.000
14	A	14	ALA	0	-0.036	-0.013	12.852	0.066	0.066	0.000	0.000	0.000	0.000
15	A	15	ALA	0	-0.003	-0.003	14.870	0.049	0.049	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.900	0.938	17.113	0.264	0.264	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.022	-0.009	17.970	0.028	0.028	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.932	0.971	18.843	0.146	0.146	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.039	-0.021	20.567	0.013	0.013	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.003	0.014	22.824	0.008	0.008	0.000	0.000	0.000	0.000
21	A	21	VAL	0	-0.013	-0.011	22.752	0.005	0.005	0.000	0.000	0.000	0.000
22	A	22	ILE	0	-0.113	-0.034	18.381	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	23	THR	0	0.050	0.017	22.386	0.024	0.024	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.813	-0.935	22.822	0.001	0.001	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.888	-0.941	22.957	-0.032	-0.032	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.809	-0.901	19.331	-0.188	-0.188	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.882	0.953	18.354	0.003	0.003	0.000	0.000	0.000	0.000
28	A	28	ALA	0	0.029	0.020	18.369	0.030	0.030	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.823	-0.887	15.542	-0.265	-0.265	0.000	0.000	0.000	0.000
30	A	30	GLN	0	0.038	-0.001	12.559	-0.023	-0.023	0.000	0.000	0.000	0.000
31	A	31	GLN	0	-0.038	-0.023	13.482	0.025	0.025	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.974	0.983	13.456	0.080	0.080	0.000	0.000	0.000	0.000
33	A	33	LEU	0	0.024	0.016	10.229	0.104	0.104	0.000	0.000	0.000	0.000
34	A	34	ARG	1	0.956	0.978	8.878	-0.064	-0.064	0.000	0.000	0.000	0.000
35	A	35	GLN	0	-0.033	-0.011	9.415	0.335	0.335	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.915	-0.967	7.515	0.295	0.295	0.000	0.000	0.000	0.000
37	A	37	TYR	0	-0.008	-0.005	3.339	0.162	0.902	0.020	-0.166	-0.593	-0.001
38	A	38	LEU	0	0.028	0.005	4.582	1.227	1.359	-0.001	-0.008	-0.123	0.000
39	A	39	LYS	1	0.914	0.968	6.931	-0.956	-0.956	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.013	0.003	2.850	-1.359	-0.444	0.363	-0.646	-0.632	0.004
41	A	41	PHE	0	0.042	0.018	2.909	3.550	4.211	1.756	-0.392	-2.024	-0.005
42	A	42	ARG	1	0.963	0.972	4.568	-2.568	-2.479	-0.001	-0.008	-0.080	0.000
43	A	43	SER	0	-0.072	-0.031	4.510	-1.299	-1.210	-0.001	-0.028	-0.061	0.000
44	A	44	SER	0	0.044	0.016	1.958	-6.778	-5.398	2.848	-1.998	-2.229	-0.010
45	A	45	MET	0	-0.030	-0.002	4.526	-0.683	-0.608	-0.001	-0.045	-0.029	0.000
46	A	46	LYS	1	0.930	0.981	7.686	-1.530	-1.530	0.000	0.000	0.000	0.000
47	A	47	ASN	0	-0.012	-0.023	6.141	0.020	0.020	0.000	0.000	0.000	0.000
48	A	48	THR	0	-0.008	-0.003	7.643	-0.108	-0.108	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.028	0.017	10.381	-0.092	-0.092	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.893	0.958	12.831	-0.526	-0.526	0.000	0.000	0.000	0.000
51	A	51	SER	0	0.029	0.006	14.802	-0.059	-0.059	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.005	0.023	16.497	0.030	0.030	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)