FMO DATABASE

FMODB ID: 52Y7Z

Calculation Name: 3LH2-S-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LH2

Chain ID: S

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-22

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	66
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-287107.493617
FMO2-HF: Nuclear repulsion	262689.825955
FMO2-HF: Total energy	-24417.667662
FMO2-MP2: Total energy	-24491.082945

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(S:6:HIS)

Summations of interaction energy for fragment #1(S:6:HIS)

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.
-14.99	-15.456	8.591	-3.928	-4.197	-0.042

Interaction energy analysis for fragmet #1(S:6:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.051 / q_NPA : -0.043

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

Sort

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	S	8	THR	0	0.008	0.005	1.897	-12.571	-13.326	8.592	-3.901	-3.936	-0.042
4	S	9	GLU	-1	-0.936	-0.959	4.275	-2.932	-2.643	-0.001	-0.027	-0.261	0.000
5	S	10	TYR	0	-0.012	-0.009	6.663	0.718	0.718	0.000	0.000	0.000	0.000
6	S	11	THR	0	-0.003	0.002	10.270	-0.050	-0.050	0.000	0.000	0.000	0.000
7	S	12	LEU	0	0.010	-0.010	13.548	0.038	0.038	0.000	0.000	0.000	0.000
8	S	13	GLN	0	-0.012	0.005	16.698	0.041	0.041	0.000	0.000	0.000	0.000
9	S	14	ALA	0	0.015	0.007	20.368	0.012	0.012	0.000	0.000	0.000	0.000
10	S	15	ASN	0	0.028	0.020	22.781	0.018	0.018	0.000	0.000	0.000	0.000
11	S	16	TRP	0	0.057	0.012	25.141	-0.024	-0.024	0.000	0.000	0.000	0.000
12	S	17	PHE	0	-0.035	-0.037	25.950	-0.018	-0.018	0.000	0.000	0.000	0.000
13	S	18	ASP	-1	-0.882	-0.923	23.902	-0.391	-0.391	0.000	0.000	0.000	0.000
14	S	19	ILE	0	-0.035	-0.008	20.061	-0.049	-0.049	0.000	0.000	0.000	0.000
15	S	20	THR	0	0.014	-0.009	21.055	-0.059	-0.059	0.000	0.000	0.000	0.000
16	S	21	GLY	0	0.042	0.026	22.370	-0.026	-0.026	0.000	0.000	0.000	0.000
17	S	22	ILE	0	0.013	0.002	17.333	-0.044	-0.044	0.000	0.000	0.000	0.000
18	S	23	LEU	0	-0.014	-0.012	16.902	-0.096	-0.096	0.000	0.000	0.000	0.000
19	S	24	TRP	0	-0.029	-0.006	18.179	-0.075	-0.075	0.000	0.000	0.000	0.000
20	S	25	LEU	0	-0.011	-0.020	18.595	-0.022	-0.022	0.000	0.000	0.000	0.000
21	S	26	LEU	0	-0.015	0.002	12.269	-0.066	-0.066	0.000	0.000	0.000	0.000
22	S	27	GLY	0	0.005	0.007	14.489	-0.162	-0.162	0.000	0.000	0.000	0.000
23	S	28	GLN	0	-0.077	-0.038	15.695	-0.011	-0.011	0.000	0.000	0.000	0.000
24	S	29	VAL	0	-0.052	-0.013	13.297	0.061	0.061	0.000	0.000	0.000	0.000
25	S	30	ASP	-1	-0.940	-0.954	10.213	-1.732	-1.732	0.000	0.000	0.000	0.000
26	S	31	GLY	0	-0.009	-0.002	9.820	-0.462	-0.462	0.000	0.000	0.000	0.000
27	S	32	LYS	1	0.913	0.948	6.669	2.896	2.896	0.000	0.000	0.000	0.000
28	S	33	ILE	0	0.000	-0.002	10.700	-0.160	-0.160	0.000	0.000	0.000	0.000
29	S	34	ILE	0	-0.006	-0.002	7.697	0.093	0.093	0.000	0.000	0.000	0.000
30	S	35	ASN	0	0.009	-0.023	11.202	0.294	0.294	0.000	0.000	0.000	0.000
31	S	36	SER	0	-0.040	-0.003	14.347	-0.062	-0.062	0.000	0.000	0.000	0.000
32	S	37	ASP	-1	-0.836	-0.904	17.633	-0.337	-0.337	0.000	0.000	0.000	0.000
33	S	38	VAL	0	-0.073	-0.037	20.584	-0.016	-0.016	0.000	0.000	0.000	0.000
34	S	39	GLN	0	-0.022	-0.023	22.000	0.051	0.051	0.000	0.000	0.000	0.000
35	S	40	ALA	0	-0.032	-0.001	25.519	-0.006	-0.006	0.000	0.000	0.000	0.000
36	S	41	PHE	0	0.029	0.004	23.065	0.009	0.009	0.000	0.000	0.000	0.000
37	S	42	VAL	0	-0.004	0.000	29.135	0.004	0.004	0.000	0.000	0.000	0.000
38	S	43	LEU	0	-0.004	0.002	29.002	0.001	0.001	0.000	0.000	0.000	0.000
39	S	44	LEU	0	0.026	0.007	32.332	0.010	0.010	0.000	0.000	0.000	0.000
40	S	45	ARG	1	0.951	0.981	33.697	0.107	0.107	0.000	0.000	0.000	0.000
41	S	46	VAL	0	0.008	0.000	34.896	0.006	0.006	0.000	0.000	0.000	0.000
42	S	47	ALA	0	0.005	-0.004	37.435	-0.002	-0.002	0.000	0.000	0.000	0.000
43	S	48	LEU	0	-0.006	0.013	35.893	0.005	0.005	0.000	0.000	0.000	0.000
44	S	49	PRO	0	0.023	0.013	40.177	-0.002	-0.002	0.000	0.000	0.000	0.000
45	S	50	ALA	0	0.109	0.035	38.643	0.002	0.002	0.000	0.000	0.000	0.000
46	S	51	ALA	0	-0.015	-0.035	39.364	0.005	0.005	0.000	0.000	0.000	0.000
47	S	52	LYS	1	0.942	0.976	39.458	-0.001	-0.001	0.000	0.000	0.000	0.000
48	S	53	VAL	0	0.037	0.046	34.078	0.002	0.002	0.000	0.000	0.000	0.000
49	S	54	ALA	0	-0.015	-0.010	33.825	0.000	0.000	0.000	0.000	0.000	0.000
50	S	55	GLU	-1	-0.889	-0.939	33.767	0.025	0.025	0.000	0.000	0.000	0.000
51	S	56	PHE	0	-0.014	-0.026	33.550	0.004	0.004	0.000	0.000	0.000	0.000
52	S	57	SER	0	0.032	0.006	29.683	-0.006	-0.006	0.000	0.000	0.000	0.000
53	S	58	ALA	0	0.013	0.021	29.480	0.001	0.001	0.000	0.000	0.000	0.000
54	S	59	LYS	1	0.933	0.960	30.216	-0.015	-0.015	0.000	0.000	0.000	0.000
55	S	60	LEU	0	-0.030	-0.006	29.107	-0.001	-0.001	0.000	0.000	0.000	0.000
56	S	61	ALA	0	0.009	0.011	25.985	-0.008	-0.008	0.000	0.000	0.000	0.000
57	S	62	ASP	-1	-0.898	-0.953	26.410	0.074	0.074	0.000	0.000	0.000	0.000
58	S	63	PHE	0	-0.103	-0.052	28.220	0.000	0.000	0.000	0.000	0.000	0.000
59	S	64	SER	0	-0.043	-0.021	25.369	-0.007	-0.007	0.000	0.000	0.000	0.000
60	S	65	GLY	0	0.034	0.023	23.613	-0.009	-0.009	0.000	0.000	0.000	0.000
61	S	66	GLY	0	-0.044	-0.023	21.602	0.005	0.005	0.000	0.000	0.000	0.000
62	S	67	SER	0	-0.043	-0.017	20.875	-0.025	-0.025	0.000	0.000	0.000	0.000
63	S	68	LEU	0	0.006	0.000	21.836	-0.033	-0.033	0.000	0.000	0.000	0.000
64	S	69	GLN	0	-0.012	-0.005	22.186	0.016	0.016	0.000	0.000	0.000	0.000
65	S	70	LEU	0	-0.019	-0.007	25.473	-0.011	-0.011	0.000	0.000	0.000	0.000
66	S	71	LEU	0	-0.020	-0.003	25.328	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(S:6:HIS)