FMO DATABASE

FMODB ID: LNNR9

Calculation Name: 5DAE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DAE

Chain ID: A

ChEMBL ID:

UniProt ID: Q1HRB8

Base Structure: X-ray

Registration Date: 2023-09-21

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	54
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-281217.973906
FMO2-HF: Nuclear repulsion	257423.77745
FMO2-HF: Total energy	-23794.196456
FMO2-MP2: Total energy	-23857.564607

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:3:GLY)

Summations of interaction energy for fragment #1(A:3: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.
2.008	3.743	-0.012	-0.87	-0.853	0.005

Interaction energy analysis for fragmet #1(A:3:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.063 / q_NPA : 0.034

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	5	CYS	0	-0.059	-0.026	3.797	0.590	2.261	-0.011	-0.864	-0.796	0.005
4	A	6	ALA	0	0.012	0.010	6.146	0.190	0.190	0.000	0.000	0.000	0.000
5	A	7	CYS	0	-0.059	-0.020	9.818	0.080	0.080	0.000	0.000	0.000	0.000
6	A	8	PRO	0	0.042	0.025	13.146	0.036	0.036	0.000	0.000	0.000	0.000
7	A	9	ARG	1	0.948	0.978	16.695	0.424	0.424	0.000	0.000	0.000	0.000
8	A	10	ILE	0	0.000	-0.002	18.563	0.047	0.047	0.000	0.000	0.000	0.000
9	A	11	TYR	0	0.002	0.006	20.096	-0.036	-0.036	0.000	0.000	0.000	0.000
10	A	12	MET	0	-0.019	-0.021	21.444	0.030	0.030	0.000	0.000	0.000	0.000
11	A	13	PRO	0	0.003	0.000	21.093	-0.020	-0.020	0.000	0.000	0.000	0.000
12	A	14	VAL	0	-0.026	0.008	17.815	0.027	0.027	0.000	0.000	0.000	0.000
13	A	15	CYS	0	0.000	0.009	20.167	-0.011	-0.011	0.000	0.000	0.000	0.000
14	A	16	GLY	0	0.045	0.016	17.308	0.012	0.012	0.000	0.000	0.000	0.000
15	A	17	SER	0	0.023	0.002	17.998	0.008	0.008	0.000	0.000	0.000	0.000
16	A	18	ASN	0	-0.002	-0.019	15.345	0.049	0.049	0.000	0.000	0.000	0.000
17	A	19	LEU	0	0.030	0.001	19.023	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	20	LYS	1	0.899	0.969	16.746	0.316	0.316	0.000	0.000	0.000	0.000
19	A	21	THR	0	0.065	0.026	19.044	0.001	0.001	0.000	0.000	0.000	0.000
20	A	22	TYR	0	-0.045	-0.040	12.952	0.003	0.003	0.000	0.000	0.000	0.000
21	A	23	ASN	0	0.031	-0.001	17.433	0.079	0.079	0.000	0.000	0.000	0.000
22	A	24	ASN	0	0.005	-0.001	15.854	-0.016	-0.016	0.000	0.000	0.000	0.000
23	A	25	ASP	-1	-0.669	-0.836	16.040	-0.374	-0.374	0.000	0.000	0.000	0.000
24	A	27	LEU	0	0.039	0.006	11.561	-0.147	-0.147	0.000	0.000	0.000	0.000
25	A	28	LEU	0	0.022	0.027	11.222	-0.129	-0.129	0.000	0.000	0.000	0.000
26	A	29	ARG	1	0.859	0.905	11.341	0.301	0.301	0.000	0.000	0.000	0.000
27	A	31	GLU	-1	-0.825	-0.875	6.724	-1.243	-1.243	0.000	0.000	0.000	0.000
28	A	32	ILE	0	-0.015	0.002	8.947	0.127	0.127	0.000	0.000	0.000	0.000
29	A	33	ASN	0	-0.075	-0.046	6.125	0.456	0.456	0.000	0.000	0.000	0.000
30	A	34	SER	0	-0.021	0.005	4.730	0.224	0.288	-0.001	-0.006	-0.057	0.000
31	A	35	ASP	-1	-0.846	-0.940	5.781	1.526	1.526	0.000	0.000	0.000	0.000
32	A	36	LEU	0	-0.011	0.005	7.655	0.137	0.137	0.000	0.000	0.000	0.000
33	A	37	GLY	0	0.038	0.016	9.015	0.113	0.113	0.000	0.000	0.000	0.000
34	A	38	ARG	1	0.909	0.945	7.768	-0.646	-0.646	0.000	0.000	0.000	0.000
35	A	39	ALA	0	-0.033	-0.004	11.319	0.038	0.038	0.000	0.000	0.000	0.000
36	A	40	ASN	0	-0.076	-0.043	13.491	0.020	0.020	0.000	0.000	0.000	0.000
37	A	41	ASN	0	-0.075	-0.033	14.729	0.017	0.017	0.000	0.000	0.000	0.000
38	A	42	LEU	0	-0.031	0.007	11.913	0.001	0.001	0.000	0.000	0.000	0.000
39	A	43	ARG	1	0.980	0.978	14.307	0.112	0.112	0.000	0.000	0.000	0.000
40	A	44	LYS	1	0.810	0.881	16.435	0.233	0.233	0.000	0.000	0.000	0.000
41	A	45	ILE	0	-0.062	-0.039	18.495	0.038	0.038	0.000	0.000	0.000	0.000
42	A	46	ALA	0	0.037	0.023	21.843	0.021	0.021	0.000	0.000	0.000	0.000
43	A	47	ASP	-1	-0.903	-0.943	22.197	-0.242	-0.242	0.000	0.000	0.000	0.000
44	A	48	GLN	0	0.038	0.019	23.781	0.008	0.008	0.000	0.000	0.000	0.000
45	A	49	ALA	0	0.001	0.001	23.473	-0.016	-0.016	0.000	0.000	0.000	0.000
46	A	51	ASP	-1	-0.871	-0.934	24.789	-0.207	-0.207	0.000	0.000	0.000	0.000
47	A	52	ASN	0	-0.086	-0.032	27.600	0.022	0.022	0.000	0.000	0.000	0.000
48	A	53	LEU	0	-0.075	-0.040	25.163	0.011	0.011	0.000	0.000	0.000	0.000
49	A	54	THR	0	-0.044	-0.037	29.393	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	55	ASP	-1	-0.854	-0.935	28.738	-0.109	-0.109	0.000	0.000	0.000	0.000
51	A	56	ASN	0	-0.008	-0.017	30.897	0.004	0.004	0.000	0.000	0.000	0.000
52	A	57	VAL	0	-0.088	-0.034	29.360	0.006	0.006	0.000	0.000	0.000	0.000
53	A	58	ASN	0	-0.108	-0.064	29.212	0.003	0.003	0.000	0.000	0.000	0.000
54	A	59	ASP	-1	-0.853	-0.880	33.276	-0.093	-0.093	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:GLY)