FMO DATABASE

FMODB ID: 94YL2

Calculation Name: 5N76-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5N76

Chain ID: A

ChEMBL ID:

UniProt ID: P72320

Base Structure: X-ray

Registration Date: 2023-06-21

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	62
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-305976.081306
FMO2-HF: Nuclear repulsion	282888.468916
FMO2-HF: Total energy	-23087.61239
FMO2-MP2: Total energy	-23154.536499

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:2:CYS)

Summations of interaction energy for fragment #1(A:2:CYS)

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.
-6.208	-2.785	0.582	-1.404	-2.601	-0.002

Interaction energy analysis for fragmet #1(A:2:CYS)

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 : -0.004

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	A	4	ALA	0	0.021	0.003	2.856	-0.925	1.818	0.542	-1.257	-2.027	-0.002
4	A	5	LYS	1	0.868	0.932	4.223	0.801	0.853	0.001	-0.020	-0.033	0.000
5	A	6	VAL	0	0.031	0.022	7.907	0.245	0.245	0.000	0.000	0.000	0.000
6	A	7	VAL	0	-0.052	-0.028	10.461	0.041	0.041	0.000	0.000	0.000	0.000
7	A	8	LEU	0	0.023	0.020	13.464	0.058	0.058	0.000	0.000	0.000	0.000
8	A	9	THR	0	-0.003	-0.016	16.874	-0.011	-0.011	0.000	0.000	0.000	0.000
9	A	10	LYS	1	0.938	0.973	20.343	0.267	0.267	0.000	0.000	0.000	0.000
10	A	11	ALA	0	0.046	0.011	23.413	0.015	0.015	0.000	0.000	0.000	0.000
11	A	12	ASP	-1	-0.899	-0.950	26.282	-0.140	-0.140	0.000	0.000	0.000	0.000
12	A	13	GLY	0	-0.001	0.010	25.099	0.008	0.008	0.000	0.000	0.000	0.000
13	A	14	GLY	0	-0.025	0.001	23.949	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	15	ARG	1	0.829	0.902	16.908	0.214	0.214	0.000	0.000	0.000	0.000
15	A	16	VAL	0	-0.011	-0.018	16.929	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	17	GLU	-1	-0.806	-0.883	13.225	-0.356	-0.356	0.000	0.000	0.000	0.000
17	A	18	ILE	0	0.027	0.027	11.920	0.025	0.025	0.000	0.000	0.000	0.000
18	A	19	GLY	0	0.005	-0.008	9.598	-0.109	-0.109	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.882	-0.946	8.399	-1.914	-1.914	0.000	0.000	0.000	0.000
20	A	21	VAL	0	-0.033	-0.020	6.744	0.222	0.222	0.000	0.000	0.000	0.000
21	A	22	LEU	0	-0.048	-0.014	6.502	-1.149	-1.149	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.919	-0.970	7.334	-0.923	-0.923	0.000	0.000	0.000	0.000
23	A	24	VAL	0	-0.022	-0.010	8.767	0.087	0.087	0.000	0.000	0.000	0.000
24	A	25	ARG	1	0.854	0.921	11.299	0.464	0.464	0.000	0.000	0.000	0.000
25	A	26	ALA	0	0.008	0.004	14.523	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.822	-0.893	17.380	-0.274	-0.274	0.000	0.000	0.000	0.000
27	A	28	GLY	0	-0.026	-0.015	20.614	-0.016	-0.016	0.000	0.000	0.000	0.000
28	A	29	GLY	0	0.036	0.027	23.504	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	30	ALA	0	-0.005	0.008	21.169	0.003	0.003	0.000	0.000	0.000	0.000
30	A	31	VAL	0	-0.030	-0.004	14.580	0.002	0.002	0.000	0.000	0.000	0.000
31	A	32	ARG	1	0.832	0.910	16.430	0.377	0.377	0.000	0.000	0.000	0.000
32	A	33	VAL	0	-0.020	-0.020	11.084	-0.042	-0.042	0.000	0.000	0.000	0.000
33	A	34	THR	0	0.050	0.029	12.231	0.094	0.094	0.000	0.000	0.000	0.000
34	A	35	THR	0	0.015	-0.009	11.068	-0.296	-0.296	0.000	0.000	0.000	0.000
35	A	36	LEU	0	-0.011	-0.015	7.606	0.075	0.075	0.000	0.000	0.000	0.000
36	A	37	PHE	0	-0.075	-0.037	11.752	0.112	0.112	0.000	0.000	0.000	0.000
37	A	38	ASP	-1	-0.938	-0.951	14.760	-0.627	-0.627	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.902	-0.923	16.097	-0.623	-0.623	0.000	0.000	0.000	0.000
39	A	40	GLU	-1	-0.893	-0.964	15.691	-0.638	-0.638	0.000	0.000	0.000	0.000
40	A	41	HIS	0	-0.087	-0.042	15.969	0.127	0.127	0.000	0.000	0.000	0.000
41	A	42	ALA	0	0.013	0.003	16.987	-0.026	-0.026	0.000	0.000	0.000	0.000
42	A	43	PHE	0	-0.062	-0.039	15.732	0.041	0.041	0.000	0.000	0.000	0.000
43	A	44	PRO	0	0.003	-0.013	20.338	0.014	0.014	0.000	0.000	0.000	0.000
44	A	45	GLY	0	0.036	0.015	23.288	0.004	0.004	0.000	0.000	0.000	0.000
45	A	46	LEU	0	-0.050	-0.010	18.563	0.017	0.017	0.000	0.000	0.000	0.000
46	A	47	ALA	0	0.047	0.018	18.237	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	48	ILE	0	-0.002	-0.014	11.894	-0.018	-0.018	0.000	0.000	0.000	0.000
48	A	49	GLY	0	-0.019	0.003	14.714	0.053	0.053	0.000	0.000	0.000	0.000
49	A	50	ARG	1	0.883	0.910	11.762	-0.411	-0.411	0.000	0.000	0.000	0.000
50	A	51	VAL	0	0.046	0.028	6.912	-0.110	-0.110	0.000	0.000	0.000	0.000
51	A	52	ASP	-1	-0.858	-0.888	8.100	1.307	1.307	0.000	0.000	0.000	0.000
52	A	53	LEU	0	0.034	-0.004	4.085	-0.440	-0.136	0.037	-0.070	-0.271	0.000
53	A	54	ARG	1	0.898	0.963	5.223	-0.597	-0.409	-0.001	-0.014	-0.174	0.000
54	A	55	SER	0	-0.055	-0.056	7.212	0.049	0.049	0.000	0.000	0.000	0.000
55	A	56	GLY	0	0.071	0.051	4.031	-0.405	-0.270	0.004	-0.041	-0.098	0.000
56	A	57	VAL	0	-0.049	-0.018	4.811	-1.083	-1.082	-0.001	-0.002	0.002	0.000
57	A	58	ILE	0	0.021	0.009	5.911	0.415	0.415	0.000	0.000	0.000	0.000
58	A	59	SER	0	-0.041	-0.024	9.012	-0.096	-0.096	0.000	0.000	0.000	0.000
59	A	60	LEU	0	-0.022	-0.010	12.823	0.046	0.046	0.000	0.000	0.000	0.000
60	A	61	ILE	0	-0.037	-0.019	15.465	0.030	0.030	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.911	-0.953	18.977	-0.088	-0.088	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.986	-0.992	21.967	-0.075	-0.075	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:CYS)