FMO DATABASE

FMODB ID: YY892

Calculation Name: 2NN4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NN4

Chain ID: A

ChEMBL ID:

UniProt ID: P54494

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-394068.336929
FMO2-HF: Nuclear repulsion	367487.15631
FMO2-HF: Total energy	-26581.180618
FMO2-MP2: Total energy	-26658.099291

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:LEU)

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

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.
-9.869	-1.158	3.296	-5.482	-6.527	-0.02

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.010

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	3	THR	0	-0.007	-0.002	3.589	-2.494	1.476	-0.041	-2.034	-1.896	-0.006
4	A	4	PHE	0	0.116	0.042	4.209	0.051	0.187	-0.001	-0.031	-0.105	0.000
5	A	5	TYR	0	0.025	0.013	6.707	0.105	0.105	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.799	-0.902	2.044	-5.529	-3.805	3.124	-2.425	-2.423	-0.016
7	A	7	VAL	0	0.017	0.007	3.788	-0.184	0.322	0.013	-0.101	-0.417	0.000
8	A	8	GLN	0	0.023	0.009	4.824	-0.266	-0.240	-0.001	-0.004	-0.021	0.000
9	A	9	GLN	0	-0.017	-0.001	6.579	0.108	0.108	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.011	0.006	4.574	-0.032	0.067	-0.001	-0.003	-0.094	0.000
11	A	11	LEU	0	0.061	0.011	6.832	0.041	0.041	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.894	0.971	9.932	0.282	0.282	0.000	0.000	0.000	0.000
13	A	13	THR	0	-0.115	-0.053	9.585	-0.023	-0.023	0.000	0.000	0.000	0.000
14	A	14	PHE	0	-0.037	-0.029	9.720	0.008	0.008	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.004	0.012	13.869	0.026	0.026	0.000	0.000	0.000	0.000
16	A	16	HIS	0	-0.032	-0.017	13.471	-0.016	-0.016	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.059	-0.030	13.448	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	18	VAL	0	-0.028	-0.012	14.610	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	19	TYR	0	-0.031	-0.026	15.571	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	20	PHE	0	-0.040	-0.028	18.082	-0.013	-0.013	0.000	0.000	0.000	0.000
21	A	21	GLY	0	-0.027	0.003	19.694	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.868	-0.938	19.708	0.136	0.136	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.876	0.927	12.071	-0.147	-0.147	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.898	-0.945	15.572	0.248	0.248	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.047	0.024	17.230	0.033	0.033	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.862	-0.939	14.573	0.140	0.140	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.046	-0.032	11.633	0.059	0.059	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.918	-0.955	13.570	0.330	0.330	0.000	0.000	0.000	0.000
29	A	29	PHE	0	0.008	0.007	15.234	0.018	0.018	0.000	0.000	0.000	0.000
30	A	30	MET	0	-0.039	-0.028	8.916	0.001	0.001	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.016	-0.010	11.298	0.108	0.108	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.857	-0.913	13.181	0.307	0.307	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.861	-0.931	13.397	0.209	0.209	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.040	-0.022	7.829	0.047	0.047	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.847	0.915	11.729	-0.331	-0.331	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.840	-0.926	14.666	0.165	0.165	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.003	0.007	11.385	-0.038	-0.038	0.000	0.000	0.000	0.000
38	A	38	TYR	0	-0.041	-0.026	12.657	-0.039	-0.039	0.000	0.000	0.000	0.000
39	A	39	MET	0	-0.068	-0.024	14.340	-0.044	-0.044	0.000	0.000	0.000	0.000
40	A	40	ASN	0	-0.102	-0.056	17.368	-0.052	-0.052	0.000	0.000	0.000	0.000
41	A	41	HIS	0	-0.042	-0.022	16.591	-0.022	-0.022	0.000	0.000	0.000	0.000
42	A	42	MET	0	-0.038	-0.011	14.449	-0.038	-0.038	0.000	0.000	0.000	0.000
43	A	43	ILE	0	-0.032	-0.006	9.146	-0.014	-0.014	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.871	-0.919	9.967	0.037	0.037	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.910	0.931	10.550	-0.163	-0.163	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.845	-0.915	8.432	0.441	0.441	0.000	0.000	0.000	0.000
47	A	47	GLN	0	-0.043	-0.036	5.987	0.302	0.302	0.000	0.000	0.000	0.000
48	A	48	TRP	0	0.029	0.025	6.328	0.835	0.835	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.006	-0.003	8.858	0.220	0.220	0.000	0.000	0.000	0.000
50	A	50	ARG	1	0.833	0.906	3.083	-2.235	-0.557	0.191	-0.682	-1.187	0.001
51	A	51	ALA	0	0.026	0.013	4.694	0.872	0.953	-0.001	-0.017	-0.063	0.000
52	A	52	ALA	0	0.057	0.021	5.635	-0.433	-0.424	-0.001	0.000	-0.009	0.000
53	A	53	ALA	0	-0.021	-0.007	7.529	-0.243	-0.243	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.057	-0.024	3.664	-1.163	-0.681	0.014	-0.185	-0.312	0.001
55	A	55	LEU	0	0.019	0.006	6.916	-0.521	-0.521	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.885	0.935	9.276	-0.702	-0.702	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.876	0.932	9.137	-0.335	-0.335	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.888	-0.945	9.349	0.071	0.071	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.020	0.004	11.364	-0.080	-0.080	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.901	-0.935	14.446	0.239	0.239	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.066	-0.015	11.056	-0.057	-0.057	0.000	0.000	0.000	0.000
62	A	62	THR	0	-0.064	-0.011	14.497	-0.065	-0.065	0.000	0.000	0.000	0.000

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