FMO DATABASE

FMODB ID: 2NM8R

Calculation Name: 3CJH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CJH

Chain ID: A

ChEMBL ID:

UniProt ID: P53299

Base Structure: X-ray

Registration Date: 2023-09-23

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	50
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-239857.972829
FMO2-HF: Nuclear repulsion	217874.22742
FMO2-HF: Total energy	-21983.745409
FMO2-MP2: Total energy	-22044.215336

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:46:ALA)

Summations of interaction energy for fragment #1(A:46:ALA)

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.
-3.78	-0.195	0.234	-1.565	-2.255	0.004

Interaction energy analysis for fragmet #1(A:46:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : 0.003

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	48	GLU	-1	-0.915	-0.958	2.703	-4.138	-1.185	0.229	-1.427	-1.755	0.004
4	A	49	LEU	0	0.055	0.024	3.204	-0.798	-0.284	0.006	-0.126	-0.394	0.000
5	A	50	VAL	0	0.001	0.000	4.960	0.355	0.473	-0.001	-0.012	-0.106	0.000
6	A	51	ASN	0	0.030	0.013	7.447	0.053	0.053	0.000	0.000	0.000	0.000
7	A	52	LYS	1	1.044	1.030	7.668	-0.045	-0.045	0.000	0.000	0.000	0.000
8	A	53	ILE	0	-0.032	0.005	8.959	0.055	0.055	0.000	0.000	0.000	0.000
9	A	54	SER	0	-0.028	-0.021	11.249	0.073	0.073	0.000	0.000	0.000	0.000
10	A	55	GLU	-1	-0.918	-0.952	12.731	0.064	0.064	0.000	0.000	0.000	0.000
11	A	56	ASN	0	-0.039	-0.033	12.452	0.032	0.032	0.000	0.000	0.000	0.000
12	A	57	CYS	0	-0.090	-0.060	15.166	-0.012	-0.012	0.000	0.000	0.000	0.000
13	A	58	PHE	0	-0.012	0.004	16.776	0.017	0.017	0.000	0.000	0.000	0.000
14	A	59	GLU	-1	-0.934	-0.972	18.356	-0.037	-0.037	0.000	0.000	0.000	0.000
15	A	60	LYS	1	0.865	0.936	19.186	0.125	0.125	0.000	0.000	0.000	0.000
16	A	61	CYS	0	-0.094	-0.029	21.278	-0.013	-0.013	0.000	0.000	0.000	0.000
17	A	62	LEU	0	-0.011	0.008	21.275	0.006	0.006	0.000	0.000	0.000	0.000
18	A	63	THR	0	0.042	0.025	24.279	0.004	0.004	0.000	0.000	0.000	0.000
19	A	64	SER	0	-0.011	-0.005	26.979	0.001	0.001	0.000	0.000	0.000	0.000
20	A	65	PRO	0	0.002	-0.023	28.813	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	66	TYR	0	-0.021	0.000	24.218	0.002	0.002	0.000	0.000	0.000	0.000
22	A	67	ALA	0	0.000	0.021	27.709	0.000	0.000	0.000	0.000	0.000	0.000
23	A	68	THR	0	0.005	-0.010	29.230	0.001	0.001	0.000	0.000	0.000	0.000
24	A	69	ARG	1	0.991	0.994	24.070	0.049	0.049	0.000	0.000	0.000	0.000
25	A	70	ASN	0	-0.015	-0.024	24.481	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	71	ASP	-1	-0.835	-0.931	21.657	-0.122	-0.122	0.000	0.000	0.000	0.000
27	A	72	ALA	0	0.008	0.012	21.871	-0.015	-0.015	0.000	0.000	0.000	0.000
28	A	74	ILE	0	0.043	0.022	17.240	-0.015	-0.015	0.000	0.000	0.000	0.000
29	A	75	ASP	-1	-0.865	-0.925	17.922	-0.214	-0.214	0.000	0.000	0.000	0.000
30	A	76	GLN	0	-0.052	-0.024	18.395	-0.023	-0.023	0.000	0.000	0.000	0.000
31	A	78	LEU	0	0.071	0.035	11.947	-0.032	-0.032	0.000	0.000	0.000	0.000
32	A	79	ALA	0	-0.014	-0.011	14.620	-0.043	-0.043	0.000	0.000	0.000	0.000
33	A	80	LYS	1	0.908	0.928	16.599	0.147	0.147	0.000	0.000	0.000	0.000
34	A	81	TYR	0	0.041	0.029	9.625	0.037	0.037	0.000	0.000	0.000	0.000
35	A	82	MET	0	0.022	0.003	9.410	-0.056	-0.056	0.000	0.000	0.000	0.000
36	A	83	ARG	1	0.912	0.954	13.305	0.219	0.219	0.000	0.000	0.000	0.000
37	A	84	SER	0	-0.015	-0.008	15.081	0.031	0.031	0.000	0.000	0.000	0.000
38	A	85	TRP	0	0.019	0.018	7.559	0.082	0.082	0.000	0.000	0.000	0.000
39	A	86	ASN	0	0.014	0.000	12.899	-0.020	-0.020	0.000	0.000	0.000	0.000
40	A	87	VAL	0	-0.015	-0.001	15.033	0.024	0.024	0.000	0.000	0.000	0.000
41	A	88	ILE	0	0.019	0.016	13.856	0.028	0.028	0.000	0.000	0.000	0.000
42	A	89	SER	0	-0.005	0.008	12.933	0.033	0.033	0.000	0.000	0.000	0.000
43	A	90	LYS	1	1.002	1.000	14.608	0.179	0.179	0.000	0.000	0.000	0.000
44	A	91	ALA	0	-0.039	-0.022	18.160	0.023	0.023	0.000	0.000	0.000	0.000
45	A	92	TYR	0	-0.021	-0.016	14.379	0.024	0.024	0.000	0.000	0.000	0.000
46	A	93	ILE	0	0.051	0.009	15.039	0.020	0.020	0.000	0.000	0.000	0.000
47	A	94	SER	0	-0.046	-0.026	18.476	0.019	0.019	0.000	0.000	0.000	0.000
48	A	95	ARG	1	0.912	0.961	20.821	0.089	0.089	0.000	0.000	0.000	0.000
49	A	96	ILE	0	-0.065	-0.012	17.220	0.012	0.012	0.000	0.000	0.000	0.000
50	A	97	GLN	0	-0.009	0.010	21.484	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:46:ALA)