FMO DATABASE

FMODB ID: 2233R

Calculation Name: 1NGM-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NGM

Chain ID: B

ChEMBL ID:

UniProt ID: P13393

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	72
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-314702.092508
FMO2-HF: Nuclear repulsion	285610.8422
FMO2-HF: Total energy	-29091.250309
FMO2-MP2: Total energy	-29176.615735

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(B:435:GLY)

Summations of interaction energy for fragment #1(B:435: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.
-22.069	-25.424	13.706	-5.716	-4.637	0.029

Interaction energy analysis for fragmet #1(B:435:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.027

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	B	437	TYR	0	0.009	0.011	3.497	0.371	2.285	-0.003	-0.997	-0.915	0.001
4	B	438	CYS	0	-0.027	-0.014	4.990	-0.559	-0.559	0.000	0.000	0.000	0.000
5	B	439	PRO	0	0.035	0.016	3.954	-1.387	-1.073	0.001	-0.119	-0.196	-0.001
6	B	440	ARG	1	0.922	0.941	1.909	-21.826	-27.455	13.706	-4.575	-3.502	0.029
7	B	441	ASN	0	0.001	0.000	3.897	-0.481	-0.435	0.002	-0.025	-0.024	0.000
8	B	442	LEU	0	0.038	0.006	6.993	0.388	0.388	0.000	0.000	0.000	0.000
9	B	443	HIS	0	0.029	0.021	9.898	0.200	0.200	0.000	0.000	0.000	0.000
10	B	444	LEU	0	-0.003	-0.002	7.791	0.076	0.076	0.000	0.000	0.000	0.000
11	B	445	LEU	0	-0.072	-0.026	7.313	0.456	0.456	0.000	0.000	0.000	0.000
12	B	446	PRO	0	0.024	0.005	10.860	-0.173	-0.173	0.000	0.000	0.000	0.000
13	B	447	THR	0	0.031	0.027	14.543	-0.048	-0.048	0.000	0.000	0.000	0.000
14	B	448	THR	0	0.066	0.022	17.022	0.017	0.017	0.000	0.000	0.000	0.000
15	B	449	ASP	-1	-0.849	-0.921	19.987	0.255	0.255	0.000	0.000	0.000	0.000
16	B	450	THR	0	-0.094	-0.047	18.972	0.021	0.021	0.000	0.000	0.000	0.000
17	B	451	TYR	0	-0.083	-0.056	17.417	0.003	0.003	0.000	0.000	0.000	0.000
18	B	452	LEU	0	0.008	0.018	22.383	-0.020	-0.020	0.000	0.000	0.000	0.000
19	B	453	SER	0	0.018	0.005	24.183	-0.003	-0.003	0.000	0.000	0.000	0.000
20	B	454	LYS	1	0.888	0.938	22.184	-0.430	-0.430	0.000	0.000	0.000	0.000
21	B	455	VAL	0	-0.060	-0.029	26.605	-0.002	-0.002	0.000	0.000	0.000	0.000
22	B	456	SER	0	-0.013	-0.027	29.647	0.004	0.004	0.000	0.000	0.000	0.000
23	B	457	ASP	-1	-0.921	-0.966	31.744	0.179	0.179	0.000	0.000	0.000	0.000
24	B	458	ASP	-1	-0.938	-0.963	34.363	0.108	0.108	0.000	0.000	0.000	0.000
25	B	459	PRO	0	-0.051	-0.017	38.127	-0.001	-0.001	0.000	0.000	0.000	0.000
26	B	460	ASP	-1	-0.951	-0.976	39.684	0.082	0.082	0.000	0.000	0.000	0.000
27	B	461	ASN	0	-0.114	-0.067	41.939	0.001	0.001	0.000	0.000	0.000	0.000
28	B	462	LEU	0	-0.030	-0.007	37.916	0.007	0.007	0.000	0.000	0.000	0.000
29	B	463	GLU	-1	-0.934	-0.960	40.347	0.097	0.097	0.000	0.000	0.000	0.000
30	B	464	ASP	-1	-0.889	-0.933	35.971	0.162	0.162	0.000	0.000	0.000	0.000
31	B	465	VAL	0	-0.060	-0.028	35.167	0.011	0.011	0.000	0.000	0.000	0.000
32	B	466	ASP	-1	-0.872	-0.914	37.754	0.108	0.108	0.000	0.000	0.000	0.000
33	B	467	ASP	-1	-0.915	-0.976	37.572	0.144	0.144	0.000	0.000	0.000	0.000
34	B	468	GLU	-1	-0.980	-0.985	40.832	0.102	0.102	0.000	0.000	0.000	0.000
35	B	469	GLU	-1	-1.003	-1.015	38.749	0.116	0.116	0.000	0.000	0.000	0.000
36	B	470	LEU	0	0.040	0.035	38.761	-0.007	-0.007	0.000	0.000	0.000	0.000
37	B	471	ASN	0	-0.105	-0.073	41.434	-0.002	-0.002	0.000	0.000	0.000	0.000
38	B	472	ALA	0	-0.003	0.004	44.266	-0.006	-0.006	0.000	0.000	0.000	0.000
39	B	473	HIS	0	-0.069	-0.028	39.418	-0.005	-0.005	0.000	0.000	0.000	0.000
40	B	474	LEU	0	-0.032	-0.007	45.016	-0.004	-0.004	0.000	0.000	0.000	0.000
41	B	475	LEU	0	-0.044	-0.021	48.400	-0.002	-0.002	0.000	0.000	0.000	0.000
42	B	476	ASN	0	0.057	0.011	51.293	-0.003	-0.003	0.000	0.000	0.000	0.000
43	B	477	GLU	-1	-0.776	-0.878	54.827	0.044	0.044	0.000	0.000	0.000	0.000
44	B	478	GLU	-1	-0.957	-0.978	58.206	0.044	0.044	0.000	0.000	0.000	0.000
45	B	479	ALA	0	0.004	-0.001	53.744	-0.001	-0.001	0.000	0.000	0.000	0.000
46	B	480	SER	0	-0.012	-0.001	54.294	-0.001	-0.001	0.000	0.000	0.000	0.000
47	B	481	LYS	1	0.865	0.905	55.218	-0.044	-0.044	0.000	0.000	0.000	0.000
48	B	482	LEU	0	-0.019	-0.003	55.748	-0.003	-0.003	0.000	0.000	0.000	0.000
49	B	483	LYS	1	0.989	0.991	48.559	-0.058	-0.058	0.000	0.000	0.000	0.000
50	B	484	GLU	-1	-0.924	-0.942	54.908	0.037	0.037	0.000	0.000	0.000	0.000
51	B	485	ARG	1	0.961	0.975	57.027	-0.035	-0.035	0.000	0.000	0.000	0.000
52	B	486	ILE	0	-0.019	-0.010	54.597	-0.002	-0.002	0.000	0.000	0.000	0.000
53	B	487	TRP	0	-0.012	-0.016	51.126	-0.002	-0.002	0.000	0.000	0.000	0.000
54	B	488	ILE	0	0.032	0.014	55.157	-0.002	-0.002	0.000	0.000	0.000	0.000
55	B	489	GLY	0	-0.014	-0.001	58.538	-0.002	-0.002	0.000	0.000	0.000	0.000
56	B	490	LEU	0	-0.047	-0.029	52.550	-0.001	-0.001	0.000	0.000	0.000	0.000
57	B	491	ASN	0	-0.035	-0.021	52.687	-0.002	-0.002	0.000	0.000	0.000	0.000
58	B	492	ALA	0	-0.003	0.006	56.248	-0.001	-0.001	0.000	0.000	0.000	0.000
59	B	493	ASP	-1	-0.941	-0.960	56.915	0.016	0.016	0.000	0.000	0.000	0.000
60	B	494	PHE	0	0.069	0.025	53.941	0.000	0.000	0.000	0.000	0.000	0.000
61	B	495	LEU	0	-0.064	-0.051	57.036	-0.001	-0.001	0.000	0.000	0.000	0.000
62	B	496	LEU	0	0.028	0.032	59.652	0.000	0.000	0.000	0.000	0.000	0.000
63	B	497	GLU	-1	-0.903	-0.952	57.369	0.015	0.015	0.000	0.000	0.000	0.000
64	B	498	GLN	0	-0.054	-0.022	55.529	-0.002	-0.002	0.000	0.000	0.000	0.000
65	B	499	GLU	-1	-0.965	-0.975	60.066	0.019	0.019	0.000	0.000	0.000	0.000
66	B	500	SER	0	0.019	0.006	63.481	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	501	LYS	1	0.837	0.901	56.975	-0.019	-0.019	0.000	0.000	0.000	0.000
68	B	502	ARG	1	0.954	0.981	62.551	-0.022	-0.022	0.000	0.000	0.000	0.000
69	B	503	LEU	0	0.040	0.029	64.710	0.000	0.000	0.000	0.000	0.000	0.000
70	B	504	LYS	1	0.887	0.939	64.501	-0.010	-0.010	0.000	0.000	0.000	0.000
71	B	505	GLN	0	-0.056	-0.026	61.030	-0.001	-0.001	0.000	0.000	0.000	0.000
72	B	506	GLU	-1	-0.964	-0.956	65.816	0.017	0.017	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:435:GLY)