FMO DATABASE

FMODB ID: 2KZ5R

Calculation Name: 1NGM-B-Xray315

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	72
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-314406.86511
FMO2-HF: Nuclear repulsion	285317.068112
FMO2-HF: Total energy	-29089.796998
FMO2-MP2: Total energy	-29175.194261

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.
-8.93	-5.312	0.651	-1.899	-2.37	0.007

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 : 0.026 / q_NPA : -0.001

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	0.022	0.019	3.471	0.108	2.027	0.002	-1.017	-0.905	0.001
4	B	438	CYS	0	-0.034	-0.024	5.114	-0.411	-0.435	0.000	-0.017	0.041	0.000
5	B	439	PRO	0	0.026	0.019	4.010	-1.466	-1.179	0.002	-0.098	-0.191	0.000
6	B	440	ARG	1	0.950	0.983	2.959	-8.936	-7.540	0.644	-0.747	-1.293	0.006
7	B	441	ASN	0	0.003	-0.003	3.908	0.166	0.206	0.003	-0.020	-0.022	0.000
8	B	442	LEU	0	0.027	-0.003	6.864	0.364	0.364	0.000	0.000	0.000	0.000
9	B	443	HIS	0	0.019	0.020	9.823	0.199	0.199	0.000	0.000	0.000	0.000
10	B	444	LEU	0	0.016	0.008	7.350	0.065	0.065	0.000	0.000	0.000	0.000
11	B	445	LEU	0	-0.080	-0.035	7.142	0.429	0.429	0.000	0.000	0.000	0.000
12	B	446	PRO	0	0.030	0.014	10.693	-0.165	-0.165	0.000	0.000	0.000	0.000
13	B	447	THR	0	0.020	0.020	14.446	-0.050	-0.050	0.000	0.000	0.000	0.000
14	B	448	THR	0	0.072	0.025	16.903	0.018	0.018	0.000	0.000	0.000	0.000
15	B	449	ASP	-1	-0.856	-0.929	20.005	0.169	0.169	0.000	0.000	0.000	0.000
16	B	450	THR	0	-0.112	-0.060	18.860	0.019	0.019	0.000	0.000	0.000	0.000
17	B	451	TYR	0	-0.086	-0.062	17.229	0.014	0.014	0.000	0.000	0.000	0.000
18	B	452	LEU	0	0.023	0.022	22.366	-0.013	-0.013	0.000	0.000	0.000	0.000
19	B	453	SER	0	0.017	0.021	24.401	-0.002	-0.002	0.000	0.000	0.000	0.000
20	B	454	LYS	1	0.912	0.948	22.839	-0.345	-0.345	0.000	0.000	0.000	0.000
21	B	455	VAL	0	-0.055	-0.023	26.554	0.000	0.000	0.000	0.000	0.000	0.000
22	B	456	SER	0	-0.010	0.003	29.634	0.000	0.000	0.000	0.000	0.000	0.000
23	B	457	ASP	-1	-0.901	-0.962	31.342	0.136	0.136	0.000	0.000	0.000	0.000
24	B	458	ASP	-1	-0.950	-0.963	34.222	0.084	0.084	0.000	0.000	0.000	0.000
25	B	459	PRO	0	-0.041	-0.017	37.995	0.000	0.000	0.000	0.000	0.000	0.000
26	B	460	ASP	-1	-0.949	-0.977	39.617	0.063	0.063	0.000	0.000	0.000	0.000
27	B	461	ASN	0	-0.060	-0.034	41.784	0.001	0.001	0.000	0.000	0.000	0.000
28	B	462	LEU	0	-0.047	-0.012	37.914	0.006	0.006	0.000	0.000	0.000	0.000
29	B	463	GLU	-1	-0.968	-0.979	40.396	0.081	0.081	0.000	0.000	0.000	0.000
30	B	464	ASP	-1	-0.947	-0.997	35.798	0.138	0.138	0.000	0.000	0.000	0.000
31	B	465	VAL	0	-0.055	-0.020	35.398	0.009	0.009	0.000	0.000	0.000	0.000
32	B	466	ASP	-1	-0.905	-0.952	37.803	0.094	0.094	0.000	0.000	0.000	0.000
33	B	467	ASP	-1	-0.964	-1.002	38.293	0.130	0.130	0.000	0.000	0.000	0.000
34	B	468	GLU	-1	-0.982	-0.987	40.896	0.091	0.091	0.000	0.000	0.000	0.000
35	B	469	GLU	-1	-0.986	-1.001	38.903	0.110	0.110	0.000	0.000	0.000	0.000
36	B	470	LEU	0	0.056	0.042	39.528	-0.005	-0.005	0.000	0.000	0.000	0.000
37	B	471	ASN	0	-0.031	-0.024	41.609	-0.004	-0.004	0.000	0.000	0.000	0.000
38	B	472	ALA	0	-0.016	0.006	44.448	-0.006	-0.006	0.000	0.000	0.000	0.000
39	B	473	HIS	0	-0.054	-0.019	39.968	-0.004	-0.004	0.000	0.000	0.000	0.000
40	B	474	LEU	0	-0.033	-0.013	45.190	-0.004	-0.004	0.000	0.000	0.000	0.000
41	B	475	LEU	0	-0.036	-0.013	48.565	-0.001	-0.001	0.000	0.000	0.000	0.000
42	B	476	ASN	0	0.066	0.009	51.468	-0.004	-0.004	0.000	0.000	0.000	0.000
43	B	477	GLU	-1	-0.836	-0.922	55.001	0.039	0.039	0.000	0.000	0.000	0.000
44	B	478	GLU	-1	-0.944	-0.977	58.375	0.041	0.041	0.000	0.000	0.000	0.000
45	B	479	ALA	0	-0.013	-0.005	53.926	-0.001	-0.001	0.000	0.000	0.000	0.000
46	B	480	SER	0	-0.024	-0.004	54.460	-0.001	-0.001	0.000	0.000	0.000	0.000
47	B	481	LYS	1	0.918	0.947	55.384	-0.039	-0.039	0.000	0.000	0.000	0.000
48	B	482	LEU	0	-0.009	-0.004	56.067	-0.002	-0.002	0.000	0.000	0.000	0.000
49	B	483	LYS	1	0.967	0.988	48.812	-0.053	-0.053	0.000	0.000	0.000	0.000
50	B	484	GLU	-1	-0.912	-0.938	55.073	0.032	0.032	0.000	0.000	0.000	0.000
51	B	485	ARG	1	0.962	0.975	57.178	-0.033	-0.033	0.000	0.000	0.000	0.000
52	B	486	ILE	0	-0.022	-0.014	54.771	-0.002	-0.002	0.000	0.000	0.000	0.000
53	B	487	TRP	0	-0.015	-0.015	51.379	-0.002	-0.002	0.000	0.000	0.000	0.000
54	B	488	ILE	0	0.023	0.010	55.307	-0.002	-0.002	0.000	0.000	0.000	0.000
55	B	489	GLY	0	-0.016	-0.002	58.679	-0.002	-0.002	0.000	0.000	0.000	0.000
56	B	490	LEU	0	-0.051	-0.033	52.514	-0.001	-0.001	0.000	0.000	0.000	0.000
57	B	491	ASN	0	-0.042	-0.023	52.854	-0.002	-0.002	0.000	0.000	0.000	0.000
58	B	492	ALA	0	0.007	0.010	56.378	-0.001	-0.001	0.000	0.000	0.000	0.000
59	B	493	ASP	-1	-0.954	-0.966	56.964	0.016	0.016	0.000	0.000	0.000	0.000
60	B	494	PHE	0	0.084	0.034	54.279	-0.001	-0.001	0.000	0.000	0.000	0.000
61	B	495	LEU	0	-0.068	-0.057	57.144	-0.001	-0.001	0.000	0.000	0.000	0.000
62	B	496	LEU	0	0.026	0.031	59.760	-0.001	-0.001	0.000	0.000	0.000	0.000
63	B	497	GLU	-1	-0.915	-0.956	57.702	0.014	0.014	0.000	0.000	0.000	0.000
64	B	498	GLN	0	-0.094	-0.053	55.861	-0.001	-0.001	0.000	0.000	0.000	0.000
65	B	499	GLU	-1	-0.954	-0.977	60.150	0.016	0.016	0.000	0.000	0.000	0.000
66	B	500	SER	0	0.024	0.005	63.578	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	501	LYS	1	0.849	0.929	56.916	-0.016	-0.016	0.000	0.000	0.000	0.000
68	B	502	ARG	1	0.956	0.976	62.617	-0.019	-0.019	0.000	0.000	0.000	0.000
69	B	503	LEU	0	0.073	0.049	64.777	0.000	0.000	0.000	0.000	0.000	0.000
70	B	504	LYS	1	0.881	0.936	64.627	-0.008	-0.008	0.000	0.000	0.000	0.000
71	B	505	GLN	0	-0.100	-0.054	61.320	-0.001	-0.001	0.000	0.000	0.000	0.000
72	B	506	GLU	-2	-1.911	-1.921	65.862	0.024	0.024	0.000	0.000	0.000	0.000

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