FMO DATABASE

FMODB ID: 6NVGZ

Calculation Name: 1YNZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YNZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q06449

Base Structure: X-ray

Registration Date: 2023-09-19

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	OptAll
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	57
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-313686.742148
FMO2-HF: Nuclear repulsion	291029.780646
FMO2-HF: Total energy	-22656.961502
FMO2-MP2: Total energy	-22722.967556

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:MET)

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

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.
-20.676	-18.725	21.61	-10.293	-13.263	0.046

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : 0.029

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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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	TYR	0	-0.004	0.001	3.041	0.942	3.466	0.016	-1.308	-1.231	0.002
4	A	4	VAL	0	-0.031	-0.013	2.757	-2.391	-0.770	0.451	-0.490	-1.581	-0.004
5	A	5	GLU	-1	-0.836	-0.911	5.164	-0.376	-0.340	-0.001	-0.002	-0.033	0.000
6	A	6	ALA	0	0.019	0.019	8.105	0.017	0.017	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.025	-0.013	9.492	0.003	0.003	0.000	0.000	0.000	0.000
8	A	8	TYR	0	-0.022	-0.013	11.512	0.040	0.040	0.000	0.000	0.000	0.000
9	A	9	GLN	0	-0.047	-0.031	14.008	-0.046	-0.046	0.000	0.000	0.000	0.000
10	A	10	PHE	0	-0.016	-0.002	14.218	0.037	0.037	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.821	-0.899	16.228	-0.066	-0.066	0.000	0.000	0.000	0.000
12	A	12	PRO	0	-0.070	-0.021	19.267	0.022	0.022	0.000	0.000	0.000	0.000
13	A	13	GLN	0	-0.053	-0.041	20.256	-0.006	-0.006	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.044	-0.023	19.626	0.006	0.006	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.921	-0.956	21.690	0.009	0.009	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.012	0.002	20.166	0.016	0.016	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.801	-0.892	17.172	0.130	0.130	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.079	-0.034	12.115	-0.054	-0.054	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.030	0.014	14.739	0.006	0.006	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.057	-0.028	10.959	-0.065	-0.065	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.905	0.931	15.176	0.186	0.186	0.000	0.000	0.000	0.000
22	A	22	PRO	0	0.006	-0.001	14.220	-0.052	-0.052	0.000	0.000	0.000	0.000
23	A	23	GLY	0	0.029	0.023	13.310	0.020	0.020	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.760	-0.876	12.929	-0.402	-0.402	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.801	0.883	9.345	0.608	0.608	0.000	0.000	0.000	0.000
26	A	26	VAL	0	-0.021	-0.003	8.129	0.106	0.106	0.000	0.000	0.000	0.000
27	A	27	GLN	0	0.039	0.032	7.011	-0.512	-0.512	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.064	-0.037	2.808	0.613	0.992	1.548	-0.412	-1.514	-0.002
29	A	29	LEU	0	-0.020	-0.015	6.324	-0.362	-0.362	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.846	-0.910	8.048	0.240	0.240	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.858	0.912	2.152	-17.208	-23.245	16.613	-6.046	-4.530	0.064
32	A	32	LEU	0	0.021	0.020	7.717	-0.092	-0.092	0.000	0.000	0.000	0.000
33	A	33	SER	0	0.022	0.015	10.306	-0.121	-0.121	0.000	0.000	0.000	0.000
34	A	34	PRO	0	-0.008	-0.023	8.436	0.370	0.370	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.923	-0.948	8.436	0.610	0.610	0.000	0.000	0.000	0.000
36	A	36	TRP	0	0.010	0.012	10.544	-0.177	-0.177	0.000	0.000	0.000	0.000
37	A	37	TYR	0	-0.032	-0.018	3.399	1.235	2.125	0.036	-0.251	-0.674	-0.001
38	A	38	LYS	1	0.906	0.939	9.182	-0.387	-0.387	0.000	0.000	0.000	0.000
39	A	39	GLY	0	-0.004	-0.010	9.482	0.005	0.005	0.000	0.000	0.000	0.000
40	A	40	SER	0	0.019	0.012	10.621	0.033	0.033	0.000	0.000	0.000	0.000
41	A	41	CYS	0	-0.018	-0.003	11.443	-0.130	-0.130	0.000	0.000	0.000	0.000
42	A	42	ASN	0	-0.003	-0.005	13.694	0.038	0.038	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.000	0.010	16.827	0.050	0.050	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.809	0.895	15.616	0.292	0.292	0.000	0.000	0.000	0.000
45	A	45	THR	0	0.005	-0.024	14.726	-0.089	-0.089	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.006	0.016	14.540	0.019	0.019	0.000	0.000	0.000	0.000
47	A	47	ILE	0	-0.025	-0.015	13.247	0.018	0.018	0.000	0.000	0.000	0.000
48	A	48	PHE	0	0.016	0.004	7.287	-0.059	-0.059	0.000	0.000	0.000	0.000
49	A	49	PRO	0	0.061	0.042	10.705	0.182	0.182	0.000	0.000	0.000	0.000
50	A	50	ALA	0	-0.002	-0.013	6.069	-0.121	-0.121	0.000	0.000	0.000	0.000
51	A	51	ASN	0	-0.015	-0.017	6.608	-0.235	-0.235	0.000	0.000	0.000	0.000
52	A	52	TYR	0	-0.007	0.000	8.861	-0.091	-0.091	0.000	0.000	0.000	0.000
53	A	53	VAL	0	-0.027	-0.008	4.777	-0.135	-0.077	-0.001	0.000	-0.056	0.000
54	A	54	LYS	1	0.866	0.942	4.922	0.823	0.823	0.000	0.000	0.000	0.000
55	A	55	PRO	0	0.022	-0.015	2.368	-1.710	-0.750	1.207	-0.356	-1.812	0.001
56	A	56	ALA	0	-0.042	-0.009	3.744	0.567	0.778	0.011	-0.026	-0.196	0.000
57	A	57	PHE	0	-0.018	-0.032	2.441	-3.032	-1.723	1.730	-1.402	-1.636	-0.014

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