FMO DATABASE

FMODB ID: ZY4ZN

Calculation Name: 3SWY-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3SWY

Chain ID: A

ChEMBL ID:
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UniProt ID: Q16281

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:

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	46
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-174133.570956
FMO2-HF: Nuclear repulsion	155518.902321
FMO2-HF: Total energy	-18614.668635
FMO2-MP2: Total energy	-18667.980607

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:GLY)

Summations of interaction energy for fragment #1(A:1: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.
-10.431	-11.271	13.197	-6.49	-5.868	-0.045

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.044 / q_NPA : 0.016

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	LEU	0	-0.041	-0.006	3.800	0.129	2.276	-0.006	-1.178	-0.963	0.004
4	A	4	GLU	-1	-0.828	-0.922	1.866	-14.497	-18.269	13.201	-5.129	-4.301	-0.049
5	A	5	GLU	-1	-0.889	-0.945	3.573	-0.550	0.156	0.003	-0.177	-0.532	0.000
6	A	6	LYS	1	0.936	0.977	5.387	2.690	2.769	-0.001	-0.006	-0.072	0.000
7	A	7	VAL	0	-0.021	-0.016	7.466	0.700	0.700	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.872	-0.926	7.515	-0.706	-0.706	0.000	0.000	0.000	0.000
9	A	9	GLN	0	-0.026	-0.007	8.837	0.486	0.486	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.046	-0.014	11.441	0.276	0.276	0.000	0.000	0.000	0.000
11	A	11	GLY	0	0.023	0.018	12.479	0.166	0.166	0.000	0.000	0.000	0.000
12	A	12	SER	0	0.056	0.016	12.959	0.144	0.144	0.000	0.000	0.000	0.000
13	A	13	SER	0	-0.048	-0.031	15.253	0.135	0.135	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.030	-0.010	17.000	0.090	0.090	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.851	-0.923	17.458	-0.414	-0.414	0.000	0.000	0.000	0.000
16	A	16	THR	0	-0.061	-0.032	19.079	0.077	0.077	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.042	-0.026	21.271	0.047	0.047	0.000	0.000	0.000	0.000
18	A	18	GLN	0	0.023	0.009	22.458	0.055	0.055	0.000	0.000	0.000	0.000
19	A	19	THR	0	-0.038	-0.027	23.419	0.041	0.041	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.896	0.937	24.728	0.302	0.302	0.000	0.000	0.000	0.000
21	A	21	PHE	0	0.012	0.009	27.203	0.021	0.021	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.025	0.009	28.617	0.018	0.018	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.910	0.971	27.541	0.212	0.212	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.079	0.042	31.813	0.012	0.012	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.006	0.009	33.112	0.012	0.012	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.005	0.006	34.930	0.011	0.011	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.908	-0.968	34.384	-0.144	-0.144	0.000	0.000	0.000	0.000
28	A	28	TYR	0	0.014	0.026	37.481	0.011	0.011	0.000	0.000	0.000	0.000
29	A	29	ASN	0	-0.027	-0.023	38.252	0.012	0.012	0.000	0.000	0.000	0.000
30	A	30	ALA	0	0.022	0.015	40.903	0.007	0.007	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.049	-0.046	41.368	0.006	0.006	0.000	0.000	0.000	0.000
32	A	32	GLN	0	-0.005	-0.002	43.273	0.011	0.011	0.000	0.000	0.000	0.000
33	A	33	MET	0	-0.031	-0.019	45.026	0.004	0.004	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.950	0.981	47.043	0.076	0.076	0.000	0.000	0.000	0.000
35	A	35	MET	0	0.003	-0.009	46.534	0.006	0.006	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.979	0.991	47.233	0.095	0.095	0.000	0.000	0.000	0.000
37	A	37	GLN	0	-0.014	-0.001	51.362	0.001	0.001	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.905	0.945	50.222	0.078	0.078	0.000	0.000	0.000	0.000
39	A	39	LEU	0	0.010	0.011	51.186	0.002	0.002	0.000	0.000	0.000	0.000
40	A	40	SER	0	0.059	0.009	55.088	0.002	0.002	0.000	0.000	0.000	0.000
41	A	41	GLN	0	-0.047	-0.009	57.154	0.002	0.002	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.006	0.020	56.852	0.002	0.002	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.874	-0.937	57.143	-0.065	-0.065	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.115	-0.059	60.853	0.002	0.002	0.000	0.000	0.000	0.000
45	A	45	GLN	0	-0.050	-0.024	62.195	0.002	0.002	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.030	-0.001	62.751	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:1:GLY)