FMO DATABASE

FMODB ID: 22VMR

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

Total energy (hartree)

FMO2-HF: Electronic energy	-174141.292063
FMO2-HF: Nuclear repulsion	155526.89641
FMO2-HF: Total energy	-18614.395654
FMO2-MP2: Total energy	-18667.710528

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.
-12.454	-14.498	15.962	-7.73	-6.186	-0.05

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	-0.038	-0.019	3.674	-0.852	1.505	-0.005	-1.311	-1.041	0.007
4	A	4	GLU	-1	-0.833	-0.924	1.779	-14.176	-19.586	15.961	-6.150	-4.401	-0.056
5	A	5	GLU	-1	-0.869	-0.922	3.298	-1.526	-0.591	0.007	-0.264	-0.677	-0.001
6	A	6	LYS	1	0.904	0.964	5.267	2.754	2.828	-0.001	-0.005	-0.067	0.000
7	A	7	VAL	0	-0.016	-0.020	7.545	0.684	0.684	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.864	-0.917	7.442	-0.889	-0.889	0.000	0.000	0.000	0.000
9	A	9	GLN	0	-0.039	-0.033	9.296	0.231	0.231	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.077	-0.040	11.376	0.273	0.273	0.000	0.000	0.000	0.000
11	A	11	GLY	0	0.034	0.025	12.422	0.170	0.170	0.000	0.000	0.000	0.000
12	A	12	SER	0	0.051	0.026	13.248	0.156	0.156	0.000	0.000	0.000	0.000
13	A	13	SER	0	-0.032	-0.030	15.318	0.136	0.136	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.032	-0.013	17.052	0.091	0.091	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.850	-0.916	17.803	-0.434	-0.434	0.000	0.000	0.000	0.000
16	A	16	THR	0	-0.061	-0.038	19.520	0.076	0.076	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.046	-0.034	21.424	0.050	0.050	0.000	0.000	0.000	0.000
18	A	18	GLN	0	0.037	0.023	22.288	0.062	0.062	0.000	0.000	0.000	0.000
19	A	19	THR	0	-0.007	0.009	24.164	0.039	0.039	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.894	0.926	25.294	0.295	0.295	0.000	0.000	0.000	0.000
21	A	21	PHE	0	0.016	0.019	27.320	0.020	0.020	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.019	0.009	28.870	0.018	0.018	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.925	0.962	27.846	0.224	0.224	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.046	0.031	31.949	0.012	0.012	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.002	0.010	33.327	0.013	0.013	0.000	0.000	0.000	0.000
26	A	26	ALA	0	-0.006	-0.007	35.021	0.011	0.011	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.916	-0.960	35.420	-0.140	-0.140	0.000	0.000	0.000	0.000
28	A	28	TYR	0	-0.018	0.004	37.770	0.010	0.010	0.000	0.000	0.000	0.000
29	A	29	ASN	0	0.006	-0.016	38.425	0.009	0.009	0.000	0.000	0.000	0.000
30	A	30	ALA	0	0.004	0.012	41.013	0.007	0.007	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.053	-0.045	41.806	0.007	0.007	0.000	0.000	0.000	0.000
32	A	32	GLN	0	0.034	0.024	43.641	0.005	0.005	0.000	0.000	0.000	0.000
33	A	33	MET	0	-0.057	-0.029	45.449	0.004	0.004	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.960	0.988	47.595	0.079	0.079	0.000	0.000	0.000	0.000
35	A	35	MET	0	0.001	-0.015	45.951	0.006	0.006	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.987	0.996	47.951	0.095	0.095	0.000	0.000	0.000	0.000
37	A	37	GLN	0	0.021	0.025	51.520	0.000	0.000	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.907	0.940	50.865	0.078	0.078	0.000	0.000	0.000	0.000
39	A	39	LEU	0	0.035	0.022	51.691	0.002	0.002	0.000	0.000	0.000	0.000
40	A	40	SER	0	0.036	0.017	55.458	0.002	0.002	0.000	0.000	0.000	0.000
41	A	41	GLN	0	-0.028	-0.012	57.440	0.002	0.002	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.000	0.011	56.855	0.002	0.002	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.931	-0.970	57.482	-0.065	-0.065	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.100	-0.054	61.329	0.002	0.002	0.000	0.000	0.000	0.000
45	A	45	GLN	0	-0.052	-0.026	62.441	0.001	0.001	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.022	0.013	63.160	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)