FMO DATABASE

FMODB ID: VRYJ1

Calculation Name: 3LKU-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LKU

Chain ID: B

ChEMBL ID:

UniProt ID: Q12125

Base Structure: X-ray

Registration Date: 2023-03-14

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	52
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-184982.761937
FMO2-HF: Nuclear repulsion	165256.075196
FMO2-HF: Total energy	-19726.686742
FMO2-MP2: Total energy	-19785.866342

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:3:THR)

Summations of interaction energy for fragment #1(B:3:THR)

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.
-5.369	-0.918	0.016	-2.151	-2.318	0.004

Interaction energy analysis for fragmet #1(B:3:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : -0.005

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	5	ALA	0	0.032	0.022	3.243	-4.061	0.026	0.017	-2.088	-2.017	0.004
4	B	6	SER	0	0.002	0.007	3.708	-1.181	-0.817	-0.001	-0.063	-0.301	0.000
5	B	7	GLY	0	0.028	0.017	5.806	-0.549	-0.549	0.000	0.000	0.000	0.000
6	B	8	PRO	0	0.015	-0.005	6.624	0.162	0.162	0.000	0.000	0.000	0.000
7	B	9	GLU	-1	-0.917	-0.951	9.049	-0.273	-0.273	0.000	0.000	0.000	0.000
8	B	10	HIS	0	-0.010	0.004	6.327	0.043	0.043	0.000	0.000	0.000	0.000
9	B	11	GLU	-1	-0.898	-0.967	8.452	-0.891	-0.891	0.000	0.000	0.000	0.000
10	B	12	PHE	0	-0.036	-0.015	11.152	0.149	0.149	0.000	0.000	0.000	0.000
11	B	13	VAL	0	0.027	0.006	11.480	0.092	0.092	0.000	0.000	0.000	0.000
12	B	14	SER	0	-0.009	-0.001	11.610	0.130	0.130	0.000	0.000	0.000	0.000
13	B	15	LYS	1	0.952	0.968	13.582	0.681	0.681	0.000	0.000	0.000	0.000
14	B	16	PHE	0	-0.006	0.007	16.365	0.071	0.071	0.000	0.000	0.000	0.000
15	B	17	LEU	0	0.009	0.002	16.185	0.051	0.051	0.000	0.000	0.000	0.000
16	B	18	THR	0	-0.011	0.007	17.402	0.040	0.040	0.000	0.000	0.000	0.000
17	B	19	LEU	0	-0.034	-0.027	19.800	0.039	0.039	0.000	0.000	0.000	0.000
18	B	20	ALA	0	-0.046	-0.016	21.512	0.030	0.030	0.000	0.000	0.000	0.000
19	B	21	THR	0	-0.106	-0.068	21.446	0.021	0.021	0.000	0.000	0.000	0.000
20	B	22	LEU	0	0.002	0.017	24.100	0.002	0.002	0.000	0.000	0.000	0.000
21	B	23	THR	0	-0.046	-0.006	25.902	0.016	0.016	0.000	0.000	0.000	0.000
22	B	24	GLU	-1	-0.897	-0.961	27.764	-0.199	-0.199	0.000	0.000	0.000	0.000
23	B	25	PRO	0	-0.003	0.005	26.206	0.012	0.012	0.000	0.000	0.000	0.000
24	B	26	LYS	1	0.944	0.975	28.975	0.113	0.113	0.000	0.000	0.000	0.000
25	B	27	LEU	0	-0.045	-0.023	31.017	0.010	0.010	0.000	0.000	0.000	0.000
26	B	28	PRO	0	0.067	0.043	29.857	-0.011	-0.011	0.000	0.000	0.000	0.000
27	B	29	LYS	1	1.007	0.977	23.398	0.248	0.248	0.000	0.000	0.000	0.000
28	B	30	SER	0	-0.017	0.001	28.624	0.004	0.004	0.000	0.000	0.000	0.000
29	B	31	TYR	0	-0.014	-0.005	31.854	0.012	0.012	0.000	0.000	0.000	0.000
30	B	32	THR	0	0.025	0.007	33.088	0.001	0.001	0.000	0.000	0.000	0.000
31	B	33	LYS	1	0.908	0.969	35.756	0.065	0.065	0.000	0.000	0.000	0.000
32	B	34	PRO	0	0.054	0.024	38.289	0.002	0.002	0.000	0.000	0.000	0.000
33	B	35	LEU	0	0.041	0.010	39.264	0.002	0.002	0.000	0.000	0.000	0.000
34	B	36	LYS	1	0.937	0.964	41.735	0.046	0.046	0.000	0.000	0.000	0.000
35	B	37	ASP	-1	-0.856	-0.923	42.684	-0.051	-0.051	0.000	0.000	0.000	0.000
36	B	38	VAL	0	-0.109	-0.051	39.319	-0.001	-0.001	0.000	0.000	0.000	0.000
37	B	39	THR	0	0.006	0.012	41.978	0.003	0.003	0.000	0.000	0.000	0.000
38	B	40	ASN	0	-0.029	-0.037	39.694	0.005	0.005	0.000	0.000	0.000	0.000
39	B	41	LEU	0	0.015	-0.004	38.131	-0.004	-0.004	0.000	0.000	0.000	0.000
40	B	42	GLY	0	-0.021	0.022	35.580	0.000	0.000	0.000	0.000	0.000	0.000
41	B	43	VAL	0	0.004	0.000	33.923	0.004	0.004	0.000	0.000	0.000	0.000
42	B	44	PRO	0	0.009	0.003	34.804	-0.001	-0.001	0.000	0.000	0.000	0.000
43	B	45	LEU	0	0.021	0.014	29.784	0.001	0.001	0.000	0.000	0.000	0.000
44	B	46	PRO	0	-0.002	0.000	29.624	0.004	0.004	0.000	0.000	0.000	0.000
45	B	47	THR	0	0.010	0.009	32.331	-0.002	-0.002	0.000	0.000	0.000	0.000
46	B	48	LEU	0	-0.003	-0.005	28.068	0.008	0.008	0.000	0.000	0.000	0.000
47	B	49	LYS	1	0.944	0.957	28.473	-0.099	-0.099	0.000	0.000	0.000	0.000
48	B	50	TYR	0	0.021	0.021	24.864	0.005	0.005	0.000	0.000	0.000	0.000
49	B	51	LYS	1	1.003	1.002	31.417	-0.067	-0.067	0.000	0.000	0.000	0.000
50	B	52	TYR	0	0.040	0.023	33.263	0.005	0.005	0.000	0.000	0.000	0.000
51	B	53	LYS	1	0.889	0.935	34.883	-0.055	-0.055	0.000	0.000	0.000	0.000
52	B	54	GLN	0	0.073	0.050	35.766	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:3:THR)