FMO DATABASE

FMODB ID: GNVZ1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-185132.963403
FMO2-HF: Nuclear repulsion	165405.869745
FMO2-HF: Total energy	-19727.093658
FMO2-MP2: Total energy	-19786.285193

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.
-7.942	-1.962	0.418	-2.938	-3.46	0.01

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 : 0.081 / q_NPA : 0.038

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	B	5	ALA	0	-0.004	0.005	2.991	-5.218	-1.102	0.312	-2.133	-2.295	0.011
4	B	6	SER	0	-0.010	-0.001	2.707	-2.929	-1.188	0.107	-0.791	-1.057	-0.001
5	B	7	GLY	0	0.008	0.005	5.074	-0.289	-0.166	-0.001	-0.014	-0.108	0.000
6	B	8	PRO	0	0.018	-0.007	6.484	0.179	0.179	0.000	0.000	0.000	0.000
7	B	9	GLU	-1	-0.917	-0.944	8.412	-0.715	-0.715	0.000	0.000	0.000	0.000
8	B	10	HIS	0	-0.018	-0.008	6.179	-0.061	-0.061	0.000	0.000	0.000	0.000
9	B	11	GLU	-1	-0.810	-0.895	8.288	-0.344	-0.344	0.000	0.000	0.000	0.000
10	B	12	PHE	0	-0.022	-0.003	11.006	0.141	0.141	0.000	0.000	0.000	0.000
11	B	13	VAL	0	0.031	0.008	11.351	0.096	0.096	0.000	0.000	0.000	0.000
12	B	14	SER	0	0.022	0.013	11.370	0.092	0.092	0.000	0.000	0.000	0.000
13	B	15	LYS	1	0.824	0.897	13.329	0.561	0.561	0.000	0.000	0.000	0.000
14	B	16	PHE	0	0.002	0.006	16.102	0.063	0.063	0.000	0.000	0.000	0.000
15	B	17	LEU	0	-0.003	-0.004	15.611	0.043	0.043	0.000	0.000	0.000	0.000
16	B	18	THR	0	-0.022	-0.011	16.871	0.041	0.041	0.000	0.000	0.000	0.000
17	B	19	LEU	0	-0.018	-0.017	19.336	0.033	0.033	0.000	0.000	0.000	0.000
18	B	20	ALA	0	-0.056	-0.021	21.174	0.025	0.025	0.000	0.000	0.000	0.000
19	B	21	THR	0	-0.097	-0.070	20.917	0.013	0.013	0.000	0.000	0.000	0.000
20	B	22	LEU	0	-0.023	0.000	23.362	0.007	0.007	0.000	0.000	0.000	0.000
21	B	23	THR	0	-0.015	0.004	25.603	0.013	0.013	0.000	0.000	0.000	0.000
22	B	24	GLU	-1	-0.903	-0.954	27.133	-0.138	-0.138	0.000	0.000	0.000	0.000
23	B	25	PRO	0	-0.017	-0.008	25.822	0.006	0.006	0.000	0.000	0.000	0.000
24	B	26	LYS	1	0.950	0.974	28.633	0.102	0.102	0.000	0.000	0.000	0.000
25	B	27	LEU	0	-0.041	-0.010	30.630	0.009	0.009	0.000	0.000	0.000	0.000
26	B	28	PRO	0	0.066	0.040	29.439	-0.010	-0.010	0.000	0.000	0.000	0.000
27	B	29	LYS	1	0.986	0.965	22.443	0.187	0.187	0.000	0.000	0.000	0.000
28	B	30	SER	0	-0.003	0.011	28.126	-0.001	-0.001	0.000	0.000	0.000	0.000
29	B	31	TYR	0	0.006	0.004	31.504	0.008	0.008	0.000	0.000	0.000	0.000
30	B	32	THR	0	-0.004	-0.019	32.727	-0.003	-0.003	0.000	0.000	0.000	0.000
31	B	33	LYS	1	0.866	0.958	35.346	0.072	0.072	0.000	0.000	0.000	0.000
32	B	34	PRO	0	0.032	0.014	37.975	0.000	0.000	0.000	0.000	0.000	0.000
33	B	35	LEU	0	0.041	0.010	39.602	0.001	0.001	0.000	0.000	0.000	0.000
34	B	36	LYS	1	0.933	0.963	41.592	0.048	0.048	0.000	0.000	0.000	0.000
35	B	37	ASP	-1	-0.831	-0.915	42.275	-0.057	-0.057	0.000	0.000	0.000	0.000
36	B	38	VAL	0	-0.077	-0.039	39.336	-0.002	-0.002	0.000	0.000	0.000	0.000
37	B	39	THR	0	0.021	0.012	41.814	0.001	0.001	0.000	0.000	0.000	0.000
38	B	40	ASN	0	-0.023	-0.011	39.168	0.000	0.000	0.000	0.000	0.000	0.000
39	B	41	LEU	0	0.022	0.004	37.549	-0.002	-0.002	0.000	0.000	0.000	0.000
40	B	42	GLY	0	-0.004	0.015	35.124	-0.004	-0.004	0.000	0.000	0.000	0.000
41	B	43	VAL	0	0.003	-0.008	33.483	0.005	0.005	0.000	0.000	0.000	0.000
42	B	44	PRO	0	-0.019	-0.011	34.085	-0.003	-0.003	0.000	0.000	0.000	0.000
43	B	45	LEU	0	0.033	0.027	29.421	-0.002	-0.002	0.000	0.000	0.000	0.000
44	B	46	PRO	0	-0.001	0.003	28.807	0.006	0.006	0.000	0.000	0.000	0.000
45	B	47	THR	0	0.001	-0.005	31.082	-0.002	-0.002	0.000	0.000	0.000	0.000
46	B	48	LEU	0	0.030	0.016	27.450	0.001	0.001	0.000	0.000	0.000	0.000
47	B	49	LYS	1	0.926	0.958	28.210	0.044	0.044	0.000	0.000	0.000	0.000
48	B	50	TYR	0	0.041	0.022	24.898	0.003	0.003	0.000	0.000	0.000	0.000
49	B	51	LYS	1	0.922	0.965	31.289	0.021	0.021	0.000	0.000	0.000	0.000
50	B	52	TYR	0	0.019	-0.003	32.736	0.002	0.002	0.000	0.000	0.000	0.000
51	B	53	LYS	1	0.939	0.960	34.638	0.017	0.017	0.000	0.000	0.000	0.000
52	B	54	GLN	0	0.092	0.074	35.190	-0.002	-0.002	0.000	0.000	0.000	0.000

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