FMO DATABASE

FMODB ID: 2JJVR

Calculation Name: 5F5U-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5F5U

Chain ID: E

ChEMBL ID:

UniProt ID: G0S6R0

Base Structure: X-ray

Registration Date: 2023-06-21

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	38
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-157006.820704
FMO2-HF: Nuclear repulsion	140669.657573
FMO2-HF: Total energy	-16337.163131
FMO2-MP2: Total energy	-16386.04822

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(E:221:VAL)

Summations of interaction energy for fragment #1(E:221:VAL)

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.
-6.405	-1.757	3.801	-3.201	-5.249	-0.02

Interaction energy analysis for fragmet #1(E:221:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : -0.009

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	E	223	PRO	0	0.065	0.046	3.081	-3.271	-1.069	0.071	-0.916	-1.357	0.000
4	E	224	GLU	-1	-0.941	-0.978	2.291	-5.944	-4.443	3.677	-1.997	-3.181	-0.020
5	E	225	ALA	0	0.000	0.004	3.072	-0.013	0.763	0.054	-0.271	-0.559	0.000
6	E	226	GLU	-1	-0.919	-0.957	4.564	0.638	0.807	-0.001	-0.017	-0.152	0.000
7	E	227	TYR	0	0.012	-0.004	7.199	0.188	0.188	0.000	0.000	0.000	0.000
8	E	228	ALA	0	-0.019	-0.018	6.710	0.187	0.187	0.000	0.000	0.000	0.000
9	E	229	ALA	0	0.016	0.007	8.394	0.180	0.180	0.000	0.000	0.000	0.000
10	E	230	TRP	0	-0.020	-0.024	10.451	0.100	0.100	0.000	0.000	0.000	0.000
11	E	231	LYS	1	0.950	0.983	9.982	0.665	0.665	0.000	0.000	0.000	0.000
12	E	232	LEU	0	-0.011	0.008	12.425	0.061	0.061	0.000	0.000	0.000	0.000
13	E	233	ARG	1	0.900	0.943	12.665	0.299	0.299	0.000	0.000	0.000	0.000
14	E	234	GLU	-1	-0.798	-0.899	16.271	-0.121	-0.121	0.000	0.000	0.000	0.000
15	E	235	LEU	0	-0.001	0.007	16.530	0.023	0.023	0.000	0.000	0.000	0.000
16	E	236	ARG	1	0.942	0.960	16.083	0.288	0.288	0.000	0.000	0.000	0.000
17	E	237	ARG	1	0.811	0.914	17.558	0.177	0.177	0.000	0.000	0.000	0.000
18	E	238	LEU	0	0.060	0.031	21.523	0.012	0.012	0.000	0.000	0.000	0.000
19	E	239	ARG	1	0.891	0.958	22.298	0.158	0.158	0.000	0.000	0.000	0.000
20	E	240	ARG	1	0.985	0.994	24.075	0.112	0.112	0.000	0.000	0.000	0.000
21	E	241	GLU	-1	-0.951	-0.973	26.319	-0.082	-0.082	0.000	0.000	0.000	0.000
22	E	242	ARG	1	0.943	0.970	27.518	0.107	0.107	0.000	0.000	0.000	0.000
23	E	243	ASP	-1	-0.850	-0.932	27.580	-0.121	-0.121	0.000	0.000	0.000	0.000
24	E	244	ALA	0	-0.045	-0.022	29.941	0.007	0.007	0.000	0.000	0.000	0.000
25	E	245	ILE	0	-0.044	-0.031	32.153	0.007	0.007	0.000	0.000	0.000	0.000
26	E	246	GLU	-1	-0.901	-0.951	31.729	-0.098	-0.098	0.000	0.000	0.000	0.000
27	E	247	ALA	0	-0.053	-0.020	34.015	0.004	0.004	0.000	0.000	0.000	0.000
28	E	248	ARG	1	0.974	0.984	34.911	0.066	0.066	0.000	0.000	0.000	0.000
29	E	249	GLU	-1	-0.943	-0.962	37.225	-0.066	-0.066	0.000	0.000	0.000	0.000
30	E	250	ARG	1	0.944	0.975	35.261	0.074	0.074	0.000	0.000	0.000	0.000
31	E	251	GLU	-1	-0.967	-0.996	39.860	-0.053	-0.053	0.000	0.000	0.000	0.000
32	E	252	LEU	0	0.001	0.010	41.736	0.003	0.003	0.000	0.000	0.000	0.000
33	E	253	ALA	0	0.047	0.024	42.846	0.002	0.002	0.000	0.000	0.000	0.000
34	E	254	GLU	-1	-0.900	-0.935	43.298	-0.046	-0.046	0.000	0.000	0.000	0.000
35	E	255	LEU	0	-0.030	-0.036	45.199	0.002	0.002	0.000	0.000	0.000	0.000
36	E	256	GLU	-1	-0.967	-0.978	47.598	-0.042	-0.042	0.000	0.000	0.000	0.000
37	E	257	ARG	1	0.792	0.896	47.034	0.048	0.048	0.000	0.000	0.000	0.000
38	E	258	ARG	1	0.872	0.950	47.346	0.044	0.044	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:221:VAL)