FMO DATABASE

FMODB ID: ZY5NN

Calculation Name: 3T5V-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3T5V

Chain ID: F

ChEMBL ID:

UniProt ID: P46674

Base Structure: X-ray

Registration Date: 2023-06-19

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	47
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-176442.127059
FMO2-HF: Nuclear repulsion	156082.847442
FMO2-HF: Total energy	-20359.279616
FMO2-MP2: Total energy	-20419.115337

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(F:30:GLU)

Summations of interaction energy for fragment #1(F:30:GLU)

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.
177.058	175.842	11.622	-5.484	-4.92	-0.047

Interaction energy analysis for fragmet #1(F:30:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -1.011 / q_NPA : -1.032

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	F	32	ASP	-1	-0.943	-0.973	1.801	21.211	18.965	11.473	-5.176	-4.050	-0.046
4	F	33	ASP	-1	-0.960	-0.971	2.926	29.992	30.898	0.150	-0.298	-0.758	-0.001
5	F	34	GLU	-1	-1.021	-0.995	4.667	25.925	26.049	-0.001	-0.010	-0.112	0.000
6	F	35	PHE	0	-0.102	-0.062	7.219	-1.917	-1.917	0.000	0.000	0.000	0.000
7	F	36	GLU	-1	-0.907	-0.950	10.757	17.877	17.877	0.000	0.000	0.000	0.000
8	F	37	ASP	-1	-0.965	-0.975	12.766	15.560	15.560	0.000	0.000	0.000	0.000
9	F	38	PHE	0	-0.029	-0.014	15.778	-0.606	-0.606	0.000	0.000	0.000	0.000
10	F	39	PRO	0	-0.074	-0.037	19.089	-0.553	-0.553	0.000	0.000	0.000	0.000
11	F	53	ALA	0	-0.023	-0.024	31.027	-0.019	-0.019	0.000	0.000	0.000	0.000
12	F	54	VAL	0	0.001	0.004	27.713	-0.108	-0.108	0.000	0.000	0.000	0.000
13	F	55	THR	0	-0.004	-0.002	30.039	0.005	0.005	0.000	0.000	0.000	0.000
14	F	56	GLN	0	0.032	-0.007	28.137	0.192	0.192	0.000	0.000	0.000	0.000
15	F	57	THR	0	-0.069	-0.028	25.920	0.173	0.173	0.000	0.000	0.000	0.000
16	F	58	ASN	0	0.019	0.004	26.365	0.600	0.600	0.000	0.000	0.000	0.000
17	F	59	ILE	0	0.004	0.007	21.287	-0.200	-0.200	0.000	0.000	0.000	0.000
18	F	60	TRP	0	-0.047	-0.013	18.873	0.425	0.425	0.000	0.000	0.000	0.000
19	F	61	GLU	-1	-0.914	-0.950	25.267	9.758	9.758	0.000	0.000	0.000	0.000
20	F	62	GLU	-1	-0.948	-0.989	27.675	9.487	9.487	0.000	0.000	0.000	0.000
21	F	63	ASN	0	-0.054	-0.029	30.486	-0.163	-0.163	0.000	0.000	0.000	0.000
22	F	64	TRP	0	0.047	0.024	26.553	0.103	0.103	0.000	0.000	0.000	0.000
23	F	65	ASP	-1	-0.935	-0.966	31.135	9.323	9.323	0.000	0.000	0.000	0.000
24	F	66	ASP	-1	-0.999	-0.993	33.727	7.665	7.665	0.000	0.000	0.000	0.000
25	F	67	VAL	0	-0.107	-0.052	33.782	-0.291	-0.291	0.000	0.000	0.000	0.000
26	F	68	GLU	-1	-0.908	-0.945	33.557	9.282	9.282	0.000	0.000	0.000	0.000
27	F	69	VAL	0	-0.080	-0.038	34.233	-0.289	-0.289	0.000	0.000	0.000	0.000
28	F	70	ASP	-1	-0.911	-0.949	36.246	7.746	7.746	0.000	0.000	0.000	0.000
29	F	71	ASP	-1	-0.752	-0.865	33.738	9.400	9.400	0.000	0.000	0.000	0.000
30	F	72	ASP	-1	-0.942	-0.960	35.341	8.257	8.257	0.000	0.000	0.000	0.000
31	F	73	PHE	0	0.021	0.022	32.082	-0.164	-0.164	0.000	0.000	0.000	0.000
32	F	74	THR	0	0.009	-0.040	34.628	-0.207	-0.207	0.000	0.000	0.000	0.000
33	F	75	ASN	0	-0.062	-0.035	36.816	-0.392	-0.392	0.000	0.000	0.000	0.000
34	F	76	GLU	-1	-0.959	-0.979	36.262	8.368	8.368	0.000	0.000	0.000	0.000
35	F	77	LEU	0	-0.011	0.001	34.747	-0.216	-0.216	0.000	0.000	0.000	0.000
36	F	78	LYS	1	0.846	0.909	39.171	-7.935	-7.935	0.000	0.000	0.000	0.000
37	F	79	ALA	0	-0.021	-0.009	42.448	-0.214	-0.214	0.000	0.000	0.000	0.000
38	F	80	GLU	-1	-0.870	-0.923	41.004	7.231	7.231	0.000	0.000	0.000	0.000
39	F	81	LEU	0	0.010	0.009	41.016	-0.159	-0.159	0.000	0.000	0.000	0.000
40	F	82	ASP	-1	-0.817	-0.890	44.349	6.172	6.172	0.000	0.000	0.000	0.000
41	F	83	ARG	1	0.832	0.895	42.209	-7.493	-7.493	0.000	0.000	0.000	0.000
42	F	84	TYR	0	0.041	0.032	45.576	-0.119	-0.119	0.000	0.000	0.000	0.000
43	F	85	LYS	1	0.895	0.938	47.628	-6.408	-6.408	0.000	0.000	0.000	0.000
44	F	86	ARG	1	0.810	0.883	48.866	-6.480	-6.480	0.000	0.000	0.000	0.000
45	F	87	GLU	-1	-0.951	-0.960	49.099	6.449	6.449	0.000	0.000	0.000	0.000
46	F	88	ASN	0	-0.100	-0.060	49.648	-0.118	-0.118	0.000	0.000	0.000	0.000
47	F	89	GLN	0	-0.083	-0.022	52.876	-0.092	-0.092	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:30:GLU)