FMO DATABASE

FMODB ID: 5JVLZ

Calculation Name: 3CA7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CA7

Chain ID: A

ChEMBL ID:

UniProt ID: Q01083

Base Structure: X-ray

Registration Date: 2023-09-23

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	-243854.829595
FMO2-HF: Nuclear repulsion	222076.367837
FMO2-HF: Total energy	-21778.461758
FMO2-MP2: Total energy	-21836.428855

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:48:THR)

Summations of interaction energy for fragment #1(A:48: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.
-2.859	-0.344	0.323	-1.204	-1.634	-0.007

Interaction energy analysis for fragmet #1(A:48:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.024

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

Sort

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	50	PRO	0	0.001	0.013	2.842	-3.539	-1.093	0.324	-1.201	-1.569	-0.007
4	A	51	THR	0	0.018	0.002	4.878	0.572	0.641	-0.001	-0.003	-0.065	0.000
5	A	52	TYR	0	-0.044	-0.018	7.036	-0.032	-0.032	0.000	0.000	0.000	0.000
6	A	53	LYS	1	0.866	0.911	10.810	0.300	0.300	0.000	0.000	0.000	0.000
7	A	54	CYS	0	-0.044	-0.015	14.175	0.013	0.013	0.000	0.000	0.000	0.000
8	A	55	PRO	0	0.043	0.019	16.168	-0.005	-0.005	0.000	0.000	0.000	0.000
9	A	56	GLU	-1	-0.883	-0.944	19.525	-0.113	-0.113	0.000	0.000	0.000	0.000
10	A	57	THR	0	-0.015	-0.007	22.284	0.007	0.007	0.000	0.000	0.000	0.000
11	A	58	PHE	0	-0.035	-0.025	18.651	0.016	0.016	0.000	0.000	0.000	0.000
12	A	59	ASP	-1	-0.834	-0.919	17.898	-0.167	-0.167	0.000	0.000	0.000	0.000
13	A	60	ALA	0	0.025	0.028	19.696	0.008	0.008	0.000	0.000	0.000	0.000
14	A	61	TRP	0	-0.023	-0.015	22.880	0.011	0.011	0.000	0.000	0.000	0.000
15	A	62	TYR	0	-0.037	-0.022	16.868	0.017	0.017	0.000	0.000	0.000	0.000
16	A	63	CYS	0	-0.017	0.030	13.581	-0.055	-0.055	0.000	0.000	0.000	0.000
17	A	64	LEU	0	0.014	0.003	20.072	-0.014	-0.014	0.000	0.000	0.000	0.000
18	A	65	ASN	0	-0.062	-0.052	21.202	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	66	ASP	-1	-0.914	-0.953	21.736	0.021	0.021	0.000	0.000	0.000	0.000
20	A	67	ALA	0	-0.044	-0.009	17.090	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	68	HIS	0	0.000	0.007	14.672	-0.045	-0.045	0.000	0.000	0.000	0.000
22	A	70	PHE	0	-0.016	-0.004	8.375	-0.070	-0.070	0.000	0.000	0.000	0.000
23	A	71	ALA	0	0.016	-0.010	11.209	0.109	0.109	0.000	0.000	0.000	0.000
24	A	72	VAL	0	0.019	0.008	6.811	-0.237	-0.237	0.000	0.000	0.000	0.000
25	A	73	LYS	1	0.840	0.903	9.255	0.431	0.431	0.000	0.000	0.000	0.000
26	A	74	ILE	0	0.001	0.003	8.616	-0.031	-0.031	0.000	0.000	0.000	0.000
27	A	75	ALA	0	-0.003	-0.008	11.096	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	76	ASP	-1	-0.861	-0.922	13.824	-0.208	-0.208	0.000	0.000	0.000	0.000
29	A	77	LEU	0	0.018	0.025	15.054	-0.043	-0.043	0.000	0.000	0.000	0.000
30	A	78	PRO	0	-0.031	-0.023	13.731	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	79	VAL	0	-0.017	-0.003	11.720	0.071	0.071	0.000	0.000	0.000	0.000
32	A	80	TYR	0	0.021	0.000	12.439	-0.103	-0.103	0.000	0.000	0.000	0.000
33	A	81	SER	0	-0.035	-0.022	11.449	0.122	0.122	0.000	0.000	0.000	0.000
34	A	83	GLU	-1	-0.927	-0.960	10.326	0.039	0.039	0.000	0.000	0.000	0.000
35	A	84	CYS	0	-0.076	-0.028	13.160	-0.050	-0.050	0.000	0.000	0.000	0.000
36	A	85	ALA	0	0.072	0.050	16.049	0.013	0.013	0.000	0.000	0.000	0.000
37	A	86	ILE	0	0.001	-0.020	18.055	0.021	0.021	0.000	0.000	0.000	0.000
38	A	87	GLY	0	0.019	0.017	19.753	-0.021	-0.021	0.000	0.000	0.000	0.000
39	A	88	PHE	0	0.010	0.005	20.378	-0.023	-0.023	0.000	0.000	0.000	0.000
40	A	89	MET	0	0.021	0.019	17.955	0.029	0.029	0.000	0.000	0.000	0.000
41	A	90	GLY	0	0.003	-0.003	18.286	-0.024	-0.024	0.000	0.000	0.000	0.000
42	A	91	GLN	0	-0.020	0.004	17.658	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	92	ARG	1	0.865	0.904	17.551	-0.074	-0.074	0.000	0.000	0.000	0.000
44	A	94	GLU	-1	-0.792	-0.894	19.718	0.140	0.140	0.000	0.000	0.000	0.000
45	A	95	TYR	0	-0.020	-0.007	22.937	-0.016	-0.016	0.000	0.000	0.000	0.000
46	A	96	LYS	1	0.839	0.920	23.164	-0.103	-0.103	0.000	0.000	0.000	0.000
47	A	97	GLU	-1	-0.949	-0.971	20.529	0.205	0.205	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:48:THR)