FMO DATABASE

FMODB ID: VR4M1

Calculation Name: 2X9A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2X9A

Chain ID: A

ChEMBL ID:

UniProt ID: O80297

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	60
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-330167.490753
FMO2-HF: Nuclear repulsion	306128.568654
FMO2-HF: Total energy	-24038.922098
FMO2-MP2: Total energy	-24108.471239

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:2:THR)

Summations of interaction energy for fragment #1(A:2: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.
-22.358	-12.325	7.782	-7.31	-10.503	-0.022

Interaction energy analysis for fragmet #1(A:2:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.004

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	A	4	ASP	-1	-0.747	-0.886	2.763	-7.116	-3.405	0.438	-2.046	-2.102	0.000
4	A	5	ALA	0	-0.036	-0.018	5.359	0.546	0.635	-0.001	-0.002	-0.086	0.000
5	A	6	GLU	-1	-0.874	-0.944	2.430	-6.357	-3.461	2.091	-2.273	-2.713	-0.025
6	A	7	CYS	0	-0.038	0.029	2.767	-2.674	-2.755	4.486	-1.556	-2.849	-0.004
7	A	8	LEU	0	-0.032	-0.018	4.402	0.621	0.682	0.000	-0.027	-0.034	0.000
8	A	9	SER	0	-0.114	-0.069	6.441	0.338	0.338	0.000	0.000	0.000	0.000
9	A	10	LYS	1	0.922	0.967	2.913	-3.907	-3.496	0.090	-0.107	-0.395	0.000
10	A	11	PRO	0	-0.008	-0.008	8.339	-0.179	-0.179	0.000	0.000	0.000	0.000
11	A	12	ALA	0	0.049	0.029	11.118	0.053	0.053	0.000	0.000	0.000	0.000
12	A	13	PHE	0	-0.078	-0.036	11.136	0.055	0.055	0.000	0.000	0.000	0.000
13	A	14	ASP	-1	-0.817	-0.895	15.620	0.091	0.091	0.000	0.000	0.000	0.000
14	A	15	GLY	0	-0.034	-0.030	18.169	0.042	0.042	0.000	0.000	0.000	0.000
15	A	16	THR	0	-0.039	-0.034	18.395	-0.042	-0.042	0.000	0.000	0.000	0.000
16	A	17	LEU	0	0.009	0.041	12.309	0.069	0.069	0.000	0.000	0.000	0.000
17	A	18	SER	0	0.018	-0.008	15.985	-0.042	-0.042	0.000	0.000	0.000	0.000
18	A	19	ASN	0	-0.074	-0.041	15.949	-0.017	-0.017	0.000	0.000	0.000	0.000
19	A	20	VAL	0	-0.039	-0.010	16.488	-0.032	-0.032	0.000	0.000	0.000	0.000
20	A	21	TRP	0	-0.086	-0.053	11.789	0.046	0.046	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.875	0.926	18.606	0.106	0.106	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.857	-0.901	15.633	-0.511	-0.511	0.000	0.000	0.000	0.000
23	A	24	GLY	0	-0.020	-0.008	20.355	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	25	ASP	-1	-0.916	-0.968	23.348	-0.148	-0.148	0.000	0.000	0.000	0.000
25	A	26	SER	0	-0.046	-0.009	18.833	0.042	0.042	0.000	0.000	0.000	0.000
26	A	27	ARG	1	0.936	0.961	18.668	0.050	0.050	0.000	0.000	0.000	0.000
27	A	28	TYR	0	0.051	0.031	13.139	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	29	ALA	0	0.044	0.012	12.779	0.051	0.051	0.000	0.000	0.000	0.000
29	A	30	ASN	0	0.000	0.003	9.491	-0.201	-0.201	0.000	0.000	0.000	0.000
30	A	31	PHE	0	0.010	-0.003	8.014	0.184	0.184	0.000	0.000	0.000	0.000
31	A	32	GLU	-1	-0.905	-0.950	5.370	1.719	1.719	0.000	0.000	0.000	0.000
32	A	33	ASN	0	-0.057	-0.035	2.650	-5.484	-2.871	0.678	-1.244	-2.047	0.007
33	A	35	ILE	0	0.025	0.015	5.050	0.438	0.481	-0.001	-0.003	-0.038	0.000
34	A	36	TYR	0	-0.035	-0.022	7.001	-0.259	-0.259	0.000	0.000	0.000	0.000
35	A	37	GLU	-1	-0.869	-0.965	10.901	-0.371	-0.371	0.000	0.000	0.000	0.000
36	A	38	LEU	0	-0.047	-0.004	14.417	0.050	0.050	0.000	0.000	0.000	0.000
37	A	39	SER	0	-0.030	-0.014	17.614	-0.034	-0.034	0.000	0.000	0.000	0.000
38	A	40	GLY	0	0.012	-0.001	20.245	0.030	0.030	0.000	0.000	0.000	0.000
39	A	41	ILE	0	-0.040	-0.023	23.495	-0.010	-0.010	0.000	0.000	0.000	0.000
40	A	42	GLY	0	0.048	0.028	23.032	0.013	0.013	0.000	0.000	0.000	0.000
41	A	43	ILE	0	-0.062	-0.038	23.820	-0.012	-0.012	0.000	0.000	0.000	0.000
42	A	44	GLY	0	0.035	0.019	23.919	0.016	0.016	0.000	0.000	0.000	0.000
43	A	45	TYR	0	-0.042	-0.040	23.005	0.003	0.003	0.000	0.000	0.000	0.000
44	A	46	ASP	-1	-0.788	-0.884	23.782	0.166	0.166	0.000	0.000	0.000	0.000
45	A	47	ASN	0	-0.043	-0.006	24.995	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	48	ASP	-1	-0.918	-0.950	24.976	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	49	THR	0	-0.046	-0.029	20.951	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	50	SER	0	-0.010	-0.022	19.866	0.035	0.035	0.000	0.000	0.000	0.000
49	A	51	TRP	0	-0.069	-0.031	19.560	-0.034	-0.034	0.000	0.000	0.000	0.000
50	A	52	ASN	0	-0.048	-0.024	19.320	0.010	0.010	0.000	0.000	0.000	0.000
51	A	53	GLY	0	0.066	0.013	19.709	-0.033	-0.033	0.000	0.000	0.000	0.000
52	A	54	HIS	0	-0.048	-0.012	17.715	0.014	0.014	0.000	0.000	0.000	0.000
53	A	55	TRP	0	-0.008	0.000	13.246	-0.063	-0.063	0.000	0.000	0.000	0.000
54	A	56	THR	0	0.001	-0.017	12.560	0.072	0.072	0.000	0.000	0.000	0.000
55	A	57	PRO	0	-0.015	0.029	7.779	-0.063	-0.063	0.000	0.000	0.000	0.000
56	A	58	VAL	0	-0.017	-0.019	9.017	-0.070	-0.070	0.000	0.000	0.000	0.000
57	A	59	ARG	1	0.883	0.946	6.733	1.022	1.022	0.000	0.000	0.000	0.000
58	A	60	ALA	0	0.039	0.009	3.812	0.075	0.255	0.002	-0.047	-0.135	0.000
59	A	61	ALA	0	-0.045	-0.023	4.697	0.816	0.926	-0.001	-0.005	-0.104	0.000
60	A	62	ASP	-1	-0.971	-0.976	6.707	-1.444	-1.444	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:THR)