FMO DATABASE

FMODB ID: 22R9R

Calculation Name: 2DGC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DGC

Chain ID: A

ChEMBL ID:

UniProt ID: P03069

Base Structure: X-ray

Registration Date: 2023-03-13

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	49
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-205734.14593
FMO2-HF: Nuclear repulsion	185332.09287
FMO2-HF: Total energy	-20402.05306
FMO2-MP2: Total energy	-20462.183432

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:229:ALA)

Summations of interaction energy for fragment #1(A:229:ALA)

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.
-24.36	-27.37	15.743	-6.285	-6.449	0.037

Interaction energy analysis for fragmet #1(A:229:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.098 / q_NPA : 0.047

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	231	LYS	1	1.008	0.999	3.451	-0.115	1.344	0.011	-0.616	-0.855	0.001
4	A	232	ARG	1	0.954	0.962	1.932	-23.281	-27.917	15.733	-5.642	-5.455	0.036
5	A	233	ALA	0	0.052	0.051	4.959	-0.173	-0.006	-0.001	-0.027	-0.139	0.000
6	A	234	ARG	1	0.996	0.984	6.583	0.483	0.483	0.000	0.000	0.000	0.000
7	A	235	ASN	0	0.020	0.013	8.288	-0.097	-0.097	0.000	0.000	0.000	0.000
8	A	236	THR	0	-0.006	-0.014	8.348	0.013	0.013	0.000	0.000	0.000	0.000
9	A	237	GLU	-1	-0.774	-0.867	10.820	0.184	0.184	0.000	0.000	0.000	0.000
10	A	238	ALA	0	-0.052	-0.020	12.644	-0.054	-0.054	0.000	0.000	0.000	0.000
11	A	239	ALA	0	0.014	0.007	13.526	-0.033	-0.033	0.000	0.000	0.000	0.000
12	A	240	ARG	1	0.820	0.876	12.981	-0.323	-0.323	0.000	0.000	0.000	0.000
13	A	241	ARG	1	1.003	1.000	13.976	-0.077	-0.077	0.000	0.000	0.000	0.000
14	A	242	SER	0	-0.001	-0.003	18.098	-0.021	-0.021	0.000	0.000	0.000	0.000
15	A	243	ARG	1	0.938	0.983	14.546	-0.449	-0.449	0.000	0.000	0.000	0.000
16	A	244	ALA	0	0.074	0.044	21.147	-0.014	-0.014	0.000	0.000	0.000	0.000
17	A	245	ARG	1	0.982	0.980	20.470	-0.082	-0.082	0.000	0.000	0.000	0.000
18	A	246	LYS	1	0.872	0.940	20.627	-0.206	-0.206	0.000	0.000	0.000	0.000
19	A	247	LEU	0	0.039	0.022	25.155	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	248	GLN	0	-0.018	-0.016	26.908	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	249	ARG	1	0.929	0.946	24.857	-0.101	-0.101	0.000	0.000	0.000	0.000
22	A	250	MET	0	-0.024	0.011	29.987	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	251	LYS	1	1.002	1.009	30.502	-0.088	-0.088	0.000	0.000	0.000	0.000
24	A	252	GLN	0	0.002	0.013	33.074	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	253	LEU	0	-0.032	-0.012	34.667	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	254	GLU	-1	-0.873	-0.955	34.835	0.082	0.082	0.000	0.000	0.000	0.000
27	A	255	ASP	-1	-0.864	-0.939	37.065	0.053	0.053	0.000	0.000	0.000	0.000
28	A	256	LYS	1	0.860	0.935	39.199	-0.042	-0.042	0.000	0.000	0.000	0.000
29	A	257	VAL	0	0.004	-0.002	40.198	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	258	GLU	-1	-0.912	-0.948	42.346	0.045	0.045	0.000	0.000	0.000	0.000
31	A	259	GLU	-1	-0.841	-0.909	43.769	0.030	0.030	0.000	0.000	0.000	0.000
32	A	260	LEU	0	0.007	-0.003	43.385	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	261	LEU	0	0.015	0.012	45.766	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	262	SER	0	-0.056	-0.024	48.329	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	263	LYS	1	0.836	0.897	47.190	-0.031	-0.031	0.000	0.000	0.000	0.000
36	A	264	ASN	0	-0.021	-0.013	50.635	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	265	TYR	0	-0.023	-0.005	52.454	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	266	HIS	0	0.027	0.002	53.306	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	267	LEU	0	-0.021	-0.007	53.255	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	268	GLU	-1	-0.879	-0.939	56.241	0.027	0.027	0.000	0.000	0.000	0.000
41	A	269	ASN	0	-0.039	-0.021	58.326	0.000	0.000	0.000	0.000	0.000	0.000
42	A	270	GLU	-1	-0.773	-0.846	59.968	0.017	0.017	0.000	0.000	0.000	0.000
43	A	271	VAL	0	-0.015	-0.012	59.725	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	272	ALA	0	0.003	-0.001	62.390	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	273	ARG	1	0.780	0.854	64.421	-0.018	-0.018	0.000	0.000	0.000	0.000
46	A	274	LEU	0	-0.017	-0.025	63.513	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	275	LYS	1	0.910	0.960	64.045	-0.020	-0.020	0.000	0.000	0.000	0.000
48	A	276	LYS	1	0.926	0.981	68.277	-0.018	-0.018	0.000	0.000	0.000	0.000
49	A	277	LEU	0	-0.025	0.005	69.711	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:229:ALA)