FMO DATABASE

FMODB ID: 7GNQK

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	OptHSide
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	-205706.658033
FMO2-HF: Nuclear repulsion	185304.782829
FMO2-HF: Total energy	-20401.875204
FMO2-MP2: Total energy	-20462.043006

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.
-25.975	-24.234	10.28	-5.341	-6.678	0.035

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 : 0.070 / q_NPA : 0.027

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	A	231	LYS	1	1.011	1.004	3.341	-2.032	0.080	0.019	-1.008	-1.123	0.000
4	A	232	ARG	1	0.955	0.963	2.047	-23.525	-24.130	10.262	-4.271	-5.384	0.035
5	A	233	ALA	0	0.054	0.046	4.367	-0.183	0.051	-0.001	-0.062	-0.171	0.000
6	A	234	ARG	1	1.008	0.995	5.966	0.722	0.722	0.000	0.000	0.000	0.000
7	A	235	ASN	0	0.005	0.006	7.684	-0.069	-0.069	0.000	0.000	0.000	0.000
8	A	236	THR	0	-0.008	-0.017	7.713	0.067	0.067	0.000	0.000	0.000	0.000
9	A	237	GLU	-1	-0.781	-0.860	10.200	-0.027	-0.027	0.000	0.000	0.000	0.000
10	A	238	ALA	0	-0.050	-0.025	12.092	-0.023	-0.023	0.000	0.000	0.000	0.000
11	A	239	ALA	0	-0.001	0.001	12.991	-0.022	-0.022	0.000	0.000	0.000	0.000
12	A	240	ARG	1	0.844	0.883	12.485	-0.131	-0.131	0.000	0.000	0.000	0.000
13	A	241	ARG	1	0.999	0.997	14.090	0.020	0.020	0.000	0.000	0.000	0.000
14	A	242	SER	0	0.007	0.007	17.682	-0.015	-0.015	0.000	0.000	0.000	0.000
15	A	243	ARG	1	0.937	0.959	14.137	-0.377	-0.377	0.000	0.000	0.000	0.000
16	A	244	ALA	0	0.071	0.042	20.694	-0.010	-0.010	0.000	0.000	0.000	0.000
17	A	245	ARG	1	0.981	0.985	19.697	-0.069	-0.069	0.000	0.000	0.000	0.000
18	A	246	LYS	1	0.881	0.933	19.907	-0.204	-0.204	0.000	0.000	0.000	0.000
19	A	247	LEU	0	0.041	0.035	24.957	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	248	GLN	0	-0.009	-0.003	26.892	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	249	ARG	1	0.923	0.955	23.928	-0.102	-0.102	0.000	0.000	0.000	0.000
22	A	250	MET	0	-0.016	0.016	29.474	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	251	LYS	1	1.012	1.009	29.850	-0.061	-0.061	0.000	0.000	0.000	0.000
24	A	252	GLN	0	-0.002	0.014	32.620	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	253	LEU	0	-0.039	-0.028	33.991	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	254	GLU	-1	-0.887	-0.969	34.213	0.072	0.072	0.000	0.000	0.000	0.000
27	A	255	ASP	-1	-0.858	-0.920	37.271	0.038	0.038	0.000	0.000	0.000	0.000
28	A	256	LYS	1	0.864	0.940	38.759	-0.038	-0.038	0.000	0.000	0.000	0.000
29	A	257	VAL	0	-0.001	-0.002	39.670	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	258	GLU	-1	-0.908	-0.944	41.878	0.036	0.036	0.000	0.000	0.000	0.000
31	A	259	GLU	-1	-0.835	-0.912	43.299	0.025	0.025	0.000	0.000	0.000	0.000
32	A	260	LEU	0	-0.022	-0.025	43.248	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	261	LEU	0	0.018	0.017	45.504	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	262	SER	0	-0.050	-0.021	48.029	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	263	LYS	1	0.851	0.904	47.110	-0.026	-0.026	0.000	0.000	0.000	0.000
36	A	264	ASN	0	-0.018	-0.008	50.242	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	265	TYR	0	0.004	0.008	51.993	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	266	HIS	0	0.038	0.009	53.093	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	267	LEU	0	-0.021	-0.007	53.152	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	268	GLU	-1	-0.908	-0.947	56.062	0.027	0.027	0.000	0.000	0.000	0.000
41	A	269	ASN	0	-0.042	-0.028	57.912	0.000	0.000	0.000	0.000	0.000	0.000
42	A	270	GLU	-1	-0.820	-0.888	59.532	0.014	0.014	0.000	0.000	0.000	0.000
43	A	271	VAL	0	-0.017	-0.011	59.612	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	272	ALA	0	0.007	0.008	62.185	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	273	ARG	1	0.804	0.878	64.048	-0.015	-0.015	0.000	0.000	0.000	0.000
46	A	274	LEU	0	-0.022	-0.023	63.255	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	275	LYS	1	0.917	0.965	63.936	-0.020	-0.020	0.000	0.000	0.000	0.000
48	A	276	LYS	1	0.907	0.971	67.875	-0.015	-0.015	0.000	0.000	0.000	0.000
49	A	277	LEU	0	-0.004	0.009	69.598	-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)