FMO DATABASE

FMODB ID: Q1G2Y

Calculation Name: 1PD3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1PD3

Chain ID: A

ChEMBL ID:

UniProt ID: P03508

Base Structure: X-ray

Registration Date: 2023-06-20

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	54
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-300787.032535
FMO2-HF: Nuclear repulsion	277601.960321
FMO2-HF: Total energy	-23185.072215
FMO2-MP2: Total energy	-23253.821157

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:63:GLY)

Summations of interaction energy for fragment #1(A:63:GLY)

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.
-2.297	0.066	-0.001	-0.984	-1.379	-0.002

Interaction energy analysis for fragmet #1(A:63:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.065 / q_NPA : 0.016

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	65	TRP	0	0.056	0.031	3.860	-0.317	1.364	-0.002	-0.842	-0.838	-0.002
4	A	66	ARG	1	1.000	0.985	4.100	-2.696	-2.315	0.002	-0.097	-0.286	0.000
5	A	67	GLU	-1	-0.882	-0.907	4.055	-1.600	-1.299	-0.001	-0.045	-0.255	0.000
6	A	68	GLN	0	-0.005	-0.018	5.846	0.431	0.431	0.000	0.000	0.000	0.000
7	A	69	LEU	0	-0.006	0.009	8.653	0.131	0.131	0.000	0.000	0.000	0.000
8	A	70	GLY	0	0.036	0.030	8.993	0.048	0.048	0.000	0.000	0.000	0.000
9	A	71	GLN	0	-0.023	-0.035	9.071	0.020	0.020	0.000	0.000	0.000	0.000
10	A	72	LYS	1	0.909	0.959	12.006	0.396	0.396	0.000	0.000	0.000	0.000
11	A	73	PHE	0	-0.008	-0.016	12.916	0.034	0.034	0.000	0.000	0.000	0.000
12	A	74	GLU	-1	-0.783	-0.833	14.128	-0.083	-0.083	0.000	0.000	0.000	0.000
13	A	75	GLU	-1	-0.865	-0.927	16.039	-0.144	-0.144	0.000	0.000	0.000	0.000
14	A	76	ILE	0	-0.041	-0.020	17.631	0.020	0.020	0.000	0.000	0.000	0.000
15	A	77	ARG	1	0.836	0.890	16.961	0.072	0.072	0.000	0.000	0.000	0.000
16	A	78	TRP	0	0.003	0.010	20.087	0.009	0.009	0.000	0.000	0.000	0.000
17	A	79	LEU	0	-0.005	-0.019	21.959	0.011	0.011	0.000	0.000	0.000	0.000
18	A	80	ILE	0	-0.037	-0.024	23.105	0.010	0.010	0.000	0.000	0.000	0.000
19	A	81	GLU	-1	-0.857	-0.944	23.731	-0.027	-0.027	0.000	0.000	0.000	0.000
20	A	82	GLU	-1	-0.850	-0.903	26.285	-0.075	-0.075	0.000	0.000	0.000	0.000
21	A	83	VAL	0	-0.094	-0.052	28.275	0.004	0.004	0.000	0.000	0.000	0.000
22	A	84	ARG	1	0.894	0.938	29.333	0.020	0.020	0.000	0.000	0.000	0.000
23	A	85	HIS	0	-0.039	-0.007	30.341	0.006	0.006	0.000	0.000	0.000	0.000
24	A	86	ARG	1	0.808	0.885	30.615	0.058	0.058	0.000	0.000	0.000	0.000
25	A	87	LEU	0	0.029	0.049	33.907	0.002	0.002	0.000	0.000	0.000	0.000
26	A	88	LYS	1	0.841	0.915	36.411	0.027	0.027	0.000	0.000	0.000	0.000
27	A	89	ILE	0	0.009	0.006	34.845	0.001	0.001	0.000	0.000	0.000	0.000
28	A	90	THR	0	0.029	0.006	38.980	0.000	0.000	0.000	0.000	0.000	0.000
29	A	91	GLU	-1	-0.815	-0.895	35.181	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	92	ASN	0	-0.021	-0.029	37.860	0.003	0.003	0.000	0.000	0.000	0.000
31	A	93	SER	0	-0.033	0.001	38.318	0.001	0.001	0.000	0.000	0.000	0.000
32	A	94	PHE	0	0.089	0.026	35.947	0.001	0.001	0.000	0.000	0.000	0.000
33	A	95	GLU	-1	-0.946	-0.976	35.062	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	96	GLN	0	0.049	0.029	32.819	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	97	ILE	0	-0.024	-0.010	32.780	0.001	0.001	0.000	0.000	0.000	0.000
36	A	98	THR	0	-0.017	-0.011	31.318	0.005	0.005	0.000	0.000	0.000	0.000
37	A	99	PHE	0	0.006	-0.013	28.583	0.002	0.002	0.000	0.000	0.000	0.000
38	A	100	MET	0	-0.008	-0.002	27.916	0.000	0.000	0.000	0.000	0.000	0.000
39	A	101	GLN	0	0.029	0.031	27.281	0.002	0.002	0.000	0.000	0.000	0.000
40	A	102	ALA	0	-0.012	-0.005	25.790	0.007	0.007	0.000	0.000	0.000	0.000
41	A	103	LEU	0	0.002	-0.004	23.445	0.005	0.005	0.000	0.000	0.000	0.000
42	A	104	GLN	0	-0.044	-0.034	22.293	0.004	0.004	0.000	0.000	0.000	0.000
43	A	105	LEU	0	0.023	0.029	22.125	0.011	0.011	0.000	0.000	0.000	0.000
44	A	106	LEU	0	-0.007	0.002	18.821	0.018	0.018	0.000	0.000	0.000	0.000
45	A	107	LEU	0	-0.010	-0.013	17.949	0.007	0.007	0.000	0.000	0.000	0.000
46	A	108	GLU	-1	-0.964	-0.964	17.196	0.144	0.144	0.000	0.000	0.000	0.000
47	A	109	VAL	0	0.052	0.010	15.842	0.038	0.038	0.000	0.000	0.000	0.000
48	A	110	GLH	0	-0.059	-0.053	12.864	0.051	0.051	0.000	0.000	0.000	0.000
49	A	111	GLN	0	0.013	0.000	12.565	0.085	0.085	0.000	0.000	0.000	0.000
50	A	112	GLU	-1	-0.891	-0.920	13.169	0.348	0.348	0.000	0.000	0.000	0.000
51	A	113	ILE	0	-0.051	-0.030	9.013	0.145	0.145	0.000	0.000	0.000	0.000
52	A	114	ARG	1	0.801	0.908	8.445	0.057	0.057	0.000	0.000	0.000	0.000
53	A	115	THR	0	-0.039	-0.045	8.958	0.207	0.207	0.000	0.000	0.000	0.000
54	A	116	PHE	0	-0.054	-0.002	8.749	0.213	0.213	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:63:GLY)