FMO DATABASE

FMODB ID: VZ3L1

Calculation Name: 1PD3-A-Xray549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1PD3

Chain ID: A

ChEMBL ID:

UniProt ID: P03508

Base Structure: X-ray

Registration Date: 2025-10-11

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	54
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230712

Total energy (hartree)

FMO2-HF: Electronic energy	-300029.451155
FMO2-HF: Nuclear repulsion	276844.364612
FMO2-HF: Total energy	-23185.086543
FMO2-MP2: Total energy	-23253.813502

3D Structure Molmil

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.
-38.502	-36.041	-0.004	-0.864	-1.593	-0.005

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 : 1 / q_Mulliken : 0.916 / q_NPA : 0.940

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	0.075	0.046	3.822	3.980	5.607	-0.005	-0.655	-0.966	-0.004
4	A	66	ARG	1	0.900	0.927	3.425	45.981	46.456	0.002	-0.143	-0.335	-0.001
5	A	67	GLU	-1	-0.910	-0.931	3.894	-44.350	-43.991	-0.001	-0.066	-0.292	0.000
6	A	68	GLN	0	-0.015	-0.024	5.714	8.771	8.771	0.000	0.000	0.000	0.000
7	A	69	LEU	0	-0.008	0.015	8.198	3.566	3.566	0.000	0.000	0.000	0.000
8	A	70	GLY	0	0.042	0.024	8.348	2.876	2.876	0.000	0.000	0.000	0.000
9	A	71	GLN	0	-0.048	-0.045	8.568	3.931	3.931	0.000	0.000	0.000	0.000
10	A	72	LYS	1	0.947	0.977	11.736	26.602	26.602	0.000	0.000	0.000	0.000
11	A	73	PHE	0	0.016	0.000	12.023	1.374	1.374	0.000	0.000	0.000	0.000
12	A	74	GLU	-1	-0.805	-0.841	13.719	-18.715	-18.715	0.000	0.000	0.000	0.000
13	A	75	GLU	-1	-0.911	-0.953	15.598	-15.090	-15.090	0.000	0.000	0.000	0.000
14	A	76	ILE	0	-0.036	-0.027	16.938	1.097	1.097	0.000	0.000	0.000	0.000
15	A	77	ARG	1	0.863	0.897	16.494	18.414	18.414	0.000	0.000	0.000	0.000
16	A	78	TRP	0	-0.022	-0.006	19.772	0.855	0.855	0.000	0.000	0.000	0.000
17	A	79	LEU	0	0.004	-0.002	21.670	0.848	0.848	0.000	0.000	0.000	0.000
18	A	80	ILE	0	-0.033	-0.014	22.570	0.757	0.757	0.000	0.000	0.000	0.000
19	A	81	GLU	-1	-0.871	-0.947	23.345	-12.452	-12.452	0.000	0.000	0.000	0.000
20	A	82	GLU	-1	-0.947	-0.968	25.638	-11.515	-11.515	0.000	0.000	0.000	0.000
21	A	83	VAL	0	-0.064	-0.037	27.941	0.594	0.594	0.000	0.000	0.000	0.000
22	A	84	ARG	1	0.884	0.941	28.893	10.265	10.265	0.000	0.000	0.000	0.000
23	A	85	HIS	0	-0.030	-0.009	30.062	0.460	0.460	0.000	0.000	0.000	0.000
24	A	86	ARG	1	0.901	0.947	31.565	10.296	10.296	0.000	0.000	0.000	0.000
25	A	87	LEU	0	-0.007	0.023	33.400	0.373	0.373	0.000	0.000	0.000	0.000
26	A	88	LYS	1	0.895	0.940	35.980	8.518	8.518	0.000	0.000	0.000	0.000
27	A	89	ILE	0	0.024	0.019	34.413	0.212	0.212	0.000	0.000	0.000	0.000
28	A	90	THR	0	0.014	-0.006	38.665	-0.101	-0.101	0.000	0.000	0.000	0.000
29	A	91	GLU	-1	-0.822	-0.905	34.608	-9.373	-9.373	0.000	0.000	0.000	0.000
30	A	92	ASN	0	-0.019	-0.014	36.832	-0.285	-0.285	0.000	0.000	0.000	0.000
31	A	93	SER	0	-0.019	-0.006	37.717	0.076	0.076	0.000	0.000	0.000	0.000
32	A	94	PHE	0	0.047	0.011	35.140	-0.169	-0.169	0.000	0.000	0.000	0.000
33	A	95	GLU	-1	-0.908	-0.940	34.478	-9.312	-9.312	0.000	0.000	0.000	0.000
34	A	96	GLN	0	0.042	0.020	32.241	-0.472	-0.472	0.000	0.000	0.000	0.000
35	A	97	ILE	0	-0.013	-0.003	31.962	-0.348	-0.348	0.000	0.000	0.000	0.000
36	A	98	THR	0	-0.001	-0.011	30.391	-0.379	-0.379	0.000	0.000	0.000	0.000
37	A	99	PHE	0	-0.005	-0.015	28.232	-0.447	-0.447	0.000	0.000	0.000	0.000
38	A	100	MET	0	-0.024	-0.002	27.194	-0.518	-0.518	0.000	0.000	0.000	0.000
39	A	101	GLN	0	0.013	0.012	26.295	-0.299	-0.299	0.000	0.000	0.000	0.000
40	A	102	ALA	0	-0.014	-0.009	24.992	-0.494	-0.494	0.000	0.000	0.000	0.000
41	A	103	LEU	0	0.007	0.001	22.712	-0.781	-0.781	0.000	0.000	0.000	0.000
42	A	104	GLN	0	-0.040	-0.026	21.502	-0.526	-0.526	0.000	0.000	0.000	0.000
43	A	105	LEU	0	0.044	0.030	21.045	-0.675	-0.675	0.000	0.000	0.000	0.000
44	A	106	LEU	0	-0.030	-0.007	18.133	-0.905	-0.905	0.000	0.000	0.000	0.000
45	A	107	LEU	0	-0.021	-0.017	17.070	-1.363	-1.363	0.000	0.000	0.000	0.000
46	A	108	GLU	-1	-0.968	-0.976	16.347	-16.002	-16.002	0.000	0.000	0.000	0.000
47	A	109	VAL	0	0.060	0.021	14.672	-1.194	-1.194	0.000	0.000	0.000	0.000
48	A	110	GLU	0	-0.069	-0.060	12.303	-1.598	-1.598	0.000	0.000	0.000	0.000
49	A	111	GLN	0	-0.008	0.005	11.693	-3.565	-3.565	0.000	0.000	0.000	0.000
50	A	112	GLU	-1	-0.909	-0.944	12.171	-20.548	-20.548	0.000	0.000	0.000	0.000
51	A	113	ILE	0	-0.032	-0.013	8.058	-2.459	-2.459	0.000	0.000	0.000	0.000
52	A	114	ARG	1	0.826	0.892	7.362	21.181	21.181	0.000	0.000	0.000	0.000
53	A	115	THR	0	-0.082	-0.044	8.370	-1.685	-1.685	0.000	0.000	0.000	0.000
54	A	116	PHE	-1	-0.851	-0.887	8.383	-33.909	-33.909	0.000	0.000	0.000	0.000

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