FMO DATABASE

FMODB ID: K3L43

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

Total energy (hartree)

FMO2-HF: Electronic energy	-301533.944758
FMO2-HF: Nuclear repulsion	278348.420752
FMO2-HF: Total energy	-23185.524006
FMO2-MP2: Total energy	-23254.300928

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.
-2.943	-0.286	0.083	-1.055	-1.686	0.001

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 : 0.076 / 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	65	TRP	0	0.045	0.023	3.726	-0.106	1.273	-0.001	-0.656	-0.722	0.000
4	A	66	ARG	1	0.941	0.959	3.065	-3.235	-2.264	0.085	-0.343	-0.714	0.001
5	A	67	GLU	-1	-0.848	-0.902	4.105	-1.974	-1.667	-0.001	-0.056	-0.250	0.000
6	A	68	GLN	0	-0.025	-0.019	5.867	0.617	0.617	0.000	0.000	0.000	0.000
7	A	69	LEU	0	-0.016	0.011	8.042	0.143	0.143	0.000	0.000	0.000	0.000
8	A	70	GLY	0	0.046	0.021	8.286	0.053	0.053	0.000	0.000	0.000	0.000
9	A	71	GLN	0	-0.004	-0.030	9.734	0.093	0.093	0.000	0.000	0.000	0.000
10	A	72	LYS	1	0.899	0.953	11.767	0.326	0.326	0.000	0.000	0.000	0.000
11	A	73	PHE	0	0.014	-0.005	12.812	0.053	0.053	0.000	0.000	0.000	0.000
12	A	74	GLU	-1	-0.788	-0.831	13.964	-0.216	-0.216	0.000	0.000	0.000	0.000
13	A	75	GLU	-1	-0.909	-0.950	15.775	-0.151	-0.151	0.000	0.000	0.000	0.000
14	A	76	ILE	0	-0.039	-0.028	16.733	0.028	0.028	0.000	0.000	0.000	0.000
15	A	77	ARG	1	0.834	0.882	17.020	0.182	0.182	0.000	0.000	0.000	0.000
16	A	78	TRP	0	-0.018	0.001	19.912	0.011	0.011	0.000	0.000	0.000	0.000
17	A	79	LEU	0	-0.012	-0.007	21.882	0.016	0.016	0.000	0.000	0.000	0.000
18	A	80	ILE	0	-0.022	-0.007	22.320	0.013	0.013	0.000	0.000	0.000	0.000
19	A	81	GLU	-1	-0.826	-0.927	22.792	-0.091	-0.091	0.000	0.000	0.000	0.000
20	A	82	GLU	-1	-0.803	-0.892	25.891	-0.090	-0.090	0.000	0.000	0.000	0.000
21	A	83	VAL	0	-0.059	-0.027	28.001	0.007	0.007	0.000	0.000	0.000	0.000
22	A	84	ARG	1	0.875	0.926	28.874	0.051	0.051	0.000	0.000	0.000	0.000
23	A	85	HIS	0	-0.016	0.001	29.955	0.006	0.006	0.000	0.000	0.000	0.000
24	A	86	ARG	1	0.806	0.883	30.511	0.079	0.079	0.000	0.000	0.000	0.000
25	A	87	LEU	0	0.005	0.016	32.872	0.004	0.004	0.000	0.000	0.000	0.000
26	A	88	LYS	1	0.791	0.893	35.605	0.047	0.047	0.000	0.000	0.000	0.000
27	A	89	ILE	0	0.018	0.019	34.093	0.003	0.003	0.000	0.000	0.000	0.000
28	A	90	THR	0	0.031	0.010	38.322	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	91	GLU	-1	-0.793	-0.877	34.306	-0.035	-0.035	0.000	0.000	0.000	0.000
30	A	92	ASN	0	-0.050	-0.039	37.299	0.003	0.003	0.000	0.000	0.000	0.000
31	A	93	SER	0	-0.030	-0.003	37.579	0.002	0.002	0.000	0.000	0.000	0.000
32	A	94	PHE	0	0.052	0.013	34.961	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	95	GLU	-1	-0.903	-0.938	34.303	-0.020	-0.020	0.000	0.000	0.000	0.000
34	A	96	GLN	0	0.047	0.013	31.945	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	97	ILE	0	-0.019	-0.005	31.888	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	98	THR	0	0.003	-0.007	30.231	0.002	0.002	0.000	0.000	0.000	0.000
37	A	99	PHE	0	0.001	-0.013	28.129	0.000	0.000	0.000	0.000	0.000	0.000
38	A	100	MET	0	-0.034	-0.007	27.154	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	101	GLN	0	0.026	0.019	26.254	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	102	ALA	0	-0.013	-0.010	24.811	0.004	0.004	0.000	0.000	0.000	0.000
41	A	103	LEU	0	0.000	0.001	22.695	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	104	GLN	0	-0.038	-0.025	21.448	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	105	LEU	0	0.045	0.029	20.896	0.000	0.000	0.000	0.000	0.000	0.000
44	A	106	LEU	0	-0.017	-0.002	17.733	0.013	0.013	0.000	0.000	0.000	0.000
45	A	107	LEU	0	-0.001	-0.012	16.892	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	108	GLU	-1	-0.972	-0.977	16.222	0.034	0.034	0.000	0.000	0.000	0.000
47	A	109	VAL	0	0.049	0.016	14.564	0.014	0.014	0.000	0.000	0.000	0.000
48	A	110	GLH	0	-0.067	-0.059	12.482	0.041	0.041	0.000	0.000	0.000	0.000
49	A	111	GLN	0	0.008	0.008	11.409	-0.048	-0.048	0.000	0.000	0.000	0.000
50	A	112	GLU	-1	-0.902	-0.927	11.797	0.217	0.217	0.000	0.000	0.000	0.000
51	A	113	ILE	0	-0.025	-0.008	7.819	0.134	0.134	0.000	0.000	0.000	0.000
52	A	114	ARG	1	0.829	0.910	6.910	0.441	0.441	0.000	0.000	0.000	0.000
53	A	115	THR	0	-0.021	-0.029	7.386	0.065	0.065	0.000	0.000	0.000	0.000
54	A	116	PHE	0	-0.039	-0.001	7.841	0.354	0.354	0.000	0.000	0.000	0.000

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