FMO DATABASE

FMODB ID: KR1M3

Calculation Name: 1PD3-A-Xray315

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	55
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-303098.159991
FMO2-HF: Nuclear repulsion	279763.189351
FMO2-HF: Total energy	-23334.97064
FMO2-MP2: Total energy	-23404.382237

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:62:ACE )

Summations of interaction energy for fragment #1(A:62:ACE )

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.
2.185	3.539	0.011	-0.701	-0.664	-0.001

Interaction energy analysis for fragmet #1(A:62:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.041 / q_NPA : 0.012

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	64	LYS	1	0.965	0.964	3.843	1.277	2.239	-0.006	-0.537	-0.419	0.000
4	A	65	TRP	0	0.037	0.026	7.395	0.261	0.261	0.000	0.000	0.000	0.000
5	A	66	ARG	1	0.958	0.957	3.412	-1.120	-0.728	0.017	-0.164	-0.245	-0.001
6	A	67	GLU	-1	-0.946	-0.941	5.851	0.673	0.673	0.000	0.000	0.000	0.000
7	A	68	GLN	0	-0.036	-0.043	7.425	0.095	0.095	0.000	0.000	0.000	0.000
8	A	69	LEU	0	0.010	0.024	9.946	0.047	0.047	0.000	0.000	0.000	0.000
9	A	70	GLY	0	0.025	0.023	9.768	0.028	0.028	0.000	0.000	0.000	0.000
10	A	71	GLN	0	-0.005	-0.018	10.314	-0.051	-0.051	0.000	0.000	0.000	0.000
11	A	72	LYS	1	0.938	0.976	13.312	0.104	0.104	0.000	0.000	0.000	0.000
12	A	73	PHE	0	0.004	-0.013	12.966	0.004	0.004	0.000	0.000	0.000	0.000
13	A	74	GLU	-1	-0.774	-0.853	14.936	0.193	0.193	0.000	0.000	0.000	0.000
14	A	75	GLU	-1	-0.872	-0.929	16.727	0.024	0.024	0.000	0.000	0.000	0.000
15	A	76	ILE	0	-0.040	-0.016	18.404	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	77	ARG	1	0.807	0.888	16.651	-0.154	-0.154	0.000	0.000	0.000	0.000
17	A	78	TRP	0	0.025	0.017	20.783	0.002	0.002	0.000	0.000	0.000	0.000
18	A	79	LEU	0	0.009	0.000	22.704	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	80	ILE	0	-0.041	-0.033	23.515	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	81	GLU	-1	-0.905	-0.953	24.238	0.081	0.081	0.000	0.000	0.000	0.000
21	A	82	GLU	-1	-0.954	-0.959	26.653	0.030	0.030	0.000	0.000	0.000	0.000
22	A	83	VAL	0	-0.083	-0.051	29.003	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	84	ARG	1	0.903	0.945	29.683	-0.048	-0.048	0.000	0.000	0.000	0.000
24	A	85	HIS	0	-0.050	-0.015	30.940	0.000	0.000	0.000	0.000	0.000	0.000
25	A	86	ARG	1	0.876	0.942	32.583	-0.028	-0.028	0.000	0.000	0.000	0.000
26	A	87	LEU	0	0.012	0.025	34.291	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	88	LYS	1	0.902	0.949	36.870	-0.032	-0.032	0.000	0.000	0.000	0.000
28	A	89	ILE	0	-0.007	-0.001	34.866	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	90	THR	0	0.011	-0.004	38.911	0.002	0.002	0.000	0.000	0.000	0.000
30	A	91	GLU	-1	-0.860	-0.941	34.987	0.053	0.053	0.000	0.000	0.000	0.000
31	A	92	ASN	0	0.006	-0.018	37.297	0.002	0.002	0.000	0.000	0.000	0.000
32	A	93	SER	0	-0.050	0.001	38.115	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	94	PHE	0	0.090	0.022	35.985	0.002	0.002	0.000	0.000	0.000	0.000
34	A	95	GLU	-1	-0.939	-0.978	35.090	0.029	0.029	0.000	0.000	0.000	0.000
35	A	96	GLN	0	0.080	0.055	32.457	0.000	0.000	0.000	0.000	0.000	0.000
36	A	97	ILE	0	-0.035	-0.012	32.413	0.004	0.004	0.000	0.000	0.000	0.000
37	A	98	THR	0	-0.015	-0.013	31.229	0.004	0.004	0.000	0.000	0.000	0.000
38	A	99	PHE	0	0.020	0.001	28.686	0.003	0.003	0.000	0.000	0.000	0.000
39	A	100	MET	0	-0.012	0.000	27.647	0.007	0.007	0.000	0.000	0.000	0.000
40	A	101	GLN	0	0.023	0.019	26.677	0.007	0.007	0.000	0.000	0.000	0.000
41	A	102	ALA	0	0.002	0.005	25.402	0.004	0.004	0.000	0.000	0.000	0.000
42	A	103	LEU	0	0.022	0.007	23.191	0.007	0.007	0.000	0.000	0.000	0.000
43	A	104	GLN	0	-0.062	-0.043	21.796	0.008	0.008	0.000	0.000	0.000	0.000
44	A	105	LEU	0	0.026	0.024	21.233	0.012	0.012	0.000	0.000	0.000	0.000
45	A	106	LEU	0	-0.018	-0.002	18.615	0.009	0.009	0.000	0.000	0.000	0.000
46	A	107	LEU	0	-0.004	-0.011	17.339	0.018	0.018	0.000	0.000	0.000	0.000
47	A	108	GLU	-1	-0.960	-0.967	16.258	0.158	0.158	0.000	0.000	0.000	0.000
48	A	109	VAL	0	0.051	0.011	15.526	0.024	0.024	0.000	0.000	0.000	0.000
49	A	110	GLH	0	-0.064	-0.036	12.507	0.001	0.001	0.000	0.000	0.000	0.000
50	A	111	GLN	0	-0.012	-0.030	11.623	0.142	0.142	0.000	0.000	0.000	0.000
51	A	112	GLU	-1	-0.903	-0.945	11.526	0.206	0.206	0.000	0.000	0.000	0.000
52	A	113	ILE	0	-0.050	-0.028	8.595	0.018	0.018	0.000	0.000	0.000	0.000
53	A	114	ARG	1	0.778	0.900	7.107	-0.599	-0.599	0.000	0.000	0.000	0.000
54	A	115	THR	0	-0.079	-0.061	6.880	0.333	0.333	0.000	0.000	0.000	0.000
55	A	116	PHE	-1	-0.869	-0.884	7.747	0.372	0.372	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:62:ACE )