FMO DATABASE

FMODB ID: G5Z21

Calculation Name: 3PGG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PGG

Chain ID: A

ChEMBL ID:

UniProt ID: Q5CXX3

Base Structure: X-ray

Registration Date: 2023-09-23

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	78
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-485075.512565
FMO2-HF: Nuclear repulsion	453973.696811
FMO2-HF: Total energy	-31101.815754
FMO2-MP2: Total energy	-31190.10873

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:25:ASN)

Summations of interaction energy for fragment #1(A:25:ASN)

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.
0.783	3.112	0.208	-0.899	-1.637	0.003

Interaction energy analysis for fragmet #1(A:25:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : -0.023

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

Sort

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	27	ILE	0	-0.008	-0.012	2.815	-0.612	1.637	0.209	-0.885	-1.572	0.003
4	A	28	LEU	0	0.039	0.023	4.673	0.446	0.526	-0.001	-0.014	-0.065	0.000
5	A	29	PRO	0	0.051	0.011	8.207	-0.008	-0.008	0.000	0.000	0.000	0.000
6	A	30	LEU	0	0.057	0.032	10.310	0.040	0.040	0.000	0.000	0.000	0.000
7	A	31	ALA	0	0.047	0.026	7.404	0.175	0.175	0.000	0.000	0.000	0.000
8	A	32	LEU	0	-0.064	-0.023	6.801	0.066	0.066	0.000	0.000	0.000	0.000
9	A	33	ILE	0	0.034	0.014	8.381	0.211	0.211	0.000	0.000	0.000	0.000
10	A	34	ASP	-1	-0.911	-0.956	10.541	0.320	0.320	0.000	0.000	0.000	0.000
11	A	35	LYS	1	0.886	0.938	5.255	0.415	0.415	0.000	0.000	0.000	0.000
12	A	36	CYS	0	-0.070	-0.024	10.689	-0.025	-0.025	0.000	0.000	0.000	0.000
13	A	37	ILE	0	0.003	0.009	13.440	0.019	0.019	0.000	0.000	0.000	0.000
14	A	38	GLY	0	-0.027	-0.015	16.261	0.049	0.049	0.000	0.000	0.000	0.000
15	A	39	ASN	0	-0.053	-0.024	15.468	0.017	0.017	0.000	0.000	0.000	0.000
16	A	40	ARG	1	0.769	0.881	17.868	0.166	0.166	0.000	0.000	0.000	0.000
17	A	41	ILE	0	-0.022	-0.008	15.419	-0.053	-0.053	0.000	0.000	0.000	0.000
18	A	42	TYR	0	-0.067	-0.071	17.981	0.072	0.072	0.000	0.000	0.000	0.000
19	A	43	VAL	0	-0.003	0.004	18.605	-0.080	-0.080	0.000	0.000	0.000	0.000
20	A	44	VAL	0	0.015	0.010	20.810	0.046	0.046	0.000	0.000	0.000	0.000
21	A	45	MET	0	-0.011	0.004	22.527	-0.037	-0.037	0.000	0.000	0.000	0.000
22	A	46	LYS	1	0.858	0.920	24.708	0.358	0.358	0.000	0.000	0.000	0.000
23	A	47	GLY	0	0.003	0.002	27.426	0.021	0.021	0.000	0.000	0.000	0.000
24	A	48	ASP	-1	-0.931	-0.961	28.986	-0.283	-0.283	0.000	0.000	0.000	0.000
25	A	49	LYS	1	0.872	0.927	28.733	0.223	0.223	0.000	0.000	0.000	0.000
26	A	50	GLU	-1	-0.849	-0.908	25.002	-0.401	-0.401	0.000	0.000	0.000	0.000
27	A	51	PHE	0	0.014	-0.003	24.273	0.035	0.035	0.000	0.000	0.000	0.000
28	A	52	SER	0	0.025	0.026	22.743	-0.038	-0.038	0.000	0.000	0.000	0.000
29	A	53	GLY	0	0.036	0.012	22.100	0.030	0.030	0.000	0.000	0.000	0.000
30	A	54	VAL	0	-0.007	-0.002	20.861	-0.036	-0.036	0.000	0.000	0.000	0.000
31	A	55	LEU	0	-0.007	0.005	15.861	0.014	0.014	0.000	0.000	0.000	0.000
32	A	56	ARG	1	0.843	0.899	19.652	0.075	0.075	0.000	0.000	0.000	0.000
33	A	57	GLY	0	0.026	0.008	19.479	0.042	0.042	0.000	0.000	0.000	0.000
34	A	58	PHE	0	-0.036	-0.019	13.902	-0.046	-0.046	0.000	0.000	0.000	0.000
35	A	59	ASP	-1	-0.746	-0.857	19.432	-0.183	-0.183	0.000	0.000	0.000	0.000
36	A	60	GLU	-1	-0.868	-0.926	17.483	-0.218	-0.218	0.000	0.000	0.000	0.000
37	A	61	TYR	0	-0.102	-0.065	18.498	-0.059	-0.059	0.000	0.000	0.000	0.000
38	A	62	VAL	0	-0.019	-0.017	16.443	-0.035	-0.035	0.000	0.000	0.000	0.000
39	A	63	ASN	0	-0.036	-0.025	19.040	-0.012	-0.012	0.000	0.000	0.000	0.000
40	A	64	MET	0	-0.039	-0.019	18.296	-0.024	-0.024	0.000	0.000	0.000	0.000
41	A	65	VAL	0	0.002	0.006	21.419	0.012	0.012	0.000	0.000	0.000	0.000
42	A	66	LEU	0	-0.026	-0.006	20.785	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	67	ASP	-1	-0.732	-0.834	24.043	-0.058	-0.058	0.000	0.000	0.000	0.000
44	A	68	ASP	-1	-0.804	-0.907	25.302	-0.142	-0.142	0.000	0.000	0.000	0.000
45	A	69	VAL	0	-0.005	0.013	25.929	-0.022	-0.022	0.000	0.000	0.000	0.000
46	A	70	GLN	0	-0.102	-0.065	27.046	0.001	0.001	0.000	0.000	0.000	0.000
47	A	71	GLU	-1	-0.800	-0.879	27.499	-0.213	-0.213	0.000	0.000	0.000	0.000
48	A	72	TYR	0	-0.013	-0.032	27.184	0.018	0.018	0.000	0.000	0.000	0.000
49	A	73	GLY	0	0.061	0.034	29.986	-0.010	-0.010	0.000	0.000	0.000	0.000
50	A	74	PHE	0	0.002	-0.001	28.051	0.006	0.006	0.000	0.000	0.000	0.000
51	A	75	LYS	1	0.898	0.953	33.884	0.162	0.162	0.000	0.000	0.000	0.000
52	A	76	ALA	0	0.038	0.025	37.551	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	77	ASP	-1	-0.833	-0.891	39.188	-0.146	-0.146	0.000	0.000	0.000	0.000
54	A	89	LYS	1	0.858	0.894	33.536	0.176	0.176	0.000	0.000	0.000	0.000
55	A	90	ARG	1	0.927	0.992	25.842	0.329	0.329	0.000	0.000	0.000	0.000
56	A	91	VAL	0	-0.046	-0.027	32.112	0.009	0.009	0.000	0.000	0.000	0.000
57	A	92	MET	0	-0.003	-0.002	30.307	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	93	VAL	0	-0.068	-0.037	32.578	0.010	0.010	0.000	0.000	0.000	0.000
59	A	94	ASN	0	0.012	-0.002	32.809	0.020	0.020	0.000	0.000	0.000	0.000
60	A	95	ARG	1	0.897	0.950	31.128	0.120	0.120	0.000	0.000	0.000	0.000
61	A	96	LEU	0	-0.018	0.007	30.503	0.008	0.008	0.000	0.000	0.000	0.000
62	A	97	GLU	-1	-0.824	-0.918	29.837	-0.093	-0.093	0.000	0.000	0.000	0.000
63	A	98	THR	0	-0.043	-0.051	27.896	-0.010	-0.010	0.000	0.000	0.000	0.000
64	A	99	ILE	0	-0.052	0.000	26.963	0.004	0.004	0.000	0.000	0.000	0.000
65	A	100	LEU	0	0.002	-0.010	25.551	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	101	LEU	0	-0.011	0.004	22.887	0.000	0.000	0.000	0.000	0.000	0.000
67	A	102	SER	0	0.010	-0.010	23.968	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	103	GLY	0	0.095	0.036	22.073	-0.016	-0.016	0.000	0.000	0.000	0.000
69	A	104	ASN	0	-0.036	-0.021	22.737	-0.033	-0.033	0.000	0.000	0.000	0.000
70	A	105	ASN	0	-0.047	-0.027	25.507	0.001	0.001	0.000	0.000	0.000	0.000
71	A	106	VAL	0	0.028	0.028	19.421	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	107	ALA	0	-0.054	-0.028	21.807	0.003	0.003	0.000	0.000	0.000	0.000
73	A	108	MET	0	-0.034	-0.017	17.100	-0.088	-0.088	0.000	0.000	0.000	0.000
74	A	109	LEU	0	0.023	0.010	13.829	0.079	0.079	0.000	0.000	0.000	0.000
75	A	110	VAL	0	0.003	-0.003	14.788	-0.147	-0.147	0.000	0.000	0.000	0.000
76	A	111	PRO	0	0.047	0.003	10.692	0.135	0.135	0.000	0.000	0.000	0.000
77	A	112	GLY	0	0.002	0.019	13.595	-0.032	-0.032	0.000	0.000	0.000	0.000
78	A	113	GLY	0	-0.063	-0.021	16.062	0.045	0.045	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:25:ASN)