FMO DATABASE

FMODB ID: VQJG1

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	OptH
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	-485468.214285
FMO2-HF: Nuclear repulsion	454366.95124
FMO2-HF: Total energy	-31101.263045
FMO2-MP2: Total energy	-31189.566662

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.
1.483	4.027	0.421	-0.955	-2.011	0.004

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 : -0.020 / q_NPA : -0.020

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	27	ILE	0	-0.004	-0.008	2.507	0.008	2.407	0.418	-0.910	-1.908	0.004
4	A	28	LEU	0	0.047	0.016	4.244	0.423	0.568	0.003	-0.045	-0.103	0.000
5	A	29	PRO	0	0.052	0.020	7.810	-0.006	-0.006	0.000	0.000	0.000	0.000
6	A	30	LEU	0	0.069	0.033	9.955	0.072	0.072	0.000	0.000	0.000	0.000
7	A	31	ALA	0	0.042	0.032	6.899	0.173	0.173	0.000	0.000	0.000	0.000
8	A	32	LEU	0	-0.066	-0.030	7.231	0.128	0.128	0.000	0.000	0.000	0.000
9	A	33	ILE	0	0.057	0.029	8.206	0.174	0.174	0.000	0.000	0.000	0.000
10	A	34	ASP	-1	-0.922	-0.957	10.856	0.488	0.488	0.000	0.000	0.000	0.000
11	A	35	LYS	1	0.881	0.926	5.368	0.342	0.342	0.000	0.000	0.000	0.000
12	A	36	CYS	0	-0.114	-0.054	10.726	-0.024	-0.024	0.000	0.000	0.000	0.000
13	A	37	ILE	0	-0.006	0.010	13.488	-0.017	-0.017	0.000	0.000	0.000	0.000
14	A	38	GLY	0	-0.017	-0.009	16.286	0.054	0.054	0.000	0.000	0.000	0.000
15	A	39	ASN	0	-0.008	-0.006	14.250	0.020	0.020	0.000	0.000	0.000	0.000
16	A	40	ARG	1	0.803	0.904	17.968	0.133	0.133	0.000	0.000	0.000	0.000
17	A	41	ILE	0	-0.010	-0.013	15.565	-0.050	-0.050	0.000	0.000	0.000	0.000
18	A	42	TYR	0	-0.069	-0.050	17.687	0.066	0.066	0.000	0.000	0.000	0.000
19	A	43	VAL	0	0.019	0.020	18.451	-0.078	-0.078	0.000	0.000	0.000	0.000
20	A	44	VAL	0	0.012	0.008	20.525	0.043	0.043	0.000	0.000	0.000	0.000
21	A	45	MET	0	-0.019	-0.002	22.204	-0.030	-0.030	0.000	0.000	0.000	0.000
22	A	46	LYS	1	0.939	0.962	24.733	0.303	0.303	0.000	0.000	0.000	0.000
23	A	47	GLY	0	-0.027	-0.021	26.962	0.020	0.020	0.000	0.000	0.000	0.000
24	A	48	ASP	-1	-0.934	-0.958	28.482	-0.277	-0.277	0.000	0.000	0.000	0.000
25	A	49	LYS	1	0.937	0.975	28.500	0.200	0.200	0.000	0.000	0.000	0.000
26	A	50	GLU	-1	-0.830	-0.921	24.805	-0.385	-0.385	0.000	0.000	0.000	0.000
27	A	51	PHE	0	0.020	0.012	24.111	0.032	0.032	0.000	0.000	0.000	0.000
28	A	52	SER	0	0.001	0.027	22.549	-0.039	-0.039	0.000	0.000	0.000	0.000
29	A	53	GLY	0	0.047	-0.001	21.910	0.029	0.029	0.000	0.000	0.000	0.000
30	A	54	VAL	0	-0.010	0.004	20.882	-0.031	-0.031	0.000	0.000	0.000	0.000
31	A	55	LEU	0	-0.007	-0.001	15.809	0.006	0.006	0.000	0.000	0.000	0.000
32	A	56	ARG	1	0.856	0.928	19.613	0.020	0.020	0.000	0.000	0.000	0.000
33	A	57	GLY	0	0.023	0.005	19.327	0.046	0.046	0.000	0.000	0.000	0.000
34	A	58	PHE	0	-0.033	-0.019	13.901	-0.060	-0.060	0.000	0.000	0.000	0.000
35	A	59	ASP	-1	-0.741	-0.867	19.198	-0.091	-0.091	0.000	0.000	0.000	0.000
36	A	60	GLU	-1	-0.935	-0.982	17.240	-0.141	-0.141	0.000	0.000	0.000	0.000
37	A	61	TYR	0	-0.064	-0.025	18.297	-0.064	-0.064	0.000	0.000	0.000	0.000
38	A	62	VAL	0	-0.027	-0.022	16.737	-0.040	-0.040	0.000	0.000	0.000	0.000
39	A	63	ASN	0	-0.023	-0.002	19.027	-0.024	-0.024	0.000	0.000	0.000	0.000
40	A	64	MET	0	-0.058	-0.034	18.599	-0.017	-0.017	0.000	0.000	0.000	0.000
41	A	65	VAL	0	0.016	0.024	21.558	0.005	0.005	0.000	0.000	0.000	0.000
42	A	66	LEU	0	-0.020	-0.002	20.347	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	67	ASP	-1	-0.740	-0.860	23.831	-0.015	-0.015	0.000	0.000	0.000	0.000
44	A	68	ASP	-1	-0.905	-0.947	25.242	-0.095	-0.095	0.000	0.000	0.000	0.000
45	A	69	VAL	0	0.012	0.016	25.571	-0.021	-0.021	0.000	0.000	0.000	0.000
46	A	70	GLN	0	-0.102	-0.060	26.887	0.001	0.001	0.000	0.000	0.000	0.000
47	A	71	GLU	-1	-0.890	-0.950	27.396	-0.190	-0.190	0.000	0.000	0.000	0.000
48	A	72	TYR	0	-0.048	-0.045	26.840	0.012	0.012	0.000	0.000	0.000	0.000
49	A	73	GLY	0	0.075	0.040	29.831	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	74	PHE	0	0.000	0.006	28.353	0.002	0.002	0.000	0.000	0.000	0.000
51	A	75	LYS	1	0.870	0.927	33.783	0.159	0.159	0.000	0.000	0.000	0.000
52	A	76	ALA	0	0.004	-0.007	37.428	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	77	ASP	-1	-0.791	-0.843	39.384	-0.156	-0.156	0.000	0.000	0.000	0.000
54	A	89	LYS	1	0.866	0.899	33.067	0.171	0.171	0.000	0.000	0.000	0.000
55	A	90	ARG	1	0.936	0.986	25.668	0.308	0.308	0.000	0.000	0.000	0.000
56	A	91	VAL	0	-0.042	-0.029	31.677	0.009	0.009	0.000	0.000	0.000	0.000
57	A	92	MET	0	-0.022	-0.012	30.267	0.001	0.001	0.000	0.000	0.000	0.000
58	A	93	VAL	0	-0.034	-0.019	32.827	0.011	0.011	0.000	0.000	0.000	0.000
59	A	94	ASN	0	0.030	0.004	33.184	0.017	0.017	0.000	0.000	0.000	0.000
60	A	95	ARG	1	0.917	0.970	31.481	0.097	0.097	0.000	0.000	0.000	0.000
61	A	96	LEU	0	-0.021	-0.004	30.441	0.006	0.006	0.000	0.000	0.000	0.000
62	A	97	GLU	-1	-0.815	-0.917	30.225	-0.061	-0.061	0.000	0.000	0.000	0.000
63	A	98	THR	0	-0.058	-0.032	27.633	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	99	ILE	0	-0.042	-0.009	26.178	0.001	0.001	0.000	0.000	0.000	0.000
65	A	100	LEU	0	0.004	-0.004	25.761	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	101	LEU	0	-0.028	-0.017	23.068	-0.007	-0.007	0.000	0.000	0.000	0.000
67	A	102	SER	0	-0.001	-0.014	24.252	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	103	GLY	0	0.155	0.060	22.147	-0.020	-0.020	0.000	0.000	0.000	0.000
69	A	104	ASN	0	-0.080	-0.033	22.773	-0.039	-0.039	0.000	0.000	0.000	0.000
70	A	105	ASN	0	-0.050	-0.050	24.998	-0.015	-0.015	0.000	0.000	0.000	0.000
71	A	106	VAL	0	0.032	0.040	19.212	0.000	0.000	0.000	0.000	0.000	0.000
72	A	107	ALA	0	-0.079	-0.024	21.483	-0.010	-0.010	0.000	0.000	0.000	0.000
73	A	108	MET	0	-0.008	-0.015	16.707	-0.100	-0.100	0.000	0.000	0.000	0.000
74	A	109	LEU	0	0.004	0.017	13.458	0.079	0.079	0.000	0.000	0.000	0.000
75	A	110	VAL	0	-0.025	-0.032	14.766	-0.143	-0.143	0.000	0.000	0.000	0.000
76	A	111	PRO	0	0.021	0.001	10.594	0.127	0.127	0.000	0.000	0.000	0.000
77	A	112	GLY	0	0.016	0.016	13.529	-0.019	-0.019	0.000	0.000	0.000	0.000
78	A	113	GLY	0	-0.034	-0.009	15.975	-0.013	-0.013	0.000	0.000	0.000	0.000

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