FMO DATABASE

FMODB ID: 1N8LZ

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	OptHSide
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	-485659.653887
FMO2-HF: Nuclear repulsion	454558.059226
FMO2-HF: Total energy	-31101.594662
FMO2-MP2: Total energy	-31189.880609

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.
1.126	3.702	0.374	-0.959	-1.991	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 : -0.024 / q_NPA : -0.022

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	-0.001	-0.006	2.535	0.014	2.446	0.372	-0.915	-1.889	0.004
4	A	28	LEU	0	0.041	0.015	4.275	0.336	0.480	0.002	-0.044	-0.102	0.000
5	A	29	PRO	0	0.053	0.021	7.832	-0.020	-0.020	0.000	0.000	0.000	0.000
6	A	30	LEU	0	0.063	0.029	9.983	0.061	0.061	0.000	0.000	0.000	0.000
7	A	31	ALA	0	0.044	0.030	6.937	0.167	0.167	0.000	0.000	0.000	0.000
8	A	32	LEU	0	-0.055	-0.021	6.910	0.132	0.132	0.000	0.000	0.000	0.000
9	A	33	ILE	0	0.050	0.025	8.221	0.163	0.163	0.000	0.000	0.000	0.000
10	A	34	ASP	-1	-0.919	-0.950	10.742	0.545	0.545	0.000	0.000	0.000	0.000
11	A	35	LYS	1	0.890	0.926	5.306	0.006	0.006	0.000	0.000	0.000	0.000
12	A	36	CYS	0	-0.095	-0.044	10.719	-0.032	-0.032	0.000	0.000	0.000	0.000
13	A	37	ILE	0	-0.019	0.001	13.489	-0.016	-0.016	0.000	0.000	0.000	0.000
14	A	38	GLY	0	-0.020	-0.012	16.282	0.051	0.051	0.000	0.000	0.000	0.000
15	A	39	ASN	0	-0.032	-0.014	14.764	0.000	0.000	0.000	0.000	0.000	0.000
16	A	40	ARG	1	0.764	0.890	17.966	0.135	0.135	0.000	0.000	0.000	0.000
17	A	41	ILE	0	-0.012	-0.007	15.314	-0.052	-0.052	0.000	0.000	0.000	0.000
18	A	42	TYR	0	-0.073	-0.075	17.703	0.065	0.065	0.000	0.000	0.000	0.000
19	A	43	VAL	0	0.016	0.019	18.473	-0.076	-0.076	0.000	0.000	0.000	0.000
20	A	44	VAL	0	0.011	0.008	20.548	0.042	0.042	0.000	0.000	0.000	0.000
21	A	45	MET	0	-0.020	-0.004	22.234	-0.029	-0.029	0.000	0.000	0.000	0.000
22	A	46	LYS	1	0.886	0.922	24.762	0.289	0.289	0.000	0.000	0.000	0.000
23	A	47	GLY	0	-0.014	-0.014	26.994	0.020	0.020	0.000	0.000	0.000	0.000
24	A	48	ASP	-1	-0.929	-0.952	28.502	-0.269	-0.269	0.000	0.000	0.000	0.000
25	A	49	LYS	1	0.864	0.929	28.577	0.193	0.193	0.000	0.000	0.000	0.000
26	A	50	GLU	-1	-0.821	-0.896	24.953	-0.377	-0.377	0.000	0.000	0.000	0.000
27	A	51	PHE	0	0.016	0.006	24.130	0.032	0.032	0.000	0.000	0.000	0.000
28	A	52	SER	0	0.002	0.017	22.565	-0.034	-0.034	0.000	0.000	0.000	0.000
29	A	53	GLY	0	0.035	0.006	21.921	0.029	0.029	0.000	0.000	0.000	0.000
30	A	54	VAL	0	-0.005	0.004	20.895	-0.030	-0.030	0.000	0.000	0.000	0.000
31	A	55	LEU	0	0.001	0.005	15.727	0.008	0.008	0.000	0.000	0.000	0.000
32	A	56	ARG	1	0.848	0.914	19.613	0.019	0.019	0.000	0.000	0.000	0.000
33	A	57	GLY	0	0.025	0.004	19.330	0.046	0.046	0.000	0.000	0.000	0.000
34	A	58	PHE	0	-0.039	-0.019	13.788	-0.057	-0.057	0.000	0.000	0.000	0.000
35	A	59	ASP	-1	-0.734	-0.854	19.246	-0.072	-0.072	0.000	0.000	0.000	0.000
36	A	60	GLU	-1	-0.883	-0.934	17.258	-0.103	-0.103	0.000	0.000	0.000	0.000
37	A	61	TYR	0	-0.116	-0.074	18.320	-0.063	-0.063	0.000	0.000	0.000	0.000
38	A	62	VAL	0	-0.037	-0.025	16.538	-0.041	-0.041	0.000	0.000	0.000	0.000
39	A	63	ASN	0	-0.026	-0.014	19.049	-0.026	-0.026	0.000	0.000	0.000	0.000
40	A	64	MET	0	-0.048	-0.024	18.408	-0.014	-0.014	0.000	0.000	0.000	0.000
41	A	65	VAL	0	0.019	0.021	21.572	0.004	0.004	0.000	0.000	0.000	0.000
42	A	66	LEU	0	-0.020	-0.005	20.483	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	67	ASP	-1	-0.730	-0.846	23.840	-0.012	-0.012	0.000	0.000	0.000	0.000
44	A	68	ASP	-1	-0.816	-0.907	25.248	-0.108	-0.108	0.000	0.000	0.000	0.000
45	A	69	VAL	0	0.011	0.017	25.734	-0.020	-0.020	0.000	0.000	0.000	0.000
46	A	70	GLN	0	-0.110	-0.061	26.897	0.000	0.000	0.000	0.000	0.000	0.000
47	A	71	GLU	-1	-0.810	-0.903	27.412	-0.182	-0.182	0.000	0.000	0.000	0.000
48	A	72	TYR	0	-0.032	-0.037	26.691	0.014	0.014	0.000	0.000	0.000	0.000
49	A	73	GLY	0	0.068	0.036	29.852	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	74	PHE	0	-0.002	0.004	28.132	0.000	0.000	0.000	0.000	0.000	0.000
51	A	75	LYS	1	0.873	0.922	33.811	0.156	0.156	0.000	0.000	0.000	0.000
52	A	76	ALA	0	0.006	-0.006	37.455	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	77	ASP	-1	-0.788	-0.836	39.201	-0.154	-0.154	0.000	0.000	0.000	0.000
54	A	89	LYS	1	0.861	0.893	33.182	0.171	0.171	0.000	0.000	0.000	0.000
55	A	90	ARG	1	0.936	0.989	25.715	0.309	0.309	0.000	0.000	0.000	0.000
56	A	91	VAL	0	-0.041	-0.029	31.701	0.008	0.008	0.000	0.000	0.000	0.000
57	A	92	MET	0	-0.020	-0.010	30.370	0.002	0.002	0.000	0.000	0.000	0.000
58	A	93	VAL	0	-0.042	-0.021	32.817	0.011	0.011	0.000	0.000	0.000	0.000
59	A	94	ASN	0	0.021	0.001	32.976	0.018	0.018	0.000	0.000	0.000	0.000
60	A	95	ARG	1	0.904	0.968	31.293	0.099	0.099	0.000	0.000	0.000	0.000
61	A	96	LEU	0	-0.019	0.001	30.406	0.006	0.006	0.000	0.000	0.000	0.000
62	A	97	GLU	-1	-0.851	-0.937	30.309	-0.061	-0.061	0.000	0.000	0.000	0.000
63	A	98	THR	0	-0.050	-0.038	27.625	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	99	ILE	0	-0.050	-0.016	26.666	0.001	0.001	0.000	0.000	0.000	0.000
65	A	100	LEU	0	-0.010	-0.009	25.657	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	101	LEU	0	-0.017	-0.007	22.943	-0.007	-0.007	0.000	0.000	0.000	0.000
67	A	102	SER	0	0.011	-0.011	24.272	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	103	GLY	0	0.148	0.062	22.175	-0.021	-0.021	0.000	0.000	0.000	0.000
69	A	104	ASN	0	-0.067	-0.025	22.801	-0.038	-0.038	0.000	0.000	0.000	0.000
70	A	105	ASN	0	-0.031	-0.031	24.997	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	106	VAL	0	0.030	0.039	19.203	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	107	ALA	0	-0.073	-0.024	21.517	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	108	MET	0	-0.022	-0.017	16.728	-0.092	-0.092	0.000	0.000	0.000	0.000
74	A	109	LEU	0	0.029	0.020	13.604	0.078	0.078	0.000	0.000	0.000	0.000
75	A	110	VAL	0	-0.032	-0.033	14.777	-0.139	-0.139	0.000	0.000	0.000	0.000
76	A	111	PRO	0	0.021	-0.002	10.566	0.122	0.122	0.000	0.000	0.000	0.000
77	A	112	GLY	0	0.017	0.021	13.544	-0.025	-0.025	0.000	0.000	0.000	0.000
78	A	113	GLY	0	-0.033	-0.009	15.984	-0.016	-0.016	0.000	0.000	0.000	0.000

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