FMO DATABASE

FMODB ID: 43YZN

Calculation Name: 3PQK-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PQK

Chain ID: F

ChEMBL ID:

UniProt ID: Q9PFB1

Base Structure: X-ray

Registration Date: 2023-03-14

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	99
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-708856.773306
FMO2-HF: Nuclear repulsion	669137.999357
FMO2-HF: Total energy	-39718.773949
FMO2-MP2: Total energy	-39833.754851

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(F:15:ARG)

Summations of interaction energy for fragment #1(F:15:ARG)

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.
-72.869	-76.967	32.083	-14.422	-13.563	-0.117

Interaction energy analysis for fragmet #1(F:15:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.801 / q_NPA : 0.857

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	F	17	ASP	-1	-0.864	-0.929	2.888	-26.249	-24.276	0.083	-0.610	-1.445	0.004
4	F	18	MET	0	-0.056	-0.018	1.908	3.282	4.427	4.822	-2.807	-3.161	0.009
5	F	19	GLU	-1	-0.820	-0.886	1.756	-128.535	-135.880	27.179	-10.999	-8.835	-0.130
6	F	20	LYS	1	0.899	0.950	5.195	33.381	33.510	-0.001	-0.006	-0.122	0.000
7	F	21	ARG	1	0.925	0.958	7.912	23.776	23.776	0.000	0.000	0.000	0.000
8	F	22	ALA	0	0.019	0.018	7.486	2.543	2.543	0.000	0.000	0.000	0.000
9	F	23	ASN	0	-0.008	-0.007	7.132	5.210	5.210	0.000	0.000	0.000	0.000
10	F	24	GLU	-1	-0.914	-0.951	10.386	-20.185	-20.185	0.000	0.000	0.000	0.000
11	F	25	VAL	0	-0.012	-0.015	12.966	1.894	1.894	0.000	0.000	0.000	0.000
12	F	26	ALA	0	0.030	0.018	12.468	1.499	1.499	0.000	0.000	0.000	0.000
13	F	27	ASN	0	-0.018	-0.024	13.747	1.217	1.217	0.000	0.000	0.000	0.000
14	F	28	LEU	0	0.017	0.016	16.263	1.170	1.170	0.000	0.000	0.000	0.000
15	F	29	LEU	0	0.022	-0.003	16.480	0.970	0.970	0.000	0.000	0.000	0.000
16	F	30	LYS	1	0.933	0.979	14.391	20.106	20.106	0.000	0.000	0.000	0.000
17	F	31	THR	0	-0.024	-0.002	19.891	0.839	0.839	0.000	0.000	0.000	0.000
18	F	32	LEU	0	0.017	0.001	22.303	0.695	0.695	0.000	0.000	0.000	0.000
19	F	33	SER	0	-0.029	0.011	21.709	0.432	0.432	0.000	0.000	0.000	0.000
20	F	34	HIS	0	-0.020	-0.017	24.196	0.154	0.154	0.000	0.000	0.000	0.000
21	F	35	PRO	0	0.066	0.031	27.885	0.025	0.025	0.000	0.000	0.000	0.000
22	F	36	VAL	0	0.029	0.012	30.841	0.135	0.135	0.000	0.000	0.000	0.000
23	F	37	ARG	1	0.843	0.910	25.162	11.623	11.623	0.000	0.000	0.000	0.000
24	F	38	LEU	0	0.030	0.009	26.355	0.026	0.026	0.000	0.000	0.000	0.000
25	F	39	MET	0	0.047	0.035	29.964	0.144	0.144	0.000	0.000	0.000	0.000
26	F	40	LEU	0	-0.043	0.003	32.493	0.165	0.165	0.000	0.000	0.000	0.000
27	F	41	VAL	0	-0.001	-0.013	28.014	0.072	0.072	0.000	0.000	0.000	0.000
28	F	42	CYS	0	-0.001	0.001	30.541	0.125	0.125	0.000	0.000	0.000	0.000
29	F	43	THR	0	0.011	-0.004	32.365	0.218	0.218	0.000	0.000	0.000	0.000
30	F	44	LEU	0	-0.058	-0.040	33.130	0.139	0.139	0.000	0.000	0.000	0.000
31	F	45	VAL	0	-0.055	-0.010	30.452	-0.027	-0.027	0.000	0.000	0.000	0.000
32	F	46	GLU	-1	-0.834	-0.866	33.192	-8.031	-8.031	0.000	0.000	0.000	0.000
33	F	47	GLY	0	-0.009	0.007	36.426	0.232	0.232	0.000	0.000	0.000	0.000
34	F	48	GLU	-1	-0.940	-0.984	37.322	-8.143	-8.143	0.000	0.000	0.000	0.000
35	F	49	PHE	0	0.036	0.022	38.377	0.219	0.219	0.000	0.000	0.000	0.000
36	F	50	SER	0	-0.056	-0.022	40.313	-0.147	-0.147	0.000	0.000	0.000	0.000
37	F	51	VAL	0	0.026	-0.011	40.304	-0.055	-0.055	0.000	0.000	0.000	0.000
38	F	52	GLY	0	0.023	0.016	42.076	-0.028	-0.028	0.000	0.000	0.000	0.000
39	F	53	GLU	-1	-0.843	-0.933	43.450	-7.012	-7.012	0.000	0.000	0.000	0.000
40	F	54	LEU	0	-0.022	-0.009	37.623	-0.048	-0.048	0.000	0.000	0.000	0.000
41	F	55	GLU	-1	-0.916	-0.970	40.970	-7.066	-7.066	0.000	0.000	0.000	0.000
42	F	56	GLN	0	-0.073	-0.034	42.621	0.097	0.097	0.000	0.000	0.000	0.000
43	F	57	GLN	0	-0.020	-0.004	40.659	-0.048	-0.048	0.000	0.000	0.000	0.000
44	F	58	ILE	0	-0.015	-0.008	36.582	-0.095	-0.095	0.000	0.000	0.000	0.000
45	F	59	GLY	0	0.017	0.029	40.103	-0.066	-0.066	0.000	0.000	0.000	0.000
46	F	60	ILE	0	-0.071	-0.036	37.259	-0.069	-0.069	0.000	0.000	0.000	0.000
47	F	61	GLY	0	0.091	0.053	40.512	0.043	0.043	0.000	0.000	0.000	0.000
48	F	62	GLN	0	0.019	0.003	40.569	-0.361	-0.361	0.000	0.000	0.000	0.000
49	F	63	PRO	0	0.004	-0.007	39.301	0.104	0.104	0.000	0.000	0.000	0.000
50	F	64	THR	0	0.021	-0.002	35.690	-0.156	-0.156	0.000	0.000	0.000	0.000
51	F	65	LEU	0	0.027	0.023	35.904	-0.325	-0.325	0.000	0.000	0.000	0.000
52	F	66	SER	0	0.021	-0.011	36.160	-0.216	-0.216	0.000	0.000	0.000	0.000
53	F	67	GLN	0	-0.037	0.003	33.950	-0.286	-0.286	0.000	0.000	0.000	0.000
54	F	68	GLN	0	0.002	-0.002	30.478	-0.636	-0.636	0.000	0.000	0.000	0.000
55	F	69	LEU	0	0.044	0.018	31.241	-0.335	-0.335	0.000	0.000	0.000	0.000
56	F	70	GLY	0	0.011	0.019	32.296	-0.150	-0.150	0.000	0.000	0.000	0.000
57	F	71	VAL	0	0.004	0.000	26.628	-0.261	-0.261	0.000	0.000	0.000	0.000
58	F	72	LEU	0	0.001	0.010	27.236	-0.465	-0.465	0.000	0.000	0.000	0.000
59	F	73	ARG	1	0.947	0.978	28.331	8.995	8.995	0.000	0.000	0.000	0.000
60	F	74	GLU	-1	-0.962	-0.968	27.321	-10.701	-10.701	0.000	0.000	0.000	0.000
61	F	75	SER	0	-0.098	-0.070	23.678	-0.525	-0.525	0.000	0.000	0.000	0.000
62	F	76	GLY	0	0.007	0.019	24.165	-0.475	-0.475	0.000	0.000	0.000	0.000
63	F	77	ILE	0	-0.074	-0.022	23.567	-0.051	-0.051	0.000	0.000	0.000	0.000
64	F	78	VAL	0	-0.006	0.003	27.155	0.261	0.261	0.000	0.000	0.000	0.000
65	F	79	GLU	-1	-0.885	-0.950	30.927	-9.691	-9.691	0.000	0.000	0.000	0.000
66	F	80	THR	0	-0.038	-0.028	33.242	0.124	0.124	0.000	0.000	0.000	0.000
67	F	81	ARG	1	0.900	0.962	34.462	8.479	8.479	0.000	0.000	0.000	0.000
68	F	82	ARG	1	0.969	0.988	39.392	6.965	6.965	0.000	0.000	0.000	0.000
69	F	83	ASN	0	0.024	0.016	42.371	-0.055	-0.055	0.000	0.000	0.000	0.000
70	F	84	ILE	0	0.005	0.005	44.805	0.100	0.100	0.000	0.000	0.000	0.000
71	F	85	LYS	1	0.953	0.960	47.921	6.153	6.153	0.000	0.000	0.000	0.000
72	F	86	GLN	0	-0.006	0.009	45.401	-0.146	-0.146	0.000	0.000	0.000	0.000
73	F	87	ILE	0	-0.001	0.001	40.998	-0.078	-0.078	0.000	0.000	0.000	0.000
74	F	88	PHE	0	0.015	0.001	40.473	0.081	0.081	0.000	0.000	0.000	0.000
75	F	89	TYR	0	-0.009	-0.014	35.618	-0.199	-0.199	0.000	0.000	0.000	0.000
76	F	90	ARG	1	0.954	0.988	32.408	9.105	9.105	0.000	0.000	0.000	0.000
77	F	91	LEU	0	0.046	0.027	29.040	-0.223	-0.223	0.000	0.000	0.000	0.000
78	F	92	THR	0	-0.055	-0.043	26.897	0.150	0.150	0.000	0.000	0.000	0.000
79	F	93	GLU	-1	-0.911	-0.964	27.613	-9.603	-9.603	0.000	0.000	0.000	0.000
80	F	94	ALA	0	-0.005	0.004	23.024	-0.302	-0.302	0.000	0.000	0.000	0.000
81	F	95	LYS	1	0.895	0.920	16.180	14.962	14.962	0.000	0.000	0.000	0.000
82	F	96	ALA	0	0.038	0.008	20.900	-0.081	-0.081	0.000	0.000	0.000	0.000
83	F	97	ALA	0	0.082	0.056	22.087	0.098	0.098	0.000	0.000	0.000	0.000
84	F	98	GLN	0	0.020	0.016	20.146	-0.218	-0.218	0.000	0.000	0.000	0.000
85	F	99	LEU	0	-0.005	0.008	19.485	0.031	0.031	0.000	0.000	0.000	0.000
86	F	100	VAL	0	0.021	0.006	22.344	0.174	0.174	0.000	0.000	0.000	0.000
87	F	101	ASN	0	0.037	0.006	25.968	0.551	0.551	0.000	0.000	0.000	0.000
88	F	102	ALA	0	-0.031	-0.002	23.286	0.279	0.279	0.000	0.000	0.000	0.000
89	F	103	LEU	0	0.001	-0.010	23.619	0.125	0.125	0.000	0.000	0.000	0.000
90	F	104	TYR	0	-0.003	-0.049	26.433	0.211	0.211	0.000	0.000	0.000	0.000
91	F	105	THR	0	-0.041	-0.019	28.141	0.327	0.327	0.000	0.000	0.000	0.000
92	F	106	ILE	0	-0.057	-0.024	24.073	0.147	0.147	0.000	0.000	0.000	0.000
93	F	107	PHE	0	-0.034	-0.025	25.179	0.082	0.082	0.000	0.000	0.000	0.000
94	F	109	ALA	0	0.016	0.011	32.722	0.279	0.279	0.000	0.000	0.000	0.000
95	F	110	GLN	0	-0.066	-0.033	31.752	0.472	0.472	0.000	0.000	0.000	0.000
96	F	111	GLU	-1	-0.949	-0.963	35.398	-8.446	-8.446	0.000	0.000	0.000	0.000
97	F	112	LYS	1	0.804	0.900	37.536	8.121	8.121	0.000	0.000	0.000	0.000
98	F	113	GLN	0	-0.009	0.004	40.112	0.053	0.053	0.000	0.000	0.000	0.000
99	F	114	ALA	0	-0.011	-0.010	43.484	0.060	0.060	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:15:ARG)