FMO DATABASE

FMODB ID: YYRG2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-713159.304172
FMO2-HF: Nuclear repulsion	673439.946787
FMO2-HF: Total energy	-39719.357386
FMO2-MP2: Total energy	-39834.326395

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.
-66.382	-69.954	29.912	-13.062	-13.276	-0.128

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 : 0.763 / q_NPA : 0.830

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	-0.826	-0.909	3.282	-25.783	-23.912	0.035	-0.639	-1.267	0.002
4	F	18	MET	0	-0.040	-0.012	2.622	2.581	4.728	0.595	-0.731	-2.010	0.002
5	F	19	GLU	-1	-0.825	-0.885	1.743	-123.676	-131.430	29.283	-11.679	-9.850	-0.132
6	F	20	LYS	1	0.875	0.938	4.952	33.655	33.819	-0.001	-0.013	-0.149	0.000
7	F	21	ARG	1	0.877	0.919	7.753	24.836	24.836	0.000	0.000	0.000	0.000
8	F	22	ALA	0	0.010	0.007	7.511	2.980	2.980	0.000	0.000	0.000	0.000
9	F	23	ASN	0	-0.032	-0.025	7.010	5.529	5.529	0.000	0.000	0.000	0.000
10	F	24	GLU	-1	-0.845	-0.912	10.266	-21.274	-21.274	0.000	0.000	0.000	0.000
11	F	25	VAL	0	0.000	-0.004	13.003	1.892	1.892	0.000	0.000	0.000	0.000
12	F	26	ALA	0	0.025	0.015	12.383	1.521	1.521	0.000	0.000	0.000	0.000
13	F	27	ASN	0	0.000	-0.003	13.620	1.458	1.458	0.000	0.000	0.000	0.000
14	F	28	LEU	0	0.022	0.021	16.148	1.092	1.092	0.000	0.000	0.000	0.000
15	F	29	LEU	0	0.025	0.000	16.137	0.951	0.951	0.000	0.000	0.000	0.000
16	F	30	LYS	1	0.885	0.956	13.447	21.053	21.053	0.000	0.000	0.000	0.000
17	F	31	THR	0	-0.010	0.004	19.700	0.547	0.547	0.000	0.000	0.000	0.000
18	F	32	LEU	0	0.009	-0.003	21.934	0.701	0.701	0.000	0.000	0.000	0.000
19	F	33	SER	0	-0.037	-0.009	21.341	0.405	0.405	0.000	0.000	0.000	0.000
20	F	34	HIS	0	0.000	-0.025	23.920	0.199	0.199	0.000	0.000	0.000	0.000
21	F	35	PRO	0	0.055	0.033	27.670	0.018	0.018	0.000	0.000	0.000	0.000
22	F	36	VAL	0	0.026	0.013	30.811	0.138	0.138	0.000	0.000	0.000	0.000
23	F	37	ARG	1	0.837	0.907	25.168	11.675	11.675	0.000	0.000	0.000	0.000
24	F	38	LEU	0	0.020	0.014	26.014	0.027	0.027	0.000	0.000	0.000	0.000
25	F	39	MET	0	0.068	0.038	29.767	0.144	0.144	0.000	0.000	0.000	0.000
26	F	40	LEU	0	-0.030	0.002	32.285	0.178	0.178	0.000	0.000	0.000	0.000
27	F	41	VAL	0	-0.011	-0.022	27.878	0.084	0.084	0.000	0.000	0.000	0.000
28	F	42	CYS	0	0.021	0.007	30.715	0.126	0.126	0.000	0.000	0.000	0.000
29	F	43	THR	0	0.016	0.003	32.381	0.239	0.239	0.000	0.000	0.000	0.000
30	F	44	LEU	0	-0.075	-0.039	32.977	0.150	0.150	0.000	0.000	0.000	0.000
31	F	45	VAL	0	-0.041	-0.010	30.594	-0.112	-0.112	0.000	0.000	0.000	0.000
32	F	46	GLU	-1	-0.803	-0.853	33.309	-8.064	-8.064	0.000	0.000	0.000	0.000
33	F	47	GLY	0	-0.004	0.002	36.762	0.261	0.261	0.000	0.000	0.000	0.000
34	F	48	GLU	-1	-0.901	-0.940	37.207	-8.514	-8.514	0.000	0.000	0.000	0.000
35	F	49	PHE	0	0.034	0.017	38.580	0.242	0.242	0.000	0.000	0.000	0.000
36	F	50	SER	0	-0.079	-0.075	40.275	-0.150	-0.150	0.000	0.000	0.000	0.000
37	F	51	VAL	0	-0.004	-0.017	40.262	-0.047	-0.047	0.000	0.000	0.000	0.000
38	F	52	GLY	0	0.031	0.019	41.770	-0.037	-0.037	0.000	0.000	0.000	0.000
39	F	53	GLU	-1	-0.805	-0.876	43.501	-7.085	-7.085	0.000	0.000	0.000	0.000
40	F	54	LEU	0	-0.005	-0.006	37.300	-0.065	-0.065	0.000	0.000	0.000	0.000
41	F	55	GLU	-1	-0.900	-0.956	40.791	-7.123	-7.123	0.000	0.000	0.000	0.000
42	F	56	GLN	0	-0.085	-0.057	42.357	0.056	0.056	0.000	0.000	0.000	0.000
43	F	57	GLN	0	-0.046	0.001	40.728	0.050	0.050	0.000	0.000	0.000	0.000
44	F	58	ILE	0	-0.021	-0.011	36.433	-0.105	-0.105	0.000	0.000	0.000	0.000
45	F	59	GLY	0	0.020	0.022	39.823	-0.075	-0.075	0.000	0.000	0.000	0.000
46	F	60	ILE	0	-0.075	-0.034	36.912	-0.031	-0.031	0.000	0.000	0.000	0.000
47	F	61	GLY	0	0.094	0.043	40.147	0.005	0.005	0.000	0.000	0.000	0.000
48	F	62	GLN	0	-0.001	-0.007	40.327	-0.370	-0.370	0.000	0.000	0.000	0.000
49	F	63	PRO	0	0.002	-0.004	39.025	0.121	0.121	0.000	0.000	0.000	0.000
50	F	64	THR	0	0.019	-0.004	35.449	-0.190	-0.190	0.000	0.000	0.000	0.000
51	F	65	LEU	0	0.004	0.025	35.561	-0.338	-0.338	0.000	0.000	0.000	0.000
52	F	66	SER	0	0.058	0.014	35.789	-0.167	-0.167	0.000	0.000	0.000	0.000
53	F	67	GLN	0	-0.026	-0.003	33.841	-0.251	-0.251	0.000	0.000	0.000	0.000
54	F	68	GLN	0	0.025	0.019	30.215	-0.716	-0.716	0.000	0.000	0.000	0.000
55	F	69	LEU	0	0.030	0.014	30.925	-0.329	-0.329	0.000	0.000	0.000	0.000
56	F	70	GLY	0	0.004	0.007	31.896	-0.178	-0.178	0.000	0.000	0.000	0.000
57	F	71	VAL	0	-0.002	-0.003	26.373	-0.275	-0.275	0.000	0.000	0.000	0.000
58	F	72	LEU	0	0.002	0.006	26.807	-0.530	-0.530	0.000	0.000	0.000	0.000
59	F	73	ARG	1	0.885	0.951	27.856	9.219	9.219	0.000	0.000	0.000	0.000
60	F	74	GLU	-1	-0.930	-0.960	27.162	-10.674	-10.674	0.000	0.000	0.000	0.000
61	F	75	SER	0	-0.076	-0.039	23.426	-0.652	-0.652	0.000	0.000	0.000	0.000
62	F	76	GLY	0	-0.001	0.009	23.838	-0.471	-0.471	0.000	0.000	0.000	0.000
63	F	77	ILE	0	-0.056	-0.019	23.397	-0.118	-0.118	0.000	0.000	0.000	0.000
64	F	78	VAL	0	-0.010	0.002	26.847	0.285	0.285	0.000	0.000	0.000	0.000
65	F	79	GLU	-1	-0.796	-0.873	30.634	-9.712	-9.712	0.000	0.000	0.000	0.000
66	F	80	THR	0	0.001	-0.004	33.197	0.117	0.117	0.000	0.000	0.000	0.000
67	F	81	ARG	1	0.844	0.910	34.334	8.683	8.683	0.000	0.000	0.000	0.000
68	F	82	ARG	1	0.950	0.972	39.564	7.023	7.023	0.000	0.000	0.000	0.000
69	F	83	ASN	0	0.016	0.016	42.675	-0.086	-0.086	0.000	0.000	0.000	0.000
70	F	84	ILE	0	0.014	0.006	45.118	0.096	0.096	0.000	0.000	0.000	0.000
71	F	85	LYS	1	0.942	0.957	48.437	6.226	6.226	0.000	0.000	0.000	0.000
72	F	86	GLN	0	0.060	0.044	45.636	-0.077	-0.077	0.000	0.000	0.000	0.000
73	F	87	ILE	0	-0.033	-0.016	41.035	-0.074	-0.074	0.000	0.000	0.000	0.000
74	F	88	PHE	0	0.010	-0.003	40.661	0.079	0.079	0.000	0.000	0.000	0.000
75	F	89	TYR	0	-0.011	-0.016	35.446	-0.190	-0.190	0.000	0.000	0.000	0.000
76	F	90	ARG	1	0.797	0.865	32.245	9.335	9.335	0.000	0.000	0.000	0.000
77	F	91	LEU	0	0.051	0.022	29.063	-0.259	-0.259	0.000	0.000	0.000	0.000
78	F	92	THR	0	-0.042	-0.028	26.770	0.208	0.208	0.000	0.000	0.000	0.000
79	F	93	GLU	-1	-0.853	-0.912	28.147	-9.591	-9.591	0.000	0.000	0.000	0.000
80	F	94	ALA	0	0.010	0.009	23.500	-0.281	-0.281	0.000	0.000	0.000	0.000
81	F	95	LYS	1	0.886	0.922	16.967	14.928	14.928	0.000	0.000	0.000	0.000
82	F	96	ALA	0	0.031	0.009	21.353	-0.143	-0.143	0.000	0.000	0.000	0.000
83	F	97	ALA	0	0.101	0.058	22.460	0.037	0.037	0.000	0.000	0.000	0.000
84	F	98	GLN	0	0.019	0.018	21.021	-0.267	-0.267	0.000	0.000	0.000	0.000
85	F	99	LEU	0	-0.006	0.005	19.258	0.059	0.059	0.000	0.000	0.000	0.000
86	F	100	VAL	0	0.015	0.010	22.344	0.141	0.141	0.000	0.000	0.000	0.000
87	F	101	ASN	0	0.027	0.002	25.994	0.532	0.532	0.000	0.000	0.000	0.000
88	F	102	ALA	0	-0.020	0.009	23.108	0.277	0.277	0.000	0.000	0.000	0.000
89	F	103	LEU	0	-0.003	-0.012	23.401	0.174	0.174	0.000	0.000	0.000	0.000
90	F	104	TYR	0	-0.005	-0.046	26.238	0.196	0.196	0.000	0.000	0.000	0.000
91	F	105	THR	0	-0.053	-0.038	27.830	0.355	0.355	0.000	0.000	0.000	0.000
92	F	106	ILE	0	-0.057	-0.021	23.933	0.141	0.141	0.000	0.000	0.000	0.000
93	F	107	PHE	0	-0.032	-0.014	25.426	0.113	0.113	0.000	0.000	0.000	0.000
94	F	109	ALA	0	0.013	0.012	32.609	0.299	0.299	0.000	0.000	0.000	0.000
95	F	110	GLN	0	-0.073	-0.044	31.528	0.488	0.488	0.000	0.000	0.000	0.000
96	F	111	GLU	-1	-0.958	-0.972	35.135	-8.600	-8.600	0.000	0.000	0.000	0.000
97	F	112	LYS	1	0.773	0.882	37.335	8.230	8.230	0.000	0.000	0.000	0.000
98	F	113	GLN	0	-0.028	-0.015	39.994	0.076	0.076	0.000	0.000	0.000	0.000
99	F	114	ALA	0	0.006	0.010	43.316	0.067	0.067	0.000	0.000	0.000	0.000

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