FMO DATABASE

FMODB ID: 5356Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-709667.042697
FMO2-HF: Nuclear repulsion	669947.865084
FMO2-HF: Total energy	-39719.177614
FMO2-MP2: Total energy	-39834.16419

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.
-68.43	-70.873	29.846	-13.351	-14.053	-0.123

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 : 0.758 / 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	-0.840	-0.918	2.903	-26.155	-24.019	0.081	-0.768	-1.449	0.003
4	F	18	MET	0	-0.069	-0.028	2.472	2.467	4.928	1.767	-1.269	-2.959	0.004
5	F	19	GLU	-1	-0.829	-0.890	1.753	-124.380	-131.569	27.999	-11.303	-9.507	-0.130
6	F	20	LYS	1	0.897	0.949	5.005	33.488	33.637	-0.001	-0.011	-0.138	0.000
7	F	21	ARG	1	0.900	0.931	7.918	24.031	24.031	0.000	0.000	0.000	0.000
8	F	22	ALA	0	0.008	0.015	7.317	2.639	2.639	0.000	0.000	0.000	0.000
9	F	23	ASN	0	-0.025	-0.021	6.801	5.420	5.420	0.000	0.000	0.000	0.000
10	F	24	GLU	-1	-0.856	-0.911	10.228	-20.851	-20.851	0.000	0.000	0.000	0.000
11	F	25	VAL	0	-0.006	-0.011	12.799	1.944	1.944	0.000	0.000	0.000	0.000
12	F	26	ALA	0	0.022	0.012	12.352	1.527	1.527	0.000	0.000	0.000	0.000
13	F	27	ASN	0	0.001	-0.007	13.559	1.509	1.509	0.000	0.000	0.000	0.000
14	F	28	LEU	0	0.022	0.021	16.118	1.121	1.121	0.000	0.000	0.000	0.000
15	F	29	LEU	0	0.026	0.001	16.173	0.955	0.955	0.000	0.000	0.000	0.000
16	F	30	LYS	1	0.899	0.967	13.806	20.562	20.562	0.000	0.000	0.000	0.000
17	F	31	THR	0	-0.012	0.004	19.777	0.623	0.623	0.000	0.000	0.000	0.000
18	F	32	LEU	0	0.024	0.003	22.164	0.717	0.717	0.000	0.000	0.000	0.000
19	F	33	SER	0	-0.035	-0.010	21.553	0.402	0.402	0.000	0.000	0.000	0.000
20	F	34	HIS	0	-0.013	-0.022	24.094	0.196	0.196	0.000	0.000	0.000	0.000
21	F	35	PRO	0	0.066	0.032	27.781	0.015	0.015	0.000	0.000	0.000	0.000
22	F	36	VAL	0	0.029	0.014	30.741	0.130	0.130	0.000	0.000	0.000	0.000
23	F	37	ARG	1	0.839	0.908	25.135	11.622	11.622	0.000	0.000	0.000	0.000
24	F	38	LEU	0	0.026	0.012	26.089	0.028	0.028	0.000	0.000	0.000	0.000
25	F	39	MET	0	0.054	0.032	29.840	0.143	0.143	0.000	0.000	0.000	0.000
26	F	40	LEU	0	-0.040	-0.002	32.342	0.180	0.180	0.000	0.000	0.000	0.000
27	F	41	VAL	0	0.006	-0.011	27.946	0.075	0.075	0.000	0.000	0.000	0.000
28	F	42	CYS	0	-0.003	0.002	30.508	0.130	0.130	0.000	0.000	0.000	0.000
29	F	43	THR	0	0.020	0.003	32.331	0.235	0.235	0.000	0.000	0.000	0.000
30	F	44	LEU	0	-0.057	-0.041	33.079	0.140	0.140	0.000	0.000	0.000	0.000
31	F	45	VAL	0	-0.049	-0.007	30.496	-0.034	-0.034	0.000	0.000	0.000	0.000
32	F	46	GLU	-1	-0.808	-0.857	33.192	-8.016	-8.016	0.000	0.000	0.000	0.000
33	F	47	GLY	0	-0.001	0.012	36.427	0.233	0.233	0.000	0.000	0.000	0.000
34	F	48	GLU	-1	-0.919	-0.961	37.310	-8.335	-8.335	0.000	0.000	0.000	0.000
35	F	49	PHE	0	0.031	0.023	38.465	0.224	0.224	0.000	0.000	0.000	0.000
36	F	50	SER	0	-0.069	-0.064	40.311	-0.135	-0.135	0.000	0.000	0.000	0.000
37	F	51	VAL	0	0.013	-0.018	40.373	-0.058	-0.058	0.000	0.000	0.000	0.000
38	F	52	GLY	0	0.021	0.014	41.918	-0.027	-0.027	0.000	0.000	0.000	0.000
39	F	53	GLU	-1	-0.791	-0.871	43.523	-7.057	-7.057	0.000	0.000	0.000	0.000
40	F	54	LEU	0	-0.031	-0.016	37.378	-0.055	-0.055	0.000	0.000	0.000	0.000
41	F	55	GLU	-1	-0.901	-0.962	40.822	-7.066	-7.066	0.000	0.000	0.000	0.000
42	F	56	GLN	0	-0.102	-0.053	42.484	0.090	0.090	0.000	0.000	0.000	0.000
43	F	57	GLN	0	-0.032	-0.005	40.612	0.023	0.023	0.000	0.000	0.000	0.000
44	F	58	ILE	0	-0.019	-0.010	36.486	-0.099	-0.099	0.000	0.000	0.000	0.000
45	F	59	GLY	0	0.019	0.030	39.988	-0.066	-0.066	0.000	0.000	0.000	0.000
46	F	60	ILE	0	-0.075	-0.036	37.117	-0.069	-0.069	0.000	0.000	0.000	0.000
47	F	61	GLY	0	0.093	0.050	40.393	0.046	0.046	0.000	0.000	0.000	0.000
48	F	62	GLN	0	0.025	0.001	40.442	-0.368	-0.368	0.000	0.000	0.000	0.000
49	F	63	PRO	0	0.000	-0.006	39.092	0.112	0.112	0.000	0.000	0.000	0.000
50	F	64	THR	0	0.021	-0.004	35.730	-0.168	-0.168	0.000	0.000	0.000	0.000
51	F	65	LEU	0	0.022	0.033	35.774	-0.330	-0.330	0.000	0.000	0.000	0.000
52	F	66	SER	0	0.038	0.003	36.017	-0.145	-0.145	0.000	0.000	0.000	0.000
53	F	67	GLN	0	-0.037	-0.006	33.857	-0.231	-0.231	0.000	0.000	0.000	0.000
54	F	68	GLN	0	0.013	0.006	30.421	-0.684	-0.684	0.000	0.000	0.000	0.000
55	F	69	LEU	0	0.040	0.017	31.093	-0.335	-0.335	0.000	0.000	0.000	0.000
56	F	70	GLY	0	0.003	0.013	32.132	-0.151	-0.151	0.000	0.000	0.000	0.000
57	F	71	VAL	0	0.011	0.004	26.522	-0.265	-0.265	0.000	0.000	0.000	0.000
58	F	72	LEU	0	0.004	0.007	26.993	-0.465	-0.465	0.000	0.000	0.000	0.000
59	F	73	ARG	1	0.904	0.960	28.158	9.091	9.091	0.000	0.000	0.000	0.000
60	F	74	GLU	-1	-0.954	-0.964	27.141	-10.782	-10.782	0.000	0.000	0.000	0.000
61	F	75	SER	0	-0.108	-0.070	23.658	-0.572	-0.572	0.000	0.000	0.000	0.000
62	F	76	GLY	0	0.010	0.018	23.982	-0.487	-0.487	0.000	0.000	0.000	0.000
63	F	77	ILE	0	-0.068	-0.024	23.471	-0.071	-0.071	0.000	0.000	0.000	0.000
64	F	78	VAL	0	-0.006	0.004	27.134	0.259	0.259	0.000	0.000	0.000	0.000
65	F	79	GLU	-1	-0.790	-0.868	30.905	-9.613	-9.613	0.000	0.000	0.000	0.000
66	F	80	THR	0	-0.007	-0.008	33.242	0.120	0.120	0.000	0.000	0.000	0.000
67	F	81	ARG	1	0.850	0.910	34.023	8.650	8.650	0.000	0.000	0.000	0.000
68	F	82	ARG	1	0.954	0.979	39.392	7.000	7.000	0.000	0.000	0.000	0.000
69	F	83	ASN	0	0.018	0.012	42.329	-0.057	-0.057	0.000	0.000	0.000	0.000
70	F	84	ILE	0	0.015	0.013	44.805	0.105	0.105	0.000	0.000	0.000	0.000
71	F	85	LYS	1	0.943	0.955	47.915	6.222	6.222	0.000	0.000	0.000	0.000
72	F	86	GLN	0	0.022	0.022	45.320	-0.099	-0.099	0.000	0.000	0.000	0.000
73	F	87	ILE	0	-0.009	-0.001	40.810	-0.085	-0.085	0.000	0.000	0.000	0.000
74	F	88	PHE	0	0.007	-0.005	40.499	0.075	0.075	0.000	0.000	0.000	0.000
75	F	89	TYR	0	-0.015	-0.013	35.508	-0.204	-0.204	0.000	0.000	0.000	0.000
76	F	90	ARG	1	0.832	0.891	32.432	9.196	9.196	0.000	0.000	0.000	0.000
77	F	91	LEU	0	0.036	0.021	29.292	-0.234	-0.234	0.000	0.000	0.000	0.000
78	F	92	THR	0	-0.049	-0.032	26.794	0.140	0.140	0.000	0.000	0.000	0.000
79	F	93	GLU	-1	-0.848	-0.926	27.613	-9.582	-9.582	0.000	0.000	0.000	0.000
80	F	94	ALA	0	-0.012	0.000	23.091	-0.306	-0.306	0.000	0.000	0.000	0.000
81	F	95	LYS	1	0.908	0.930	16.376	15.060	15.060	0.000	0.000	0.000	0.000
82	F	96	ALA	0	0.034	0.005	20.900	-0.082	-0.082	0.000	0.000	0.000	0.000
83	F	97	ALA	0	0.081	0.056	22.087	0.101	0.101	0.000	0.000	0.000	0.000
84	F	98	GLN	0	0.029	0.022	20.394	-0.260	-0.260	0.000	0.000	0.000	0.000
85	F	99	LEU	0	-0.009	0.006	19.368	0.038	0.038	0.000	0.000	0.000	0.000
86	F	100	VAL	0	0.019	0.008	22.306	0.182	0.182	0.000	0.000	0.000	0.000
87	F	101	ASN	0	0.014	-0.011	25.932	0.522	0.522	0.000	0.000	0.000	0.000
88	F	102	ALA	0	-0.022	0.003	23.226	0.288	0.288	0.000	0.000	0.000	0.000
89	F	103	LEU	0	0.004	-0.009	23.478	0.133	0.133	0.000	0.000	0.000	0.000
90	F	104	TYR	0	-0.010	-0.043	26.398	0.217	0.217	0.000	0.000	0.000	0.000
91	F	105	THR	0	-0.046	-0.025	28.058	0.333	0.333	0.000	0.000	0.000	0.000
92	F	106	ILE	0	-0.051	-0.018	24.086	0.150	0.150	0.000	0.000	0.000	0.000
93	F	107	PHE	0	-0.027	-0.018	25.103	0.083	0.083	0.000	0.000	0.000	0.000
94	F	109	ALA	0	0.015	0.009	32.687	0.282	0.282	0.000	0.000	0.000	0.000
95	F	110	GLN	0	-0.071	-0.039	31.508	0.478	0.478	0.000	0.000	0.000	0.000
96	F	111	GLU	-1	-0.959	-0.970	35.288	-8.489	-8.489	0.000	0.000	0.000	0.000
97	F	112	LYS	1	0.770	0.879	37.559	8.155	8.155	0.000	0.000	0.000	0.000
98	F	113	GLN	0	-0.014	0.003	40.077	0.074	0.074	0.000	0.000	0.000	0.000
99	F	114	ALA	0	-0.002	-0.004	43.444	0.057	0.057	0.000	0.000	0.000	0.000

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