FMO DATABASE

FMODB ID: 2JNGR

Calculation Name: 1PUE-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1PUE

Chain ID: E

ChEMBL ID:

UniProt ID: P17433

Base Structure: X-ray

Registration Date: 2023-06-22

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	88
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-682174.137727
FMO2-HF: Nuclear repulsion	645765.590338
FMO2-HF: Total energy	-36408.547388
FMO2-MP2: Total energy	-36515.591091

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(E:171:LYS)

Summations of interaction energy for fragment #1(E:171:LYS)

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.
142.001	145.293	13.766	-8.388	-8.67	-0.084

Interaction energy analysis for fragmet #1(E:171:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.940 / q_NPA : 0.962

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	E	173	ARG	1	0.886	0.920	3.137	19.173	22.074	0.079	-1.554	-1.426	-0.001
4	E	174	LEU	0	0.002	-0.009	5.905	1.548	1.548	0.000	0.000	0.000	0.000
5	E	175	TYR	0	0.044	0.011	8.137	0.050	0.050	0.000	0.000	0.000	0.000
6	E	176	GLN	0	0.006	-0.003	8.344	1.970	1.970	0.000	0.000	0.000	0.000
7	E	177	PHE	0	-0.019	-0.004	7.158	0.585	0.585	0.000	0.000	0.000	0.000
8	E	178	LEU	0	-0.018	-0.019	9.139	1.252	1.252	0.000	0.000	0.000	0.000
9	E	179	LEU	0	0.000	0.014	12.619	1.195	1.195	0.000	0.000	0.000	0.000
10	E	180	ASP	-1	-0.804	-0.906	10.615	-21.059	-21.059	0.000	0.000	0.000	0.000
11	E	181	LEU	0	-0.043	-0.001	13.106	0.885	0.885	0.000	0.000	0.000	0.000
12	E	182	LEU	0	-0.029	-0.018	14.766	1.066	1.066	0.000	0.000	0.000	0.000
13	E	183	ARG	1	0.882	0.940	16.230	16.359	16.359	0.000	0.000	0.000	0.000
14	E	184	SER	0	-0.010	-0.007	15.837	0.548	0.548	0.000	0.000	0.000	0.000
15	E	185	GLY	0	-0.058	-0.023	18.450	0.669	0.669	0.000	0.000	0.000	0.000
16	E	186	ASP	-1	-0.721	-0.848	16.534	-16.746	-16.746	0.000	0.000	0.000	0.000
17	E	187	MET	0	-0.044	-0.016	16.013	-0.878	-0.878	0.000	0.000	0.000	0.000
18	E	188	LYS	1	0.955	0.980	19.325	12.736	12.736	0.000	0.000	0.000	0.000
19	E	189	ASP	-1	-0.874	-0.918	22.315	-12.482	-12.482	0.000	0.000	0.000	0.000
20	E	190	SER	0	-0.084	-0.084	18.508	0.103	0.103	0.000	0.000	0.000	0.000
21	E	191	ILE	0	-0.067	-0.040	16.173	-0.208	-0.208	0.000	0.000	0.000	0.000
22	E	192	TRP	0	0.012	0.011	19.943	0.068	0.068	0.000	0.000	0.000	0.000
23	E	193	TRP	0	0.021	-0.006	18.907	-0.151	-0.151	0.000	0.000	0.000	0.000
24	E	194	VAL	0	-0.073	-0.041	23.437	0.291	0.291	0.000	0.000	0.000	0.000
25	E	195	ASP	-1	-0.794	-0.885	25.589	-9.830	-9.830	0.000	0.000	0.000	0.000
26	E	196	LYS	1	0.885	0.920	23.961	10.592	10.592	0.000	0.000	0.000	0.000
27	E	197	ASP	-1	-0.808	-0.881	24.065	-10.908	-10.908	0.000	0.000	0.000	0.000
28	E	198	LYS	1	0.843	0.920	25.989	9.899	9.899	0.000	0.000	0.000	0.000
29	E	199	GLY	0	0.072	0.043	22.002	-0.276	-0.276	0.000	0.000	0.000	0.000
30	E	200	THR	0	-0.053	-0.038	21.286	-0.548	-0.548	0.000	0.000	0.000	0.000
31	E	201	PHE	0	0.035	0.012	16.560	0.002	0.002	0.000	0.000	0.000	0.000
32	E	202	GLN	0	-0.016	-0.012	21.724	0.283	0.283	0.000	0.000	0.000	0.000
33	E	203	PHE	0	0.024	0.018	15.691	-0.366	-0.366	0.000	0.000	0.000	0.000
34	E	204	SER	0	0.043	0.033	21.223	0.670	0.670	0.000	0.000	0.000	0.000
35	E	205	SER	0	-0.036	-0.053	22.606	-0.304	-0.304	0.000	0.000	0.000	0.000
36	E	206	LYS	1	0.985	1.000	24.126	10.099	10.099	0.000	0.000	0.000	0.000
37	E	207	HIS	0	0.123	0.077	21.793	-0.340	-0.340	0.000	0.000	0.000	0.000
38	E	208	LYS	1	0.813	0.917	18.663	13.265	13.265	0.000	0.000	0.000	0.000
39	E	209	GLU	-1	-0.760	-0.883	16.906	-17.244	-17.244	0.000	0.000	0.000	0.000
40	E	210	ALA	0	0.000	0.015	16.170	-1.085	-1.085	0.000	0.000	0.000	0.000
41	E	211	LEU	0	0.044	0.025	13.175	-1.228	-1.228	0.000	0.000	0.000	0.000
42	E	212	ALA	0	0.002	-0.008	12.439	-1.832	-1.832	0.000	0.000	0.000	0.000
43	E	213	HIS	0	0.038	0.014	11.398	-2.356	-2.356	0.000	0.000	0.000	0.000
44	E	214	ARG	1	0.888	0.914	10.908	18.805	18.805	0.000	0.000	0.000	0.000
45	E	215	TRP	0	0.031	0.013	4.829	-3.793	-3.793	0.000	0.000	0.000	0.000
46	E	216	GLY	0	-0.046	-0.041	6.586	-4.815	-4.815	0.000	0.000	0.000	0.000
47	E	217	ILE	0	0.023	0.009	6.671	-5.078	-5.078	0.000	0.000	0.000	0.000
48	E	218	GLN	0	0.032	0.020	5.332	-2.501	-2.501	0.000	0.000	0.000	0.000
49	E	219	LYS	1	0.839	0.923	2.285	44.493	46.951	1.998	-1.454	-3.002	-0.005
50	E	220	GLY	0	0.054	0.045	1.743	-45.253	-47.433	11.690	-5.381	-4.130	-0.078
51	E	221	ASN	0	-0.016	0.002	4.050	-4.190	-4.077	-0.001	0.001	-0.112	0.000
52	E	222	ARG	1	1.016	1.003	6.171	31.463	31.463	0.000	0.000	0.000	0.000
53	E	223	LYS	1	0.964	0.976	9.105	22.367	22.367	0.000	0.000	0.000	0.000
54	E	224	LYS	1	0.944	0.985	10.602	16.857	16.857	0.000	0.000	0.000	0.000
55	E	225	MET	0	-0.052	-0.007	9.005	1.511	1.511	0.000	0.000	0.000	0.000
56	E	226	THR	0	0.005	-0.026	12.372	0.598	0.598	0.000	0.000	0.000	0.000
57	E	227	TYR	0	0.036	0.002	14.661	-0.622	-0.622	0.000	0.000	0.000	0.000
58	E	228	GLU	-1	-0.809	-0.885	16.671	-16.600	-16.600	0.000	0.000	0.000	0.000
59	E	229	LYS	1	0.877	0.942	13.293	20.623	20.623	0.000	0.000	0.000	0.000
60	E	230	MET	0	0.006	0.016	11.553	-1.312	-1.312	0.000	0.000	0.000	0.000
61	E	231	ALA	0	0.024	0.007	13.140	-0.167	-0.167	0.000	0.000	0.000	0.000
62	E	232	ARG	1	0.829	0.895	15.285	17.671	17.671	0.000	0.000	0.000	0.000
63	E	233	ALA	0	-0.002	0.011	10.880	0.233	0.233	0.000	0.000	0.000	0.000
64	E	234	LEU	0	0.008	-0.001	13.018	0.299	0.299	0.000	0.000	0.000	0.000
65	E	235	ARG	1	0.961	0.973	14.360	16.022	16.022	0.000	0.000	0.000	0.000
66	E	236	ASN	0	0.016	0.025	13.340	1.818	1.818	0.000	0.000	0.000	0.000
67	E	237	TYR	0	0.043	0.033	9.283	-0.148	-0.148	0.000	0.000	0.000	0.000
68	E	238	GLY	0	0.011	0.019	15.926	0.696	0.696	0.000	0.000	0.000	0.000
69	E	239	LYS	1	0.871	0.918	18.566	14.164	14.164	0.000	0.000	0.000	0.000
70	E	240	THR	0	-0.022	-0.024	15.212	0.315	0.315	0.000	0.000	0.000	0.000
71	E	241	GLY	0	0.022	0.001	17.970	0.484	0.484	0.000	0.000	0.000	0.000
72	E	242	GLU	-1	-0.753	-0.839	12.827	-18.990	-18.990	0.000	0.000	0.000	0.000
73	E	243	VAL	0	-0.008	-0.013	14.666	-0.023	-0.023	0.000	0.000	0.000	0.000
74	E	244	LYS	1	0.895	0.970	17.567	13.612	13.612	0.000	0.000	0.000	0.000
75	E	245	LYS	1	0.789	0.888	20.725	12.166	12.166	0.000	0.000	0.000	0.000
76	E	246	VAL	0	0.050	0.031	22.458	0.310	0.310	0.000	0.000	0.000	0.000
77	E	247	LYN	0	0.059	0.044	25.754	-0.363	-0.363	0.000	0.000	0.000	0.000
78	E	248	LYS	1	0.967	0.977	27.450	10.973	10.973	0.000	0.000	0.000	0.000
79	E	249	LYS	1	1.002	0.997	26.550	10.034	10.034	0.000	0.000	0.000	0.000
80	E	250	LEU	0	-0.016	-0.015	21.448	0.000	0.000	0.000	0.000	0.000	0.000
81	E	251	THR	0	0.050	0.031	22.216	-0.300	-0.300	0.000	0.000	0.000	0.000
82	E	252	TYR	0	-0.064	-0.040	19.236	0.095	0.095	0.000	0.000	0.000	0.000
83	E	253	GLN	0	0.008	0.001	20.775	0.734	0.734	0.000	0.000	0.000	0.000
84	E	254	PHE	0	-0.017	0.008	14.160	-0.412	-0.412	0.000	0.000	0.000	0.000
85	E	255	SER	0	-0.043	-0.038	18.358	0.789	0.789	0.000	0.000	0.000	0.000
86	E	256	GLY	0	0.044	0.020	20.341	0.151	0.151	0.000	0.000	0.000	0.000
87	E	257	GLU	-1	-0.787	-0.875	15.386	-16.019	-16.019	0.000	0.000	0.000	0.000
88	E	258	VAL	0	-0.055	-0.017	17.822	-0.163	-0.163	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:171:LYS)