FMO DATABASE

FMODB ID: 7264K

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

Total energy (hartree)

FMO2-HF: Electronic energy	-681090.793478
FMO2-HF: Nuclear repulsion	644682.813761
FMO2-HF: Total energy	-36407.979717
FMO2-MP2: Total energy	-36515.029736

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.
145.897	150.162	11.156	-7.216	-8.207	-0.066

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 : 0.942 / q_NPA : 0.966

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	E	173	ARG	1	0.870	0.923	3.555	19.910	22.700	-0.003	-1.526	-1.261	0.006
4	E	174	LEU	0	0.003	-0.009	6.303	1.321	1.321	0.000	0.000	0.000	0.000
5	E	175	TYR	0	0.043	0.002	8.294	0.104	0.104	0.000	0.000	0.000	0.000
6	E	176	GLN	0	-0.002	0.002	8.497	2.037	2.037	0.000	0.000	0.000	0.000
7	E	177	PHE	0	-0.009	0.001	7.217	0.831	0.831	0.000	0.000	0.000	0.000
8	E	178	LEU	0	0.001	-0.013	9.172	1.311	1.311	0.000	0.000	0.000	0.000
9	E	179	LEU	0	-0.015	0.009	12.672	1.294	1.294	0.000	0.000	0.000	0.000
10	E	180	ASP	-1	-0.826	-0.925	10.635	-21.012	-21.012	0.000	0.000	0.000	0.000
11	E	181	LEU	0	-0.038	-0.003	12.769	0.819	0.819	0.000	0.000	0.000	0.000
12	E	182	LEU	0	-0.045	-0.016	14.953	1.047	1.047	0.000	0.000	0.000	0.000
13	E	183	ARG	1	0.905	0.943	17.067	15.945	15.945	0.000	0.000	0.000	0.000
14	E	184	SER	0	-0.040	-0.005	15.833	0.461	0.461	0.000	0.000	0.000	0.000
15	E	185	GLY	0	-0.043	-0.029	18.547	0.682	0.682	0.000	0.000	0.000	0.000
16	E	186	ASP	-1	-0.736	-0.850	16.883	-16.352	-16.352	0.000	0.000	0.000	0.000
17	E	187	MET	0	-0.035	-0.006	15.970	-1.006	-1.006	0.000	0.000	0.000	0.000
18	E	188	LYS	1	0.989	1.006	19.205	12.596	12.596	0.000	0.000	0.000	0.000
19	E	189	ASP	-1	-0.871	-0.916	22.260	-12.156	-12.156	0.000	0.000	0.000	0.000
20	E	190	SER	0	-0.087	-0.084	18.716	0.074	0.074	0.000	0.000	0.000	0.000
21	E	191	ILE	0	-0.058	-0.037	16.524	-0.169	-0.169	0.000	0.000	0.000	0.000
22	E	192	TRP	0	0.029	0.021	20.186	0.036	0.036	0.000	0.000	0.000	0.000
23	E	193	TRP	0	0.014	-0.004	19.095	-0.192	-0.192	0.000	0.000	0.000	0.000
24	E	194	VAL	0	-0.070	-0.047	23.689	0.301	0.301	0.000	0.000	0.000	0.000
25	E	195	ASP	-1	-0.836	-0.935	25.791	-9.809	-9.809	0.000	0.000	0.000	0.000
26	E	196	LYS	1	0.966	0.971	23.997	10.954	10.954	0.000	0.000	0.000	0.000
27	E	197	ASP	-1	-0.866	-0.918	24.640	-10.551	-10.551	0.000	0.000	0.000	0.000
28	E	198	LYS	1	0.882	0.961	26.622	9.907	9.907	0.000	0.000	0.000	0.000
29	E	199	GLY	0	0.052	0.037	22.474	-0.270	-0.270	0.000	0.000	0.000	0.000
30	E	200	THR	0	-0.062	-0.040	21.718	-0.551	-0.551	0.000	0.000	0.000	0.000
31	E	201	PHE	0	0.038	0.037	16.883	0.076	0.076	0.000	0.000	0.000	0.000
32	E	202	GLN	0	-0.010	-0.021	21.834	0.192	0.192	0.000	0.000	0.000	0.000
33	E	203	PHE	0	-0.026	-0.007	15.924	-0.273	-0.273	0.000	0.000	0.000	0.000
34	E	204	SER	0	0.054	0.049	21.397	0.712	0.712	0.000	0.000	0.000	0.000
35	E	205	SER	0	-0.053	-0.065	22.761	-0.324	-0.324	0.000	0.000	0.000	0.000
36	E	206	LYS	1	0.994	0.982	23.917	9.830	9.830	0.000	0.000	0.000	0.000
37	E	207	HIS	0	0.108	0.067	21.871	-0.251	-0.251	0.000	0.000	0.000	0.000
38	E	208	LYS	1	0.829	0.942	18.961	13.332	13.332	0.000	0.000	0.000	0.000
39	E	209	GLU	-1	-0.770	-0.901	17.258	-17.225	-17.225	0.000	0.000	0.000	0.000
40	E	210	ALA	0	0.002	0.016	16.311	-1.094	-1.094	0.000	0.000	0.000	0.000
41	E	211	LEU	0	0.036	0.019	13.271	-1.019	-1.019	0.000	0.000	0.000	0.000
42	E	212	ALA	0	-0.025	-0.021	12.763	-1.728	-1.728	0.000	0.000	0.000	0.000
43	E	213	HIS	0	0.033	-0.006	11.635	-2.729	-2.729	0.000	0.000	0.000	0.000
44	E	214	ARG	1	0.881	0.915	10.810	18.458	18.458	0.000	0.000	0.000	0.000
45	E	215	TRP	0	0.038	0.024	5.151	-4.170	-4.170	0.000	0.000	0.000	0.000
46	E	216	GLY	0	-0.046	-0.038	6.593	-4.792	-4.792	0.000	0.000	0.000	0.000
47	E	217	ILE	0	0.016	0.002	6.513	-5.174	-5.174	0.000	0.000	0.000	0.000
48	E	218	GLN	0	0.024	0.016	5.137	-1.072	-1.072	0.000	0.000	0.000	0.000
49	E	219	LYS	1	0.871	0.946	2.256	44.549	46.128	2.869	-1.179	-3.270	-0.002
50	E	220	GLY	0	0.062	0.051	1.838	-42.431	-42.639	8.291	-4.509	-3.575	-0.070
51	E	221	ASN	0	-0.074	-0.030	4.165	-4.462	-4.358	-0.001	-0.002	-0.101	0.000
52	E	222	ARG	1	1.043	1.014	6.094	31.188	31.188	0.000	0.000	0.000	0.000
53	E	223	LYS	1	0.956	0.982	9.266	22.377	22.377	0.000	0.000	0.000	0.000
54	E	224	LYS	1	1.023	1.014	10.176	16.283	16.283	0.000	0.000	0.000	0.000
55	E	225	MET	0	-0.070	-0.011	9.267	1.653	1.653	0.000	0.000	0.000	0.000
56	E	226	THR	0	0.068	0.032	12.255	0.624	0.624	0.000	0.000	0.000	0.000
57	E	227	TYR	0	0.043	0.001	14.808	-0.669	-0.669	0.000	0.000	0.000	0.000
58	E	228	GLU	-1	-0.924	-0.950	16.936	-15.763	-15.763	0.000	0.000	0.000	0.000
59	E	229	LYS	1	0.886	0.924	13.313	21.567	21.567	0.000	0.000	0.000	0.000
60	E	230	MET	0	0.013	0.024	11.908	-1.320	-1.320	0.000	0.000	0.000	0.000
61	E	231	ALA	0	0.028	0.007	13.565	-0.131	-0.131	0.000	0.000	0.000	0.000
62	E	232	ARG	1	0.851	0.918	15.305	17.818	17.818	0.000	0.000	0.000	0.000
63	E	233	ALA	0	-0.004	-0.003	11.127	0.338	0.338	0.000	0.000	0.000	0.000
64	E	234	LEU	0	0.025	0.013	13.213	0.257	0.257	0.000	0.000	0.000	0.000
65	E	235	ARG	1	0.946	0.968	15.131	15.966	15.966	0.000	0.000	0.000	0.000
66	E	236	ASN	0	0.013	0.012	13.558	1.808	1.808	0.000	0.000	0.000	0.000
67	E	237	TYR	0	0.040	0.034	9.520	-0.509	-0.509	0.000	0.000	0.000	0.000
68	E	238	GLY	0	-0.015	0.011	16.043	0.649	0.649	0.000	0.000	0.000	0.000
69	E	239	LYS	1	0.856	0.923	18.228	14.482	14.482	0.000	0.000	0.000	0.000
70	E	240	THR	0	0.002	-0.035	15.033	0.454	0.454	0.000	0.000	0.000	0.000
71	E	241	GLY	0	-0.046	-0.021	17.681	0.213	0.213	0.000	0.000	0.000	0.000
72	E	242	GLU	-1	-0.684	-0.812	12.461	-19.535	-19.535	0.000	0.000	0.000	0.000
73	E	243	VAL	0	-0.010	-0.005	15.331	0.102	0.102	0.000	0.000	0.000	0.000
74	E	244	LYS	1	0.929	0.985	18.172	12.761	12.761	0.000	0.000	0.000	0.000
75	E	245	LYS	1	0.790	0.890	21.335	12.353	12.353	0.000	0.000	0.000	0.000
76	E	246	VAL	0	0.028	0.015	22.979	0.386	0.386	0.000	0.000	0.000	0.000
77	E	247	LYN	0	0.057	0.040	26.053	-0.393	-0.393	0.000	0.000	0.000	0.000
78	E	248	LYS	1	0.983	0.993	27.503	10.899	10.899	0.000	0.000	0.000	0.000
79	E	249	LYS	1	0.998	0.988	26.700	10.061	10.061	0.000	0.000	0.000	0.000
80	E	250	LEU	0	-0.007	-0.008	21.914	0.012	0.012	0.000	0.000	0.000	0.000
81	E	251	THR	0	0.050	0.030	22.435	-0.282	-0.282	0.000	0.000	0.000	0.000
82	E	252	TYR	0	-0.036	-0.017	19.512	0.112	0.112	0.000	0.000	0.000	0.000
83	E	253	GLN	0	0.009	-0.006	21.078	0.584	0.584	0.000	0.000	0.000	0.000
84	E	254	PHE	0	-0.017	-0.004	14.426	-0.224	-0.224	0.000	0.000	0.000	0.000
85	E	255	SER	0	-0.040	-0.015	18.223	0.841	0.841	0.000	0.000	0.000	0.000
86	E	256	GLY	0	0.098	0.030	20.131	-0.132	-0.132	0.000	0.000	0.000	0.000
87	E	257	GLU	-1	-0.827	-0.898	15.590	-16.704	-16.704	0.000	0.000	0.000	0.000
88	E	258	VAL	0	-0.093	-0.046	17.618	-0.196	-0.196	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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