FMO DATABASE

FMODB ID: MVNZZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-680604.48548
FMO2-HF: Nuclear repulsion	644197.501733
FMO2-HF: Total energy	-36406.983747
FMO2-MP2: Total energy	-36514.053008

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.
171.118	176.399	5.604	-4.603	-6.28	-0.019

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 : 0.995 / q_NPA : 1.000

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	0.969	0.984	3.646	22.212	24.890	-0.005	-1.519	-1.152	0.007
4	E	174	LEU	0	0.008	-0.005	6.176	1.507	1.507	0.000	0.000	0.000	0.000
5	E	175	TYR	0	0.074	0.014	8.742	0.206	0.206	0.000	0.000	0.000	0.000
6	E	176	GLN	0	0.035	0.025	8.634	1.993	1.993	0.000	0.000	0.000	0.000
7	E	177	PHE	0	-0.033	-0.005	7.559	1.067	1.067	0.000	0.000	0.000	0.000
8	E	178	LEU	0	0.000	-0.017	9.425	1.335	1.335	0.000	0.000	0.000	0.000
9	E	179	LEU	0	-0.002	0.017	12.992	1.262	1.262	0.000	0.000	0.000	0.000
10	E	180	ASP	-1	-0.851	-0.941	10.672	-21.044	-21.044	0.000	0.000	0.000	0.000
11	E	181	LEU	0	-0.025	0.026	12.438	0.885	0.885	0.000	0.000	0.000	0.000
12	E	182	LEU	0	-0.039	-0.010	15.054	1.026	1.026	0.000	0.000	0.000	0.000
13	E	183	ARG	1	0.898	0.935	17.347	15.566	15.566	0.000	0.000	0.000	0.000
14	E	184	SER	0	-0.061	-0.045	15.775	0.294	0.294	0.000	0.000	0.000	0.000
15	E	185	GLY	0	-0.018	-0.020	18.522	0.648	0.648	0.000	0.000	0.000	0.000
16	E	186	ASP	-1	-0.869	-0.918	17.024	-14.792	-14.792	0.000	0.000	0.000	0.000
17	E	187	MET	0	-0.048	-0.025	15.933	-1.025	-1.025	0.000	0.000	0.000	0.000
18	E	188	LYS	1	1.017	1.007	19.274	12.184	12.184	0.000	0.000	0.000	0.000
19	E	189	ASP	-1	-0.852	-0.903	22.317	-11.799	-11.799	0.000	0.000	0.000	0.000
20	E	190	SER	0	-0.096	-0.072	18.868	0.076	0.076	0.000	0.000	0.000	0.000
21	E	191	ILE	0	-0.047	-0.031	16.832	-0.192	-0.192	0.000	0.000	0.000	0.000
22	E	192	TRP	0	0.020	0.019	20.453	0.018	0.018	0.000	0.000	0.000	0.000
23	E	193	TRP	0	0.012	-0.002	19.712	-0.186	-0.186	0.000	0.000	0.000	0.000
24	E	194	VAL	0	-0.082	-0.059	23.989	0.293	0.293	0.000	0.000	0.000	0.000
25	E	195	ASP	-1	-0.840	-0.935	26.202	-9.703	-9.703	0.000	0.000	0.000	0.000
26	E	196	LYS	1	0.955	0.968	23.980	11.085	11.085	0.000	0.000	0.000	0.000
27	E	197	ASP	-1	-0.868	-0.913	24.963	-10.444	-10.444	0.000	0.000	0.000	0.000
28	E	198	LYS	1	0.913	0.964	26.840	10.200	10.200	0.000	0.000	0.000	0.000
29	E	199	GLY	0	0.063	0.042	22.849	-0.277	-0.277	0.000	0.000	0.000	0.000
30	E	200	THR	0	-0.047	-0.032	22.152	-0.493	-0.493	0.000	0.000	0.000	0.000
31	E	201	PHE	0	0.009	0.026	17.409	0.095	0.095	0.000	0.000	0.000	0.000
32	E	202	GLN	0	-0.031	-0.034	22.227	0.163	0.163	0.000	0.000	0.000	0.000
33	E	203	PHE	0	-0.017	-0.002	16.320	-0.257	-0.257	0.000	0.000	0.000	0.000
34	E	204	SER	0	0.053	0.046	21.769	0.717	0.717	0.000	0.000	0.000	0.000
35	E	205	SER	0	-0.059	-0.070	23.013	-0.362	-0.362	0.000	0.000	0.000	0.000
36	E	206	LYS	1	0.980	0.967	24.214	9.705	9.705	0.000	0.000	0.000	0.000
37	E	207	HIS	0	0.112	0.069	22.277	-0.238	-0.238	0.000	0.000	0.000	0.000
38	E	208	LYS	1	0.914	0.980	19.242	12.906	12.906	0.000	0.000	0.000	0.000
39	E	209	GLU	-1	-0.841	-0.947	17.635	-17.449	-17.449	0.000	0.000	0.000	0.000
40	E	210	ALA	0	0.004	0.019	16.785	-1.023	-1.023	0.000	0.000	0.000	0.000
41	E	211	LEU	0	0.014	0.013	13.658	-0.984	-0.984	0.000	0.000	0.000	0.000
42	E	212	ALA	0	-0.018	-0.027	13.168	-1.662	-1.662	0.000	0.000	0.000	0.000
43	E	213	HIS	0	0.031	-0.007	12.079	-2.935	-2.935	0.000	0.000	0.000	0.000
44	E	214	ARG	1	0.993	1.001	10.948	18.901	18.901	0.000	0.000	0.000	0.000
45	E	215	TRP	0	0.013	0.011	5.357	-3.789	-3.789	0.000	0.000	0.000	0.000
46	E	216	GLY	0	-0.040	-0.036	7.077	-4.450	-4.450	0.000	0.000	0.000	0.000
47	E	217	ILE	0	0.012	0.005	7.137	-4.476	-4.476	0.000	0.000	0.000	0.000
48	E	218	GLN	0	0.035	0.021	4.834	-0.381	-0.381	0.000	0.000	0.000	0.000
49	E	219	LYS	1	0.855	0.933	1.923	50.456	49.978	4.979	-1.188	-3.313	-0.002
50	E	220	GLY	0	0.046	0.039	2.496	-27.813	-24.795	0.631	-1.895	-1.754	-0.024
51	E	221	ASN	0	-0.076	-0.031	4.760	-6.345	-6.282	-0.001	-0.001	-0.061	0.000
52	E	222	ARG	1	1.041	1.013	6.406	30.843	30.843	0.000	0.000	0.000	0.000
53	E	223	LYS	1	0.954	0.982	9.456	22.170	22.170	0.000	0.000	0.000	0.000
54	E	224	LYS	1	1.026	1.011	10.581	15.647	15.647	0.000	0.000	0.000	0.000
55	E	225	MET	0	-0.072	-0.007	9.120	1.209	1.209	0.000	0.000	0.000	0.000
56	E	226	THR	0	0.093	0.055	12.683	0.509	0.509	0.000	0.000	0.000	0.000
57	E	227	TYR	0	0.044	0.000	14.856	-0.649	-0.649	0.000	0.000	0.000	0.000
58	E	228	GLU	-1	-0.922	-0.952	16.845	-15.454	-15.454	0.000	0.000	0.000	0.000
59	E	229	LYS	1	0.873	0.916	12.068	22.748	22.748	0.000	0.000	0.000	0.000
60	E	230	MET	0	0.015	0.019	11.614	-1.261	-1.261	0.000	0.000	0.000	0.000
61	E	231	ALA	0	0.029	0.005	13.411	-0.222	-0.222	0.000	0.000	0.000	0.000
62	E	232	ARG	1	0.899	0.956	15.195	18.174	18.174	0.000	0.000	0.000	0.000
63	E	233	ALA	0	-0.015	-0.012	11.161	0.260	0.260	0.000	0.000	0.000	0.000
64	E	234	LEU	0	0.030	0.017	13.230	0.197	0.197	0.000	0.000	0.000	0.000
65	E	235	ARG	1	0.938	0.964	15.056	16.024	16.024	0.000	0.000	0.000	0.000
66	E	236	ASN	0	-0.003	-0.007	13.932	2.031	2.031	0.000	0.000	0.000	0.000
67	E	237	TYR	0	0.019	0.029	9.341	-0.696	-0.696	0.000	0.000	0.000	0.000
68	E	238	GLY	0	-0.017	0.012	15.831	0.661	0.661	0.000	0.000	0.000	0.000
69	E	239	LYS	1	0.860	0.926	18.036	14.738	14.738	0.000	0.000	0.000	0.000
70	E	240	THR	0	-0.033	-0.070	15.172	0.346	0.346	0.000	0.000	0.000	0.000
71	E	241	GLY	0	-0.037	-0.015	17.644	0.238	0.238	0.000	0.000	0.000	0.000
72	E	242	GLU	-1	-0.758	-0.837	13.206	-18.567	-18.567	0.000	0.000	0.000	0.000
73	E	243	VAL	0	-0.027	-0.013	15.269	0.167	0.167	0.000	0.000	0.000	0.000
74	E	244	LYS	1	0.943	0.979	18.038	12.799	12.799	0.000	0.000	0.000	0.000
75	E	245	LYS	1	0.803	0.916	21.193	12.427	12.427	0.000	0.000	0.000	0.000
76	E	246	VAL	0	0.032	0.019	23.052	0.369	0.369	0.000	0.000	0.000	0.000
77	E	247	LYN	0	0.051	0.025	26.265	-0.400	-0.400	0.000	0.000	0.000	0.000
78	E	248	LYS	1	0.979	1.002	27.818	10.755	10.755	0.000	0.000	0.000	0.000
79	E	249	LYS	1	0.987	0.979	26.967	9.950	9.950	0.000	0.000	0.000	0.000
80	E	250	LEU	0	-0.019	-0.013	22.343	0.027	0.027	0.000	0.000	0.000	0.000
81	E	251	THR	0	0.051	0.034	22.828	-0.292	-0.292	0.000	0.000	0.000	0.000
82	E	252	TYR	0	-0.026	-0.020	19.528	0.043	0.043	0.000	0.000	0.000	0.000
83	E	253	GLN	0	0.012	-0.013	21.310	0.588	0.588	0.000	0.000	0.000	0.000
84	E	254	PHE	0	0.005	0.013	14.924	-0.272	-0.272	0.000	0.000	0.000	0.000
85	E	255	SER	0	0.011	0.020	18.068	0.794	0.794	0.000	0.000	0.000	0.000
86	E	256	GLY	0	0.077	0.019	20.035	-0.132	-0.132	0.000	0.000	0.000	0.000
87	E	257	GLU	-1	-0.902	-0.942	15.583	-17.254	-17.254	0.000	0.000	0.000	0.000
88	E	258	VAL	0	-0.114	-0.055	17.933	-0.078	-0.078	0.000	0.000	0.000	0.000

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