FMO DATABASE

FMODB ID: 6YL2Z

Calculation Name: 2PJW-V-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2PJW

Chain ID: V

ChEMBL ID:

UniProt ID: P38753

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	91
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-511057.745382
FMO2-HF: Nuclear repulsion	473607.759128
FMO2-HF: Total energy	-37449.986254
FMO2-MP2: Total energy	-37557.870446

3D Structure Molmil

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(V:348:VAL)

Summations of interaction energy for fragment #1(V:348:VAL)

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.
-7.226	0.828	2.648	-4.08	-6.622	0.001

Interaction energy analysis for fragmet #1(V:348:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : -0.007

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	V	350	LEU	0	-0.078	-0.006	3.795	0.898	2.938	-0.023	-0.964	-1.053	0.000
4	V	351	SER	0	0.005	-0.028	5.970	-0.298	-0.298	0.000	0.000	0.000	0.000
5	V	352	ASP	-1	-0.792	-0.902	9.139	0.002	0.002	0.000	0.000	0.000	0.000
6	V	353	GLU	-1	-0.780	-0.863	11.897	0.611	0.611	0.000	0.000	0.000	0.000
7	V	354	GLU	-1	-0.791	-0.858	7.197	1.596	1.596	0.000	0.000	0.000	0.000
8	V	355	LYS	1	0.825	0.894	9.629	-0.149	-0.149	0.000	0.000	0.000	0.000
9	V	356	ASP	-1	-0.874	-0.942	12.526	0.085	0.085	0.000	0.000	0.000	0.000
10	V	357	SER	0	-0.095	-0.052	14.313	-0.014	-0.014	0.000	0.000	0.000	0.000
11	V	358	ILE	0	0.012	0.011	11.471	-0.022	-0.022	0.000	0.000	0.000	0.000
12	V	359	TYR	0	0.045	0.029	15.788	-0.021	-0.021	0.000	0.000	0.000	0.000
13	V	360	MET	0	0.009	0.019	18.703	-0.013	-0.013	0.000	0.000	0.000	0.000
14	V	361	PHE	0	0.016	-0.007	18.322	-0.006	-0.006	0.000	0.000	0.000	0.000
15	V	362	ALA	0	0.008	-0.001	19.599	-0.011	-0.011	0.000	0.000	0.000	0.000
16	V	363	SER	0	0.001	-0.004	21.316	-0.006	-0.006	0.000	0.000	0.000	0.000
17	V	364	LEU	0	-0.014	-0.011	23.457	-0.005	-0.005	0.000	0.000	0.000	0.000
18	V	365	VAL	0	-0.005	-0.008	22.673	-0.002	-0.002	0.000	0.000	0.000	0.000
19	V	366	GLU	-1	-0.802	-0.898	25.389	0.012	0.012	0.000	0.000	0.000	0.000
20	V	367	LYS	1	0.856	0.945	28.003	-0.037	-0.037	0.000	0.000	0.000	0.000
21	V	368	MET	0	-0.028	-0.018	27.711	-0.001	-0.001	0.000	0.000	0.000	0.000
22	V	369	LYS	1	0.812	0.918	27.201	-0.021	-0.021	0.000	0.000	0.000	0.000
23	V	370	SER	0	-0.011	-0.008	30.827	-0.003	-0.003	0.000	0.000	0.000	0.000
24	V	371	ARG	1	0.924	0.959	32.378	-0.053	-0.053	0.000	0.000	0.000	0.000
25	V	372	PRO	0	0.011	0.005	35.352	0.001	0.001	0.000	0.000	0.000	0.000
26	V	373	LEU	0	-0.080	-0.017	35.785	-0.001	-0.001	0.000	0.000	0.000	0.000
27	V	374	ASN	0	0.064	0.031	31.812	-0.001	-0.001	0.000	0.000	0.000	0.000
28	V	375	GLU	-1	-0.742	-0.896	31.469	0.054	0.054	0.000	0.000	0.000	0.000
29	V	376	ILE	0	-0.076	-0.023	32.823	0.004	0.004	0.000	0.000	0.000	0.000
30	V	377	LEU	0	-0.003	-0.014	29.318	0.002	0.002	0.000	0.000	0.000	0.000
31	V	378	GLU	-1	-0.999	-0.966	27.859	0.085	0.085	0.000	0.000	0.000	0.000
32	V	379	ASP	-1	-0.876	-0.942	29.292	0.080	0.080	0.000	0.000	0.000	0.000
33	V	380	SER	0	-0.054	-0.069	25.897	0.007	0.007	0.000	0.000	0.000	0.000
34	V	381	LYS	1	0.881	0.950	24.447	-0.127	-0.127	0.000	0.000	0.000	0.000
35	V	382	LEU	0	0.067	0.052	23.229	0.012	0.012	0.000	0.000	0.000	0.000
36	V	383	GLN	0	0.083	0.016	22.478	0.009	0.009	0.000	0.000	0.000	0.000
37	V	384	ASN	0	-0.044	-0.024	21.205	0.001	0.001	0.000	0.000	0.000	0.000
38	V	385	LEU	0	-0.043	-0.003	17.880	0.036	0.036	0.000	0.000	0.000	0.000
39	V	386	ALA	0	0.034	0.015	17.734	0.021	0.021	0.000	0.000	0.000	0.000
40	V	387	GLN	0	-0.011	0.005	17.289	0.006	0.006	0.000	0.000	0.000	0.000
41	V	388	ARG	1	0.884	0.942	14.430	-0.320	-0.320	0.000	0.000	0.000	0.000
42	V	389	VAL	0	0.026	0.002	13.190	0.042	0.042	0.000	0.000	0.000	0.000
43	V	390	PHE	0	-0.034	-0.035	13.055	-0.013	-0.013	0.000	0.000	0.000	0.000
44	V	391	ALA	0	0.011	0.016	12.186	-0.029	-0.029	0.000	0.000	0.000	0.000
45	V	392	SER	0	-0.017	-0.011	8.836	-0.017	-0.017	0.000	0.000	0.000	0.000
46	V	393	LYS	1	0.949	0.978	8.615	-0.049	-0.049	0.000	0.000	0.000	0.000
47	V	394	ALA	0	0.039	0.019	8.613	-0.119	-0.119	0.000	0.000	0.000	0.000
48	V	395	ARG	1	0.809	0.873	3.448	-6.667	-5.695	0.147	-0.424	-0.695	0.002
49	V	396	LEU	0	0.060	0.047	4.347	-0.870	-0.816	-0.001	-0.017	-0.036	0.000
50	V	397	ASN	0	0.007	-0.002	6.651	-0.238	-0.238	0.000	0.000	0.000	0.000
51	V	398	TYR	0	-0.004	0.021	2.441	-2.914	-0.839	2.164	-1.487	-2.753	0.005
52	V	399	ALA	0	-0.012	-0.019	2.911	-1.160	-0.390	0.160	-0.300	-0.630	-0.001
53	V	400	LEU	0	-0.029	-0.018	3.866	-0.053	0.109	0.004	-0.013	-0.152	0.000
54	V	401	ASN	0	-0.025	-0.036	7.116	0.152	0.152	0.000	0.000	0.000	0.000
55	V	402	ASP	-1	-0.832	-0.901	3.129	-3.980	-2.656	0.186	-0.662	-0.848	-0.006
56	V	403	LYS	1	0.858	0.920	3.240	3.809	4.279	0.008	-0.179	-0.300	0.001
57	V	404	ALA	0	0.020	0.013	7.655	0.204	0.204	0.000	0.000	0.000	0.000
58	V	405	GLN	0	0.020	0.015	7.332	0.020	0.020	0.000	0.000	0.000	0.000
59	V	406	LYS	1	0.857	0.915	3.619	1.888	2.075	0.003	-0.034	-0.155	0.000
60	V	407	TYR	0	0.044	0.031	9.686	0.110	0.110	0.000	0.000	0.000	0.000
61	V	408	ASN	0	0.014	-0.008	12.558	0.113	0.113	0.000	0.000	0.000	0.000
62	V	409	THR	0	-0.033	-0.017	11.911	0.056	0.056	0.000	0.000	0.000	0.000
63	V	410	LEU	0	0.000	-0.006	11.556	0.040	0.040	0.000	0.000	0.000	0.000
64	V	411	ILE	0	-0.046	-0.004	15.275	0.043	0.043	0.000	0.000	0.000	0.000
65	V	412	GLU	-1	-0.857	-0.924	17.514	-0.206	-0.206	0.000	0.000	0.000	0.000
66	V	413	MET	0	-0.006	-0.006	16.218	0.014	0.014	0.000	0.000	0.000	0.000
67	V	414	ASN	0	-0.017	-0.003	19.196	0.027	0.027	0.000	0.000	0.000	0.000
68	V	415	GLY	0	0.007	0.005	21.051	0.020	0.020	0.000	0.000	0.000	0.000
69	V	416	LYS	1	0.875	0.920	20.662	0.222	0.222	0.000	0.000	0.000	0.000
70	V	417	ILE	0	0.003	-0.003	21.040	0.014	0.014	0.000	0.000	0.000	0.000
71	V	418	SER	0	-0.018	-0.005	24.891	0.013	0.013	0.000	0.000	0.000	0.000
72	V	419	GLU	-1	-0.931	-0.980	27.124	-0.129	-0.129	0.000	0.000	0.000	0.000
73	V	420	ILE	0	0.026	0.029	26.041	0.011	0.011	0.000	0.000	0.000	0.000
74	V	421	MET	0	-0.086	-0.025	26.526	0.011	0.011	0.000	0.000	0.000	0.000
75	V	422	ASN	0	-0.043	-0.035	30.660	0.002	0.002	0.000	0.000	0.000	0.000
76	V	423	ILE	0	-0.010	-0.010	32.008	0.008	0.008	0.000	0.000	0.000	0.000
77	V	424	TYR	0	0.001	-0.008	33.667	0.007	0.007	0.000	0.000	0.000	0.000
78	V	425	ASP	-1	-0.811	-0.900	34.238	-0.090	-0.090	0.000	0.000	0.000	0.000
79	V	426	ARG	1	0.908	0.956	34.176	0.099	0.099	0.000	0.000	0.000	0.000
80	V	427	LEU	0	-0.052	-0.027	37.347	0.004	0.004	0.000	0.000	0.000	0.000
81	V	428	LEU	0	-0.012	-0.014	38.486	0.004	0.004	0.000	0.000	0.000	0.000
82	V	429	GLU	-1	-0.916	-0.952	40.947	-0.060	-0.060	0.000	0.000	0.000	0.000
83	V	430	GLN	0	-0.019	-0.017	42.751	0.004	0.004	0.000	0.000	0.000	0.000
84	V	431	GLN	0	-0.041	-0.007	43.990	0.005	0.005	0.000	0.000	0.000	0.000
85	V	432	LEU	0	0.029	0.009	43.502	0.003	0.003	0.000	0.000	0.000	0.000
86	V	433	GLN	0	0.015	0.005	46.826	0.003	0.003	0.000	0.000	0.000	0.000
87	V	434	SER	0	-0.049	-0.032	48.653	0.002	0.002	0.000	0.000	0.000	0.000
88	V	435	ILE	0	-0.038	-0.013	48.149	0.002	0.002	0.000	0.000	0.000	0.000
89	V	436	ASN	0	-0.039	-0.013	50.955	0.002	0.002	0.000	0.000	0.000	0.000
90	V	437	LEU	0	-0.052	-0.006	52.361	0.002	0.002	0.000	0.000	0.000	0.000
91	V	438	SER	0	-0.072	-0.036	54.976	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(V:348:VAL)