FMO DATABASE

FMODB ID: ZVR8N

Calculation Name: 2PJW-V-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

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:

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	91
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-510706.991474
FMO2-HF: Nuclear repulsion	473256.445069
FMO2-HF: Total energy	-37450.546405
FMO2-MP2: Total energy	-37558.271526

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(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.
-6.92	0.636	4.313	-4.643	-7.225	-0.013

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 : 0.009 / q_NPA : -0.010

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	V	350	LEU	0	-0.042	-0.009	3.689	1.802	3.461	-0.014	-0.750	-0.895	0.002
4	V	351	SER	0	0.008	-0.026	6.298	-0.295	-0.295	0.000	0.000	0.000	0.000
5	V	352	ASP	-1	-0.794	-0.900	9.187	0.017	0.017	0.000	0.000	0.000	0.000
6	V	353	GLU	-1	-0.764	-0.865	11.939	0.635	0.635	0.000	0.000	0.000	0.000
7	V	354	GLU	-1	-0.798	-0.844	7.703	1.542	1.542	0.000	0.000	0.000	0.000
8	V	355	LYS	1	0.808	0.892	9.912	-0.197	-0.197	0.000	0.000	0.000	0.000
9	V	356	ASP	-1	-0.842	-0.923	13.067	0.099	0.099	0.000	0.000	0.000	0.000
10	V	357	SER	0	-0.076	-0.051	14.489	-0.023	-0.023	0.000	0.000	0.000	0.000
11	V	358	ILE	0	0.000	0.001	11.448	-0.030	-0.030	0.000	0.000	0.000	0.000
12	V	359	TYR	0	0.021	0.010	15.950	-0.031	-0.031	0.000	0.000	0.000	0.000
13	V	360	MET	0	-0.005	0.003	18.931	-0.020	-0.020	0.000	0.000	0.000	0.000
14	V	361	PHE	0	0.004	-0.009	18.521	-0.009	-0.009	0.000	0.000	0.000	0.000
15	V	362	ALA	0	0.022	0.013	19.994	-0.011	-0.011	0.000	0.000	0.000	0.000
16	V	363	SER	0	0.001	-0.002	21.736	-0.010	-0.010	0.000	0.000	0.000	0.000
17	V	364	LEU	0	-0.013	-0.012	23.792	-0.006	-0.006	0.000	0.000	0.000	0.000
18	V	365	VAL	0	0.019	0.001	22.823	-0.004	-0.004	0.000	0.000	0.000	0.000
19	V	366	GLU	-1	-0.802	-0.879	25.624	0.018	0.018	0.000	0.000	0.000	0.000
20	V	367	LYS	1	0.876	0.939	28.083	-0.043	-0.043	0.000	0.000	0.000	0.000
21	V	368	MET	0	-0.012	-0.008	27.899	-0.001	-0.001	0.000	0.000	0.000	0.000
22	V	369	LYS	1	0.781	0.892	27.409	-0.030	-0.030	0.000	0.000	0.000	0.000
23	V	370	SER	0	0.010	0.005	31.062	-0.003	-0.003	0.000	0.000	0.000	0.000
24	V	371	ARG	1	0.879	0.949	32.327	-0.060	-0.060	0.000	0.000	0.000	0.000
25	V	372	PRO	0	-0.006	-0.020	35.766	0.000	0.000	0.000	0.000	0.000	0.000
26	V	373	LEU	0	-0.039	0.005	36.368	-0.001	-0.001	0.000	0.000	0.000	0.000
27	V	374	ASN	0	0.006	-0.007	32.005	-0.001	-0.001	0.000	0.000	0.000	0.000
28	V	375	GLU	-1	-0.754	-0.902	31.718	0.057	0.057	0.000	0.000	0.000	0.000
29	V	376	ILE	0	-0.058	-0.004	32.729	0.005	0.005	0.000	0.000	0.000	0.000
30	V	377	LEU	0	-0.044	-0.044	29.313	0.000	0.000	0.000	0.000	0.000	0.000
31	V	378	GLU	-1	-0.925	-0.949	27.906	0.091	0.091	0.000	0.000	0.000	0.000
32	V	379	ASP	-1	-0.895	-0.931	28.915	0.088	0.088	0.000	0.000	0.000	0.000
33	V	380	SER	0	-0.044	-0.040	25.863	0.006	0.006	0.000	0.000	0.000	0.000
34	V	381	LYS	1	0.874	0.931	25.012	-0.130	-0.130	0.000	0.000	0.000	0.000
35	V	382	LEU	0	0.066	0.051	23.567	0.011	0.011	0.000	0.000	0.000	0.000
36	V	383	GLN	0	0.045	0.000	22.486	0.014	0.014	0.000	0.000	0.000	0.000
37	V	384	ASN	0	-0.005	-0.009	20.977	0.001	0.001	0.000	0.000	0.000	0.000
38	V	385	LEU	0	-0.061	-0.011	18.009	0.039	0.039	0.000	0.000	0.000	0.000
39	V	386	ALA	0	0.048	0.019	17.664	0.025	0.025	0.000	0.000	0.000	0.000
40	V	387	GLN	0	0.001	0.008	17.270	0.008	0.008	0.000	0.000	0.000	0.000
41	V	388	ARG	1	0.879	0.938	14.392	-0.337	-0.337	0.000	0.000	0.000	0.000
42	V	389	VAL	0	0.020	0.012	12.997	0.064	0.064	0.000	0.000	0.000	0.000
43	V	390	PHE	0	-0.018	-0.026	13.017	-0.013	-0.013	0.000	0.000	0.000	0.000
44	V	391	ALA	0	0.010	0.016	11.996	-0.026	-0.026	0.000	0.000	0.000	0.000
45	V	392	SER	0	-0.029	-0.032	8.851	-0.033	-0.033	0.000	0.000	0.000	0.000
46	V	393	LYS	1	0.961	0.981	8.375	-0.023	-0.023	0.000	0.000	0.000	0.000
47	V	394	ALA	0	0.009	0.015	8.251	-0.138	-0.138	0.000	0.000	0.000	0.000
48	V	395	ARG	1	0.799	0.880	3.490	-6.650	-5.873	0.038	-0.303	-0.512	0.002
49	V	396	LEU	0	0.024	0.020	4.178	-0.942	-0.881	-0.001	-0.036	-0.024	0.000
50	V	397	ASN	0	-0.011	-0.023	6.898	-0.202	-0.202	0.000	0.000	0.000	0.000
51	V	398	TYR	0	0.017	0.020	2.320	-2.367	-0.979	3.107	-1.787	-2.708	-0.002
52	V	399	ALA	0	0.008	0.004	3.244	-0.952	-0.376	0.040	-0.194	-0.423	0.000
53	V	400	LEU	0	-0.008	-0.003	4.179	0.025	0.192	0.001	-0.024	-0.143	0.000
54	V	401	ASN	0	0.010	0.001	6.891	0.175	0.175	0.000	0.000	0.000	0.000
55	V	402	ASP	-1	-0.817	-0.897	2.655	-5.229	-3.332	1.039	-1.162	-1.775	-0.016
56	V	403	LYS	1	0.802	0.880	3.096	3.827	4.578	0.087	-0.315	-0.522	0.001
57	V	404	ALA	0	0.025	0.016	7.546	0.203	0.203	0.000	0.000	0.000	0.000
58	V	405	GLN	0	0.009	0.009	7.316	0.026	0.026	0.000	0.000	0.000	0.000
59	V	406	LYS	1	0.853	0.924	3.250	1.770	2.050	0.016	-0.072	-0.223	0.000
60	V	407	TYR	0	0.022	0.019	9.453	0.102	0.102	0.000	0.000	0.000	0.000
61	V	408	ASN	0	-0.013	-0.024	12.309	0.110	0.110	0.000	0.000	0.000	0.000
62	V	409	THR	0	-0.021	-0.018	11.855	0.058	0.058	0.000	0.000	0.000	0.000
63	V	410	LEU	0	-0.006	-0.010	11.741	0.045	0.045	0.000	0.000	0.000	0.000
64	V	411	ILE	0	-0.014	0.002	15.037	0.043	0.043	0.000	0.000	0.000	0.000
65	V	412	GLU	-1	-0.841	-0.897	17.305	-0.199	-0.199	0.000	0.000	0.000	0.000
66	V	413	MET	0	-0.011	-0.013	15.790	0.012	0.012	0.000	0.000	0.000	0.000
67	V	414	ASN	0	-0.010	-0.006	18.931	0.025	0.025	0.000	0.000	0.000	0.000
68	V	415	GLY	0	0.009	0.009	20.805	0.019	0.019	0.000	0.000	0.000	0.000
69	V	416	LYS	1	0.890	0.924	20.618	0.219	0.219	0.000	0.000	0.000	0.000
70	V	417	ILE	0	-0.034	-0.019	20.615	0.014	0.014	0.000	0.000	0.000	0.000
71	V	418	SER	0	-0.012	-0.010	24.542	0.012	0.012	0.000	0.000	0.000	0.000
72	V	419	GLU	-1	-0.959	-0.981	26.706	-0.128	-0.128	0.000	0.000	0.000	0.000
73	V	420	ILE	0	-0.022	-0.008	26.062	0.010	0.010	0.000	0.000	0.000	0.000
74	V	421	MET	0	-0.097	-0.051	26.400	0.011	0.011	0.000	0.000	0.000	0.000
75	V	422	ASN	0	0.039	0.032	30.608	0.003	0.003	0.000	0.000	0.000	0.000
76	V	423	ILE	0	-0.014	-0.004	31.775	0.004	0.004	0.000	0.000	0.000	0.000
77	V	424	TYR	0	-0.002	-0.001	33.600	0.006	0.006	0.000	0.000	0.000	0.000
78	V	425	ASP	-1	-0.814	-0.910	34.167	-0.086	-0.086	0.000	0.000	0.000	0.000
79	V	426	ARG	1	0.897	0.943	34.185	0.096	0.096	0.000	0.000	0.000	0.000
80	V	427	LEU	0	-0.006	-0.001	37.257	0.004	0.004	0.000	0.000	0.000	0.000
81	V	428	LEU	0	-0.020	-0.012	38.423	0.004	0.004	0.000	0.000	0.000	0.000
82	V	429	GLU	-1	-0.902	-0.945	40.922	-0.058	-0.058	0.000	0.000	0.000	0.000
83	V	430	GLN	0	-0.020	-0.015	42.808	0.003	0.003	0.000	0.000	0.000	0.000
84	V	431	GLN	0	-0.034	0.005	43.947	0.005	0.005	0.000	0.000	0.000	0.000
85	V	432	LEU	0	0.010	-0.003	43.496	0.003	0.003	0.000	0.000	0.000	0.000
86	V	433	GLN	0	0.023	0.000	46.875	0.003	0.003	0.000	0.000	0.000	0.000
87	V	434	SER	0	-0.052	-0.039	48.341	0.002	0.002	0.000	0.000	0.000	0.000
88	V	435	ILE	0	-0.047	-0.019	48.059	0.002	0.002	0.000	0.000	0.000	0.000
89	V	436	ASN	0	-0.044	-0.015	51.012	0.002	0.002	0.000	0.000	0.000	0.000
90	V	437	LEU	0	-0.038	-0.005	52.397	0.002	0.002	0.000	0.000	0.000	0.000
91	V	438	SER	0	-0.075	-0.031	54.970	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)