FMO DATABASE

FMODB ID: 4JRVN

Calculation Name: 2P3W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2P3W

Chain ID: A

ChEMBL ID:

UniProt ID: P83110

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	112
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-823231.371573
FMO2-HF: Nuclear repulsion	780644.058707
FMO2-HF: Total energy	-42587.312866
FMO2-MP2: Total energy	-42711.758562

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(A:350:GLY)

Summations of interaction energy for fragment #1(A:350:GLY)

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.
0.927	1.824	-0.006	-0.393	-0.498	0.001

Interaction energy analysis for fragmet #1(A:350:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : 0.005

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	A	352	HIS	0	0.037	0.016	3.857	0.050	0.947	-0.006	-0.393	-0.498	0.001
4	A	353	MET	0	-0.018	0.018	6.326	0.527	0.527	0.000	0.000	0.000	0.000
5	A	354	LYS	1	0.914	0.970	8.601	0.117	0.117	0.000	0.000	0.000	0.000
6	A	355	ARG	1	0.910	0.954	11.877	-0.107	-0.107	0.000	0.000	0.000	0.000
7	A	356	PHE	0	-0.044	-0.032	15.385	-0.037	-0.037	0.000	0.000	0.000	0.000
8	A	357	ILE	0	0.136	0.064	19.006	0.017	0.017	0.000	0.000	0.000	0.000
9	A	358	GLY	0	-0.028	0.007	22.531	0.003	0.003	0.000	0.000	0.000	0.000
10	A	359	ILE	0	0.062	0.039	24.077	0.003	0.003	0.000	0.000	0.000	0.000
11	A	360	ARG	1	0.804	0.910	25.558	0.045	0.045	0.000	0.000	0.000	0.000
12	A	361	MET	0	-0.025	-0.003	24.409	0.008	0.008	0.000	0.000	0.000	0.000
13	A	362	ARG	1	0.786	0.865	29.449	0.026	0.026	0.000	0.000	0.000	0.000
14	A	363	THR	0	0.019	-0.006	30.890	0.004	0.004	0.000	0.000	0.000	0.000
15	A	364	ILE	0	-0.037	0.004	32.872	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	365	THR	0	0.017	0.004	36.048	0.000	0.000	0.000	0.000	0.000	0.000
17	A	366	PRO	0	0.029	0.002	38.733	0.000	0.000	0.000	0.000	0.000	0.000
18	A	367	SER	0	0.039	0.020	40.770	0.000	0.000	0.000	0.000	0.000	0.000
19	A	368	LEU	0	0.013	0.022	36.389	0.000	0.000	0.000	0.000	0.000	0.000
20	A	369	VAL	0	-0.003	-0.010	40.434	0.002	0.002	0.000	0.000	0.000	0.000
21	A	370	ASP	-1	-0.899	-0.956	42.705	-0.014	-0.014	0.000	0.000	0.000	0.000
22	A	371	GLU	-1	-0.857	-0.903	40.183	-0.028	-0.028	0.000	0.000	0.000	0.000
23	A	372	LEU	0	-0.004	0.007	39.284	0.001	0.001	0.000	0.000	0.000	0.000
24	A	373	LYS	1	0.880	0.939	43.841	0.009	0.009	0.000	0.000	0.000	0.000
25	A	374	ALA	0	-0.054	-0.027	47.387	0.001	0.001	0.000	0.000	0.000	0.000
26	A	375	SER	0	-0.066	-0.036	45.178	0.000	0.000	0.000	0.000	0.000	0.000
27	A	376	ASN	0	-0.064	-0.032	43.897	0.001	0.001	0.000	0.000	0.000	0.000
28	A	377	PRO	0	0.020	0.010	47.901	0.001	0.001	0.000	0.000	0.000	0.000
29	A	378	ASP	-1	-0.935	-0.979	50.900	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	379	PHE	0	-0.022	-0.001	44.070	0.001	0.001	0.000	0.000	0.000	0.000
31	A	380	PRO	0	-0.037	0.017	45.692	0.001	0.001	0.000	0.000	0.000	0.000
32	A	381	GLU	-1	-0.855	-0.945	43.954	0.000	0.000	0.000	0.000	0.000	0.000
33	A	382	VAL	0	-0.043	-0.027	39.277	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	383	SER	0	0.012	0.009	41.423	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	384	SER	0	-0.037	-0.030	36.066	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	385	GLY	0	0.042	0.031	34.276	0.003	0.003	0.000	0.000	0.000	0.000
37	A	386	ILE	0	-0.075	-0.041	29.037	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	387	TYR	0	0.047	0.036	32.434	0.003	0.003	0.000	0.000	0.000	0.000
39	A	388	VAL	0	-0.014	-0.017	30.798	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	389	GLN	0	-0.023	-0.020	31.860	0.001	0.001	0.000	0.000	0.000	0.000
41	A	390	GLU	-1	-0.805	-0.905	30.203	-0.042	-0.042	0.000	0.000	0.000	0.000
42	A	391	VAL	0	0.030	0.019	29.069	0.000	0.000	0.000	0.000	0.000	0.000
43	A	392	ALA	0	-0.026	-0.004	25.732	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	393	PRO	0	0.040	0.021	27.757	0.006	0.006	0.000	0.000	0.000	0.000
45	A	394	ASN	0	0.012	-0.004	25.336	0.009	0.009	0.000	0.000	0.000	0.000
46	A	395	SER	0	-0.029	-0.008	24.135	0.008	0.008	0.000	0.000	0.000	0.000
47	A	396	PRO	0	0.001	-0.007	21.920	0.003	0.003	0.000	0.000	0.000	0.000
48	A	397	SER	0	0.033	-0.001	25.144	0.005	0.005	0.000	0.000	0.000	0.000
49	A	398	GLN	0	-0.011	0.004	27.837	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	399	ARG	1	0.752	0.838	22.632	-0.034	-0.034	0.000	0.000	0.000	0.000
51	A	400	GLY	0	0.002	0.013	29.450	0.005	0.005	0.000	0.000	0.000	0.000
52	A	401	GLY	0	-0.007	0.004	30.725	0.001	0.001	0.000	0.000	0.000	0.000
53	A	402	ILE	0	-0.015	-0.002	29.254	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	403	GLN	0	-0.058	-0.044	32.805	0.001	0.001	0.000	0.000	0.000	0.000
55	A	404	ASP	-1	-0.918	-0.965	34.495	-0.016	-0.016	0.000	0.000	0.000	0.000
56	A	405	GLY	0	0.009	0.003	35.271	0.002	0.002	0.000	0.000	0.000	0.000
57	A	406	ASP	-1	-0.762	-0.837	34.449	0.004	0.004	0.000	0.000	0.000	0.000
58	A	407	ILE	0	-0.009	-0.011	35.221	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	408	ILE	0	-0.009	0.008	29.271	0.003	0.003	0.000	0.000	0.000	0.000
60	A	409	VAL	0	0.003	-0.010	33.212	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	410	LYS	1	0.845	0.925	32.266	-0.020	-0.020	0.000	0.000	0.000	0.000
62	A	411	VAL	0	0.030	0.006	25.732	0.000	0.000	0.000	0.000	0.000	0.000
63	A	412	ASN	0	-0.043	-0.025	25.113	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	413	GLY	0	0.009	0.015	29.145	0.002	0.002	0.000	0.000	0.000	0.000
65	A	414	ARG	1	0.828	0.886	24.833	-0.041	-0.041	0.000	0.000	0.000	0.000
66	A	415	PRO	0	-0.005	-0.005	31.715	0.000	0.000	0.000	0.000	0.000	0.000
67	A	416	LEU	0	-0.019	0.002	28.166	0.000	0.000	0.000	0.000	0.000	0.000
68	A	417	VAL	0	-0.035	-0.029	31.618	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	418	ASP	-1	-0.754	-0.849	28.321	-0.040	-0.040	0.000	0.000	0.000	0.000
70	A	419	SER	0	-0.037	-0.015	26.973	0.001	0.001	0.000	0.000	0.000	0.000
71	A	420	SER	0	-0.062	-0.059	24.112	0.001	0.001	0.000	0.000	0.000	0.000
72	A	421	GLU	-1	-0.770	-0.885	23.555	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	422	LEU	0	0.020	0.009	24.441	0.008	0.008	0.000	0.000	0.000	0.000
74	A	423	GLN	0	-0.061	-0.033	19.509	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	424	GLU	-1	-0.875	-0.949	18.725	-0.009	-0.009	0.000	0.000	0.000	0.000
76	A	425	ALA	0	0.015	0.029	19.714	0.015	0.015	0.000	0.000	0.000	0.000
77	A	426	VAL	0	-0.027	-0.019	18.733	0.014	0.014	0.000	0.000	0.000	0.000
78	A	427	LEU	0	-0.050	-0.013	13.312	0.003	0.003	0.000	0.000	0.000	0.000
79	A	428	THR	0	-0.067	-0.050	15.483	0.031	0.031	0.000	0.000	0.000	0.000
80	A	429	GLU	-1	-0.787	-0.844	17.793	0.075	0.075	0.000	0.000	0.000	0.000
81	A	430	SER	0	-0.030	-0.015	19.311	-0.010	-0.010	0.000	0.000	0.000	0.000
82	A	431	PRO	0	-0.009	-0.006	21.300	0.013	0.013	0.000	0.000	0.000	0.000
83	A	432	LEU	0	-0.015	-0.016	22.342	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	433	LEU	0	-0.001	-0.002	25.671	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	434	LEU	0	-0.017	-0.015	26.877	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	435	GLU	-1	-0.789	-0.878	30.760	0.018	0.018	0.000	0.000	0.000	0.000
87	A	436	VAL	0	-0.040	-0.032	33.204	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	437	ARG	1	0.843	0.902	35.820	-0.010	-0.010	0.000	0.000	0.000	0.000
89	A	438	ARG	1	0.798	0.847	35.884	-0.008	-0.008	0.000	0.000	0.000	0.000
90	A	439	GLY	0	0.022	0.007	40.490	0.001	0.001	0.000	0.000	0.000	0.000
91	A	440	ASN	0	-0.016	-0.020	43.771	0.000	0.000	0.000	0.000	0.000	0.000
92	A	441	ASP	-1	-0.932	-0.942	42.431	0.009	0.009	0.000	0.000	0.000	0.000
93	A	442	ASP	-1	-0.883	-0.945	39.786	0.013	0.013	0.000	0.000	0.000	0.000
94	A	443	LEU	0	-0.022	0.000	37.300	0.002	0.002	0.000	0.000	0.000	0.000
95	A	444	LEU	0	-0.020	-0.010	33.211	0.000	0.000	0.000	0.000	0.000	0.000
96	A	445	PHE	0	0.014	0.015	31.092	0.002	0.002	0.000	0.000	0.000	0.000
97	A	446	SER	0	-0.018	-0.021	28.936	0.004	0.004	0.000	0.000	0.000	0.000
98	A	447	ILE	0	-0.014	0.000	24.596	0.002	0.002	0.000	0.000	0.000	0.000
99	A	448	ALA	0	0.029	0.012	21.717	0.002	0.002	0.000	0.000	0.000	0.000
100	A	449	PRO	0	-0.027	-0.013	18.349	-0.008	-0.008	0.000	0.000	0.000	0.000
101	A	450	GLU	-1	-0.839	-0.882	18.211	0.054	0.054	0.000	0.000	0.000	0.000
102	A	451	VAL	0	-0.038	-0.038	12.350	-0.021	-0.021	0.000	0.000	0.000	0.000
103	A	452	VAL	0	-0.015	0.002	13.022	0.026	0.026	0.000	0.000	0.000	0.000
104	A	453	MET	0	0.018	-0.006	8.163	-0.038	-0.038	0.000	0.000	0.000	0.000
105	A	454	GLY	0	0.023	0.002	7.192	-0.030	-0.030	0.000	0.000	0.000	0.000
106	A	455	GLY	0	0.005	0.003	8.215	-0.069	-0.069	0.000	0.000	0.000	0.000
107	A	456	GLY	0	-0.020	-0.015	10.370	0.071	0.071	0.000	0.000	0.000	0.000
108	A	457	PHE	0	-0.022	-0.011	13.351	0.046	0.046	0.000	0.000	0.000	0.000
109	A	458	GLY	0	0.016	0.022	14.581	0.028	0.028	0.000	0.000	0.000	0.000
110	A	459	ARG	1	0.912	0.936	16.009	0.246	0.246	0.000	0.000	0.000	0.000
111	A	460	TRP	0	0.045	0.033	18.823	0.013	0.013	0.000	0.000	0.000	0.000
112	A	461	VAL	0	-0.004	0.006	22.495	-0.009	-0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:350:GLY)