FMO DATABASE

FMODB ID: ZVY5N

Calculation Name: 1WWC-A-Xray372

Preferred Name: NT-3 growth factor receptor

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1WWC

Chain ID: A

ChEMBL ID: CHEMBL5608

UniProt ID: Q16288

Base Structure: X-ray

Registration Date: 2023-09-21

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	104
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-715938.858092
FMO2-HF: Nuclear repulsion	673943.444277
FMO2-HF: Total energy	-41995.413816
FMO2-MP2: Total energy	-42119.442314

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:300:THR)

Summations of interaction energy for fragment #1(A:300:THR)

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.
-3.715	-0.112	1.712	-1.835	-3.48	-0.012

Interaction energy analysis for fragmet #1(A:300:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : -0.020

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	302	TYR	0	0.001	-0.003	2.614	-4.676	-1.145	1.713	-1.832	-3.412	-0.012
4	A	303	TYR	0	0.020	0.004	5.309	0.602	0.674	-0.001	-0.003	-0.068	0.000
5	A	304	PRO	0	0.027	0.020	8.534	-0.069	-0.069	0.000	0.000	0.000	0.000
6	A	305	PRO	0	-0.005	-0.019	11.467	0.056	0.056	0.000	0.000	0.000	0.000
7	A	306	ARG	1	0.935	0.970	10.078	0.573	0.573	0.000	0.000	0.000	0.000
8	A	307	VAL	0	0.033	0.024	15.125	0.006	0.006	0.000	0.000	0.000	0.000
9	A	308	VAL	0	-0.058	-0.030	15.473	0.006	0.006	0.000	0.000	0.000	0.000
10	A	309	SER	0	-0.074	-0.060	18.382	0.018	0.018	0.000	0.000	0.000	0.000
11	A	310	LEU	0	-0.004	-0.009	21.359	-0.013	-0.013	0.000	0.000	0.000	0.000
12	A	311	GLU	-1	-0.855	-0.896	24.139	-0.091	-0.091	0.000	0.000	0.000	0.000
13	A	312	GLU	-1	-0.954	-0.970	27.529	-0.076	-0.076	0.000	0.000	0.000	0.000
14	A	313	PRO	0	-0.045	-0.024	30.968	0.004	0.004	0.000	0.000	0.000	0.000
15	A	314	GLU	-1	-0.841	-0.903	30.413	-0.034	-0.034	0.000	0.000	0.000	0.000
16	A	315	LEU	0	-0.050	-0.026	33.156	0.001	0.001	0.000	0.000	0.000	0.000
17	A	316	ARG	1	0.869	0.917	27.012	0.033	0.033	0.000	0.000	0.000	0.000
18	A	317	LEU	0	-0.002	0.004	34.440	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	318	GLU	-1	-0.809	-0.887	30.770	0.001	0.001	0.000	0.000	0.000	0.000
20	A	319	HIS	0	-0.010	0.001	35.515	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	320	CYS	0	0.051	0.025	31.699	0.003	0.003	0.000	0.000	0.000	0.000
22	A	321	ILE	0	-0.051	0.001	35.842	0.000	0.000	0.000	0.000	0.000	0.000
23	A	322	GLU	-1	-0.900	-0.966	35.846	-0.007	-0.007	0.000	0.000	0.000	0.000
24	A	323	PHE	0	-0.058	-0.023	30.980	0.003	0.003	0.000	0.000	0.000	0.000
25	A	324	VAL	0	0.055	0.014	36.139	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	325	VAL	0	-0.050	-0.018	34.794	0.003	0.003	0.000	0.000	0.000	0.000
27	A	326	ARG	1	0.974	0.978	35.945	0.004	0.004	0.000	0.000	0.000	0.000
28	A	327	GLY	0	-0.020	-0.020	36.384	0.004	0.004	0.000	0.000	0.000	0.000
29	A	328	ASN	0	-0.031	-0.004	35.155	0.001	0.001	0.000	0.000	0.000	0.000
30	A	329	PRO	0	0.020	-0.016	32.365	0.001	0.001	0.000	0.000	0.000	0.000
31	A	330	PRO	0	0.013	0.012	29.776	0.002	0.002	0.000	0.000	0.000	0.000
32	A	331	PRO	0	-0.056	-0.005	30.968	0.007	0.007	0.000	0.000	0.000	0.000
33	A	332	THR	0	-0.023	0.017	27.940	0.002	0.002	0.000	0.000	0.000	0.000
34	A	333	LEU	0	0.047	0.001	29.483	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	334	HIS	0	-0.047	-0.015	28.211	0.009	0.009	0.000	0.000	0.000	0.000
36	A	335	TRP	0	0.091	0.041	30.495	-0.007	-0.007	0.000	0.000	0.000	0.000
37	A	336	LEU	0	-0.052	-0.030	33.462	0.007	0.007	0.000	0.000	0.000	0.000
38	A	337	HIS	0	-0.029	-0.023	36.076	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	338	ASN	0	-0.016	-0.021	37.730	0.000	0.000	0.000	0.000	0.000	0.000
40	A	339	GLY	0	-0.001	-0.004	40.311	0.001	0.001	0.000	0.000	0.000	0.000
41	A	340	GLN	0	-0.001	0.014	36.703	0.008	0.008	0.000	0.000	0.000	0.000
42	A	341	PRO	0	0.018	0.010	32.141	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	342	LEU	0	0.002	0.016	31.238	0.002	0.002	0.000	0.000	0.000	0.000
44	A	343	ARG	1	0.931	0.964	28.124	-0.092	-0.092	0.000	0.000	0.000	0.000
45	A	344	GLU	-1	-0.857	-0.924	26.018	0.055	0.055	0.000	0.000	0.000	0.000
46	A	345	SER	0	-0.111	-0.091	24.830	0.012	0.012	0.000	0.000	0.000	0.000
47	A	346	LYS	1	0.976	1.003	23.555	-0.023	-0.023	0.000	0.000	0.000	0.000
48	A	347	ILE	0	-0.056	-0.024	25.943	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	348	ILE	0	0.042	0.036	28.842	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	349	HIS	1	0.779	0.858	25.873	0.000	0.000	0.000	0.000	0.000	0.000
51	A	350	VAL	0	0.072	0.040	26.892	-0.007	-0.007	0.000	0.000	0.000	0.000
52	A	351	GLU	-1	-0.881	-0.908	25.721	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	352	TYR	0	0.005	-0.003	25.765	0.002	0.002	0.000	0.000	0.000	0.000
54	A	353	TYR	0	-0.018	-0.020	28.170	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	354	GLN	0	-0.060	-0.047	29.581	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	355	GLU	-1	-0.912	-0.949	24.978	0.017	0.017	0.000	0.000	0.000	0.000
57	A	356	GLY	0	0.013	0.007	29.184	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	357	GLU	-1	-0.913	-0.966	30.500	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	358	ILE	0	-0.040	-0.019	33.868	0.004	0.004	0.000	0.000	0.000	0.000
60	A	359	SER	0	-0.031	0.003	31.420	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	360	GLU	-1	-0.876	-0.941	32.283	-0.016	-0.016	0.000	0.000	0.000	0.000
62	A	361	GLY	0	0.031	0.007	31.835	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	363	LEU	0	0.002	0.027	30.870	0.002	0.002	0.000	0.000	0.000	0.000
64	A	364	LEU	0	-0.044	-0.033	29.720	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	365	PHE	0	0.011	-0.010	31.537	0.007	0.007	0.000	0.000	0.000	0.000
66	A	366	ASN	0	-0.061	-0.042	30.872	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	367	LYS	1	0.870	0.917	31.982	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	368	PRO	0	0.030	0.035	35.489	0.004	0.004	0.000	0.000	0.000	0.000
69	A	369	THR	0	0.004	-0.013	36.873	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	370	HIS	0	-0.017	-0.031	39.495	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	371	TYR	0	0.039	0.022	38.704	0.001	0.001	0.000	0.000	0.000	0.000
72	A	372	ASN	0	-0.007	0.015	34.848	0.002	0.002	0.000	0.000	0.000	0.000
73	A	373	ASN	0	0.017	0.003	38.743	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	374	GLY	0	0.005	0.010	41.749	0.004	0.004	0.000	0.000	0.000	0.000
75	A	375	ASN	0	-0.011	-0.006	42.383	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	376	TYR	0	0.013	-0.010	35.502	0.005	0.005	0.000	0.000	0.000	0.000
77	A	377	THR	0	-0.058	-0.043	38.219	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	378	LEU	0	0.014	0.020	33.577	0.004	0.004	0.000	0.000	0.000	0.000
79	A	379	ILE	0	-0.009	-0.019	35.201	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	380	ALA	0	0.037	0.016	34.212	0.002	0.002	0.000	0.000	0.000	0.000
81	A	381	LYS	1	0.911	0.952	33.746	-0.057	-0.057	0.000	0.000	0.000	0.000
82	A	382	ASN	0	0.032	0.008	33.213	0.004	0.004	0.000	0.000	0.000	0.000
83	A	383	PRO	0	-0.005	-0.019	33.424	0.001	0.001	0.000	0.000	0.000	0.000
84	A	384	LEU	0	-0.008	0.005	36.347	0.000	0.000	0.000	0.000	0.000	0.000
85	A	385	GLY	0	-0.012	0.001	38.421	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	386	THR	0	-0.047	-0.026	37.393	0.005	0.005	0.000	0.000	0.000	0.000
87	A	387	ALA	0	0.007	0.009	38.539	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	388	ASN	0	-0.040	-0.021	38.673	0.003	0.003	0.000	0.000	0.000	0.000
89	A	389	GLN	0	0.053	0.047	40.232	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	390	THR	0	0.001	0.004	40.704	0.003	0.003	0.000	0.000	0.000	0.000
91	A	391	ILE	0	0.004	0.017	40.417	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	392	ASN	0	-0.028	-0.029	42.962	0.002	0.002	0.000	0.000	0.000	0.000
93	A	393	GLY	0	0.035	0.019	41.636	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	394	HIS	0	-0.048	-0.024	42.719	0.001	0.001	0.000	0.000	0.000	0.000
95	A	395	PHE	0	-0.003	-0.004	38.064	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	396	LEU	0	-0.006	-0.005	41.472	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	397	LYS	1	0.953	0.988	44.635	-0.016	-0.016	0.000	0.000	0.000	0.000
98	A	398	GLU	-1	-0.781	-0.878	45.380	0.030	0.030	0.000	0.000	0.000	0.000
99	A	399	PRO	0	-0.099	-0.060	46.419	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	400	PHE	0	0.011	0.015	49.514	0.001	0.001	0.000	0.000	0.000	0.000
101	A	401	PRO	0	0.027	0.006	51.957	0.001	0.001	0.000	0.000	0.000	0.000
102	A	402	VAL	0	-0.023	-0.014	50.745	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	403	ASP	-1	-0.917	-0.940	52.340	0.032	0.032	0.000	0.000	0.000	0.000
104	A	404	GLU	-1	-1.042	-1.018	55.305	0.022	0.022	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:300:THR)