FMO DATABASE

FMODB ID: R85G8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-715730.315921
FMO2-HF: Nuclear repulsion	673734.420118
FMO2-HF: Total energy	-41995.895804
FMO2-MP2: Total energy	-42119.938791

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.
-7.422	-2.842	3.924	-2.962	-5.542	-0.021

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 : -0.019 / q_NPA : -0.019

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	0.024	0.003	2.620	-8.593	-4.073	3.925	-2.958	-5.488	-0.021
4	A	303	TYR	0	0.030	0.005	5.024	0.725	0.785	-0.001	-0.004	-0.054	0.000
5	A	304	PRO	0	0.018	0.017	8.532	-0.068	-0.068	0.000	0.000	0.000	0.000
6	A	305	PRO	0	0.016	-0.007	11.489	0.049	0.049	0.000	0.000	0.000	0.000
7	A	306	ARG	1	0.896	0.953	10.191	0.681	0.681	0.000	0.000	0.000	0.000
8	A	307	VAL	0	0.020	0.015	15.452	0.006	0.006	0.000	0.000	0.000	0.000
9	A	308	VAL	0	-0.045	-0.022	15.548	0.007	0.007	0.000	0.000	0.000	0.000
10	A	309	SER	0	-0.073	-0.061	18.575	0.025	0.025	0.000	0.000	0.000	0.000
11	A	310	LEU	0	-0.031	-0.035	21.480	-0.020	-0.020	0.000	0.000	0.000	0.000
12	A	311	GLU	-1	-0.828	-0.867	24.323	-0.107	-0.107	0.000	0.000	0.000	0.000
13	A	312	GLU	-1	-0.932	-0.961	27.622	-0.083	-0.083	0.000	0.000	0.000	0.000
14	A	313	PRO	0	-0.050	-0.028	31.116	0.005	0.005	0.000	0.000	0.000	0.000
15	A	314	GLU	-1	-0.822	-0.883	30.095	-0.030	-0.030	0.000	0.000	0.000	0.000
16	A	315	LEU	0	-0.031	-0.017	33.570	0.000	0.000	0.000	0.000	0.000	0.000
17	A	316	ARG	1	0.821	0.889	26.907	0.035	0.035	0.000	0.000	0.000	0.000
18	A	317	LEU	0	0.001	0.001	34.390	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	318	GLU	-1	-0.801	-0.886	30.658	0.004	0.004	0.000	0.000	0.000	0.000
20	A	319	HIS	0	-0.005	0.005	35.414	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	320	CYS	0	0.020	0.010	31.813	0.002	0.002	0.000	0.000	0.000	0.000
22	A	321	ILE	0	-0.051	-0.004	36.059	0.000	0.000	0.000	0.000	0.000	0.000
23	A	322	GLU	-1	-0.905	-0.963	35.935	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	323	PHE	0	-0.060	-0.027	30.715	0.004	0.004	0.000	0.000	0.000	0.000
25	A	324	VAL	0	0.054	0.023	35.943	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	325	VAL	0	-0.034	-0.010	34.751	0.003	0.003	0.000	0.000	0.000	0.000
27	A	326	ARG	1	0.939	0.968	35.926	0.002	0.002	0.000	0.000	0.000	0.000
28	A	327	GLY	0	-0.001	-0.006	36.581	0.004	0.004	0.000	0.000	0.000	0.000
29	A	328	ASN	0	-0.024	-0.012	35.279	0.002	0.002	0.000	0.000	0.000	0.000
30	A	329	PRO	0	0.031	-0.012	32.168	0.002	0.002	0.000	0.000	0.000	0.000
31	A	330	PRO	0	0.009	0.014	29.967	0.002	0.002	0.000	0.000	0.000	0.000
32	A	331	PRO	0	-0.051	-0.011	31.170	0.007	0.007	0.000	0.000	0.000	0.000
33	A	332	THR	0	-0.010	0.020	27.900	0.002	0.002	0.000	0.000	0.000	0.000
34	A	333	LEU	0	0.043	0.002	29.519	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	334	HIS	0	-0.034	-0.015	28.549	0.010	0.010	0.000	0.000	0.000	0.000
36	A	335	TRP	0	0.060	0.028	30.543	-0.008	-0.008	0.000	0.000	0.000	0.000
37	A	336	LEU	0	-0.046	-0.019	33.467	0.007	0.007	0.000	0.000	0.000	0.000
38	A	337	HIS	0	-0.030	-0.019	36.203	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	338	ASN	0	-0.013	-0.016	38.147	0.001	0.001	0.000	0.000	0.000	0.000
40	A	339	GLY	0	0.013	0.010	40.449	0.001	0.001	0.000	0.000	0.000	0.000
41	A	340	GLN	0	-0.027	-0.008	36.993	0.008	0.008	0.000	0.000	0.000	0.000
42	A	341	PRO	0	0.013	-0.008	32.075	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	342	LEU	0	0.015	0.021	31.513	0.001	0.001	0.000	0.000	0.000	0.000
44	A	343	ARG	1	0.930	0.959	28.278	-0.103	-0.103	0.000	0.000	0.000	0.000
45	A	344	GLU	-1	-0.798	-0.894	26.706	0.058	0.058	0.000	0.000	0.000	0.000
46	A	345	SER	0	-0.074	-0.053	25.224	0.016	0.016	0.000	0.000	0.000	0.000
47	A	346	LYS	1	0.927	0.964	23.896	-0.033	-0.033	0.000	0.000	0.000	0.000
48	A	347	ILE	0	-0.050	-0.024	25.926	-0.009	-0.009	0.000	0.000	0.000	0.000
49	A	348	ILE	0	0.030	0.030	29.660	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	349	HIS	1	0.763	0.850	26.234	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	350	VAL	0	0.039	0.021	27.290	-0.009	-0.009	0.000	0.000	0.000	0.000
52	A	351	GLU	-1	-0.878	-0.907	25.758	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	352	TYR	0	-0.021	-0.022	25.879	0.003	0.003	0.000	0.000	0.000	0.000
54	A	353	TYR	0	-0.032	-0.028	28.395	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	354	GLN	0	-0.070	-0.046	29.502	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	355	GLU	-1	-0.881	-0.942	25.179	0.027	0.027	0.000	0.000	0.000	0.000
57	A	356	GLY	0	0.012	0.006	29.190	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	357	GLU	-1	-0.917	-0.964	30.676	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	358	ILE	0	-0.059	-0.032	33.654	0.002	0.002	0.000	0.000	0.000	0.000
60	A	359	SER	0	-0.011	0.002	31.334	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	360	GLU	-1	-0.880	-0.934	31.936	-0.015	-0.015	0.000	0.000	0.000	0.000
62	A	361	GLY	0	0.061	0.021	31.710	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	363	LEU	0	0.002	0.014	31.038	0.002	0.002	0.000	0.000	0.000	0.000
64	A	364	LEU	0	-0.011	-0.003	29.893	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	365	PHE	0	0.015	-0.004	31.827	0.008	0.008	0.000	0.000	0.000	0.000
66	A	366	ASN	0	-0.045	-0.045	30.796	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	367	LYS	1	0.854	0.925	32.333	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	368	PRO	0	-0.003	0.018	35.836	0.004	0.004	0.000	0.000	0.000	0.000
69	A	369	THR	0	-0.013	-0.022	37.266	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	370	HIS	0	0.003	-0.016	39.835	0.000	0.000	0.000	0.000	0.000	0.000
71	A	371	TYR	0	0.035	0.019	39.339	0.001	0.001	0.000	0.000	0.000	0.000
72	A	372	ASN	0	0.001	0.018	35.348	0.002	0.002	0.000	0.000	0.000	0.000
73	A	373	ASN	0	0.035	0.004	39.294	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	374	GLY	0	0.013	0.020	42.357	0.004	0.004	0.000	0.000	0.000	0.000
75	A	375	ASN	0	0.006	0.002	43.058	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	376	TYR	0	-0.011	-0.025	35.967	0.005	0.005	0.000	0.000	0.000	0.000
77	A	377	THR	0	-0.044	-0.038	38.437	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	378	LEU	0	0.020	0.035	33.837	0.005	0.005	0.000	0.000	0.000	0.000
79	A	379	ILE	0	-0.016	-0.027	35.288	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	380	ALA	0	0.038	0.023	34.339	0.002	0.002	0.000	0.000	0.000	0.000
81	A	381	LYS	1	0.892	0.943	33.680	-0.061	-0.061	0.000	0.000	0.000	0.000
82	A	382	ASN	0	0.023	0.022	33.205	0.004	0.004	0.000	0.000	0.000	0.000
83	A	383	PRO	0	-0.013	-0.029	33.350	0.003	0.003	0.000	0.000	0.000	0.000
84	A	384	LEU	0	0.009	0.013	36.080	0.001	0.001	0.000	0.000	0.000	0.000
85	A	385	GLY	0	0.006	0.012	38.435	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	386	THR	0	-0.052	-0.036	37.567	0.005	0.005	0.000	0.000	0.000	0.000
87	A	387	ALA	0	0.011	0.011	38.766	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	388	ASN	0	-0.042	-0.028	38.886	0.003	0.003	0.000	0.000	0.000	0.000
89	A	389	GLN	0	0.025	0.021	40.230	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	390	THR	0	-0.001	0.016	40.739	0.003	0.003	0.000	0.000	0.000	0.000
91	A	391	ILE	0	0.007	0.017	40.536	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	392	ASN	0	-0.039	-0.039	43.419	0.002	0.002	0.000	0.000	0.000	0.000
93	A	393	GLY	0	0.043	0.031	41.994	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	394	HIS	0	-0.054	-0.029	43.083	0.001	0.001	0.000	0.000	0.000	0.000
95	A	395	PHE	0	0.006	0.005	38.573	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	396	LEU	0	0.003	0.001	41.919	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	397	LYS	1	0.881	0.942	45.151	-0.019	-0.019	0.000	0.000	0.000	0.000
98	A	398	GLU	-1	-0.751	-0.869	45.916	0.033	0.033	0.000	0.000	0.000	0.000
99	A	399	PRO	0	-0.059	-0.030	46.764	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	400	PHE	0	0.010	0.021	49.775	0.001	0.001	0.000	0.000	0.000	0.000
101	A	401	PRO	0	0.003	-0.008	52.462	0.001	0.001	0.000	0.000	0.000	0.000
102	A	402	VAL	0	-0.020	-0.010	51.056	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	403	ASP	-1	-0.900	-0.928	52.651	0.037	0.037	0.000	0.000	0.000	0.000
104	A	404	GLU	-1	-1.050	-1.029	55.789	0.026	0.026	0.000	0.000	0.000	0.000

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