FMO DATABASE

FMODB ID: 6Y6VZ

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	OptH
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	-715310.421995
FMO2-HF: Nuclear repulsion	673315.771451
FMO2-HF: Total energy	-41994.650544
FMO2-MP2: Total energy	-42118.71899

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.
-1.842	1.915	2.091	-1.968	-3.879	-0.008

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 : 0.022 / q_NPA : 0.012

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	0.006	-0.009	2.288	-3.070	0.602	2.092	-1.960	-3.804	-0.008
4	A	303	TYR	0	0.016	0.001	4.782	0.442	0.527	-0.001	-0.008	-0.075	0.000
5	A	304	PRO	0	0.024	0.018	8.082	0.037	0.037	0.000	0.000	0.000	0.000
6	A	305	PRO	0	0.004	-0.007	10.982	0.049	0.049	0.000	0.000	0.000	0.000
7	A	306	ARG	1	0.931	0.965	10.222	0.507	0.507	0.000	0.000	0.000	0.000
8	A	307	VAL	0	0.032	0.023	14.834	0.032	0.032	0.000	0.000	0.000	0.000
9	A	308	VAL	0	-0.051	-0.024	15.471	-0.011	-0.011	0.000	0.000	0.000	0.000
10	A	309	SER	0	-0.018	-0.017	18.268	0.011	0.011	0.000	0.000	0.000	0.000
11	A	310	LEU	0	-0.002	-0.012	21.241	0.001	0.001	0.000	0.000	0.000	0.000
12	A	311	GLU	-1	-0.931	-0.949	24.003	-0.037	-0.037	0.000	0.000	0.000	0.000
13	A	312	GLU	-1	-0.953	-0.968	27.431	-0.038	-0.038	0.000	0.000	0.000	0.000
14	A	313	PRO	0	-0.053	-0.027	30.894	0.007	0.007	0.000	0.000	0.000	0.000
15	A	314	GLU	-1	-0.901	-0.944	30.732	0.013	0.013	0.000	0.000	0.000	0.000
16	A	315	LEU	0	-0.052	-0.032	32.997	0.005	0.005	0.000	0.000	0.000	0.000
17	A	316	ARG	1	0.950	0.969	26.884	-0.063	-0.063	0.000	0.000	0.000	0.000
18	A	317	LEU	0	0.002	0.003	34.319	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	318	GLU	-1	-0.858	-0.939	30.602	0.105	0.105	0.000	0.000	0.000	0.000
20	A	319	HIS	0	-0.017	0.000	35.457	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	320	CYS	0	0.024	0.014	31.733	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	321	ILE	0	-0.039	0.010	35.869	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	322	GLU	-1	-0.902	-0.976	35.898	0.080	0.080	0.000	0.000	0.000	0.000
24	A	323	PHE	0	-0.051	-0.017	31.056	0.000	0.000	0.000	0.000	0.000	0.000
25	A	324	VAL	0	0.053	0.018	36.226	0.000	0.000	0.000	0.000	0.000	0.000
26	A	325	VAL	0	-0.053	-0.020	34.905	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	326	ARG	1	0.973	0.978	36.092	-0.087	-0.087	0.000	0.000	0.000	0.000
28	A	327	GLY	0	-0.027	-0.023	36.581	0.001	0.001	0.000	0.000	0.000	0.000
29	A	328	ASN	0	0.053	0.036	35.248	0.012	0.012	0.000	0.000	0.000	0.000
30	A	329	PRO	0	-0.022	-0.032	32.629	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	330	PRO	0	0.022	0.014	30.004	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	331	PRO	0	-0.036	0.001	31.189	0.012	0.012	0.000	0.000	0.000	0.000
33	A	332	THR	0	-0.030	0.005	28.172	0.007	0.007	0.000	0.000	0.000	0.000
34	A	333	LEU	0	0.041	-0.006	29.659	-0.015	-0.015	0.000	0.000	0.000	0.000
35	A	334	HIS	0	-0.022	0.002	28.541	0.015	0.015	0.000	0.000	0.000	0.000
36	A	335	TRP	0	0.098	0.039	30.769	-0.019	-0.019	0.000	0.000	0.000	0.000
37	A	336	LEU	0	-0.060	-0.033	33.596	0.009	0.009	0.000	0.000	0.000	0.000
38	A	337	HIS	0	-0.029	-0.023	36.202	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	338	ASN	0	-0.008	-0.025	37.826	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	339	GLY	0	-0.008	-0.008	40.432	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	340	GLN	0	-0.009	0.007	36.747	0.013	0.013	0.000	0.000	0.000	0.000
42	A	341	PRO	0	0.013	0.010	32.216	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	342	LEU	0	0.014	0.022	31.668	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	343	ARG	1	0.944	0.973	28.407	-0.189	-0.189	0.000	0.000	0.000	0.000
45	A	344	GLU	-1	-0.869	-0.932	26.107	0.210	0.210	0.000	0.000	0.000	0.000
46	A	345	SER	0	-0.130	-0.088	24.872	0.008	0.008	0.000	0.000	0.000	0.000
47	A	346	LYS	1	0.987	0.999	23.642	-0.128	-0.128	0.000	0.000	0.000	0.000
48	A	347	ILE	0	-0.054	-0.024	25.903	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	348	ILE	0	0.056	0.045	28.848	-0.010	-0.010	0.000	0.000	0.000	0.000
50	A	349	HIS	1	0.758	0.860	25.812	-0.121	-0.121	0.000	0.000	0.000	0.000
51	A	350	VAL	0	0.067	0.036	26.897	-0.018	-0.018	0.000	0.000	0.000	0.000
52	A	351	GLU	-1	-0.845	-0.890	25.544	0.169	0.169	0.000	0.000	0.000	0.000
53	A	352	TYR	0	0.006	-0.001	26.110	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	353	TYR	0	-0.022	-0.016	28.210	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	354	GLN	0	-0.035	-0.023	29.676	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	355	GLU	-1	-0.908	-0.947	25.083	0.219	0.219	0.000	0.000	0.000	0.000
57	A	356	GLY	0	0.013	0.008	29.311	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	357	GLU	-1	-0.977	-1.001	30.665	0.110	0.110	0.000	0.000	0.000	0.000
59	A	358	ILE	0	-0.036	-0.016	33.997	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	359	SER	0	-0.024	0.005	31.451	0.008	0.008	0.000	0.000	0.000	0.000
61	A	360	GLU	-1	-0.925	-0.979	32.383	0.077	0.077	0.000	0.000	0.000	0.000
62	A	361	GLY	0	0.024	0.000	31.903	0.006	0.006	0.000	0.000	0.000	0.000
63	A	363	LEU	0	0.011	0.036	30.838	0.010	0.010	0.000	0.000	0.000	0.000
64	A	364	LEU	0	-0.052	-0.041	29.638	-0.011	-0.011	0.000	0.000	0.000	0.000
65	A	365	PHE	0	0.011	-0.005	31.539	0.010	0.010	0.000	0.000	0.000	0.000
66	A	366	ASN	0	-0.029	-0.019	29.696	-0.017	-0.017	0.000	0.000	0.000	0.000
67	A	367	LYS	1	0.877	0.933	31.831	-0.074	-0.074	0.000	0.000	0.000	0.000
68	A	368	PRO	0	0.043	0.037	35.434	0.004	0.004	0.000	0.000	0.000	0.000
69	A	369	THR	0	0.003	-0.009	36.841	-0.007	-0.007	0.000	0.000	0.000	0.000
70	A	370	HIS	0	-0.018	-0.029	39.464	0.000	0.000	0.000	0.000	0.000	0.000
71	A	371	TYR	0	0.028	0.014	38.749	0.001	0.001	0.000	0.000	0.000	0.000
72	A	372	ASN	0	-0.014	0.012	34.892	0.002	0.002	0.000	0.000	0.000	0.000
73	A	373	ASN	0	0.034	0.025	38.763	0.002	0.002	0.000	0.000	0.000	0.000
74	A	374	GLY	0	-0.001	0.015	41.797	0.004	0.004	0.000	0.000	0.000	0.000
75	A	375	ASN	0	-0.021	-0.013	42.447	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	376	TYR	0	0.010	-0.022	35.781	0.009	0.009	0.000	0.000	0.000	0.000
77	A	377	THR	0	-0.046	-0.032	38.342	-0.006	-0.006	0.000	0.000	0.000	0.000
78	A	378	LEU	0	0.019	0.020	33.858	0.009	0.009	0.000	0.000	0.000	0.000
79	A	379	ILE	0	-0.012	-0.020	35.344	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	380	ALA	0	0.036	0.015	34.398	0.010	0.010	0.000	0.000	0.000	0.000
81	A	381	LYS	1	0.892	0.936	33.954	-0.184	-0.184	0.000	0.000	0.000	0.000
82	A	382	ASN	0	0.045	0.027	33.441	0.010	0.010	0.000	0.000	0.000	0.000
83	A	383	PRO	0	0.006	-0.020	33.623	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	384	LEU	0	-0.012	0.002	36.617	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	385	GLY	0	-0.011	0.004	38.669	-0.009	-0.009	0.000	0.000	0.000	0.000
86	A	386	THR	0	-0.081	-0.040	37.779	0.011	0.011	0.000	0.000	0.000	0.000
87	A	387	ALA	0	0.050	0.029	38.744	-0.008	-0.008	0.000	0.000	0.000	0.000
88	A	388	ASN	0	-0.051	-0.024	38.859	0.005	0.005	0.000	0.000	0.000	0.000
89	A	389	GLN	0	0.066	0.053	40.382	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	390	THR	0	-0.002	0.001	40.837	0.008	0.008	0.000	0.000	0.000	0.000
91	A	391	ILE	0	0.008	0.021	40.575	-0.006	-0.006	0.000	0.000	0.000	0.000
92	A	392	ASN	0	-0.014	-0.017	43.049	0.002	0.002	0.000	0.000	0.000	0.000
93	A	393	GLY	0	0.030	0.015	41.679	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	394	HIS	0	-0.041	-0.019	42.762	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	395	PHE	0	-0.016	-0.010	38.187	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	396	LEU	0	-0.002	-0.011	41.623	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	397	LYS	1	0.946	0.999	44.608	-0.054	-0.054	0.000	0.000	0.000	0.000
98	A	398	GLU	-1	-0.784	-0.895	45.668	0.081	0.081	0.000	0.000	0.000	0.000
99	A	399	PRO	0	-0.104	-0.067	46.362	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	400	PHE	0	0.013	0.015	49.491	0.002	0.002	0.000	0.000	0.000	0.000
101	A	401	PRO	0	0.012	-0.004	51.938	0.001	0.001	0.000	0.000	0.000	0.000
102	A	402	VAL	0	-0.024	-0.011	50.721	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	403	ASP	-1	-0.916	-0.938	52.651	0.060	0.060	0.000	0.000	0.000	0.000
104	A	404	GLU	-1	-1.028	-1.010	55.303	0.046	0.046	0.000	0.000	0.000	0.000

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