FMO DATABASE

FMODB ID: 1N8YZ

Calculation Name: 3CTD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CTD

Chain ID: A

ChEMBL ID:

UniProt ID: Q7V3J8

Base Structure: X-ray

Registration Date: 2023-09-23

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	163
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1427124.670761
FMO2-HF: Nuclear repulsion	1362972.556583
FMO2-HF: Total energy	-64152.114178
FMO2-MP2: Total energy	-64339.968906

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:258:ASN)

Summations of interaction energy for fragment #1(A:258:ASN)

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.
-21.239	-12.813	4.266	-6.441	-6.252	-0.02

Interaction energy analysis for fragmet #1(A:258:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.058 / q_NPA : 0.018

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	260	PHE	0	-0.009	-0.026	2.872	-10.448	-5.745	0.382	-2.381	-2.704	0.022
4	A	261	ASP	-1	-0.856	-0.938	2.303	-11.403	-7.854	3.884	-4.016	-3.418	-0.042
5	A	262	VAL	0	0.018	0.019	4.114	-0.279	-0.105	0.000	-0.044	-0.130	0.000
6	A	263	ILE	0	0.026	0.017	6.619	-0.002	-0.002	0.000	0.000	0.000	0.000
7	A	264	SER	0	-0.058	-0.008	7.098	-0.273	-0.273	0.000	0.000	0.000	0.000
8	A	265	ALA	0	0.031	0.023	8.226	-0.094	-0.094	0.000	0.000	0.000	0.000
9	A	266	PHE	0	0.043	0.026	10.164	0.023	0.023	0.000	0.000	0.000	0.000
10	A	267	ILE	0	-0.001	-0.003	11.934	-0.015	-0.015	0.000	0.000	0.000	0.000
11	A	268	LYS	1	0.848	0.908	10.349	-0.388	-0.388	0.000	0.000	0.000	0.000
12	A	269	SER	0	0.014	0.001	13.910	-0.087	-0.087	0.000	0.000	0.000	0.000
13	A	270	ILE	0	0.025	0.020	16.142	-0.008	-0.008	0.000	0.000	0.000	0.000
14	A	271	ARG	1	0.742	0.832	16.455	-0.440	-0.440	0.000	0.000	0.000	0.000
15	A	272	GLY	0	-0.025	-0.015	18.434	-0.012	-0.012	0.000	0.000	0.000	0.000
16	A	273	SER	0	-0.073	-0.027	20.148	-0.019	-0.019	0.000	0.000	0.000	0.000
17	A	274	ASP	-1	-0.811	-0.890	19.180	-0.234	-0.234	0.000	0.000	0.000	0.000
18	A	275	PRO	0	-0.003	-0.005	19.731	0.013	0.013	0.000	0.000	0.000	0.000
19	A	276	ASP	-1	-0.867	-0.937	20.724	-0.146	-0.146	0.000	0.000	0.000	0.000
20	A	277	ALA	0	0.006	0.001	16.041	-0.035	-0.035	0.000	0.000	0.000	0.000
21	A	278	THR	0	-0.068	-0.047	15.777	0.012	0.012	0.000	0.000	0.000	0.000
22	A	279	LEU	0	0.002	0.003	16.103	0.054	0.054	0.000	0.000	0.000	0.000
23	A	280	TYR	0	-0.004	0.022	12.450	-0.059	-0.059	0.000	0.000	0.000	0.000
24	A	281	TRP	0	-0.003	-0.026	9.384	-0.153	-0.153	0.000	0.000	0.000	0.000
25	A	282	LEU	0	-0.025	-0.013	12.417	0.093	0.093	0.000	0.000	0.000	0.000
26	A	283	ALA	0	0.009	-0.009	14.398	0.095	0.095	0.000	0.000	0.000	0.000
27	A	284	ASN	0	-0.010	-0.007	9.039	0.041	0.041	0.000	0.000	0.000	0.000
28	A	285	MET	0	-0.034	-0.015	9.426	0.209	0.209	0.000	0.000	0.000	0.000
29	A	286	VAL	0	-0.013	-0.006	11.368	0.201	0.201	0.000	0.000	0.000	0.000
30	A	287	GLU	-1	-0.909	-0.940	12.816	-0.194	-0.194	0.000	0.000	0.000	0.000
31	A	288	ALA	0	-0.102	-0.042	7.965	-0.083	-0.083	0.000	0.000	0.000	0.000
32	A	289	GLY	0	-0.015	-0.006	9.780	0.291	0.291	0.000	0.000	0.000	0.000
33	A	290	GLU	-1	-0.871	-0.910	8.354	4.143	4.143	0.000	0.000	0.000	0.000
34	A	291	ASP	-1	-0.794	-0.899	10.942	1.180	1.180	0.000	0.000	0.000	0.000
35	A	292	PRO	0	0.036	0.005	13.390	0.080	0.080	0.000	0.000	0.000	0.000
36	A	293	ASN	0	-0.054	-0.034	16.346	-0.136	-0.136	0.000	0.000	0.000	0.000
37	A	294	PHE	0	-0.043	-0.011	8.056	0.194	0.194	0.000	0.000	0.000	0.000
38	A	295	ILE	0	0.006	-0.003	12.940	0.032	0.032	0.000	0.000	0.000	0.000
39	A	296	PHE	0	0.051	0.008	14.678	-0.085	-0.085	0.000	0.000	0.000	0.000
40	A	297	ARG	1	0.957	0.989	13.963	-1.552	-1.552	0.000	0.000	0.000	0.000
41	A	298	ARG	1	0.903	0.945	10.081	-1.779	-1.779	0.000	0.000	0.000	0.000
42	A	299	LEU	0	0.061	0.048	15.783	-0.110	-0.110	0.000	0.000	0.000	0.000
43	A	300	LEU	0	0.025	0.008	18.507	-0.084	-0.084	0.000	0.000	0.000	0.000
44	A	301	ILE	0	-0.012	-0.007	16.569	-0.042	-0.042	0.000	0.000	0.000	0.000
45	A	302	SER	0	-0.011	-0.008	17.578	-0.091	-0.091	0.000	0.000	0.000	0.000
46	A	303	ALA	0	0.019	-0.002	19.498	-0.074	-0.074	0.000	0.000	0.000	0.000
47	A	304	CYS	0	-0.023	-0.019	22.564	-0.061	-0.061	0.000	0.000	0.000	0.000
48	A	305	GLU	-1	-0.906	-0.934	18.377	0.617	0.617	0.000	0.000	0.000	0.000
49	A	306	ASP	-1	-0.796	-0.864	18.590	0.424	0.424	0.000	0.000	0.000	0.000
50	A	307	ILE	0	0.013	0.031	22.048	-0.049	-0.049	0.000	0.000	0.000	0.000
51	A	308	GLY	0	0.042	0.019	25.168	-0.024	-0.024	0.000	0.000	0.000	0.000
52	A	309	LEU	0	-0.005	-0.024	27.194	-0.014	-0.014	0.000	0.000	0.000	0.000
53	A	310	ALA	0	-0.016	0.005	28.400	-0.024	-0.024	0.000	0.000	0.000	0.000
54	A	311	ASP	-1	-0.763	-0.886	29.275	0.180	0.180	0.000	0.000	0.000	0.000
55	A	312	PRO	0	-0.024	-0.001	29.514	0.020	0.020	0.000	0.000	0.000	0.000
56	A	313	ASN	0	-0.032	-0.017	31.142	0.018	0.018	0.000	0.000	0.000	0.000
57	A	314	ALA	0	0.051	0.042	25.985	0.013	0.013	0.000	0.000	0.000	0.000
58	A	315	ILE	0	0.014	-0.010	25.236	0.024	0.024	0.000	0.000	0.000	0.000
59	A	316	VAL	0	-0.008	0.014	27.072	0.026	0.026	0.000	0.000	0.000	0.000
60	A	317	VAL	0	0.025	0.021	27.303	0.013	0.013	0.000	0.000	0.000	0.000
61	A	318	VAL	0	0.054	0.021	22.120	0.009	0.009	0.000	0.000	0.000	0.000
62	A	319	GLN	0	-0.023	-0.020	24.833	0.049	0.049	0.000	0.000	0.000	0.000
63	A	320	SER	0	-0.018	0.004	26.528	0.002	0.002	0.000	0.000	0.000	0.000
64	A	321	CYS	0	-0.083	-0.040	24.535	-0.016	-0.016	0.000	0.000	0.000	0.000
65	A	322	CYS	0	-0.061	-0.031	22.800	0.031	0.031	0.000	0.000	0.000	0.000
66	A	323	ASP	-1	-0.756	-0.849	24.316	0.368	0.368	0.000	0.000	0.000	0.000
67	A	324	ALA	0	-0.054	-0.018	27.594	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	325	PHE	0	0.013	-0.010	20.064	-0.011	-0.011	0.000	0.000	0.000	0.000
69	A	326	ASP	-1	-0.935	-0.952	24.656	0.582	0.582	0.000	0.000	0.000	0.000
70	A	327	ARG	1	0.723	0.842	25.691	-0.342	-0.342	0.000	0.000	0.000	0.000
71	A	328	VAL	0	-0.059	-0.030	27.073	-0.020	-0.020	0.000	0.000	0.000	0.000
72	A	329	GLY	0	0.024	0.027	23.206	-0.011	-0.011	0.000	0.000	0.000	0.000
73	A	330	PHE	0	-0.064	-0.028	17.154	-0.036	-0.036	0.000	0.000	0.000	0.000
74	A	331	PRO	0	0.061	0.019	22.832	0.000	0.000	0.000	0.000	0.000	0.000
75	A	332	GLU	-1	-0.826	-0.938	23.916	0.151	0.151	0.000	0.000	0.000	0.000
76	A	333	GLY	0	0.003	0.008	23.794	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	334	LEU	0	0.004	-0.004	19.515	0.036	0.036	0.000	0.000	0.000	0.000
78	A	335	PHE	0	0.013	-0.003	22.382	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	336	PHE	0	0.007	0.009	24.084	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	337	LEU	0	0.025	0.026	17.022	0.017	0.017	0.000	0.000	0.000	0.000
81	A	338	SER	0	-0.002	0.014	20.705	-0.007	-0.007	0.000	0.000	0.000	0.000
82	A	339	GLN	0	0.018	0.004	22.131	-0.028	-0.028	0.000	0.000	0.000	0.000
83	A	340	ALA	0	0.012	0.005	21.941	-0.010	-0.010	0.000	0.000	0.000	0.000
84	A	341	SER	0	-0.031	-0.047	18.710	0.029	0.029	0.000	0.000	0.000	0.000
85	A	342	LEU	0	0.009	-0.005	20.436	-0.023	-0.023	0.000	0.000	0.000	0.000
86	A	343	TYR	0	-0.067	-0.041	23.072	-0.019	-0.019	0.000	0.000	0.000	0.000
87	A	344	LEU	0	0.002	-0.003	20.133	-0.012	-0.012	0.000	0.000	0.000	0.000
88	A	345	ALA	0	-0.004	0.003	20.653	-0.014	-0.014	0.000	0.000	0.000	0.000
89	A	346	ILE	0	0.022	0.010	22.151	-0.027	-0.027	0.000	0.000	0.000	0.000
90	A	347	SER	0	-0.043	-0.006	25.330	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	348	PRO	0	-0.022	0.001	26.147	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	349	LYS	1	0.813	0.890	21.842	-0.116	-0.116	0.000	0.000	0.000	0.000
93	A	350	SER	0	-0.067	-0.079	25.503	-0.018	-0.018	0.000	0.000	0.000	0.000
94	A	351	ASN	0	0.045	0.034	23.462	0.002	0.002	0.000	0.000	0.000	0.000
95	A	352	SER	0	-0.058	-0.048	25.245	0.025	0.025	0.000	0.000	0.000	0.000
96	A	353	THR	0	0.031	0.001	25.584	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	354	LYS	1	0.905	0.947	19.476	-0.570	-0.570	0.000	0.000	0.000	0.000
98	A	355	SER	0	-0.127	-0.092	25.986	-0.014	-0.014	0.000	0.000	0.000	0.000
99	A	356	ILE	0	0.017	0.022	27.232	-0.016	-0.016	0.000	0.000	0.000	0.000
100	A	357	PHE	0	0.046	0.005	23.036	0.002	0.002	0.000	0.000	0.000	0.000
101	A	358	LYS	1	0.921	0.975	27.767	-0.230	-0.230	0.000	0.000	0.000	0.000
102	A	359	ALA	0	-0.012	-0.003	30.447	-0.011	-0.011	0.000	0.000	0.000	0.000
103	A	360	MET	0	-0.018	-0.003	26.179	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	361	GLU	-1	-0.895	-0.962	27.249	0.328	0.328	0.000	0.000	0.000	0.000
105	A	362	ALA	0	-0.027	-0.008	31.170	-0.009	-0.009	0.000	0.000	0.000	0.000
106	A	363	ILE	0	-0.020	0.006	33.856	-0.006	-0.006	0.000	0.000	0.000	0.000
107	A	364	LYS	1	0.902	0.963	28.087	-0.353	-0.353	0.000	0.000	0.000	0.000
108	A	365	ALA	0	0.041	0.025	34.078	-0.008	-0.008	0.000	0.000	0.000	0.000
109	A	366	THR	0	-0.034	-0.034	36.935	-0.017	-0.017	0.000	0.000	0.000	0.000
110	A	367	ASN	0	-0.061	-0.020	39.524	0.001	0.001	0.000	0.000	0.000	0.000
111	A	368	VAL	0	0.005	-0.003	42.338	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	369	SER	0	-0.003	-0.001	40.532	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	370	LEU	0	-0.001	-0.010	43.201	0.004	0.004	0.000	0.000	0.000	0.000
114	A	371	VAL	0	-0.005	0.010	44.340	-0.003	-0.003	0.000	0.000	0.000	0.000
115	A	372	PRO	0	0.078	0.043	46.394	-0.006	-0.006	0.000	0.000	0.000	0.000
116	A	373	ASN	0	0.039	0.003	49.469	0.008	0.008	0.000	0.000	0.000	0.000
117	A	374	HIS	0	0.012	0.005	49.978	0.001	0.001	0.000	0.000	0.000	0.000
118	A	375	LEU	0	-0.023	-0.016	46.113	0.001	0.001	0.000	0.000	0.000	0.000
119	A	376	LYS	1	0.839	0.935	48.100	-0.124	-0.124	0.000	0.000	0.000	0.000
120	A	377	ASN	0	0.026	-0.002	48.697	-0.004	-0.004	0.000	0.000	0.000	0.000
121	A	378	ASN	0	-0.039	-0.020	50.289	-0.004	-0.004	0.000	0.000	0.000	0.000
122	A	379	ALA	0	0.001	0.030	52.663	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	380	SER	0	0.006	-0.007	54.427	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	381	ASN	0	-0.008	-0.017	56.019	0.000	0.000	0.000	0.000	0.000	0.000
125	A	382	TYR	0	0.019	0.025	48.927	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	383	LEU	0	-0.012	0.003	53.961	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	384	ASN	0	0.036	0.004	52.278	0.005	0.005	0.000	0.000	0.000	0.000
128	A	385	PRO	0	0.030	0.003	49.144	-0.005	-0.005	0.000	0.000	0.000	0.000
129	A	386	HIS	0	-0.017	-0.012	48.561	-0.008	-0.008	0.000	0.000	0.000	0.000
130	A	387	ASN	0	-0.074	-0.015	53.324	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	388	TYR	0	0.031	0.014	54.587	-0.005	-0.005	0.000	0.000	0.000	0.000
132	A	389	GLN	0	0.012	-0.001	56.012	0.002	0.002	0.000	0.000	0.000	0.000
133	A	390	GLY	0	0.030	0.002	51.595	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	391	LYS	1	0.860	0.944	49.282	-0.079	-0.079	0.000	0.000	0.000	0.000
135	A	392	TRP	0	0.018	-0.010	50.843	-0.003	-0.003	0.000	0.000	0.000	0.000
136	A	393	LEU	0	0.036	0.047	52.052	-0.004	-0.004	0.000	0.000	0.000	0.000
137	A	394	GLN	0	-0.031	-0.016	51.790	0.005	0.005	0.000	0.000	0.000	0.000
138	A	395	GLN	0	0.018	-0.006	50.611	-0.002	-0.002	0.000	0.000	0.000	0.000
139	A	396	GLU	-1	-0.879	-0.910	48.648	0.107	0.107	0.000	0.000	0.000	0.000
140	A	397	TYR	0	0.031	0.004	44.364	0.002	0.002	0.000	0.000	0.000	0.000
141	A	398	LEU	0	-0.026	-0.006	40.278	0.010	0.010	0.000	0.000	0.000	0.000
142	A	399	PRO	0	0.044	0.013	42.780	-0.006	-0.006	0.000	0.000	0.000	0.000
143	A	400	THR	0	0.077	0.033	45.708	-0.002	-0.002	0.000	0.000	0.000	0.000
144	A	401	ASP	-1	-0.942	-0.963	44.113	0.132	0.132	0.000	0.000	0.000	0.000
145	A	402	LEU	0	-0.024	0.007	40.016	0.003	0.003	0.000	0.000	0.000	0.000
146	A	403	GLN	0	-0.101	-0.082	43.736	0.002	0.002	0.000	0.000	0.000	0.000
147	A	404	GLY	0	0.025	0.024	44.465	-0.007	-0.007	0.000	0.000	0.000	0.000
148	A	405	ILE	0	-0.016	-0.016	37.775	-0.001	-0.001	0.000	0.000	0.000	0.000
149	A	406	LYS	1	0.910	0.968	36.818	-0.122	-0.122	0.000	0.000	0.000	0.000
150	A	407	PHE	0	0.098	0.036	33.849	0.002	0.002	0.000	0.000	0.000	0.000
151	A	408	TRP	0	-0.045	-0.028	32.076	0.002	0.002	0.000	0.000	0.000	0.000
152	A	409	LYS	1	0.855	0.908	30.892	-0.157	-0.157	0.000	0.000	0.000	0.000
153	A	410	PRO	0	0.013	0.022	31.140	0.012	0.012	0.000	0.000	0.000	0.000
154	A	411	LYS	1	0.878	0.929	27.404	-0.131	-0.131	0.000	0.000	0.000	0.000
155	A	412	ASP	-1	-0.829	-0.896	29.550	0.079	0.079	0.000	0.000	0.000	0.000
156	A	413	SER	0	-0.049	-0.056	31.549	-0.014	-0.014	0.000	0.000	0.000	0.000
157	A	414	GLY	0	0.058	0.039	31.506	0.007	0.007	0.000	0.000	0.000	0.000
158	A	415	TRP	0	0.022	0.004	33.468	-0.008	-0.008	0.000	0.000	0.000	0.000
159	A	416	GLU	-1	-0.735	-0.830	31.229	0.177	0.177	0.000	0.000	0.000	0.000
160	A	417	LYS	1	0.888	0.947	35.126	-0.075	-0.075	0.000	0.000	0.000	0.000
161	A	418	ASN	0	-0.001	-0.008	36.852	-0.008	-0.008	0.000	0.000	0.000	0.000
162	A	419	LYS	1	0.880	0.960	37.969	-0.136	-0.136	0.000	0.000	0.000	0.000
163	A	420	TYR	0	-0.009	0.033	38.077	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:258:ASN)