FMO DATABASE

FMODB ID: VQJN1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1426636.802671
FMO2-HF: Nuclear repulsion	1362485.705341
FMO2-HF: Total energy	-64151.09733
FMO2-MP2: Total energy	-64339.011872

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.
-19.836	-11.414	1.494	-4.829	-5.086	-0.008

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 : 0.064 / q_NPA : 0.027

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	-0.023	2.871	-10.402	-5.944	0.345	-2.256	-2.546	0.020
4	A	261	ASP	-1	-0.871	-0.942	2.692	-9.848	-6.030	1.149	-2.539	-2.428	-0.028
5	A	262	VAL	0	0.009	0.013	4.141	-0.362	-0.216	0.000	-0.034	-0.112	0.000
6	A	263	ILE	0	0.024	0.014	6.628	-0.082	-0.082	0.000	0.000	0.000	0.000
7	A	264	SER	0	-0.032	-0.001	7.230	-0.339	-0.339	0.000	0.000	0.000	0.000
8	A	265	ALA	0	0.006	0.009	8.248	-0.149	-0.149	0.000	0.000	0.000	0.000
9	A	266	PHE	0	0.050	0.021	10.177	-0.010	-0.010	0.000	0.000	0.000	0.000
10	A	267	ILE	0	0.001	0.005	11.974	-0.041	-0.041	0.000	0.000	0.000	0.000
11	A	268	LYS	1	0.826	0.896	10.178	-0.541	-0.541	0.000	0.000	0.000	0.000
12	A	269	SER	0	0.010	0.008	13.954	-0.100	-0.100	0.000	0.000	0.000	0.000
13	A	270	ILE	0	0.035	0.026	16.158	-0.018	-0.018	0.000	0.000	0.000	0.000
14	A	271	ARG	1	0.786	0.861	15.115	-0.535	-0.535	0.000	0.000	0.000	0.000
15	A	272	GLY	0	-0.032	-0.016	18.456	-0.019	-0.019	0.000	0.000	0.000	0.000
16	A	273	SER	0	-0.062	-0.026	20.167	-0.021	-0.021	0.000	0.000	0.000	0.000
17	A	274	ASP	-1	-0.821	-0.897	19.173	-0.154	-0.154	0.000	0.000	0.000	0.000
18	A	275	PRO	0	0.010	-0.013	19.737	0.019	0.019	0.000	0.000	0.000	0.000
19	A	276	ASP	-1	-0.874	-0.931	20.728	-0.080	-0.080	0.000	0.000	0.000	0.000
20	A	277	ALA	0	0.000	0.000	16.018	-0.028	-0.028	0.000	0.000	0.000	0.000
21	A	278	THR	0	-0.057	-0.033	15.773	0.029	0.029	0.000	0.000	0.000	0.000
22	A	279	LEU	0	-0.001	0.001	16.110	0.063	0.063	0.000	0.000	0.000	0.000
23	A	280	TYR	0	-0.003	0.023	12.468	0.028	0.028	0.000	0.000	0.000	0.000
24	A	281	TRP	0	-0.013	-0.027	9.389	-0.149	-0.149	0.000	0.000	0.000	0.000
25	A	282	LEU	0	-0.030	-0.014	12.412	0.112	0.112	0.000	0.000	0.000	0.000
26	A	283	ALA	0	0.017	-0.003	14.398	0.100	0.100	0.000	0.000	0.000	0.000
27	A	284	ASN	0	-0.025	-0.008	8.784	0.108	0.108	0.000	0.000	0.000	0.000
28	A	285	MET	0	-0.029	-0.018	9.338	0.251	0.251	0.000	0.000	0.000	0.000
29	A	286	VAL	0	0.009	0.006	11.305	0.192	0.192	0.000	0.000	0.000	0.000
30	A	287	GLU	-1	-0.923	-0.949	13.042	-0.144	-0.144	0.000	0.000	0.000	0.000
31	A	288	ALA	0	-0.105	-0.044	8.121	-0.094	-0.094	0.000	0.000	0.000	0.000
32	A	289	GLY	0	-0.021	-0.009	9.870	0.277	0.277	0.000	0.000	0.000	0.000
33	A	290	GLU	-1	-0.859	-0.890	8.385	4.365	4.365	0.000	0.000	0.000	0.000
34	A	291	ASP	-1	-0.867	-0.951	10.815	1.258	1.258	0.000	0.000	0.000	0.000
35	A	292	PRO	0	0.044	0.003	13.238	0.091	0.091	0.000	0.000	0.000	0.000
36	A	293	ASN	0	0.019	0.006	16.198	-0.122	-0.122	0.000	0.000	0.000	0.000
37	A	294	PHE	0	-0.075	-0.022	8.052	0.183	0.183	0.000	0.000	0.000	0.000
38	A	295	ILE	0	0.016	-0.002	12.937	0.035	0.035	0.000	0.000	0.000	0.000
39	A	296	PHE	0	0.055	0.012	14.678	-0.087	-0.087	0.000	0.000	0.000	0.000
40	A	297	ARG	1	0.955	0.990	13.811	-1.660	-1.660	0.000	0.000	0.000	0.000
41	A	298	ARG	1	0.912	0.944	10.029	-2.016	-2.016	0.000	0.000	0.000	0.000
42	A	299	LEU	0	0.064	0.047	15.783	-0.115	-0.115	0.000	0.000	0.000	0.000
43	A	300	LEU	0	0.039	0.018	18.564	-0.086	-0.086	0.000	0.000	0.000	0.000
44	A	301	ILE	0	-0.042	-0.016	16.629	-0.045	-0.045	0.000	0.000	0.000	0.000
45	A	302	SER	0	0.022	0.033	17.669	-0.094	-0.094	0.000	0.000	0.000	0.000
46	A	303	ALA	0	0.034	0.004	19.558	-0.078	-0.078	0.000	0.000	0.000	0.000
47	A	304	CYS	0	-0.040	-0.031	22.623	-0.064	-0.064	0.000	0.000	0.000	0.000
48	A	305	GLU	-1	-0.908	-0.953	18.512	0.693	0.693	0.000	0.000	0.000	0.000
49	A	306	ASP	-1	-0.857	-0.919	18.543	0.495	0.495	0.000	0.000	0.000	0.000
50	A	307	ILE	0	0.016	0.036	22.101	-0.053	-0.053	0.000	0.000	0.000	0.000
51	A	308	GLY	0	0.041	0.019	25.219	-0.028	-0.028	0.000	0.000	0.000	0.000
52	A	309	LEU	0	-0.008	-0.022	27.253	-0.016	-0.016	0.000	0.000	0.000	0.000
53	A	310	ALA	0	0.005	0.011	28.497	-0.026	-0.026	0.000	0.000	0.000	0.000
54	A	311	ASP	-1	-0.790	-0.877	29.364	0.211	0.211	0.000	0.000	0.000	0.000
55	A	312	PRO	0	-0.018	-0.003	29.568	0.022	0.022	0.000	0.000	0.000	0.000
56	A	313	ASN	0	-0.003	-0.004	31.202	0.021	0.021	0.000	0.000	0.000	0.000
57	A	314	ALA	0	0.062	0.048	26.004	0.014	0.014	0.000	0.000	0.000	0.000
58	A	315	ILE	0	0.020	-0.007	25.205	0.027	0.027	0.000	0.000	0.000	0.000
59	A	316	VAL	0	-0.020	0.004	27.133	0.027	0.027	0.000	0.000	0.000	0.000
60	A	317	VAL	0	0.018	0.010	27.258	0.012	0.012	0.000	0.000	0.000	0.000
61	A	318	VAL	0	0.044	0.017	22.299	0.009	0.009	0.000	0.000	0.000	0.000
62	A	319	GLN	0	-0.011	-0.014	24.833	0.057	0.057	0.000	0.000	0.000	0.000
63	A	320	SER	0	-0.017	0.010	26.528	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	321	CYS	0	-0.082	-0.033	24.511	-0.017	-0.017	0.000	0.000	0.000	0.000
65	A	322	CYS	0	-0.034	-0.015	22.937	0.032	0.032	0.000	0.000	0.000	0.000
66	A	323	ASP	-1	-0.859	-0.920	24.316	0.460	0.460	0.000	0.000	0.000	0.000
67	A	324	ALA	0	-0.106	-0.053	27.549	-0.015	-0.015	0.000	0.000	0.000	0.000
68	A	325	PHE	0	0.024	-0.003	20.113	-0.016	-0.016	0.000	0.000	0.000	0.000
69	A	326	ASP	-1	-0.919	-0.946	24.324	0.618	0.618	0.000	0.000	0.000	0.000
70	A	327	ARG	1	0.830	0.923	25.536	-0.379	-0.379	0.000	0.000	0.000	0.000
71	A	328	VAL	0	-0.050	-0.026	26.920	-0.021	-0.021	0.000	0.000	0.000	0.000
72	A	329	GLY	0	0.029	0.029	23.070	-0.013	-0.013	0.000	0.000	0.000	0.000
73	A	330	PHE	0	-0.053	-0.023	17.317	-0.036	-0.036	0.000	0.000	0.000	0.000
74	A	331	PRO	0	0.061	0.016	22.784	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	332	GLU	-1	-0.833	-0.943	23.904	0.182	0.182	0.000	0.000	0.000	0.000
76	A	333	GLY	0	-0.007	0.002	23.676	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	334	LEU	0	0.005	0.000	19.503	0.042	0.042	0.000	0.000	0.000	0.000
78	A	335	PHE	0	0.006	-0.009	22.278	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	336	PHE	0	0.004	0.014	23.998	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	337	LEU	0	0.036	0.022	17.437	0.018	0.018	0.000	0.000	0.000	0.000
81	A	338	SER	0	0.000	0.024	20.705	0.004	0.004	0.000	0.000	0.000	0.000
82	A	339	GLN	0	0.030	0.013	22.131	-0.029	-0.029	0.000	0.000	0.000	0.000
83	A	340	ALA	0	0.009	-0.002	21.898	-0.011	-0.011	0.000	0.000	0.000	0.000
84	A	341	SER	0	-0.036	-0.056	18.644	0.035	0.035	0.000	0.000	0.000	0.000
85	A	342	LEU	0	-0.001	-0.008	20.467	-0.024	-0.024	0.000	0.000	0.000	0.000
86	A	343	TYR	0	-0.090	-0.071	23.096	-0.018	-0.018	0.000	0.000	0.000	0.000
87	A	344	LEU	0	0.007	0.005	20.092	-0.016	-0.016	0.000	0.000	0.000	0.000
88	A	345	ALA	0	-0.027	-0.005	20.657	-0.015	-0.015	0.000	0.000	0.000	0.000
89	A	346	ILE	0	0.018	0.002	22.177	-0.029	-0.029	0.000	0.000	0.000	0.000
90	A	347	SER	0	-0.041	-0.013	25.357	-0.011	-0.011	0.000	0.000	0.000	0.000
91	A	348	PRO	0	-0.030	-0.006	26.180	-0.006	-0.006	0.000	0.000	0.000	0.000
92	A	349	LYS	1	0.842	0.918	21.875	-0.182	-0.182	0.000	0.000	0.000	0.000
93	A	350	SER	0	-0.079	-0.072	25.542	-0.018	-0.018	0.000	0.000	0.000	0.000
94	A	351	ASN	0	0.058	0.041	23.572	0.001	0.001	0.000	0.000	0.000	0.000
95	A	352	SER	0	-0.059	-0.054	25.300	0.023	0.023	0.000	0.000	0.000	0.000
96	A	353	THR	0	0.040	0.018	25.734	-0.006	-0.006	0.000	0.000	0.000	0.000
97	A	354	LYS	1	0.908	0.955	19.286	-0.621	-0.621	0.000	0.000	0.000	0.000
98	A	355	SER	0	-0.149	-0.116	26.053	-0.017	-0.017	0.000	0.000	0.000	0.000
99	A	356	ILE	0	0.022	0.027	27.103	-0.019	-0.019	0.000	0.000	0.000	0.000
100	A	357	PHE	0	0.043	0.000	23.255	0.002	0.002	0.000	0.000	0.000	0.000
101	A	358	LYS	1	0.921	0.978	27.712	-0.260	-0.260	0.000	0.000	0.000	0.000
102	A	359	ALA	0	-0.010	-0.004	30.392	-0.013	-0.013	0.000	0.000	0.000	0.000
103	A	360	MET	0	-0.028	-0.012	26.403	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	361	GLU	-1	-0.915	-0.956	27.316	0.342	0.342	0.000	0.000	0.000	0.000
105	A	362	ALA	0	-0.031	-0.017	31.118	-0.011	-0.011	0.000	0.000	0.000	0.000
106	A	363	ILE	0	-0.021	0.007	33.780	-0.007	-0.007	0.000	0.000	0.000	0.000
107	A	364	LYS	1	0.948	0.972	27.931	-0.379	-0.379	0.000	0.000	0.000	0.000
108	A	365	ALA	0	0.027	0.018	34.029	-0.008	-0.008	0.000	0.000	0.000	0.000
109	A	366	THR	0	-0.027	-0.019	36.811	-0.018	-0.018	0.000	0.000	0.000	0.000
110	A	367	ASN	0	-0.077	-0.033	39.405	0.000	0.000	0.000	0.000	0.000	0.000
111	A	368	VAL	0	0.013	0.001	42.329	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	369	SER	0	0.002	0.001	40.430	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	370	LEU	0	0.000	-0.014	43.139	0.004	0.004	0.000	0.000	0.000	0.000
114	A	371	VAL	0	-0.016	0.007	44.302	-0.003	-0.003	0.000	0.000	0.000	0.000
115	A	372	PRO	0	0.061	0.037	46.401	-0.006	-0.006	0.000	0.000	0.000	0.000
116	A	373	ASN	0	0.011	-0.016	49.415	0.007	0.007	0.000	0.000	0.000	0.000
117	A	374	HIS	0	-0.003	-0.003	50.166	0.001	0.001	0.000	0.000	0.000	0.000
118	A	375	LEU	0	-0.001	-0.004	46.054	0.002	0.002	0.000	0.000	0.000	0.000
119	A	376	LYS	1	0.912	0.968	48.062	-0.133	-0.133	0.000	0.000	0.000	0.000
120	A	377	ASN	0	0.024	0.000	48.704	-0.005	-0.005	0.000	0.000	0.000	0.000
121	A	378	ASN	0	-0.040	-0.017	50.289	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	379	ALA	0	-0.012	0.024	52.642	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	380	SER	0	-0.001	-0.011	54.407	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	381	ASN	0	0.000	-0.009	56.246	0.000	0.000	0.000	0.000	0.000	0.000
125	A	382	TYR	0	0.014	0.017	49.258	0.000	0.000	0.000	0.000	0.000	0.000
126	A	383	LEU	0	-0.018	0.003	53.969	-0.004	-0.004	0.000	0.000	0.000	0.000
127	A	384	ASN	0	0.039	0.006	51.813	0.004	0.004	0.000	0.000	0.000	0.000
128	A	385	PRO	0	0.031	0.005	49.149	-0.005	-0.005	0.000	0.000	0.000	0.000
129	A	386	HIS	0	-0.006	-0.006	48.807	-0.008	-0.008	0.000	0.000	0.000	0.000
130	A	387	ASN	0	-0.068	-0.008	53.324	-0.003	-0.003	0.000	0.000	0.000	0.000
131	A	388	TYR	0	0.102	0.053	55.047	-0.005	-0.005	0.000	0.000	0.000	0.000
132	A	389	GLN	0	0.006	0.008	56.302	0.002	0.002	0.000	0.000	0.000	0.000
133	A	390	GLY	0	-0.026	-0.036	52.440	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	391	LYS	1	0.846	0.917	50.090	-0.089	-0.089	0.000	0.000	0.000	0.000
135	A	392	TRP	0	0.008	0.002	51.149	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	393	LEU	0	0.025	0.041	51.997	-0.004	-0.004	0.000	0.000	0.000	0.000
137	A	394	GLN	0	-0.023	-0.019	51.856	0.007	0.007	0.000	0.000	0.000	0.000
138	A	395	GLN	0	0.030	0.004	50.427	-0.003	-0.003	0.000	0.000	0.000	0.000
139	A	396	GLU	-1	-0.923	-0.945	48.583	0.116	0.116	0.000	0.000	0.000	0.000
140	A	397	TYR	0	0.028	-0.002	44.289	0.003	0.003	0.000	0.000	0.000	0.000
141	A	398	LEU	0	-0.030	-0.012	40.117	0.010	0.010	0.000	0.000	0.000	0.000
142	A	399	PRO	0	0.037	0.012	42.649	-0.006	-0.006	0.000	0.000	0.000	0.000
143	A	400	THR	0	0.076	0.034	45.654	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	401	ASP	-1	-0.932	-0.952	44.419	0.142	0.142	0.000	0.000	0.000	0.000
145	A	402	LEU	0	-0.012	0.004	40.051	0.004	0.004	0.000	0.000	0.000	0.000
146	A	403	GLN	0	-0.070	-0.051	43.681	0.003	0.003	0.000	0.000	0.000	0.000
147	A	404	GLY	0	0.011	0.016	44.494	-0.008	-0.008	0.000	0.000	0.000	0.000
148	A	405	ILE	0	-0.014	-0.013	37.945	0.000	0.000	0.000	0.000	0.000	0.000
149	A	406	LYS	1	0.909	0.978	36.865	-0.141	-0.141	0.000	0.000	0.000	0.000
150	A	407	PHE	0	0.077	0.019	33.814	0.003	0.003	0.000	0.000	0.000	0.000
151	A	408	TRP	0	-0.036	-0.025	32.203	0.002	0.002	0.000	0.000	0.000	0.000
152	A	409	LYS	1	0.877	0.931	30.856	-0.181	-0.181	0.000	0.000	0.000	0.000
153	A	410	PRO	0	0.008	0.017	31.193	0.014	0.014	0.000	0.000	0.000	0.000
154	A	411	LYS	1	0.909	0.957	27.104	-0.187	-0.187	0.000	0.000	0.000	0.000
155	A	412	ASP	-1	-0.869	-0.929	29.653	0.111	0.111	0.000	0.000	0.000	0.000
156	A	413	SER	0	-0.050	-0.053	31.502	-0.016	-0.016	0.000	0.000	0.000	0.000
157	A	414	GLY	0	0.041	0.031	31.465	0.010	0.010	0.000	0.000	0.000	0.000
158	A	415	TRP	0	-0.017	-0.010	33.515	-0.010	-0.010	0.000	0.000	0.000	0.000
159	A	416	GLU	-1	-0.727	-0.843	31.201	0.209	0.209	0.000	0.000	0.000	0.000
160	A	417	LYS	1	0.950	0.983	35.179	-0.098	-0.098	0.000	0.000	0.000	0.000
161	A	418	ASN	0	-0.022	-0.018	36.899	-0.012	-0.012	0.000	0.000	0.000	0.000
162	A	419	LYS	1	0.882	0.954	38.004	-0.154	-0.154	0.000	0.000	0.000	0.000
163	A	420	TYR	0	0.001	0.026	38.109	-0.002	-0.002	0.000	0.000	0.000	0.000

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