FMO DATABASE

FMODB ID: QYVVY

Calculation Name: 1AT0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1AT0

Chain ID: A

ChEMBL ID:

UniProt ID: Q02936

Base Structure: X-ray

Registration Date: 2023-06-22

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	145
LigandResidueName
LigandFragmentNumber	0
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1328673.107543
FMO2-HF: Nuclear repulsion	1272992.283138
FMO2-HF: Total energy	-55680.824406
FMO2-MP2: Total energy	-55842.846702

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:CYM)

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

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.
-23.342	-28.732	45.924	-18.729	-21.802	0.1

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.827 / q_NPA : -0.891

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	THR	0	-0.010	-0.021	3.101	2.590	5.297	0.139	-1.558	-1.287	0.001
4	A	261	PRO	0	-0.013	-0.012	5.735	-1.228	-1.228	0.000	0.000	0.000	0.000
5	A	262	GLU	-1	-0.845	-0.917	8.081	24.850	24.850	0.000	0.000	0.000	0.000
6	A	263	SER	0	-0.046	-0.004	7.744	-1.279	-1.279	0.000	0.000	0.000	0.000
7	A	264	THR	0	-0.042	-0.026	9.716	-0.989	-0.989	0.000	0.000	0.000	0.000
8	A	265	ALA	0	0.061	0.039	10.646	0.553	0.553	0.000	0.000	0.000	0.000
9	A	266	LEU	0	-0.027	-0.019	12.260	-1.045	-1.045	0.000	0.000	0.000	0.000
10	A	267	LEU	0	0.046	0.018	15.480	0.190	0.190	0.000	0.000	0.000	0.000
11	A	268	GLU	-1	-0.818	-0.916	17.721	12.541	12.541	0.000	0.000	0.000	0.000
12	A	269	SER	0	-0.045	-0.027	20.633	-0.309	-0.309	0.000	0.000	0.000	0.000
13	A	270	GLY	0	0.014	0.012	21.249	-0.529	-0.529	0.000	0.000	0.000	0.000
14	A	271	VAL	0	-0.050	-0.021	19.385	-0.089	-0.089	0.000	0.000	0.000	0.000
15	A	272	ARG	1	0.967	0.980	16.304	-14.193	-14.193	0.000	0.000	0.000	0.000
16	A	273	LYS	1	0.870	0.927	14.550	-17.507	-17.507	0.000	0.000	0.000	0.000
17	A	274	PRO	0	0.065	0.036	12.380	1.248	1.248	0.000	0.000	0.000	0.000
18	A	275	LEU	0	0.032	0.015	5.724	-0.446	-0.446	0.000	0.000	0.000	0.000
19	A	276	GLY	0	-0.001	-0.011	9.544	0.578	0.578	0.000	0.000	0.000	0.000
20	A	277	GLU	-1	-0.944	-0.962	10.414	15.799	15.799	0.000	0.000	0.000	0.000
21	A	278	LEU	0	-0.070	-0.017	9.465	-1.205	-1.205	0.000	0.000	0.000	0.000
22	A	279	SER	0	-0.029	-0.014	12.745	0.459	0.459	0.000	0.000	0.000	0.000
23	A	280	ILE	0	-0.031	-0.015	13.413	0.094	0.094	0.000	0.000	0.000	0.000
24	A	281	GLY	0	-0.010	-0.003	15.076	-0.918	-0.918	0.000	0.000	0.000	0.000
25	A	282	ASP	-1	-0.852	-0.917	14.843	16.414	16.414	0.000	0.000	0.000	0.000
26	A	283	ARG	1	0.844	0.901	15.683	-12.971	-12.971	0.000	0.000	0.000	0.000
27	A	284	VAL	0	0.001	-0.003	11.676	-0.491	-0.491	0.000	0.000	0.000	0.000
28	A	285	LEU	0	-0.040	-0.019	15.007	-0.342	-0.342	0.000	0.000	0.000	0.000
29	A	286	SER	0	-0.034	-0.039	12.879	1.339	1.339	0.000	0.000	0.000	0.000
30	A	287	MET	0	-0.049	-0.008	14.632	-0.730	-0.730	0.000	0.000	0.000	0.000
31	A	288	THR	0	0.050	0.045	16.220	0.708	0.708	0.000	0.000	0.000	0.000
32	A	289	ALA	0	0.037	0.005	18.497	0.329	0.329	0.000	0.000	0.000	0.000
33	A	290	ASN	0	-0.070	-0.045	19.696	0.408	0.408	0.000	0.000	0.000	0.000
34	A	291	GLY	0	0.027	0.000	18.938	-0.418	-0.418	0.000	0.000	0.000	0.000
35	A	292	GLN	0	-0.003	0.021	20.017	-0.209	-0.209	0.000	0.000	0.000	0.000
36	A	293	ALA	0	0.025	0.022	18.814	0.691	0.691	0.000	0.000	0.000	0.000
37	A	294	VAL	0	0.006	0.001	17.965	-0.737	-0.737	0.000	0.000	0.000	0.000
38	A	295	TYR	0	0.011	0.029	17.699	0.694	0.694	0.000	0.000	0.000	0.000
39	A	296	SER	0	0.026	0.002	15.121	-0.534	-0.534	0.000	0.000	0.000	0.000
40	A	297	GLU	-1	-0.864	-0.910	15.559	15.095	15.095	0.000	0.000	0.000	0.000
41	A	298	VAL	0	0.004	0.003	10.761	0.738	0.738	0.000	0.000	0.000	0.000
42	A	299	ILE	0	-0.001	-0.012	12.932	-1.197	-1.197	0.000	0.000	0.000	0.000
43	A	300	LEU	0	-0.020	-0.015	10.123	-0.847	-0.847	0.000	0.000	0.000	0.000
44	A	301	PHE	0	-0.007	-0.009	7.152	0.890	0.890	0.000	0.000	0.000	0.000
45	A	302	MET	0	-0.038	-0.021	6.164	-3.318	-3.318	0.000	0.000	0.000	0.000
46	A	303	ASP	-1	-0.849	-0.927	3.099	52.771	53.329	0.034	-0.109	-0.483	0.000
47	A	304	ARG	1	0.884	0.939	5.020	-25.554	-25.506	-0.001	-0.002	-0.045	0.000
48	A	305	ASN	0	0.026	0.030	6.266	-6.782	-6.782	0.000	0.000	0.000	0.000
49	A	306	LEU	0	0.007	-0.006	7.302	2.979	2.979	0.000	0.000	0.000	0.000
50	A	307	GLU	-1	-0.802	-0.891	9.267	20.397	20.397	0.000	0.000	0.000	0.000
51	A	308	GLN	0	-0.006	0.006	5.304	-7.743	-7.676	-0.001	-0.015	-0.051	0.000
52	A	309	MET	0	-0.004	0.012	7.611	3.195	3.195	0.000	0.000	0.000	0.000
53	A	310	GLN	0	-0.038	-0.011	3.744	-5.951	-4.825	0.175	-0.642	-0.657	0.009
54	A	311	ASN	0	0.007	0.009	7.245	-4.701	-4.701	0.000	0.000	0.000	0.000
55	A	312	PHE	0	0.030	-0.001	3.247	6.096	6.849	0.032	-0.205	-0.579	0.001
56	A	313	VAL	0	0.018	0.014	7.147	-4.593	-4.593	0.000	0.000	0.000	0.000
57	A	314	GLN	0	-0.034	-0.027	8.517	0.250	0.250	0.000	0.000	0.000	0.000
58	A	315	LEU	0	0.036	0.024	10.396	-1.841	-1.841	0.000	0.000	0.000	0.000
59	A	316	HIS	0	0.036	0.019	12.782	-0.341	-0.341	0.000	0.000	0.000	0.000
60	A	317	THR	0	0.034	0.000	15.749	-0.302	-0.302	0.000	0.000	0.000	0.000
61	A	318	ASP	-1	-0.837	-0.929	18.193	12.516	12.516	0.000	0.000	0.000	0.000
62	A	319	GLY	0	-0.004	0.012	21.018	-0.507	-0.507	0.000	0.000	0.000	0.000
63	A	320	GLY	0	-0.037	-0.015	20.491	-0.304	-0.304	0.000	0.000	0.000	0.000
64	A	321	ALA	0	-0.034	0.004	15.828	0.379	0.379	0.000	0.000	0.000	0.000
65	A	322	VAL	0	0.027	-0.010	12.874	-0.020	-0.020	0.000	0.000	0.000	0.000
66	A	323	LEU	0	-0.019	0.008	7.845	0.562	0.562	0.000	0.000	0.000	0.000
67	A	324	THR	0	-0.010	-0.005	7.525	-1.005	-1.005	0.000	0.000	0.000	0.000
68	A	325	VAL	0	0.037	0.016	4.217	1.381	1.514	-0.001	-0.065	-0.067	0.000
69	A	326	THR	0	-0.031	-0.037	1.862	-21.243	-37.493	36.767	-11.051	-9.466	0.087
70	A	327	PRO	0	-0.015	-0.025	3.795	-4.262	-3.768	0.004	-0.299	-0.199	0.002
71	A	328	ALA	0	0.006	-0.001	5.726	-4.329	-4.329	0.000	0.000	0.000	0.000
72	A	329	HIS	0	0.026	0.014	2.744	7.469	7.659	3.265	-1.076	-2.380	-0.005
73	A	330	LEU	0	-0.072	-0.020	4.696	-5.747	-5.720	-0.001	-0.006	-0.020	0.000
74	A	331	VAL	0	0.027	-0.002	7.504	1.085	1.085	0.000	0.000	0.000	0.000
75	A	332	SER	0	0.000	-0.008	9.834	-0.946	-0.946	0.000	0.000	0.000	0.000
76	A	333	VAL	0	0.008	-0.005	13.508	-0.092	-0.092	0.000	0.000	0.000	0.000
77	A	334	TRP	0	-0.022	-0.015	16.072	-0.398	-0.398	0.000	0.000	0.000	0.000
78	A	335	GLN	0	-0.030	-0.011	19.675	0.399	0.399	0.000	0.000	0.000	0.000
79	A	336	PRO	0	-0.003	-0.012	22.518	-0.346	-0.346	0.000	0.000	0.000	0.000
80	A	337	GLU	-1	-0.821	-0.884	25.409	11.419	11.419	0.000	0.000	0.000	0.000
81	A	338	SER	0	-0.038	-0.053	25.595	-0.188	-0.188	0.000	0.000	0.000	0.000
82	A	339	GLN	0	-0.080	-0.038	25.607	-0.257	-0.257	0.000	0.000	0.000	0.000
83	A	340	LYS	1	0.914	0.971	20.973	-13.470	-13.470	0.000	0.000	0.000	0.000
84	A	341	LEU	0	0.018	0.020	17.286	0.280	0.280	0.000	0.000	0.000	0.000
85	A	342	THR	0	-0.068	-0.044	17.436	-0.116	-0.116	0.000	0.000	0.000	0.000
86	A	343	PHE	0	0.038	0.017	11.832	0.364	0.364	0.000	0.000	0.000	0.000
87	A	344	VAL	0	0.003	0.005	12.258	-0.691	-0.691	0.000	0.000	0.000	0.000
88	A	345	PHE	0	-0.004	-0.003	8.233	0.755	0.755	0.000	0.000	0.000	0.000
89	A	346	ALA	0	0.068	0.027	6.645	-2.378	-2.378	0.000	0.000	0.000	0.000
90	A	347	ASP	-1	-0.864	-0.926	8.592	24.874	24.874	0.000	0.000	0.000	0.000
91	A	348	ARG	1	0.803	0.887	10.689	-25.427	-25.427	0.000	0.000	0.000	0.000
92	A	349	ILE	0	-0.048	0.002	10.918	-1.453	-1.453	0.000	0.000	0.000	0.000
93	A	350	GLU	-1	-0.932	-0.967	13.992	14.656	14.656	0.000	0.000	0.000	0.000
94	A	351	GLU	-1	-0.877	-0.962	17.073	14.018	14.018	0.000	0.000	0.000	0.000
95	A	352	LYS	1	0.871	0.928	19.494	-12.196	-12.196	0.000	0.000	0.000	0.000
96	A	353	ASN	0	0.001	0.025	17.037	0.337	0.337	0.000	0.000	0.000	0.000
97	A	354	GLN	0	0.021	-0.004	18.963	-0.117	-0.117	0.000	0.000	0.000	0.000
98	A	355	VAL	0	0.053	0.041	13.503	0.470	0.470	0.000	0.000	0.000	0.000
99	A	356	LEU	0	-0.020	-0.010	15.687	-0.876	-0.876	0.000	0.000	0.000	0.000
100	A	357	VAL	0	0.008	-0.010	15.741	1.201	1.201	0.000	0.000	0.000	0.000
101	A	358	ARG	1	0.875	0.958	17.582	-14.065	-14.065	0.000	0.000	0.000	0.000
102	A	359	ASP	-1	-0.816	-0.883	19.410	11.411	11.411	0.000	0.000	0.000	0.000
103	A	360	VAL	0	-0.057	-0.043	22.637	0.028	0.028	0.000	0.000	0.000	0.000
104	A	361	GLU	-1	-0.941	-0.968	24.232	9.528	9.528	0.000	0.000	0.000	0.000
105	A	362	THR	0	-0.016	-0.043	26.443	-0.055	-0.055	0.000	0.000	0.000	0.000
106	A	363	GLY	0	-0.039	-0.021	22.877	-0.031	-0.031	0.000	0.000	0.000	0.000
107	A	364	GLU	-1	-0.871	-0.913	21.997	11.443	11.443	0.000	0.000	0.000	0.000
108	A	365	LEU	0	-0.044	-0.021	16.711	0.328	0.328	0.000	0.000	0.000	0.000
109	A	366	ARG	1	0.873	0.914	20.448	-11.471	-11.471	0.000	0.000	0.000	0.000
110	A	367	PRO	0	-0.013	0.000	20.048	0.569	0.569	0.000	0.000	0.000	0.000
111	A	368	GLN	0	0.059	0.047	19.239	-0.035	-0.035	0.000	0.000	0.000	0.000
112	A	369	ARG	1	0.875	0.922	19.239	-11.338	-11.338	0.000	0.000	0.000	0.000
113	A	370	VAL	0	0.024	0.023	15.472	0.112	0.112	0.000	0.000	0.000	0.000
114	A	371	VAL	0	-0.060	-0.047	18.144	-0.623	-0.623	0.000	0.000	0.000	0.000
115	A	372	LYS	1	0.901	0.954	17.654	-16.550	-16.550	0.000	0.000	0.000	0.000
116	A	373	VAL	0	-0.003	0.017	13.212	0.841	0.841	0.000	0.000	0.000	0.000
117	A	374	GLY	0	-0.040	-0.018	14.077	-0.905	-0.905	0.000	0.000	0.000	0.000
118	A	375	SER	0	-0.058	-0.043	11.353	1.259	1.259	0.000	0.000	0.000	0.000
119	A	376	VAL	0	0.015	0.014	10.383	-1.814	-1.814	0.000	0.000	0.000	0.000
120	A	377	ARG	1	0.884	0.945	9.582	-26.347	-26.347	0.000	0.000	0.000	0.000
121	A	378	SER	0	0.007	0.010	8.293	-2.174	-2.174	0.000	0.000	0.000	0.000
122	A	379	LYS	1	0.843	0.894	8.966	-20.131	-20.131	0.000	0.000	0.000	0.000
123	A	380	GLY	0	-0.029	-0.016	7.067	-2.184	-2.184	0.000	0.000	0.000	0.000
124	A	381	VAL	0	-0.001	-0.006	2.306	-0.542	0.497	2.195	-1.018	-2.216	0.008
125	A	382	VAL	0	-0.025	-0.021	2.694	-8.826	-8.056	0.262	-0.197	-0.835	0.000
126	A	383	ALA	0	0.055	0.027	2.269	2.622	4.557	2.136	-1.858	-2.213	-0.009
127	A	384	PRO	0	-0.028	-0.002	3.467	-5.168	-5.041	0.033	0.044	-0.203	0.000
128	A	385	LEU	0	0.054	0.008	6.900	1.219	1.219	0.000	0.000	0.000	0.000
129	A	386	THR	0	0.010	-0.020	9.294	-1.928	-1.928	0.000	0.000	0.000	0.000
130	A	387	ARG	1	0.824	0.889	12.366	-14.617	-14.617	0.000	0.000	0.000	0.000
131	A	388	GLU	-1	-0.914	-0.958	14.941	15.073	15.073	0.000	0.000	0.000	0.000
132	A	389	GLY	0	-0.007	0.022	12.011	-0.243	-0.243	0.000	0.000	0.000	0.000
133	A	390	THR	0	-0.007	-0.030	10.717	1.993	1.993	0.000	0.000	0.000	0.000
134	A	391	ILE	0	0.007	0.002	7.280	-0.701	-0.701	0.000	0.000	0.000	0.000
135	A	392	VAL	0	-0.024	0.004	10.228	0.728	0.728	0.000	0.000	0.000	0.000
136	A	393	VAL	0	-0.006	0.005	7.020	-0.504	-0.504	0.000	0.000	0.000	0.000
137	A	394	ASN	0	-0.009	-0.005	10.233	-0.250	-0.250	0.000	0.000	0.000	0.000
138	A	395	SER	0	-0.021	-0.021	12.962	-0.660	-0.660	0.000	0.000	0.000	0.000
139	A	396	VAL	0	0.027	0.025	11.775	-1.167	-1.167	0.000	0.000	0.000	0.000
140	A	397	ALA	0	-0.022	-0.009	11.631	1.378	1.378	0.000	0.000	0.000	0.000
141	A	398	ALA	0	0.000	0.004	7.844	0.238	0.238	0.000	0.000	0.000	0.000
142	A	399	SER	0	0.041	0.023	8.846	-1.399	-1.399	0.000	0.000	0.000	0.000
143	A	400	CYS	0	-0.038	0.004	6.622	1.739	1.739	0.000	0.000	0.000	0.000
144	A	401	TYR	0	-0.054	-0.019	5.732	5.519	5.519	0.000	0.000	0.000	0.000
145	A	402	ALA	0	0.061	0.043	3.000	-3.996	-3.110	0.886	-0.672	-1.101	0.006

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