FMO DATABASE

FMODB ID: R9888

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1328080.078403
FMO2-HF: Nuclear repulsion	1272399.705934
FMO2-HF: Total energy	-55680.372469
FMO2-MP2: Total energy	-55842.408023

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.
-27.821	-32.738	47.108	-20.377	-21.812	0.046

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 : -0.887 / q_NPA : -0.896

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	0.022	0.020	3.180	3.552	6.141	0.129	-1.490	-1.228	0.003
4	A	261	PRO	0	-0.017	-0.013	5.903	-0.508	-0.508	0.000	0.000	0.000	0.000
5	A	262	GLU	-1	-0.871	-0.952	7.968	24.199	24.199	0.000	0.000	0.000	0.000
6	A	263	SER	0	-0.023	0.004	7.699	-1.504	-1.504	0.000	0.000	0.000	0.000
7	A	264	THR	0	-0.056	-0.026	9.689	-0.848	-0.848	0.000	0.000	0.000	0.000
8	A	265	ALA	0	0.061	0.043	10.717	0.427	0.427	0.000	0.000	0.000	0.000
9	A	266	LEU	0	-0.028	-0.020	12.263	-1.091	-1.091	0.000	0.000	0.000	0.000
10	A	267	LEU	0	0.034	0.006	15.351	0.220	0.220	0.000	0.000	0.000	0.000
11	A	268	GLU	-1	-0.808	-0.901	17.723	12.576	12.576	0.000	0.000	0.000	0.000
12	A	269	SER	0	-0.056	-0.028	20.639	-0.348	-0.348	0.000	0.000	0.000	0.000
13	A	270	GLY	0	0.029	0.018	21.258	-0.557	-0.557	0.000	0.000	0.000	0.000
14	A	271	VAL	0	-0.052	-0.017	19.393	-0.119	-0.119	0.000	0.000	0.000	0.000
15	A	272	ARG	1	0.969	0.975	16.320	-14.072	-14.072	0.000	0.000	0.000	0.000
16	A	273	LYS	1	0.884	0.949	14.376	-18.293	-18.293	0.000	0.000	0.000	0.000
17	A	274	PRO	0	0.069	0.034	12.144	1.257	1.257	0.000	0.000	0.000	0.000
18	A	275	LEU	0	0.039	0.016	5.850	-0.379	-0.379	0.000	0.000	0.000	0.000
19	A	276	GLY	0	0.000	-0.008	9.273	0.990	0.990	0.000	0.000	0.000	0.000
20	A	277	GLU	-1	-0.986	-1.001	10.049	16.514	16.514	0.000	0.000	0.000	0.000
21	A	278	LEU	0	-0.056	-0.011	9.554	-1.425	-1.425	0.000	0.000	0.000	0.000
22	A	279	SER	0	-0.032	-0.013	12.607	0.661	0.661	0.000	0.000	0.000	0.000
23	A	280	ILE	0	-0.029	-0.013	13.538	0.096	0.096	0.000	0.000	0.000	0.000
24	A	281	GLY	0	-0.005	0.001	15.063	-1.010	-1.010	0.000	0.000	0.000	0.000
25	A	282	ASP	-1	-0.856	-0.923	14.834	17.194	17.194	0.000	0.000	0.000	0.000
26	A	283	ARG	1	0.857	0.906	15.682	-13.145	-13.145	0.000	0.000	0.000	0.000
27	A	284	VAL	0	0.008	0.002	11.729	-0.571	-0.571	0.000	0.000	0.000	0.000
28	A	285	LEU	0	-0.036	-0.021	15.014	-0.389	-0.389	0.000	0.000	0.000	0.000
29	A	286	SER	0	-0.048	-0.022	13.529	1.902	1.902	0.000	0.000	0.000	0.000
30	A	287	MET	0	-0.039	-0.002	14.087	-0.793	-0.793	0.000	0.000	0.000	0.000
31	A	288	THR	0	0.043	0.044	15.817	0.688	0.688	0.000	0.000	0.000	0.000
32	A	289	ALA	0	0.051	0.010	17.798	0.262	0.262	0.000	0.000	0.000	0.000
33	A	290	ASN	0	-0.072	-0.035	18.858	0.398	0.398	0.000	0.000	0.000	0.000
34	A	291	GLY	0	0.032	0.000	18.149	-0.418	-0.418	0.000	0.000	0.000	0.000
35	A	292	GLN	0	0.005	0.014	19.233	-0.039	-0.039	0.000	0.000	0.000	0.000
36	A	293	ALA	0	0.031	0.022	18.784	0.704	0.704	0.000	0.000	0.000	0.000
37	A	294	VAL	0	0.011	0.005	18.038	-0.718	-0.718	0.000	0.000	0.000	0.000
38	A	295	TYR	0	0.017	0.023	17.717	0.631	0.631	0.000	0.000	0.000	0.000
39	A	296	SER	0	0.008	-0.006	15.175	-0.435	-0.435	0.000	0.000	0.000	0.000
40	A	297	GLU	-1	-0.855	-0.907	15.566	15.924	15.924	0.000	0.000	0.000	0.000
41	A	298	VAL	0	-0.003	0.006	10.854	0.727	0.727	0.000	0.000	0.000	0.000
42	A	299	ILE	0	-0.007	-0.016	12.932	-1.277	-1.277	0.000	0.000	0.000	0.000
43	A	300	LEU	0	-0.020	-0.017	10.211	-0.937	-0.937	0.000	0.000	0.000	0.000
44	A	301	PHE	0	-0.015	-0.012	7.268	0.545	0.545	0.000	0.000	0.000	0.000
45	A	302	MET	0	-0.052	-0.025	6.013	-4.477	-4.477	0.000	0.000	0.000	0.000
46	A	303	ASP	-1	-0.846	-0.914	3.110	61.666	61.394	2.742	-0.971	-1.499	0.006
47	A	304	ARG	1	0.901	0.944	5.049	-27.870	-27.690	-0.001	-0.044	-0.136	0.000
48	A	305	ASN	0	0.017	0.027	6.075	-8.698	-8.698	0.000	0.000	0.000	0.000
49	A	306	LEU	0	0.008	-0.008	7.239	2.495	2.495	0.000	0.000	0.000	0.000
50	A	307	GLU	-1	-0.804	-0.897	9.151	20.173	20.173	0.000	0.000	0.000	0.000
51	A	308	GLN	0	-0.008	0.004	5.584	-6.503	-6.429	-0.001	-0.004	-0.069	0.000
52	A	309	MET	0	-0.009	0.013	7.727	2.303	2.303	0.000	0.000	0.000	0.000
53	A	310	GLN	0	-0.026	-0.012	3.782	-0.583	-0.283	0.001	-0.040	-0.260	0.000
54	A	311	ASN	0	-0.020	0.004	7.202	-3.935	-3.935	0.000	0.000	0.000	0.000
55	A	312	PHE	0	0.016	-0.003	3.181	3.595	4.209	0.036	-0.220	-0.430	0.001
56	A	313	VAL	0	0.027	0.022	7.733	-3.770	-3.770	0.000	0.000	0.000	0.000
57	A	314	GLN	0	-0.037	-0.030	9.477	0.518	0.518	0.000	0.000	0.000	0.000
58	A	315	LEU	0	0.033	0.023	10.625	-1.747	-1.747	0.000	0.000	0.000	0.000
59	A	316	HIS	0	-0.018	-0.007	13.411	-0.055	-0.055	0.000	0.000	0.000	0.000
60	A	317	THR	0	0.032	0.009	16.028	-0.291	-0.291	0.000	0.000	0.000	0.000
61	A	318	ASP	-1	-0.909	-0.968	18.524	12.234	12.234	0.000	0.000	0.000	0.000
62	A	319	GLY	0	0.025	0.020	21.253	-0.458	-0.458	0.000	0.000	0.000	0.000
63	A	320	GLY	0	-0.054	-0.024	20.861	-0.264	-0.264	0.000	0.000	0.000	0.000
64	A	321	ALA	0	-0.040	-0.002	15.932	0.382	0.382	0.000	0.000	0.000	0.000
65	A	322	VAL	0	0.018	-0.015	13.259	-0.123	-0.123	0.000	0.000	0.000	0.000
66	A	323	LEU	0	-0.025	0.004	7.853	0.603	0.603	0.000	0.000	0.000	0.000
67	A	324	THR	0	-0.009	-0.013	7.543	-1.257	-1.257	0.000	0.000	0.000	0.000
68	A	325	VAL	0	0.026	0.011	4.493	1.734	1.854	-0.001	-0.058	-0.061	0.000
69	A	326	THR	0	-0.003	-0.027	1.816	-29.677	-36.524	19.644	-7.433	-5.365	0.051
70	A	327	PRO	0	-0.010	-0.021	4.721	-3.089	-2.901	-0.001	-0.054	-0.133	0.000
71	A	328	ALA	0	0.014	0.004	6.197	-3.451	-3.451	0.000	0.000	0.000	0.000
72	A	329	HIS	0	0.043	0.019	1.960	1.162	-3.863	12.800	-4.245	-3.529	-0.038
73	A	330	LEU	0	-0.071	-0.019	4.500	-4.953	-4.914	-0.001	-0.009	-0.028	0.000
74	A	331	VAL	0	0.026	0.000	7.183	1.027	1.027	0.000	0.000	0.000	0.000
75	A	332	SER	0	-0.002	-0.006	9.430	-0.923	-0.923	0.000	0.000	0.000	0.000
76	A	333	VAL	0	0.016	-0.002	12.990	-0.055	-0.055	0.000	0.000	0.000	0.000
77	A	334	TRP	0	-0.023	-0.015	15.786	-0.385	-0.385	0.000	0.000	0.000	0.000
78	A	335	GLN	0	-0.012	-0.004	19.335	0.256	0.256	0.000	0.000	0.000	0.000
79	A	336	PRO	0	-0.029	-0.025	22.248	-0.325	-0.325	0.000	0.000	0.000	0.000
80	A	337	GLU	-1	-0.828	-0.921	25.154	11.217	11.217	0.000	0.000	0.000	0.000
81	A	338	SER	0	-0.039	-0.020	25.058	-0.186	-0.186	0.000	0.000	0.000	0.000
82	A	339	GLN	0	-0.048	-0.026	25.202	-0.231	-0.231	0.000	0.000	0.000	0.000
83	A	340	LYS	1	0.932	0.980	21.582	-12.669	-12.669	0.000	0.000	0.000	0.000
84	A	341	LEU	0	0.020	0.015	16.704	0.230	0.230	0.000	0.000	0.000	0.000
85	A	342	THR	0	-0.088	-0.046	16.863	-0.148	-0.148	0.000	0.000	0.000	0.000
86	A	343	PHE	0	0.033	0.014	10.777	0.327	0.327	0.000	0.000	0.000	0.000
87	A	344	VAL	0	0.000	0.005	11.907	-0.672	-0.672	0.000	0.000	0.000	0.000
88	A	345	PHE	0	-0.016	-0.009	7.965	0.349	0.349	0.000	0.000	0.000	0.000
89	A	346	ALA	0	0.068	0.024	7.041	-2.198	-2.198	0.000	0.000	0.000	0.000
90	A	347	ASP	-1	-0.922	-0.979	9.013	23.430	23.430	0.000	0.000	0.000	0.000
91	A	348	ARG	1	0.863	0.948	11.410	-22.317	-22.317	0.000	0.000	0.000	0.000
92	A	349	ILE	0	-0.035	0.004	11.110	-1.339	-1.339	0.000	0.000	0.000	0.000
93	A	350	GLU	-1	-0.944	-0.968	14.398	14.182	14.182	0.000	0.000	0.000	0.000
94	A	351	GLU	-1	-0.909	-0.974	17.618	13.263	13.263	0.000	0.000	0.000	0.000
95	A	352	LYS	1	0.866	0.924	20.042	-11.679	-11.679	0.000	0.000	0.000	0.000
96	A	353	ASN	0	0.025	0.035	17.483	0.178	0.178	0.000	0.000	0.000	0.000
97	A	354	GLN	0	0.003	-0.013	18.961	-0.133	-0.133	0.000	0.000	0.000	0.000
98	A	355	VAL	0	0.053	0.044	13.533	0.442	0.442	0.000	0.000	0.000	0.000
99	A	356	LEU	0	-0.017	-0.010	15.346	-0.831	-0.831	0.000	0.000	0.000	0.000
100	A	357	VAL	0	0.010	-0.007	15.404	1.170	1.170	0.000	0.000	0.000	0.000
101	A	358	ARG	1	0.926	0.966	17.465	-14.259	-14.259	0.000	0.000	0.000	0.000
102	A	359	ASP	-1	-0.854	-0.911	19.361	11.347	11.347	0.000	0.000	0.000	0.000
103	A	360	VAL	0	-0.061	-0.045	22.714	0.052	0.052	0.000	0.000	0.000	0.000
104	A	361	GLU	-1	-0.958	-0.970	24.249	9.499	9.499	0.000	0.000	0.000	0.000
105	A	362	THR	0	-0.027	-0.030	26.188	-0.024	-0.024	0.000	0.000	0.000	0.000
106	A	363	GLY	0	-0.033	-0.011	22.905	-0.016	-0.016	0.000	0.000	0.000	0.000
107	A	364	GLU	-1	-0.879	-0.925	22.018	11.401	11.401	0.000	0.000	0.000	0.000
108	A	365	LEU	0	-0.048	-0.021	16.726	0.337	0.337	0.000	0.000	0.000	0.000
109	A	366	ARG	1	0.879	0.916	20.060	-11.410	-11.410	0.000	0.000	0.000	0.000
110	A	367	PRO	0	-0.019	-0.007	19.790	0.547	0.547	0.000	0.000	0.000	0.000
111	A	368	GLN	0	0.072	0.047	19.274	-0.155	-0.155	0.000	0.000	0.000	0.000
112	A	369	ARG	1	0.932	0.960	19.285	-11.189	-11.189	0.000	0.000	0.000	0.000
113	A	370	VAL	0	0.026	0.025	15.852	0.114	0.114	0.000	0.000	0.000	0.000
114	A	371	VAL	0	-0.067	-0.050	18.520	-0.630	-0.630	0.000	0.000	0.000	0.000
115	A	372	LYS	1	0.982	0.994	18.640	-15.362	-15.362	0.000	0.000	0.000	0.000
116	A	373	VAL	0	0.021	0.029	14.140	0.767	0.767	0.000	0.000	0.000	0.000
117	A	374	GLY	0	-0.046	-0.021	15.022	-0.883	-0.883	0.000	0.000	0.000	0.000
118	A	375	SER	0	-0.023	-0.025	12.343	1.792	1.792	0.000	0.000	0.000	0.000
119	A	376	VAL	0	0.017	0.018	10.151	-1.519	-1.519	0.000	0.000	0.000	0.000
120	A	377	ARG	1	0.911	0.948	10.044	-24.202	-24.202	0.000	0.000	0.000	0.000
121	A	378	SER	0	-0.010	-0.003	8.968	-1.270	-1.270	0.000	0.000	0.000	0.000
122	A	379	LYS	1	0.818	0.891	8.954	-20.701	-20.701	0.000	0.000	0.000	0.000
123	A	380	GLY	0	-0.011	-0.009	7.219	-1.890	-1.890	0.000	0.000	0.000	0.000
124	A	381	VAL	0	-0.008	-0.007	2.490	-4.098	-2.717	1.814	-1.034	-2.161	0.013
125	A	382	VAL	0	-0.010	-0.018	2.381	-7.801	-6.725	0.814	-0.509	-1.381	-0.002
126	A	383	ALA	0	0.062	0.021	2.432	-1.726	-2.035	7.888	-3.510	-4.069	0.007
127	A	384	PRO	0	-0.048	-0.016	3.452	-7.240	-6.846	0.044	-0.109	-0.329	0.003
128	A	385	LEU	0	0.057	0.009	6.895	0.450	0.450	0.000	0.000	0.000	0.000
129	A	386	THR	0	0.015	-0.024	9.300	-1.800	-1.800	0.000	0.000	0.000	0.000
130	A	387	ARG	1	0.810	0.879	12.375	-15.319	-15.319	0.000	0.000	0.000	0.000
131	A	388	GLU	-1	-0.943	-0.974	15.052	15.248	15.248	0.000	0.000	0.000	0.000
132	A	389	GLY	0	0.000	0.031	11.943	-0.340	-0.340	0.000	0.000	0.000	0.000
133	A	390	THR	0	-0.013	-0.038	10.335	1.737	1.737	0.000	0.000	0.000	0.000
134	A	391	ILE	0	0.000	-0.007	7.250	-0.389	-0.389	0.000	0.000	0.000	0.000
135	A	392	VAL	0	-0.024	-0.002	10.164	0.465	0.465	0.000	0.000	0.000	0.000
136	A	393	VAL	0	0.000	0.008	6.959	-0.415	-0.415	0.000	0.000	0.000	0.000
137	A	394	ASN	0	0.001	-0.009	10.249	0.720	0.720	0.000	0.000	0.000	0.000
138	A	395	SER	0	-0.025	-0.023	12.975	-0.736	-0.736	0.000	0.000	0.000	0.000
139	A	396	VAL	0	0.033	0.028	11.643	-1.219	-1.219	0.000	0.000	0.000	0.000
140	A	397	ALA	0	-0.027	-0.011	11.395	1.382	1.382	0.000	0.000	0.000	0.000
141	A	398	ALA	0	0.003	0.006	7.193	0.096	0.096	0.000	0.000	0.000	0.000
142	A	399	SER	0	0.051	0.028	7.896	-0.906	-0.906	0.000	0.000	0.000	0.000
143	A	400	CYS	0	-0.031	0.027	6.475	1.306	1.306	0.000	0.000	0.000	0.000
144	A	401	TYR	0	-0.052	-0.022	5.335	5.248	5.248	0.000	0.000	0.000	0.000
145	A	402	ALA	0	0.057	0.039	2.464	-3.065	-2.484	1.201	-0.647	-1.134	0.002

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