FMO DATABASE

FMODB ID: K9GG3

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	OptAll
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	-1329100.623454
FMO2-HF: Nuclear repulsion	1273419.486926
FMO2-HF: Total energy	-55681.136529
FMO2-MP2: Total energy	-55843.124886

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.
-37.962	-59.419	73.589	-30.368	-21.76	0.133

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 : -0.783 / q_NPA : -0.806

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	-0.019	-0.024	3.841	1.569	3.348	-0.001	-0.951	-0.827	0.004
4	A	261	PRO	0	0.002	-0.007	6.224	-0.792	-0.792	0.000	0.000	0.000	0.000
5	A	262	GLU	-1	-0.853	-0.911	8.703	23.836	23.836	0.000	0.000	0.000	0.000
6	A	263	SER	0	-0.050	-0.017	7.618	-1.484	-1.484	0.000	0.000	0.000	0.000
7	A	264	THR	0	-0.045	-0.030	9.775	-0.302	-0.302	0.000	0.000	0.000	0.000
8	A	265	ALA	0	0.066	0.047	10.655	0.312	0.312	0.000	0.000	0.000	0.000
9	A	266	LEU	0	-0.029	-0.025	12.161	-1.190	-1.190	0.000	0.000	0.000	0.000
10	A	267	LEU	0	0.026	0.011	15.413	0.436	0.436	0.000	0.000	0.000	0.000
11	A	268	GLU	-1	-0.818	-0.909	17.811	12.901	12.901	0.000	0.000	0.000	0.000
12	A	269	SER	0	-0.042	-0.020	20.881	-0.368	-0.368	0.000	0.000	0.000	0.000
13	A	270	GLY	0	0.011	0.008	21.470	-0.481	-0.481	0.000	0.000	0.000	0.000
14	A	271	VAL	0	-0.027	-0.007	19.203	0.028	0.028	0.000	0.000	0.000	0.000
15	A	272	ARG	1	0.957	0.971	16.197	-14.353	-14.353	0.000	0.000	0.000	0.000
16	A	273	LYS	1	0.856	0.921	13.968	-17.619	-17.619	0.000	0.000	0.000	0.000
17	A	274	PRO	0	0.039	0.025	11.926	1.305	1.305	0.000	0.000	0.000	0.000
18	A	275	LEU	0	0.010	0.008	5.239	-0.482	-0.482	0.000	0.000	0.000	0.000
19	A	276	GLY	0	0.007	-0.004	9.071	0.500	0.500	0.000	0.000	0.000	0.000
20	A	277	GLU	-1	-0.915	-0.943	10.710	15.782	15.782	0.000	0.000	0.000	0.000
21	A	278	LEU	0	-0.071	-0.018	9.187	-1.019	-1.019	0.000	0.000	0.000	0.000
22	A	279	SER	0	-0.026	-0.017	12.113	0.584	0.584	0.000	0.000	0.000	0.000
23	A	280	ILE	0	-0.045	-0.022	13.406	0.168	0.168	0.000	0.000	0.000	0.000
24	A	281	GLY	0	-0.004	0.001	15.068	-1.071	-1.071	0.000	0.000	0.000	0.000
25	A	282	ASP	-1	-0.833	-0.919	14.412	16.736	16.736	0.000	0.000	0.000	0.000
26	A	283	ARG	1	0.787	0.875	15.263	-13.239	-13.239	0.000	0.000	0.000	0.000
27	A	284	VAL	0	0.009	0.010	11.868	-0.566	-0.566	0.000	0.000	0.000	0.000
28	A	285	LEU	0	-0.013	-0.004	14.991	-0.507	-0.507	0.000	0.000	0.000	0.000
29	A	286	SER	0	-0.036	-0.043	13.417	1.465	1.465	0.000	0.000	0.000	0.000
30	A	287	MET	0	-0.039	0.010	14.021	-0.846	-0.846	0.000	0.000	0.000	0.000
31	A	288	THR	0	0.046	0.031	15.733	0.798	0.798	0.000	0.000	0.000	0.000
32	A	289	ALA	0	0.020	0.000	17.742	0.349	0.349	0.000	0.000	0.000	0.000
33	A	290	ASN	0	-0.054	-0.027	18.792	0.226	0.226	0.000	0.000	0.000	0.000
34	A	291	GLY	0	0.026	0.001	18.167	-0.477	-0.477	0.000	0.000	0.000	0.000
35	A	292	GLN	0	0.002	0.016	19.243	-0.052	-0.052	0.000	0.000	0.000	0.000
36	A	293	ALA	0	0.032	0.018	18.895	0.751	0.751	0.000	0.000	0.000	0.000
37	A	294	VAL	0	-0.009	0.001	17.916	-0.749	-0.749	0.000	0.000	0.000	0.000
38	A	295	TYR	0	-0.007	0.006	18.127	0.641	0.641	0.000	0.000	0.000	0.000
39	A	296	SER	0	0.030	-0.001	15.505	-0.551	-0.551	0.000	0.000	0.000	0.000
40	A	297	GLU	-1	-0.814	-0.875	15.674	15.566	15.566	0.000	0.000	0.000	0.000
41	A	298	VAL	0	0.002	-0.001	10.704	0.783	0.783	0.000	0.000	0.000	0.000
42	A	299	ILE	0	-0.026	-0.025	13.100	-1.380	-1.380	0.000	0.000	0.000	0.000
43	A	300	LEU	0	-0.033	-0.017	10.153	-0.963	-0.963	0.000	0.000	0.000	0.000
44	A	301	PHE	0	-0.001	-0.011	6.830	0.949	0.949	0.000	0.000	0.000	0.000
45	A	302	MET	0	-0.029	-0.011	5.869	-3.955	-3.955	0.000	0.000	0.000	0.000
46	A	303	ASP	-1	-0.745	-0.876	3.604	45.491	45.764	0.003	-0.032	-0.242	0.000
47	A	304	ARG	1	0.865	0.928	5.504	-23.437	-23.437	0.000	0.000	0.000	0.000
48	A	305	ASN	0	0.011	0.010	6.480	-6.278	-6.278	0.000	0.000	0.000	0.000
49	A	306	LEU	0	0.020	0.003	7.516	2.084	2.084	0.000	0.000	0.000	0.000
50	A	307	GLU	-1	-0.800	-0.894	9.540	19.767	19.767	0.000	0.000	0.000	0.000
51	A	308	GLN	0	-0.046	-0.014	5.227	-7.217	-7.217	0.000	0.000	0.000	0.000
52	A	309	MET	0	-0.021	-0.002	7.441	2.655	2.655	0.000	0.000	0.000	0.000
53	A	310	GLN	0	-0.017	0.011	3.853	-3.893	-3.592	0.003	-0.087	-0.217	0.001
54	A	311	ASN	0	0.000	0.000	7.190	-3.821	-3.821	0.000	0.000	0.000	0.000
55	A	312	PHE	0	0.028	0.007	2.870	6.126	6.782	0.080	-0.184	-0.552	0.000
56	A	313	VAL	0	0.016	0.025	7.394	-4.631	-4.631	0.000	0.000	0.000	0.000
57	A	314	GLN	0	-0.052	-0.046	9.152	0.283	0.283	0.000	0.000	0.000	0.000
58	A	315	LEU	0	0.025	0.014	10.339	-1.603	-1.603	0.000	0.000	0.000	0.000
59	A	316	HIS	0	0.035	0.016	13.090	-0.200	-0.200	0.000	0.000	0.000	0.000
60	A	317	THR	0	0.016	-0.011	15.969	-0.318	-0.318	0.000	0.000	0.000	0.000
61	A	318	ASP	-1	-0.809	-0.906	18.545	12.714	12.714	0.000	0.000	0.000	0.000
62	A	319	GLY	0	-0.017	0.005	21.215	-0.544	-0.544	0.000	0.000	0.000	0.000
63	A	320	GLY	0	-0.038	-0.014	20.690	-0.180	-0.180	0.000	0.000	0.000	0.000
64	A	321	ALA	0	-0.012	0.011	15.755	0.326	0.326	0.000	0.000	0.000	0.000
65	A	322	VAL	0	0.015	-0.016	13.309	-0.094	-0.094	0.000	0.000	0.000	0.000
66	A	323	LEU	0	0.008	0.030	7.651	0.718	0.718	0.000	0.000	0.000	0.000
67	A	324	THR	0	-0.015	-0.014	7.388	-1.462	-1.462	0.000	0.000	0.000	0.000
68	A	325	VAL	0	0.029	0.018	4.235	0.863	1.005	-0.001	-0.071	-0.070	0.000
69	A	326	THR	0	-0.080	-0.129	1.853	-29.198	-57.185	59.366	-22.039	-9.338	0.147
70	A	327	PRO	0	-0.026	-0.027	4.900	-4.457	-3.877	0.000	-0.401	-0.178	0.003
71	A	328	ALA	0	0.027	0.014	5.770	-5.139	-5.084	-0.001	-0.007	-0.047	0.000
72	A	329	HIS	0	0.021	0.011	2.223	0.083	-0.533	6.266	-2.347	-3.303	-0.017
73	A	330	LEU	0	-0.038	-0.006	4.608	-6.018	-5.990	-0.001	-0.007	-0.020	0.000
74	A	331	VAL	0	0.030	0.004	7.336	0.350	0.350	0.000	0.000	0.000	0.000
75	A	332	SER	0	-0.007	-0.025	9.197	-0.919	-0.919	0.000	0.000	0.000	0.000
76	A	333	VAL	0	-0.006	-0.009	12.743	-0.376	-0.376	0.000	0.000	0.000	0.000
77	A	334	TRP	0	0.002	-0.005	15.571	-0.415	-0.415	0.000	0.000	0.000	0.000
78	A	335	GLN	0	0.009	0.012	19.309	0.553	0.553	0.000	0.000	0.000	0.000
79	A	336	PRO	0	0.008	0.004	22.406	-0.353	-0.353	0.000	0.000	0.000	0.000
80	A	337	GLU	-1	-0.833	-0.899	25.246	11.556	11.556	0.000	0.000	0.000	0.000
81	A	338	SER	0	-0.046	-0.052	25.606	-0.248	-0.248	0.000	0.000	0.000	0.000
82	A	339	GLN	0	-0.088	-0.049	25.262	-0.149	-0.149	0.000	0.000	0.000	0.000
83	A	340	LYS	1	0.902	0.966	20.574	-13.752	-13.752	0.000	0.000	0.000	0.000
84	A	341	LEU	0	0.027	0.021	16.374	0.320	0.320	0.000	0.000	0.000	0.000
85	A	342	THR	0	-0.074	-0.048	16.980	-0.157	-0.157	0.000	0.000	0.000	0.000
86	A	343	PHE	0	0.026	0.012	11.099	0.365	0.365	0.000	0.000	0.000	0.000
87	A	344	VAL	0	-0.013	0.000	11.807	-0.731	-0.731	0.000	0.000	0.000	0.000
88	A	345	PHE	0	-0.010	0.001	8.568	0.805	0.805	0.000	0.000	0.000	0.000
89	A	346	ALA	0	0.073	0.035	7.131	-2.685	-2.685	0.000	0.000	0.000	0.000
90	A	347	ASP	-1	-0.856	-0.907	9.038	26.263	26.263	0.000	0.000	0.000	0.000
91	A	348	ARG	1	0.771	0.853	11.442	-27.046	-27.046	0.000	0.000	0.000	0.000
92	A	349	ILE	0	-0.029	0.013	10.932	-1.272	-1.272	0.000	0.000	0.000	0.000
93	A	350	GLU	-1	-0.910	-0.953	14.322	14.863	14.863	0.000	0.000	0.000	0.000
94	A	351	GLU	-1	-0.857	-0.956	17.470	14.457	14.457	0.000	0.000	0.000	0.000
95	A	352	LYS	1	0.885	0.932	19.784	-12.627	-12.627	0.000	0.000	0.000	0.000
96	A	353	ASN	0	-0.008	0.009	17.405	0.370	0.370	0.000	0.000	0.000	0.000
97	A	354	GLN	0	0.012	0.002	18.967	-0.186	-0.186	0.000	0.000	0.000	0.000
98	A	355	VAL	0	0.048	0.026	13.481	0.477	0.477	0.000	0.000	0.000	0.000
99	A	356	LEU	0	-0.009	0.000	15.186	-0.860	-0.860	0.000	0.000	0.000	0.000
100	A	357	VAL	0	-0.005	-0.012	15.010	1.291	1.291	0.000	0.000	0.000	0.000
101	A	358	ARG	1	0.849	0.936	17.188	-14.143	-14.143	0.000	0.000	0.000	0.000
102	A	359	ASP	-1	-0.771	-0.866	19.136	11.468	11.468	0.000	0.000	0.000	0.000
103	A	360	VAL	0	-0.022	-0.015	22.745	0.211	0.211	0.000	0.000	0.000	0.000
104	A	361	GLU	-1	-0.974	-0.977	24.240	9.675	9.675	0.000	0.000	0.000	0.000
105	A	362	THR	0	-0.009	-0.044	26.200	0.009	0.009	0.000	0.000	0.000	0.000
106	A	363	GLY	0	-0.043	-0.020	22.761	0.002	0.002	0.000	0.000	0.000	0.000
107	A	364	GLU	-1	-0.853	-0.908	21.756	11.675	11.675	0.000	0.000	0.000	0.000
108	A	365	LEU	0	-0.055	-0.021	16.298	0.313	0.313	0.000	0.000	0.000	0.000
109	A	366	ARG	1	0.842	0.903	19.890	-11.809	-11.809	0.000	0.000	0.000	0.000
110	A	367	PRO	0	-0.020	0.000	19.605	0.660	0.660	0.000	0.000	0.000	0.000
111	A	368	GLN	0	0.060	0.043	18.777	-0.105	-0.105	0.000	0.000	0.000	0.000
112	A	369	ARG	1	0.869	0.916	19.064	-11.354	-11.354	0.000	0.000	0.000	0.000
113	A	370	VAL	0	0.025	0.016	15.751	0.053	0.053	0.000	0.000	0.000	0.000
114	A	371	VAL	0	-0.070	-0.046	18.366	-0.719	-0.719	0.000	0.000	0.000	0.000
115	A	372	LYS	1	0.884	0.945	18.129	-16.803	-16.803	0.000	0.000	0.000	0.000
116	A	373	VAL	0	-0.006	0.021	14.149	0.906	0.906	0.000	0.000	0.000	0.000
117	A	374	GLY	0	-0.026	-0.016	14.511	-1.181	-1.181	0.000	0.000	0.000	0.000
118	A	375	SER	0	-0.077	-0.047	11.163	1.365	1.365	0.000	0.000	0.000	0.000
119	A	376	VAL	0	0.020	0.017	9.809	-1.927	-1.927	0.000	0.000	0.000	0.000
120	A	377	ARG	1	0.862	0.923	9.804	-24.142	-24.142	0.000	0.000	0.000	0.000
121	A	378	SER	0	-0.002	0.006	8.749	-1.632	-1.632	0.000	0.000	0.000	0.000
122	A	379	LYS	1	0.851	0.900	8.686	-19.456	-19.456	0.000	0.000	0.000	0.000
123	A	380	GLY	0	0.003	0.005	7.569	-1.891	-1.891	0.000	0.000	0.000	0.000
124	A	381	VAL	0	-0.041	-0.023	2.242	0.988	1.731	1.689	-0.742	-1.690	0.006
125	A	382	VAL	0	-0.032	-0.023	3.372	-6.635	-6.029	0.017	-0.168	-0.455	0.000
126	A	383	ALA	0	0.052	0.033	2.377	2.169	4.115	2.854	-2.334	-2.467	-0.015
127	A	384	PRO	0	-0.008	0.003	3.355	-6.647	-6.579	0.050	0.090	-0.208	0.000
128	A	385	LEU	0	0.030	-0.007	6.975	1.952	1.952	0.000	0.000	0.000	0.000
129	A	386	THR	0	0.022	-0.011	9.726	-1.915	-1.915	0.000	0.000	0.000	0.000
130	A	387	ARG	1	0.840	0.890	12.911	-14.988	-14.988	0.000	0.000	0.000	0.000
131	A	388	GLU	-1	-0.895	-0.943	14.829	15.544	15.544	0.000	0.000	0.000	0.000
132	A	389	GLY	0	-0.011	0.011	11.803	-0.007	-0.007	0.000	0.000	0.000	0.000
133	A	390	THR	0	-0.007	-0.022	10.393	2.128	2.128	0.000	0.000	0.000	0.000
134	A	391	ILE	0	0.000	0.019	7.690	-0.742	-0.742	0.000	0.000	0.000	0.000
135	A	392	VAL	0	-0.011	0.008	10.555	0.374	0.374	0.000	0.000	0.000	0.000
136	A	393	VAL	0	-0.003	-0.005	7.543	-0.451	-0.451	0.000	0.000	0.000	0.000
137	A	394	ASN	0	-0.023	-0.017	10.734	-0.394	-0.394	0.000	0.000	0.000	0.000
138	A	395	SER	0	0.000	-0.008	13.281	-0.700	-0.700	0.000	0.000	0.000	0.000
139	A	396	VAL	0	0.012	0.020	11.502	-1.028	-1.028	0.000	0.000	0.000	0.000
140	A	397	ALA	0	-0.001	-0.002	11.334	1.365	1.365	0.000	0.000	0.000	0.000
141	A	398	ALA	0	-0.007	-0.003	7.196	0.190	0.190	0.000	0.000	0.000	0.000
142	A	399	SER	0	0.027	0.018	8.043	-0.926	-0.926	0.000	0.000	0.000	0.000
143	A	400	CYS	0	-0.065	-0.016	6.481	1.771	1.771	0.000	0.000	0.000	0.000
144	A	401	TYR	0	-0.028	-0.007	5.377	6.654	6.778	-0.001	-0.004	-0.119	0.000
145	A	402	ALA	0	0.047	0.031	2.328	-3.592	-3.747	3.266	-1.084	-2.027	0.004

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