FMO DATABASE

FMODB ID: 6YG1Z

Calculation Name: 1XAO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XAO

Chain ID: A

ChEMBL ID:

UniProt ID: P25491

Base Structure: X-ray

Registration Date: 2023-09-22

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	121
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-787574.604225
FMO2-HF: Nuclear repulsion	741588.748858
FMO2-HF: Total energy	-45985.855367
FMO2-MP2: Total energy	-46120.9205

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:SER)

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

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.
1.986	5.001	0.071	-1.543	-1.542	0.005

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : 0.016

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	LYS	1	0.819	0.899	3.740	2.861	5.331	0.009	-1.338	-1.141	0.005
4	A	261	ARG	1	0.861	0.907	6.455	-0.484	-0.484	0.000	0.000	0.000	0.000
5	A	262	ASP	-1	-0.920	-0.953	9.571	-0.326	-0.326	0.000	0.000	0.000	0.000
6	A	263	GLY	0	0.053	0.022	12.955	-0.001	-0.001	0.000	0.000	0.000	0.000
7	A	264	ASP	-1	-0.856	-0.937	14.883	0.148	0.148	0.000	0.000	0.000	0.000
8	A	265	ASP	-1	-0.776	-0.866	13.779	-0.191	-0.191	0.000	0.000	0.000	0.000
9	A	266	LEU	0	-0.092	-0.040	8.032	0.121	0.121	0.000	0.000	0.000	0.000
10	A	267	VAL	0	-0.008	-0.006	8.591	-0.107	-0.107	0.000	0.000	0.000	0.000
11	A	268	TYR	0	0.035	0.009	2.825	-0.232	0.313	0.062	-0.205	-0.401	0.000
12	A	269	GLU	-1	-0.828	-0.903	5.389	-0.967	-0.967	0.000	0.000	0.000	0.000
13	A	270	ALA	0	0.029	0.031	6.237	-0.334	-0.334	0.000	0.000	0.000	0.000
14	A	271	GLU	-1	-0.908	-0.970	8.561	-0.349	-0.349	0.000	0.000	0.000	0.000
15	A	272	ILE	0	-0.026	0.001	11.282	0.030	0.030	0.000	0.000	0.000	0.000
16	A	273	ASP	-1	-0.781	-0.876	14.675	-0.248	-0.248	0.000	0.000	0.000	0.000
17	A	274	LEU	0	0.010	-0.002	17.987	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	275	LEU	0	0.011	0.006	20.806	0.005	0.005	0.000	0.000	0.000	0.000
19	A	276	THR	0	0.010	0.001	17.599	0.008	0.008	0.000	0.000	0.000	0.000
20	A	277	ALA	0	-0.025	-0.010	18.699	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	278	ILE	0	-0.008	-0.007	20.205	0.005	0.005	0.000	0.000	0.000	0.000
22	A	279	ALA	0	-0.011	-0.001	23.728	0.017	0.017	0.000	0.000	0.000	0.000
23	A	280	GLY	0	0.020	0.021	21.969	0.015	0.015	0.000	0.000	0.000	0.000
24	A	281	GLY	0	-0.031	-0.031	20.511	0.007	0.007	0.000	0.000	0.000	0.000
25	A	282	GLU	-1	-0.856	-0.916	17.615	-0.189	-0.189	0.000	0.000	0.000	0.000
26	A	283	PHE	0	0.002	0.005	10.623	-0.013	-0.013	0.000	0.000	0.000	0.000
27	A	284	ALA	0	-0.006	-0.014	11.719	0.046	0.046	0.000	0.000	0.000	0.000
28	A	285	LEU	0	-0.031	-0.006	6.274	-0.078	-0.078	0.000	0.000	0.000	0.000
29	A	286	GLU	-1	-0.871	-0.902	6.665	0.892	0.892	0.000	0.000	0.000	0.000
30	A	287	HIS	0	0.013	-0.019	6.254	-0.314	-0.314	0.000	0.000	0.000	0.000
31	A	288	VAL	0	-0.005	-0.011	5.491	0.295	0.295	0.000	0.000	0.000	0.000
32	A	289	SER	0	-0.058	-0.049	7.658	0.130	0.130	0.000	0.000	0.000	0.000
33	A	290	GLY	0	0.027	0.017	9.802	0.010	0.010	0.000	0.000	0.000	0.000
34	A	291	ASP	-1	-0.866	-0.905	11.167	0.063	0.063	0.000	0.000	0.000	0.000
35	A	292	TRP	0	-0.048	-0.047	9.408	-0.189	-0.189	0.000	0.000	0.000	0.000
36	A	293	LEU	0	-0.047	-0.008	10.252	0.024	0.024	0.000	0.000	0.000	0.000
37	A	294	LYS	1	0.840	0.895	12.102	0.108	0.108	0.000	0.000	0.000	0.000
38	A	295	VAL	0	-0.025	-0.014	13.286	0.027	0.027	0.000	0.000	0.000	0.000
39	A	296	GLY	0	0.039	0.032	15.904	-0.013	-0.013	0.000	0.000	0.000	0.000
40	A	297	ILE	0	-0.030	-0.018	16.002	-0.021	-0.021	0.000	0.000	0.000	0.000
41	A	298	VAL	0	0.035	0.010	20.080	0.021	0.021	0.000	0.000	0.000	0.000
42	A	299	PRO	0	0.027	0.005	23.882	-0.010	-0.010	0.000	0.000	0.000	0.000
43	A	300	GLY	0	0.020	0.017	25.911	0.014	0.014	0.000	0.000	0.000	0.000
44	A	301	GLU	-1	-0.899	-0.929	22.402	-0.251	-0.251	0.000	0.000	0.000	0.000
45	A	302	VAL	0	-0.044	-0.016	22.091	-0.025	-0.025	0.000	0.000	0.000	0.000
46	A	303	ILE	0	-0.006	-0.017	16.569	-0.016	-0.016	0.000	0.000	0.000	0.000
47	A	304	ALA	0	0.016	-0.003	19.368	0.022	0.022	0.000	0.000	0.000	0.000
48	A	305	PRO	0	0.035	0.001	17.207	-0.052	-0.052	0.000	0.000	0.000	0.000
49	A	306	GLY	0	0.006	0.016	15.111	0.030	0.030	0.000	0.000	0.000	0.000
50	A	307	MET	0	-0.079	-0.013	16.156	0.001	0.001	0.000	0.000	0.000	0.000
51	A	308	ARG	1	0.908	0.946	14.535	0.418	0.418	0.000	0.000	0.000	0.000
52	A	309	LYS	1	0.842	0.918	14.947	0.384	0.384	0.000	0.000	0.000	0.000
53	A	310	VAL	0	-0.006	-0.009	14.804	-0.084	-0.084	0.000	0.000	0.000	0.000
54	A	311	ILE	0	-0.005	0.008	11.837	0.029	0.029	0.000	0.000	0.000	0.000
55	A	312	GLU	-1	-0.836	-0.925	15.354	-0.187	-0.187	0.000	0.000	0.000	0.000
56	A	313	GLY	0	-0.004	-0.001	17.427	0.006	0.006	0.000	0.000	0.000	0.000
57	A	314	LYS	1	0.835	0.919	12.508	0.054	0.054	0.000	0.000	0.000	0.000
58	A	315	GLY	0	0.030	0.026	11.787	-0.051	-0.051	0.000	0.000	0.000	0.000
59	A	316	MET	0	-0.061	-0.044	10.887	0.148	0.148	0.000	0.000	0.000	0.000
60	A	317	PRO	0	0.040	0.001	14.241	-0.046	-0.046	0.000	0.000	0.000	0.000
61	A	318	ILE	0	0.027	0.037	17.430	-0.019	-0.019	0.000	0.000	0.000	0.000
62	A	319	PRO	0	-0.013	0.003	18.522	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	320	LYS	1	0.816	0.891	20.016	-0.033	-0.033	0.000	0.000	0.000	0.000
64	A	321	TYR	0	-0.027	-0.014	22.891	-0.013	-0.013	0.000	0.000	0.000	0.000
65	A	322	GLY	0	0.011	0.018	22.260	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	323	GLY	0	-0.005	0.019	22.025	0.003	0.003	0.000	0.000	0.000	0.000
67	A	324	TYR	0	-0.046	-0.039	15.124	0.045	0.045	0.000	0.000	0.000	0.000
68	A	325	GLY	0	0.011	0.028	16.745	-0.019	-0.019	0.000	0.000	0.000	0.000
69	A	326	ASN	0	-0.045	-0.037	15.716	0.026	0.026	0.000	0.000	0.000	0.000
70	A	327	LEU	0	-0.008	-0.001	8.593	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	328	ILE	0	0.010	0.003	12.034	-0.018	-0.018	0.000	0.000	0.000	0.000
72	A	329	ILE	0	0.001	-0.004	9.286	-0.267	-0.267	0.000	0.000	0.000	0.000
73	A	330	LYS	1	0.860	0.923	9.766	1.322	1.322	0.000	0.000	0.000	0.000
74	A	331	PHE	0	0.025	0.003	10.529	-0.202	-0.202	0.000	0.000	0.000	0.000
75	A	332	THR	0	0.011	0.011	10.506	0.122	0.122	0.000	0.000	0.000	0.000
76	A	333	ILE	0	-0.029	-0.025	13.165	0.005	0.005	0.000	0.000	0.000	0.000
77	A	334	LYS	1	0.855	0.931	15.163	0.295	0.295	0.000	0.000	0.000	0.000
78	A	335	PHE	0	0.007	-0.012	17.076	0.021	0.021	0.000	0.000	0.000	0.000
79	A	336	PRO	0	-0.023	-0.013	20.842	0.004	0.004	0.000	0.000	0.000	0.000
80	A	337	GLU	-1	-0.807	-0.894	22.854	-0.140	-0.140	0.000	0.000	0.000	0.000
81	A	338	ASN	0	-0.050	-0.042	24.856	0.005	0.005	0.000	0.000	0.000	0.000
82	A	339	HIS	0	-0.024	-0.022	28.455	0.005	0.005	0.000	0.000	0.000	0.000
83	A	340	PHE	0	-0.007	0.018	27.007	0.005	0.005	0.000	0.000	0.000	0.000
84	A	341	THR	0	-0.043	-0.031	28.988	0.001	0.001	0.000	0.000	0.000	0.000
85	A	342	SER	0	0.038	0.024	32.158	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	343	GLU	-1	-0.770	-0.891	35.772	-0.079	-0.079	0.000	0.000	0.000	0.000
87	A	344	GLU	-1	-0.897	-0.929	37.705	-0.062	-0.062	0.000	0.000	0.000	0.000
88	A	345	ASN	0	0.008	-0.008	34.269	0.000	0.000	0.000	0.000	0.000	0.000
89	A	346	LEU	0	0.013	0.007	31.620	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	347	LYS	1	0.866	0.918	34.567	0.072	0.072	0.000	0.000	0.000	0.000
91	A	348	LYS	1	0.854	0.921	35.990	0.069	0.069	0.000	0.000	0.000	0.000
92	A	349	LEU	0	-0.005	0.004	30.389	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	350	GLU	-1	-0.843	-0.900	33.886	-0.093	-0.093	0.000	0.000	0.000	0.000
94	A	351	GLU	-1	-0.970	-0.975	36.613	-0.073	-0.073	0.000	0.000	0.000	0.000
95	A	352	ILE	0	-0.072	-0.032	31.743	0.000	0.000	0.000	0.000	0.000	0.000
96	A	353	LEU	0	-0.041	-0.009	29.118	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	354	PRO	0	-0.012	-0.016	31.448	0.007	0.007	0.000	0.000	0.000	0.000
98	A	355	PRO	0	0.011	0.004	34.348	0.000	0.000	0.000	0.000	0.000	0.000
99	A	356	ARG	1	0.815	0.884	35.598	0.092	0.092	0.000	0.000	0.000	0.000
100	A	357	ILE	0	0.015	0.014	33.690	0.005	0.005	0.000	0.000	0.000	0.000
101	A	358	VAL	0	0.003	-0.010	37.182	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	359	PRO	0	0.002	-0.003	38.620	0.001	0.001	0.000	0.000	0.000	0.000
103	A	360	ALA	0	0.021	0.020	40.803	0.005	0.005	0.000	0.000	0.000	0.000
104	A	361	ILE	0	0.005	0.002	43.086	0.000	0.000	0.000	0.000	0.000	0.000
105	A	362	PRO	0	-0.014	-0.011	44.890	0.003	0.003	0.000	0.000	0.000	0.000
106	A	363	LYS	1	0.981	0.979	48.091	0.057	0.057	0.000	0.000	0.000	0.000
107	A	364	LYS	1	0.944	0.971	51.462	0.052	0.052	0.000	0.000	0.000	0.000
108	A	365	ALA	0	-0.021	0.006	48.095	0.002	0.002	0.000	0.000	0.000	0.000
109	A	366	THR	0	0.022	0.010	48.010	0.001	0.001	0.000	0.000	0.000	0.000
110	A	367	VAL	0	-0.047	-0.028	46.093	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	368	ASP	-1	-0.879	-0.934	43.889	-0.061	-0.061	0.000	0.000	0.000	0.000
112	A	369	GLU	-1	-0.957	-0.973	43.001	-0.065	-0.065	0.000	0.000	0.000	0.000
113	A	370	CYS	0	-0.087	-0.046	38.966	0.001	0.001	0.000	0.000	0.000	0.000
114	A	371	VAL	0	-0.014	-0.008	37.551	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	372	LEU	0	-0.041	-0.020	31.753	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	373	ALA	0	0.004	-0.004	33.273	0.005	0.005	0.000	0.000	0.000	0.000
117	A	374	ASP	-1	-0.913	-0.949	29.048	-0.112	-0.112	0.000	0.000	0.000	0.000
118	A	375	PHE	0	-0.047	-0.027	25.235	0.004	0.004	0.000	0.000	0.000	0.000
119	A	376	ASP	-1	-0.879	-0.932	26.463	-0.098	-0.098	0.000	0.000	0.000	0.000
120	A	377	PRO	0	-0.060	-0.043	22.240	-0.004	-0.004	0.000	0.000	0.000	0.000
121	A	378	ALA	0	-0.053	-0.010	23.952	-0.004	-0.004	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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