FMO DATABASE

FMODB ID: 89Y4Y

Calculation Name: 1HY5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1HY5

Chain ID: A

ChEMBL ID:

UniProt ID: P31493

Base Structure: X-ray

Registration Date: 2023-09-24

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	120
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-914766.616921
FMO2-HF: Nuclear repulsion	868881.563768
FMO2-HF: Total energy	-45885.053153
FMO2-MP2: Total energy	-46014.105455

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:1100:THR)

Summations of interaction energy for fragment #1(A:1100:THR)

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.
-6.202	-1.294	3.602	-3.706	-4.805	-0.002

Interaction energy analysis for fragmet #1(A:1100:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.019

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	1102	PHE	0	0.037	0.028	3.204	0.885	4.288	0.372	-1.710	-2.065	0.008
4	A	1103	SER	0	0.070	0.013	4.930	0.153	0.265	-0.001	-0.003	-0.108	0.000
5	A	1104	ASP	-1	-0.784	-0.860	3.844	1.321	1.534	0.002	-0.062	-0.153	0.000
6	A	1105	SER	0	0.008	0.016	2.196	-8.183	-7.124	3.228	-1.876	-2.412	-0.010
7	A	1106	ILE	0	-0.045	-0.015	4.070	-0.615	-0.494	0.001	-0.055	-0.067	0.000
8	A	1107	LYS	1	0.905	0.935	7.767	-1.220	-1.220	0.000	0.000	0.000	0.000
9	A	1108	GLN	0	-0.069	-0.035	5.591	0.894	0.894	0.000	0.000	0.000	0.000
10	A	1109	LEU	0	0.017	0.017	7.724	-0.243	-0.243	0.000	0.000	0.000	0.000
11	A	1110	ALA	0	0.026	0.016	9.222	-0.095	-0.095	0.000	0.000	0.000	0.000
12	A	1111	ALA	0	-0.010	-0.002	11.355	-0.074	-0.074	0.000	0.000	0.000	0.000
13	A	1112	GLU	-1	-0.907	-0.950	9.486	0.734	0.734	0.000	0.000	0.000	0.000
14	A	1113	THR	0	-0.089	-0.067	13.130	-0.087	-0.087	0.000	0.000	0.000	0.000
15	A	1114	LEU	0	0.000	-0.006	15.263	-0.044	-0.044	0.000	0.000	0.000	0.000
16	A	1115	PRO	0	0.036	0.013	16.504	-0.042	-0.042	0.000	0.000	0.000	0.000
17	A	1116	LYS	1	0.874	0.947	18.716	-0.169	-0.169	0.000	0.000	0.000	0.000
18	A	1117	TYR	0	0.047	0.015	17.022	-0.022	-0.022	0.000	0.000	0.000	0.000
19	A	1118	MET	0	-0.011	0.028	19.461	-0.017	-0.017	0.000	0.000	0.000	0.000
20	A	1119	GLN	0	0.051	0.025	23.279	-0.018	-0.018	0.000	0.000	0.000	0.000
21	A	1120	GLN	0	-0.020	-0.013	23.339	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	1121	LEU	0	0.039	0.031	24.574	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	1122	ASN	0	-0.018	-0.011	27.332	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	1123	SER	0	-0.095	-0.071	29.281	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	1124	LEU	0	-0.046	-0.030	29.837	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	1125	ASP	-1	-0.805	-0.914	32.649	0.053	0.053	0.000	0.000	0.000	0.000
27	A	1126	ALA	0	0.063	0.037	36.131	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	1127	GLU	-1	-0.822	-0.887	38.442	0.036	0.036	0.000	0.000	0.000	0.000
29	A	1128	MET	0	-0.041	-0.022	31.308	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	1129	LEU	0	-0.053	-0.034	32.881	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	1130	GLN	0	-0.012	-0.007	34.871	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	1131	LYS	1	0.741	0.873	36.518	-0.039	-0.039	0.000	0.000	0.000	0.000
33	A	1132	ASN	0	-0.021	-0.009	31.409	-0.007	-0.007	0.000	0.000	0.000	0.000
34	A	1133	HIS	0	0.042	0.044	31.082	0.005	0.005	0.000	0.000	0.000	0.000
35	A	1134	ASP	-1	-0.805	-0.919	30.419	0.004	0.004	0.000	0.000	0.000	0.000
36	A	1135	GLN	0	0.002	-0.008	29.296	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	1136	PHE	0	0.014	-0.024	27.036	0.002	0.002	0.000	0.000	0.000	0.000
38	A	1137	ALA	0	-0.042	-0.004	25.905	0.004	0.004	0.000	0.000	0.000	0.000
39	A	1138	THR	0	0.029	-0.005	26.008	-0.014	-0.014	0.000	0.000	0.000	0.000
40	A	1139	GLY	0	-0.040	-0.016	22.496	0.006	0.006	0.000	0.000	0.000	0.000
41	A	1140	SER	0	-0.015	-0.014	18.878	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	1141	GLY	0	0.013	0.015	21.118	0.017	0.017	0.000	0.000	0.000	0.000
43	A	1142	PRO	0	0.000	0.006	22.444	0.001	0.001	0.000	0.000	0.000	0.000
44	A	1143	LEU	0	0.026	0.033	22.943	0.010	0.010	0.000	0.000	0.000	0.000
45	A	1144	ARG	1	0.991	1.008	20.878	0.039	0.039	0.000	0.000	0.000	0.000
46	A	1145	GLY	0	-0.014	0.010	19.022	-0.007	-0.007	0.000	0.000	0.000	0.000
47	A	1146	SER	0	0.026	-0.019	18.229	0.010	0.010	0.000	0.000	0.000	0.000
48	A	1147	ILE	0	-0.012	0.013	19.313	0.014	0.014	0.000	0.000	0.000	0.000
49	A	1148	THR	0	-0.062	-0.047	15.956	-0.009	-0.009	0.000	0.000	0.000	0.000
50	A	1149	GLN	0	-0.003	-0.006	12.585	0.027	0.027	0.000	0.000	0.000	0.000
51	A	1150	CYS	0	-0.045	-0.025	15.428	0.032	0.032	0.000	0.000	0.000	0.000
52	A	1151	GLN	0	0.004	-0.009	17.691	0.001	0.001	0.000	0.000	0.000	0.000
53	A	1152	GLY	0	0.033	0.026	13.712	-0.016	-0.016	0.000	0.000	0.000	0.000
54	A	1153	LEU	0	0.009	0.005	12.346	0.014	0.014	0.000	0.000	0.000	0.000
55	A	1154	MET	0	-0.017	-0.013	14.604	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	1155	GLN	0	-0.022	-0.004	15.751	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	1156	PHE	0	-0.026	-0.031	11.579	-0.039	-0.039	0.000	0.000	0.000	0.000
58	A	1157	CYS	0	-0.084	-0.019	12.010	0.093	0.093	0.000	0.000	0.000	0.000
59	A	1158	GLY	0	0.077	0.037	13.935	-0.055	-0.055	0.000	0.000	0.000	0.000
60	A	1159	GLY	0	-0.018	-0.021	16.952	0.038	0.038	0.000	0.000	0.000	0.000
61	A	1160	GLU	-1	-0.878	-0.951	19.586	0.167	0.167	0.000	0.000	0.000	0.000
62	A	1161	LEU	0	-0.007	0.005	13.620	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	1162	GLN	0	-0.031	-0.006	17.621	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	1163	ALA	0	-0.007	-0.015	18.753	-0.022	-0.022	0.000	0.000	0.000	0.000
65	A	1164	GLU	-1	-0.744	-0.873	20.936	0.128	0.128	0.000	0.000	0.000	0.000
66	A	1165	ALA	0	0.015	0.002	18.244	-0.009	-0.009	0.000	0.000	0.000	0.000
67	A	1166	SER	0	-0.015	-0.001	20.382	-0.021	-0.021	0.000	0.000	0.000	0.000
68	A	1167	ALA	0	0.016	0.007	23.086	-0.013	-0.013	0.000	0.000	0.000	0.000
69	A	1168	ILE	0	-0.006	0.019	21.942	-0.008	-0.008	0.000	0.000	0.000	0.000
70	A	1169	LEU	0	-0.040	-0.021	20.443	-0.012	-0.012	0.000	0.000	0.000	0.000
71	A	1170	ASN	0	-0.058	-0.040	24.796	-0.018	-0.018	0.000	0.000	0.000	0.000
72	A	1171	THR	0	-0.025	-0.009	27.980	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	1172	PRO	0	-0.084	-0.030	30.059	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	1173	VAL	0	0.030	0.011	30.617	0.005	0.005	0.000	0.000	0.000	0.000
75	A	1174	CYS	0	-0.058	-0.040	33.644	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	1175	GLY	0	-0.007	0.005	36.398	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	1176	ILE	0	-0.043	-0.016	32.315	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	1177	PRO	0	0.023	0.016	29.699	0.005	0.005	0.000	0.000	0.000	0.000
79	A	1178	PHE	0	0.101	0.051	23.521	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	1179	SER	0	0.027	0.012	25.192	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	1180	GLN	0	-0.037	-0.037	26.119	-0.008	-0.008	0.000	0.000	0.000	0.000
82	A	1181	TRP	0	-0.010	-0.017	28.404	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	1182	GLY	0	-0.021	-0.009	25.363	0.002	0.002	0.000	0.000	0.000	0.000
84	A	1183	THR	0	-0.067	-0.041	26.169	-0.012	-0.012	0.000	0.000	0.000	0.000
85	A	1184	ILE	0	-0.021	-0.002	28.606	0.004	0.004	0.000	0.000	0.000	0.000
86	A	1185	GLY	0	0.001	0.002	31.686	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	1186	GLY	0	0.020	0.006	33.885	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	1187	ALA	0	0.012	0.004	34.744	0.002	0.002	0.000	0.000	0.000	0.000
89	A	1188	ALA	0	0.038	0.030	32.574	0.002	0.002	0.000	0.000	0.000	0.000
90	A	1189	SER	0	0.074	0.039	34.374	0.001	0.001	0.000	0.000	0.000	0.000
91	A	1190	ALA	0	-0.011	-0.010	36.026	0.001	0.001	0.000	0.000	0.000	0.000
92	A	1191	TYR	0	0.029	0.022	37.415	0.001	0.001	0.000	0.000	0.000	0.000
93	A	1192	VAL	0	0.023	0.017	35.557	0.002	0.002	0.000	0.000	0.000	0.000
94	A	1193	ALA	0	-0.073	-0.022	38.789	0.000	0.000	0.000	0.000	0.000	0.000
95	A	1194	SER	0	-0.047	-0.055	41.268	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	1195	GLY	0	-0.031	-0.011	43.239	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	1196	VAL	0	-0.053	-0.019	42.215	0.001	0.001	0.000	0.000	0.000	0.000
98	A	1197	ASP	-1	-0.813	-0.882	42.742	0.038	0.038	0.000	0.000	0.000	0.000
99	A	1198	LEU	0	-0.005	-0.003	37.486	0.001	0.001	0.000	0.000	0.000	0.000
100	A	1199	THR	0	-0.025	-0.047	38.085	0.005	0.005	0.000	0.000	0.000	0.000
101	A	1200	GLN	0	-0.078	-0.048	38.063	0.002	0.002	0.000	0.000	0.000	0.000
102	A	1201	ALA	0	0.091	0.036	35.414	0.004	0.004	0.000	0.000	0.000	0.000
103	A	1202	ALA	0	0.001	0.007	33.599	0.004	0.004	0.000	0.000	0.000	0.000
104	A	1203	ASN	0	-0.008	-0.017	33.078	0.009	0.009	0.000	0.000	0.000	0.000
105	A	1204	GLU	-1	-0.783	-0.880	33.077	0.056	0.056	0.000	0.000	0.000	0.000
106	A	1205	ILE	0	-0.013	-0.007	28.083	0.007	0.007	0.000	0.000	0.000	0.000
107	A	1206	LYS	1	0.844	0.940	28.408	-0.072	-0.072	0.000	0.000	0.000	0.000
108	A	1207	GLY	0	0.037	0.024	28.858	0.011	0.011	0.000	0.000	0.000	0.000
109	A	1208	LEU	0	0.019	0.013	26.489	0.012	0.012	0.000	0.000	0.000	0.000
110	A	1209	ALA	0	-0.006	-0.013	24.422	0.015	0.015	0.000	0.000	0.000	0.000
111	A	1210	GLN	0	-0.019	-0.012	24.379	0.014	0.014	0.000	0.000	0.000	0.000
112	A	1211	GLN	0	-0.035	-0.026	25.175	0.010	0.010	0.000	0.000	0.000	0.000
113	A	1212	MET	0	0.016	0.008	20.378	0.016	0.016	0.000	0.000	0.000	0.000
114	A	1213	GLN	0	0.044	0.023	20.136	0.034	0.034	0.000	0.000	0.000	0.000
115	A	1214	LYS	1	0.782	0.915	21.031	-0.115	-0.115	0.000	0.000	0.000	0.000
116	A	1215	LEU	0	0.019	0.027	17.215	0.019	0.019	0.000	0.000	0.000	0.000
117	A	1216	LEU	0	-0.003	0.003	15.848	0.056	0.056	0.000	0.000	0.000	0.000
118	A	1217	SER	0	-0.053	-0.046	16.951	0.044	0.044	0.000	0.000	0.000	0.000
119	A	1218	LEU	0	-0.053	-0.022	17.856	0.016	0.016	0.000	0.000	0.000	0.000
120	A	1219	MET	0	-0.119	-0.045	12.860	0.150	0.150	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:1100:THR)