FMO DATABASE

FMODB ID: 52R8Z

Calculation Name: 5U2U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5U2U

Chain ID: A

ChEMBL ID:

UniProt ID: P31539

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:

Apendix: None

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	157
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1583439.454008
FMO2-HF: Nuclear repulsion	1522593.768744
FMO2-HF: Total energy	-60845.685264
FMO2-MP2: Total energy	-61028.822435

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:6:GLN)

Summations of interaction energy for fragment #1(A:6:GLN)

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.
-24.706	-16.629	4.29	-5.213	-7.154	-0.022

Interaction energy analysis for fragmet #1(A:6:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : -0.020

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	8	THR	0	-0.046	-0.046	3.841	-2.338	-0.561	-0.021	-0.916	-0.840	0.002
4	A	9	GLU	-1	-0.890	-0.965	6.468	-0.173	-0.173	0.000	0.000	0.000	0.000
5	A	10	ARG	1	0.935	0.981	8.703	0.652	0.652	0.000	0.000	0.000	0.000
6	A	11	ALA	0	0.012	0.016	7.663	0.177	0.177	0.000	0.000	0.000	0.000
7	A	12	LEU	0	-0.012	-0.015	6.010	0.303	0.303	0.000	0.000	0.000	0.000
8	A	13	THR	0	0.009	0.001	9.243	0.036	0.036	0.000	0.000	0.000	0.000
9	A	14	ILE	0	0.018	0.017	12.600	0.034	0.034	0.000	0.000	0.000	0.000
10	A	15	LEU	0	0.000	-0.003	8.381	0.020	0.020	0.000	0.000	0.000	0.000
11	A	16	THR	0	-0.040	-0.020	12.194	-0.027	-0.027	0.000	0.000	0.000	0.000
12	A	17	LEU	0	-0.012	-0.001	14.411	-0.034	-0.034	0.000	0.000	0.000	0.000
13	A	18	ALA	0	-0.021	-0.008	15.319	-0.032	-0.032	0.000	0.000	0.000	0.000
14	A	19	GLN	0	-0.003	-0.009	15.159	-0.074	-0.074	0.000	0.000	0.000	0.000
15	A	20	LYS	1	0.955	0.981	17.870	-0.286	-0.286	0.000	0.000	0.000	0.000
16	A	21	LEU	0	0.027	0.026	20.078	-0.029	-0.029	0.000	0.000	0.000	0.000
17	A	22	ALA	0	0.016	0.011	20.796	-0.025	-0.025	0.000	0.000	0.000	0.000
18	A	23	SER	0	0.024	0.001	22.107	-0.030	-0.030	0.000	0.000	0.000	0.000
19	A	24	ASP	-1	-0.968	-0.984	23.865	0.231	0.231	0.000	0.000	0.000	0.000
20	A	25	HIS	0	-0.087	-0.042	25.669	-0.040	-0.040	0.000	0.000	0.000	0.000
21	A	26	GLN	0	-0.010	-0.012	27.118	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	27	HIS	0	0.046	0.032	24.142	0.021	0.021	0.000	0.000	0.000	0.000
23	A	28	PRO	0	0.014	0.010	24.430	0.016	0.016	0.000	0.000	0.000	0.000
24	A	29	GLN	0	0.006	-0.013	21.220	0.055	0.055	0.000	0.000	0.000	0.000
25	A	30	LEU	0	0.034	0.024	15.048	-0.012	-0.012	0.000	0.000	0.000	0.000
26	A	31	GLN	0	-0.068	-0.056	18.555	0.051	0.051	0.000	0.000	0.000	0.000
27	A	32	PRO	0	0.057	0.009	17.112	0.009	0.009	0.000	0.000	0.000	0.000
28	A	33	ILE	0	0.020	0.022	18.184	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	34	HIS	0	0.048	0.025	18.429	0.016	0.016	0.000	0.000	0.000	0.000
30	A	35	ILE	0	0.011	0.014	13.739	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	36	LEU	0	-0.032	-0.016	16.606	-0.042	-0.042	0.000	0.000	0.000	0.000
32	A	37	ALA	0	-0.009	-0.028	19.233	-0.048	-0.048	0.000	0.000	0.000	0.000
33	A	38	ALA	0	0.024	0.020	17.038	-0.044	-0.044	0.000	0.000	0.000	0.000
34	A	39	PHE	0	-0.059	-0.031	13.816	-0.038	-0.038	0.000	0.000	0.000	0.000
35	A	40	ILE	0	-0.084	-0.036	18.826	-0.052	-0.052	0.000	0.000	0.000	0.000
36	A	41	GLU	-1	-0.937	-0.949	20.849	0.207	0.207	0.000	0.000	0.000	0.000
37	A	42	THR	0	-0.038	-0.039	22.034	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	43	PRO	0	-0.018	-0.004	19.295	0.006	0.006	0.000	0.000	0.000	0.000
39	A	44	GLU	-1	-0.897	-0.962	19.781	0.029	0.029	0.000	0.000	0.000	0.000
40	A	45	ASP	-1	-1.007	-1.012	18.449	-0.162	-0.162	0.000	0.000	0.000	0.000
41	A	46	GLY	0	0.003	0.028	20.943	-0.017	-0.017	0.000	0.000	0.000	0.000
42	A	47	SER	0	-0.039	-0.020	21.405	-0.011	-0.011	0.000	0.000	0.000	0.000
43	A	48	VAL	0	-0.006	-0.009	23.532	0.024	0.024	0.000	0.000	0.000	0.000
44	A	49	PRO	0	0.002	0.009	20.886	-0.018	-0.018	0.000	0.000	0.000	0.000
45	A	50	TYR	0	0.045	0.015	16.472	0.028	0.028	0.000	0.000	0.000	0.000
46	A	51	LEU	0	0.036	0.016	19.604	0.001	0.001	0.000	0.000	0.000	0.000
47	A	52	GLN	0	0.011	0.001	21.008	0.003	0.003	0.000	0.000	0.000	0.000
48	A	53	ASN	0	0.002	-0.004	22.164	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	54	LEU	0	-0.048	-0.008	19.204	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	55	ILE	0	-0.003	-0.007	23.838	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	56	GLU	-1	-0.870	-0.934	26.426	0.086	0.086	0.000	0.000	0.000	0.000
52	A	57	LYS	1	0.872	0.943	25.381	-0.040	-0.040	0.000	0.000	0.000	0.000
53	A	58	GLY	0	0.008	0.009	27.641	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	59	ARG	1	0.836	0.923	28.654	-0.076	-0.076	0.000	0.000	0.000	0.000
55	A	60	TYR	0	0.033	0.017	28.790	0.003	0.003	0.000	0.000	0.000	0.000
56	A	61	ASP	-1	-0.842	-0.929	31.442	0.129	0.129	0.000	0.000	0.000	0.000
57	A	62	TYR	0	0.094	0.026	24.924	0.026	0.026	0.000	0.000	0.000	0.000
58	A	63	ASP	-1	-0.901	-0.948	29.566	0.137	0.137	0.000	0.000	0.000	0.000
59	A	64	LEU	0	-0.065	-0.038	32.012	0.009	0.009	0.000	0.000	0.000	0.000
60	A	65	PHE	0	0.032	0.012	23.492	0.013	0.013	0.000	0.000	0.000	0.000
61	A	66	LYS	1	0.976	0.992	26.656	-0.137	-0.137	0.000	0.000	0.000	0.000
62	A	67	LYS	1	0.902	0.961	28.406	-0.134	-0.134	0.000	0.000	0.000	0.000
63	A	68	VAL	0	-0.002	0.008	28.888	0.004	0.004	0.000	0.000	0.000	0.000
64	A	69	VAL	0	0.060	0.055	23.596	0.015	0.015	0.000	0.000	0.000	0.000
65	A	70	ASN	0	0.034	0.000	26.688	0.031	0.031	0.000	0.000	0.000	0.000
66	A	71	ARG	1	0.899	0.952	28.073	-0.223	-0.223	0.000	0.000	0.000	0.000
67	A	72	ASN	0	-0.079	-0.062	27.038	0.002	0.002	0.000	0.000	0.000	0.000
68	A	73	LEU	0	0.023	0.019	23.475	0.016	0.016	0.000	0.000	0.000	0.000
69	A	74	VAL	0	-0.015	-0.009	26.603	0.002	0.002	0.000	0.000	0.000	0.000
70	A	75	ARG	1	0.903	0.952	29.650	-0.235	-0.235	0.000	0.000	0.000	0.000
71	A	76	ILE	0	-0.029	0.003	24.749	0.003	0.003	0.000	0.000	0.000	0.000
72	A	77	PRO	0	-0.049	-0.017	29.013	-0.012	-0.012	0.000	0.000	0.000	0.000
73	A	78	GLN	0	-0.015	-0.016	29.825	0.015	0.015	0.000	0.000	0.000	0.000
74	A	79	GLN	0	-0.045	-0.030	28.835	0.001	0.001	0.000	0.000	0.000	0.000
75	A	80	GLN	0	-0.038	-0.027	30.334	-0.006	-0.006	0.000	0.000	0.000	0.000
76	A	81	PRO	0	-0.010	0.004	31.835	-0.011	-0.011	0.000	0.000	0.000	0.000
77	A	82	ALA	0	0.044	0.026	27.927	0.016	0.016	0.000	0.000	0.000	0.000
78	A	83	PRO	0	-0.057	-0.010	24.892	-0.016	-0.016	0.000	0.000	0.000	0.000
79	A	84	ALA	0	0.001	-0.002	25.008	0.002	0.002	0.000	0.000	0.000	0.000
80	A	85	GLU	-1	-0.925	-0.969	19.059	0.557	0.557	0.000	0.000	0.000	0.000
81	A	86	ILE	0	0.008	0.011	19.915	-0.017	-0.017	0.000	0.000	0.000	0.000
82	A	87	THR	0	0.029	0.006	18.629	0.045	0.045	0.000	0.000	0.000	0.000
83	A	88	PRO	0	-0.053	0.002	14.537	-0.012	-0.012	0.000	0.000	0.000	0.000
84	A	89	SER	0	0.048	0.031	17.040	0.002	0.002	0.000	0.000	0.000	0.000
85	A	90	TYR	0	0.032	-0.006	17.367	0.113	0.113	0.000	0.000	0.000	0.000
86	A	91	ALA	0	-0.002	-0.004	17.338	0.098	0.098	0.000	0.000	0.000	0.000
87	A	92	LEU	0	0.026	0.019	13.415	0.087	0.087	0.000	0.000	0.000	0.000
88	A	93	GLY	0	0.044	0.026	13.072	0.195	0.195	0.000	0.000	0.000	0.000
89	A	94	LYS	1	0.964	0.971	12.529	-0.871	-0.871	0.000	0.000	0.000	0.000
90	A	95	VAL	0	0.024	0.035	12.508	0.216	0.216	0.000	0.000	0.000	0.000
91	A	96	LEU	0	0.008	-0.004	8.658	0.260	0.260	0.000	0.000	0.000	0.000
92	A	97	GLN	0	-0.044	-0.021	8.519	0.642	0.642	0.000	0.000	0.000	0.000
93	A	98	ASP	-1	-0.902	-0.972	9.430	2.032	2.032	0.000	0.000	0.000	0.000
94	A	99	ALA	0	0.007	0.016	8.219	0.098	0.098	0.000	0.000	0.000	0.000
95	A	100	ALA	0	0.039	0.014	4.809	0.495	0.630	-0.001	-0.004	-0.130	0.000
96	A	101	LYS	1	0.875	0.939	6.003	-1.805	-1.805	0.000	0.000	0.000	0.000
97	A	102	ILE	0	0.025	0.013	8.875	-0.378	-0.378	0.000	0.000	0.000	0.000
98	A	103	GLN	0	-0.007	-0.020	2.690	4.695	6.169	0.193	-0.743	-0.924	0.001
99	A	104	LYS	1	0.874	0.937	3.962	-11.898	-11.632	-0.001	-0.073	-0.192	0.000
100	A	105	GLN	0	-0.033	-0.013	7.970	-0.784	-0.784	0.000	0.000	0.000	0.000
101	A	106	GLN	0	0.002	0.014	10.330	-0.263	-0.263	0.000	0.000	0.000	0.000
102	A	107	LYS	1	0.887	0.945	9.218	-0.212	-0.212	0.000	0.000	0.000	0.000
103	A	108	ASP	-1	-0.733	-0.837	7.042	-0.712	-0.712	0.000	0.000	0.000	0.000
104	A	109	SER	0	-0.016	-0.001	4.115	1.008	1.259	-0.001	-0.102	-0.148	0.000
105	A	110	PHE	0	-0.092	-0.044	2.072	-16.424	-14.742	3.914	-2.391	-3.205	-0.032
106	A	111	ILE	0	-0.007	0.002	3.008	-0.365	2.053	0.208	-0.945	-1.681	0.007
107	A	112	ALA	0	0.027	0.001	5.431	-1.139	-1.211	-0.001	-0.006	0.080	0.000
108	A	113	GLN	0	-0.028	-0.038	8.898	0.555	0.555	0.000	0.000	0.000	0.000
109	A	114	ASP	-1	-0.781	-0.909	11.696	0.318	0.318	0.000	0.000	0.000	0.000
110	A	115	HIS	0	-0.018	0.010	7.628	0.719	0.719	0.000	0.000	0.000	0.000
111	A	116	ILE	0	0.020	0.008	8.358	0.123	0.123	0.000	0.000	0.000	0.000
112	A	117	LEU	0	-0.009	0.012	11.446	-0.052	-0.052	0.000	0.000	0.000	0.000
113	A	118	PHE	0	-0.004	-0.016	13.100	-0.049	-0.049	0.000	0.000	0.000	0.000
114	A	119	ALA	0	-0.035	-0.011	11.988	-0.039	-0.039	0.000	0.000	0.000	0.000
115	A	120	LEU	0	-0.032	-0.024	14.120	-0.085	-0.085	0.000	0.000	0.000	0.000
116	A	121	PHE	0	0.018	0.008	16.679	-0.083	-0.083	0.000	0.000	0.000	0.000
117	A	122	ASN	0	-0.038	-0.001	15.769	-0.179	-0.179	0.000	0.000	0.000	0.000
118	A	123	ASP	-1	-0.831	-0.901	18.439	0.696	0.696	0.000	0.000	0.000	0.000
119	A	124	SER	0	0.050	0.006	20.289	-0.033	-0.033	0.000	0.000	0.000	0.000
120	A	125	SER	0	-0.072	-0.034	22.069	-0.052	-0.052	0.000	0.000	0.000	0.000
121	A	126	ILE	0	0.016	0.011	19.180	-0.050	-0.050	0.000	0.000	0.000	0.000
122	A	127	GLN	0	-0.031	-0.039	22.023	-0.086	-0.086	0.000	0.000	0.000	0.000
123	A	128	GLN	0	-0.064	-0.023	24.926	-0.037	-0.037	0.000	0.000	0.000	0.000
124	A	129	ILE	0	0.025	0.003	23.909	-0.031	-0.031	0.000	0.000	0.000	0.000
125	A	130	PHE	0	0.006	-0.011	21.952	-0.025	-0.025	0.000	0.000	0.000	0.000
126	A	131	LYS	1	0.941	0.985	26.892	-0.316	-0.316	0.000	0.000	0.000	0.000
127	A	132	GLU	-1	-0.959	-0.988	30.044	0.268	0.268	0.000	0.000	0.000	0.000
128	A	133	ALA	0	-0.058	-0.024	28.779	-0.021	-0.021	0.000	0.000	0.000	0.000
129	A	134	GLN	0	-0.067	-0.028	30.848	-0.018	-0.018	0.000	0.000	0.000	0.000
130	A	135	VAL	0	-0.008	-0.004	26.663	-0.013	-0.013	0.000	0.000	0.000	0.000
131	A	136	ASP	-1	-0.868	-0.938	28.214	0.301	0.301	0.000	0.000	0.000	0.000
132	A	137	ILE	0	0.025	0.003	22.031	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	138	GLU	-1	-0.860	-0.930	23.395	0.460	0.460	0.000	0.000	0.000	0.000
134	A	139	ALA	0	0.020	0.021	24.482	-0.011	-0.011	0.000	0.000	0.000	0.000
135	A	140	ILE	0	-0.018	-0.006	21.298	-0.019	-0.019	0.000	0.000	0.000	0.000
136	A	141	LYS	1	0.843	0.917	18.955	-0.560	-0.560	0.000	0.000	0.000	0.000
137	A	142	GLN	0	-0.036	-0.014	20.534	0.018	0.018	0.000	0.000	0.000	0.000
138	A	143	GLN	0	0.020	0.002	22.822	-0.046	-0.046	0.000	0.000	0.000	0.000
139	A	144	ALA	0	0.001	-0.001	17.665	-0.038	-0.038	0.000	0.000	0.000	0.000
140	A	145	LEU	0	-0.040	-0.025	17.275	-0.032	-0.032	0.000	0.000	0.000	0.000
141	A	146	GLU	-1	-0.925	-0.957	19.388	0.041	0.041	0.000	0.000	0.000	0.000
142	A	147	LEU	0	-0.095	-0.036	18.117	-0.041	-0.041	0.000	0.000	0.000	0.000
143	A	148	ARG	1	0.849	0.943	14.228	0.070	0.070	0.000	0.000	0.000	0.000
144	A	149	GLY	0	0.058	0.035	17.615	-0.090	-0.090	0.000	0.000	0.000	0.000
145	A	150	ASN	0	-0.104	-0.063	17.453	-0.005	-0.005	0.000	0.000	0.000	0.000
146	A	151	THR	0	-0.005	0.004	13.771	-0.096	-0.096	0.000	0.000	0.000	0.000
147	A	152	ARG	1	0.821	0.908	9.529	0.709	0.709	0.000	0.000	0.000	0.000
148	A	153	ILE	0	0.021	-0.004	7.890	-0.170	-0.170	0.000	0.000	0.000	0.000
149	A	154	ASP	-1	-0.896	-0.966	7.285	-2.392	-2.392	0.000	0.000	0.000	0.000
150	A	155	SER	0	0.037	0.018	8.534	-0.364	-0.364	0.000	0.000	0.000	0.000
151	A	156	ARG	1	0.855	0.927	3.626	1.688	1.834	0.000	-0.033	-0.114	0.000
152	A	157	GLY	0	0.090	0.042	7.377	0.481	0.481	0.000	0.000	0.000	0.000
153	A	158	ALA	0	-0.012	0.002	10.449	0.224	0.224	0.000	0.000	0.000	0.000
154	A	159	ASP	-1	-0.743	-0.852	10.778	-0.225	-0.225	0.000	0.000	0.000	0.000
155	A	160	THR	0	-0.047	-0.023	12.799	0.153	0.153	0.000	0.000	0.000	0.000
156	A	161	ASN	0	0.093	0.038	16.239	0.054	0.054	0.000	0.000	0.000	0.000
157	A	162	THR	0	0.025	0.024	18.621	0.045	0.045	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:GLN)