FMO DATABASE

FMODB ID: YZ9M2

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1583862.431895
FMO2-HF: Nuclear repulsion	1523015.60428
FMO2-HF: Total energy	-60846.827615
FMO2-MP2: Total energy	-61029.893745

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.
-25.19	-18.07	5.858	-5.343	-7.637	-0.023

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 : -0.021

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	-0.036	-0.045	3.838	-2.121	-0.328	-0.019	-0.917	-0.857	0.001
4	A	9	GLU	-1	-0.845	-0.928	6.409	-0.794	-0.794	0.000	0.000	0.000	0.000
5	A	10	ARG	1	0.882	0.937	8.636	1.145	1.145	0.000	0.000	0.000	0.000
6	A	11	ALA	0	0.007	0.011	7.662	0.224	0.224	0.000	0.000	0.000	0.000
7	A	12	LEU	0	-0.015	-0.009	6.359	0.328	0.328	0.000	0.000	0.000	0.000
8	A	13	THR	0	0.015	0.006	9.157	0.142	0.142	0.000	0.000	0.000	0.000
9	A	14	ILE	0	0.017	0.016	12.588	0.080	0.080	0.000	0.000	0.000	0.000
10	A	15	LEU	0	-0.005	-0.003	8.430	0.079	0.079	0.000	0.000	0.000	0.000
11	A	16	THR	0	-0.048	-0.029	12.094	0.048	0.048	0.000	0.000	0.000	0.000
12	A	17	LEU	0	0.009	0.007	14.398	0.007	0.007	0.000	0.000	0.000	0.000
13	A	18	ALA	0	-0.026	-0.007	15.334	0.003	0.003	0.000	0.000	0.000	0.000
14	A	19	GLN	0	0.018	-0.004	15.923	-0.013	-0.013	0.000	0.000	0.000	0.000
15	A	20	LYS	1	0.845	0.911	17.904	-0.095	-0.095	0.000	0.000	0.000	0.000
16	A	21	LEU	0	0.015	0.020	20.220	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	22	ALA	0	0.022	0.018	20.781	-0.009	-0.009	0.000	0.000	0.000	0.000
18	A	23	SER	0	0.028	0.003	22.119	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	24	ASP	-1	-0.894	-0.935	23.841	0.083	0.083	0.000	0.000	0.000	0.000
20	A	25	HIS	0	-0.082	-0.046	25.441	-0.026	-0.026	0.000	0.000	0.000	0.000
21	A	26	GLN	0	-0.020	-0.005	27.143	0.000	0.000	0.000	0.000	0.000	0.000
22	A	27	HIS	0	0.054	0.033	24.151	0.016	0.016	0.000	0.000	0.000	0.000
23	A	28	PRO	0	0.018	0.009	24.449	0.011	0.011	0.000	0.000	0.000	0.000
24	A	29	GLN	0	-0.005	-0.014	21.331	0.051	0.051	0.000	0.000	0.000	0.000
25	A	30	LEU	0	0.038	0.034	15.122	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	31	GLN	0	-0.039	-0.034	18.582	0.060	0.060	0.000	0.000	0.000	0.000
27	A	32	PRO	0	0.047	0.013	17.133	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	33	ILE	0	0.012	0.019	18.207	-0.020	-0.020	0.000	0.000	0.000	0.000
29	A	34	HIS	0	0.051	0.020	18.474	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	35	ILE	0	0.008	0.000	13.727	-0.024	-0.024	0.000	0.000	0.000	0.000
31	A	36	LEU	0	-0.029	-0.012	16.633	-0.051	-0.051	0.000	0.000	0.000	0.000
32	A	37	ALA	0	-0.007	-0.026	19.256	-0.041	-0.041	0.000	0.000	0.000	0.000
33	A	38	ALA	0	0.027	0.019	17.053	-0.031	-0.031	0.000	0.000	0.000	0.000
34	A	39	PHE	0	-0.065	-0.033	13.906	-0.044	-0.044	0.000	0.000	0.000	0.000
35	A	40	ILE	0	-0.081	-0.036	18.850	-0.037	-0.037	0.000	0.000	0.000	0.000
36	A	41	GLU	-1	-0.923	-0.948	20.880	0.027	0.027	0.000	0.000	0.000	0.000
37	A	42	THR	0	-0.041	-0.034	21.954	-0.015	-0.015	0.000	0.000	0.000	0.000
38	A	43	PRO	0	-0.019	-0.006	19.307	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	44	GLU	-1	-0.888	-0.955	19.343	-0.156	-0.156	0.000	0.000	0.000	0.000
40	A	45	ASP	-1	-0.970	-1.004	19.189	-0.378	-0.378	0.000	0.000	0.000	0.000
41	A	46	GLY	0	-0.003	0.023	20.877	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	47	SER	0	-0.077	-0.028	21.332	0.018	0.018	0.000	0.000	0.000	0.000
43	A	48	VAL	0	0.027	0.005	23.467	0.024	0.024	0.000	0.000	0.000	0.000
44	A	49	PRO	0	0.024	0.015	20.825	-0.033	-0.033	0.000	0.000	0.000	0.000
45	A	50	TYR	0	-0.024	-0.041	15.979	0.041	0.041	0.000	0.000	0.000	0.000
46	A	51	LEU	0	0.030	0.015	19.598	0.015	0.015	0.000	0.000	0.000	0.000
47	A	52	GLN	0	-0.007	-0.018	21.024	0.014	0.014	0.000	0.000	0.000	0.000
48	A	53	ASN	0	0.027	0.008	22.406	0.023	0.023	0.000	0.000	0.000	0.000
49	A	54	LEU	0	-0.031	0.002	19.279	0.009	0.009	0.000	0.000	0.000	0.000
50	A	55	ILE	0	0.003	-0.003	23.847	0.014	0.014	0.000	0.000	0.000	0.000
51	A	56	GLU	-1	-0.851	-0.916	26.438	-0.043	-0.043	0.000	0.000	0.000	0.000
52	A	57	LYS	1	0.827	0.927	24.789	0.127	0.127	0.000	0.000	0.000	0.000
53	A	58	GLY	0	0.022	0.011	27.770	0.004	0.004	0.000	0.000	0.000	0.000
54	A	59	ARG	1	0.826	0.920	28.833	0.038	0.038	0.000	0.000	0.000	0.000
55	A	60	TYR	0	0.036	0.017	29.110	0.011	0.011	0.000	0.000	0.000	0.000
56	A	61	ASP	-1	-0.843	-0.923	31.456	0.018	0.018	0.000	0.000	0.000	0.000
57	A	62	TYR	0	0.102	0.026	25.131	0.018	0.018	0.000	0.000	0.000	0.000
58	A	63	ASP	-1	-0.825	-0.922	29.586	0.013	0.013	0.000	0.000	0.000	0.000
59	A	64	LEU	0	-0.075	-0.033	32.034	0.008	0.008	0.000	0.000	0.000	0.000
60	A	65	PHE	0	0.038	0.011	23.481	0.011	0.011	0.000	0.000	0.000	0.000
61	A	66	LYS	1	0.884	0.948	26.790	0.011	0.011	0.000	0.000	0.000	0.000
62	A	67	LYS	1	0.874	0.953	28.429	-0.027	-0.027	0.000	0.000	0.000	0.000
63	A	68	VAL	0	-0.008	-0.001	28.847	0.008	0.008	0.000	0.000	0.000	0.000
64	A	69	VAL	0	0.054	0.037	23.622	0.016	0.016	0.000	0.000	0.000	0.000
65	A	70	ASN	0	0.039	0.003	26.647	0.022	0.022	0.000	0.000	0.000	0.000
66	A	71	ARG	1	0.881	0.955	28.100	-0.109	-0.109	0.000	0.000	0.000	0.000
67	A	72	ASN	0	-0.074	-0.059	27.105	0.010	0.010	0.000	0.000	0.000	0.000
68	A	73	LEU	0	0.024	0.025	23.397	0.016	0.016	0.000	0.000	0.000	0.000
69	A	74	VAL	0	-0.020	-0.012	26.632	0.006	0.006	0.000	0.000	0.000	0.000
70	A	75	ARG	1	0.902	0.953	29.680	-0.124	-0.124	0.000	0.000	0.000	0.000
71	A	76	ILE	0	-0.032	0.003	24.672	0.008	0.008	0.000	0.000	0.000	0.000
72	A	77	PRO	0	-0.051	-0.020	29.042	-0.010	-0.010	0.000	0.000	0.000	0.000
73	A	78	GLN	0	0.022	0.004	29.855	0.011	0.011	0.000	0.000	0.000	0.000
74	A	79	GLN	0	-0.049	-0.023	28.830	0.007	0.007	0.000	0.000	0.000	0.000
75	A	80	GLN	0	-0.030	-0.042	30.311	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	81	PRO	0	-0.034	-0.012	31.808	-0.006	-0.006	0.000	0.000	0.000	0.000
77	A	82	ALA	0	0.052	0.032	27.981	0.013	0.013	0.000	0.000	0.000	0.000
78	A	83	PRO	0	-0.056	-0.005	24.855	-0.009	-0.009	0.000	0.000	0.000	0.000
79	A	84	ALA	0	0.006	-0.003	25.029	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	85	GLU	-1	-0.951	-0.976	19.155	0.421	0.421	0.000	0.000	0.000	0.000
81	A	86	ILE	0	0.012	0.017	19.878	-0.009	-0.009	0.000	0.000	0.000	0.000
82	A	87	THR	0	0.031	0.014	18.608	0.029	0.029	0.000	0.000	0.000	0.000
83	A	88	PRO	0	-0.031	-0.003	14.506	-0.020	-0.020	0.000	0.000	0.000	0.000
84	A	89	SER	0	0.027	0.011	17.068	0.022	0.022	0.000	0.000	0.000	0.000
85	A	90	TYR	0	0.024	-0.010	17.388	0.073	0.073	0.000	0.000	0.000	0.000
86	A	91	ALA	0	0.006	-0.001	17.353	0.081	0.081	0.000	0.000	0.000	0.000
87	A	92	LEU	0	0.028	0.021	13.499	0.063	0.063	0.000	0.000	0.000	0.000
88	A	93	GLY	0	0.046	0.028	13.091	0.124	0.124	0.000	0.000	0.000	0.000
89	A	94	LYS	1	0.862	0.910	12.541	-0.731	-0.731	0.000	0.000	0.000	0.000
90	A	95	VAL	0	0.012	0.023	12.711	0.172	0.172	0.000	0.000	0.000	0.000
91	A	96	LEU	0	0.016	0.003	8.660	0.145	0.145	0.000	0.000	0.000	0.000
92	A	97	GLN	0	0.004	0.011	8.528	0.435	0.435	0.000	0.000	0.000	0.000
93	A	98	ASP	-1	-0.783	-0.893	9.517	1.618	1.618	0.000	0.000	0.000	0.000
94	A	99	ALA	0	0.039	0.038	8.275	0.082	0.082	0.000	0.000	0.000	0.000
95	A	100	ALA	0	0.033	0.012	4.959	0.262	0.357	-0.001	-0.003	-0.091	0.000
96	A	101	LYS	1	0.777	0.875	6.202	-1.266	-1.266	0.000	0.000	0.000	0.000
97	A	102	ILE	0	0.019	0.011	8.932	-0.250	-0.250	0.000	0.000	0.000	0.000
98	A	103	GLN	0	0.027	0.014	3.106	4.548	5.854	0.121	-0.619	-0.807	0.001
99	A	104	LYS	1	0.856	0.913	3.130	-15.141	-14.258	0.024	-0.384	-0.523	0.004
100	A	105	GLN	0	-0.020	-0.005	7.998	-0.566	-0.566	0.000	0.000	0.000	0.000
101	A	106	GLN	0	0.005	0.013	10.312	-0.161	-0.161	0.000	0.000	0.000	0.000
102	A	107	LYS	1	0.882	0.940	9.146	-0.260	-0.260	0.000	0.000	0.000	0.000
103	A	108	ASP	-1	-0.749	-0.840	6.881	-1.078	-1.078	0.000	0.000	0.000	0.000
104	A	109	SER	0	-0.016	-0.005	4.143	0.981	1.260	-0.001	-0.112	-0.167	0.000
105	A	110	PHE	0	-0.080	-0.034	2.037	-14.801	-13.898	5.658	-2.739	-3.822	-0.031
106	A	111	ILE	0	-0.026	-0.011	3.224	1.014	2.735	0.076	-0.539	-1.259	0.002
107	A	112	ALA	0	0.030	0.006	5.546	-0.767	-0.767	0.000	0.000	0.000	0.000
108	A	113	GLN	0	-0.020	-0.035	8.905	0.522	0.522	0.000	0.000	0.000	0.000
109	A	114	ASP	-1	-0.763	-0.857	11.710	-0.235	-0.235	0.000	0.000	0.000	0.000
110	A	115	HIS	0	0.002	0.013	7.512	0.375	0.375	0.000	0.000	0.000	0.000
111	A	116	ILE	0	0.023	0.008	8.294	0.208	0.208	0.000	0.000	0.000	0.000
112	A	117	LEU	0	-0.009	0.013	11.459	0.052	0.052	0.000	0.000	0.000	0.000
113	A	118	PHE	0	0.007	-0.014	13.662	0.022	0.022	0.000	0.000	0.000	0.000
114	A	119	ALA	0	-0.041	-0.011	12.250	0.029	0.029	0.000	0.000	0.000	0.000
115	A	120	LEU	0	-0.039	-0.026	14.347	-0.010	-0.010	0.000	0.000	0.000	0.000
116	A	121	PHE	0	0.030	0.015	16.692	-0.034	-0.034	0.000	0.000	0.000	0.000
117	A	122	ASN	0	-0.035	-0.010	15.875	-0.108	-0.108	0.000	0.000	0.000	0.000
118	A	123	ASP	-1	-0.823	-0.899	18.477	0.474	0.474	0.000	0.000	0.000	0.000
119	A	124	SER	0	0.031	0.005	20.300	-0.035	-0.035	0.000	0.000	0.000	0.000
120	A	125	SER	0	-0.073	-0.040	22.006	-0.043	-0.043	0.000	0.000	0.000	0.000
121	A	126	ILE	0	0.017	0.008	19.167	-0.041	-0.041	0.000	0.000	0.000	0.000
122	A	127	GLN	0	-0.026	-0.026	22.274	-0.059	-0.059	0.000	0.000	0.000	0.000
123	A	128	GLN	0	-0.058	-0.033	24.938	-0.026	-0.026	0.000	0.000	0.000	0.000
124	A	129	ILE	0	0.016	-0.002	24.260	-0.024	-0.024	0.000	0.000	0.000	0.000
125	A	130	PHE	0	0.019	-0.003	21.939	-0.022	-0.022	0.000	0.000	0.000	0.000
126	A	131	LYS	1	0.900	0.963	26.907	-0.207	-0.207	0.000	0.000	0.000	0.000
127	A	132	GLU	-1	-0.890	-0.949	30.055	0.146	0.146	0.000	0.000	0.000	0.000
128	A	133	ALA	0	-0.068	-0.026	28.792	-0.014	-0.014	0.000	0.000	0.000	0.000
129	A	134	GLN	0	-0.066	-0.026	30.865	-0.016	-0.016	0.000	0.000	0.000	0.000
130	A	135	VAL	0	-0.011	-0.003	26.606	-0.012	-0.012	0.000	0.000	0.000	0.000
131	A	136	ASP	-1	-0.844	-0.928	28.359	0.162	0.162	0.000	0.000	0.000	0.000
132	A	137	ILE	0	0.007	-0.003	22.494	-0.008	-0.008	0.000	0.000	0.000	0.000
133	A	138	GLU	-1	-0.812	-0.888	23.789	0.271	0.271	0.000	0.000	0.000	0.000
134	A	139	ALA	0	0.025	0.022	24.897	-0.014	-0.014	0.000	0.000	0.000	0.000
135	A	140	ILE	0	-0.021	-0.006	21.541	-0.023	-0.023	0.000	0.000	0.000	0.000
136	A	141	LYS	1	0.790	0.875	19.554	-0.330	-0.330	0.000	0.000	0.000	0.000
137	A	142	GLN	0	-0.050	-0.034	20.738	0.003	0.003	0.000	0.000	0.000	0.000
138	A	143	GLN	0	-0.012	-0.022	22.734	-0.045	-0.045	0.000	0.000	0.000	0.000
139	A	144	ALA	0	0.007	-0.001	17.801	-0.042	-0.042	0.000	0.000	0.000	0.000
140	A	145	LEU	0	-0.046	-0.024	17.100	-0.052	-0.052	0.000	0.000	0.000	0.000
141	A	146	GLU	-1	-0.878	-0.919	19.241	-0.078	-0.078	0.000	0.000	0.000	0.000
142	A	147	LEU	0	-0.083	-0.030	17.998	-0.034	-0.034	0.000	0.000	0.000	0.000
143	A	148	ARG	1	0.843	0.907	13.344	0.411	0.411	0.000	0.000	0.000	0.000
144	A	149	GLY	0	0.061	0.045	17.495	-0.073	-0.073	0.000	0.000	0.000	0.000
145	A	150	ASN	0	-0.088	-0.055	17.363	-0.011	-0.011	0.000	0.000	0.000	0.000
146	A	151	THR	0	-0.037	-0.020	13.947	-0.061	-0.061	0.000	0.000	0.000	0.000
147	A	152	ARG	1	0.829	0.916	9.414	0.818	0.818	0.000	0.000	0.000	0.000
148	A	153	ILE	0	0.021	-0.007	8.080	-0.145	-0.145	0.000	0.000	0.000	0.000
149	A	154	ASP	-1	-0.901	-0.968	7.206	-2.470	-2.470	0.000	0.000	0.000	0.000
150	A	155	SER	0	0.037	0.019	8.502	-0.263	-0.263	0.000	0.000	0.000	0.000
151	A	156	ARG	1	0.834	0.906	3.743	2.192	2.332	0.000	-0.030	-0.111	0.000
152	A	157	GLY	0	0.111	0.053	7.355	0.437	0.437	0.000	0.000	0.000	0.000
153	A	158	ALA	0	-0.018	0.004	10.397	0.277	0.277	0.000	0.000	0.000	0.000
154	A	159	ASP	-1	-0.743	-0.837	10.703	-0.905	-0.905	0.000	0.000	0.000	0.000
155	A	160	THR	0	-0.023	-0.009	12.809	0.165	0.165	0.000	0.000	0.000	0.000
156	A	161	ASN	0	0.071	0.039	16.239	0.031	0.031	0.000	0.000	0.000	0.000
157	A	162	THR	0	0.012	0.018	18.595	0.067	0.067	0.000	0.000	0.000	0.000

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