FMO DATABASE

FMODB ID: V5V61

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1589049.493954
FMO2-HF: Nuclear repulsion	1528202.290483
FMO2-HF: Total energy	-60847.203471
FMO2-MP2: Total energy	-61030.197945

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.
-36.29	-27.295	8.217	-7.194	-10.017	0.004

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 : 0.018 / q_NPA : -0.018

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	-0.009	-0.023	3.879	-2.597	-1.066	-0.014	-0.776	-0.741	0.001
4	A	9	GLU	-1	-0.789	-0.893	6.729	-1.649	-1.649	0.000	0.000	0.000	0.000
5	A	10	ARG	1	0.840	0.923	9.040	1.344	1.344	0.000	0.000	0.000	0.000
6	A	11	ALA	0	0.016	0.016	7.543	0.263	0.263	0.000	0.000	0.000	0.000
7	A	12	LEU	0	-0.006	-0.006	6.326	0.332	0.332	0.000	0.000	0.000	0.000
8	A	13	THR	0	0.011	0.002	8.825	0.202	0.202	0.000	0.000	0.000	0.000
9	A	14	ILE	0	0.011	0.009	12.409	0.107	0.107	0.000	0.000	0.000	0.000
10	A	15	LEU	0	-0.024	-0.018	8.483	0.113	0.113	0.000	0.000	0.000	0.000
11	A	16	THR	0	-0.039	-0.031	11.677	0.072	0.072	0.000	0.000	0.000	0.000
12	A	17	LEU	0	-0.007	0.004	14.040	0.020	0.020	0.000	0.000	0.000	0.000
13	A	18	ALA	0	-0.005	0.002	15.603	0.020	0.020	0.000	0.000	0.000	0.000
14	A	19	GLN	0	0.016	-0.009	15.839	0.013	0.013	0.000	0.000	0.000	0.000
15	A	20	LYS	1	0.830	0.904	17.803	0.022	0.022	0.000	0.000	0.000	0.000
16	A	21	LEU	0	-0.004	0.004	20.279	0.011	0.011	0.000	0.000	0.000	0.000
17	A	22	ALA	0	-0.001	0.011	20.630	0.004	0.004	0.000	0.000	0.000	0.000
18	A	23	SER	0	0.021	-0.001	21.988	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	24	ASP	-1	-0.872	-0.919	23.778	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	25	HIS	0	-0.081	-0.044	25.526	-0.018	-0.018	0.000	0.000	0.000	0.000
21	A	26	GLN	0	-0.012	-0.007	27.089	0.007	0.007	0.000	0.000	0.000	0.000
22	A	27	HIS	0	0.054	0.036	23.987	0.019	0.019	0.000	0.000	0.000	0.000
23	A	28	PRO	0	0.016	0.005	23.978	0.006	0.006	0.000	0.000	0.000	0.000
24	A	29	GLN	0	-0.018	-0.019	20.919	0.051	0.051	0.000	0.000	0.000	0.000
25	A	30	LEU	0	0.028	0.038	14.836	-0.015	-0.015	0.000	0.000	0.000	0.000
26	A	31	GLN	0	-0.018	-0.015	18.108	0.078	0.078	0.000	0.000	0.000	0.000
27	A	32	PRO	0	0.019	0.006	16.813	-0.027	-0.027	0.000	0.000	0.000	0.000
28	A	33	ILE	0	0.019	0.013	17.885	-0.027	-0.027	0.000	0.000	0.000	0.000
29	A	34	HIS	0	0.046	0.013	18.592	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	35	ILE	0	0.006	0.000	13.575	-0.037	-0.037	0.000	0.000	0.000	0.000
31	A	36	LEU	0	-0.033	-0.016	16.607	-0.051	-0.051	0.000	0.000	0.000	0.000
32	A	37	ALA	0	0.012	-0.002	19.126	-0.037	-0.037	0.000	0.000	0.000	0.000
33	A	38	ALA	0	0.033	0.014	16.909	-0.033	-0.033	0.000	0.000	0.000	0.000
34	A	39	PHE	0	-0.062	-0.036	13.301	-0.050	-0.050	0.000	0.000	0.000	0.000
35	A	40	ILE	0	-0.063	-0.033	18.544	-0.025	-0.025	0.000	0.000	0.000	0.000
36	A	41	GLU	-1	-0.908	-0.944	21.267	-0.065	-0.065	0.000	0.000	0.000	0.000
37	A	42	THR	0	-0.029	-0.028	22.087	-0.017	-0.017	0.000	0.000	0.000	0.000
38	A	43	PRO	0	-0.010	0.001	19.561	-0.011	-0.011	0.000	0.000	0.000	0.000
39	A	44	GLU	-1	-0.905	-0.961	19.178	-0.307	-0.307	0.000	0.000	0.000	0.000
40	A	45	ASP	-1	-0.922	-0.939	19.130	-0.508	-0.508	0.000	0.000	0.000	0.000
41	A	46	GLY	0	-0.012	0.006	20.921	0.001	0.001	0.000	0.000	0.000	0.000
42	A	47	SER	0	-0.093	-0.050	21.253	0.028	0.028	0.000	0.000	0.000	0.000
43	A	48	VAL	0	0.025	0.008	23.430	0.015	0.015	0.000	0.000	0.000	0.000
44	A	49	PRO	0	0.041	0.021	20.533	-0.038	-0.038	0.000	0.000	0.000	0.000
45	A	50	TYR	0	-0.030	-0.044	15.806	0.061	0.061	0.000	0.000	0.000	0.000
46	A	51	LEU	0	0.024	0.013	19.213	0.030	0.030	0.000	0.000	0.000	0.000
47	A	52	GLN	0	-0.024	-0.021	20.596	0.016	0.016	0.000	0.000	0.000	0.000
48	A	53	ASN	0	0.026	-0.003	22.107	0.040	0.040	0.000	0.000	0.000	0.000
49	A	54	LEU	0	-0.036	-0.005	18.771	0.010	0.010	0.000	0.000	0.000	0.000
50	A	55	ILE	0	-0.017	-0.009	23.308	0.018	0.018	0.000	0.000	0.000	0.000
51	A	56	GLU	-1	-0.838	-0.915	25.931	-0.064	-0.064	0.000	0.000	0.000	0.000
52	A	57	LYS	1	0.816	0.920	24.856	0.135	0.135	0.000	0.000	0.000	0.000
53	A	58	GLY	0	0.039	0.014	27.153	0.007	0.007	0.000	0.000	0.000	0.000
54	A	59	ARG	1	0.826	0.918	28.473	0.031	0.031	0.000	0.000	0.000	0.000
55	A	60	TYR	0	0.044	0.032	28.583	0.009	0.009	0.000	0.000	0.000	0.000
56	A	61	ASP	-1	-0.822	-0.915	30.711	0.004	0.004	0.000	0.000	0.000	0.000
57	A	62	TYR	0	0.090	0.020	24.552	0.018	0.018	0.000	0.000	0.000	0.000
58	A	63	ASP	-1	-0.799	-0.894	29.061	-0.017	-0.017	0.000	0.000	0.000	0.000
59	A	64	LEU	0	-0.041	0.003	31.740	0.004	0.004	0.000	0.000	0.000	0.000
60	A	65	PHE	0	0.029	0.007	22.965	0.007	0.007	0.000	0.000	0.000	0.000
61	A	66	LYS	1	0.871	0.939	26.683	0.045	0.045	0.000	0.000	0.000	0.000
62	A	67	LYS	1	0.815	0.895	28.079	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	68	VAL	0	-0.021	-0.009	28.278	0.007	0.007	0.000	0.000	0.000	0.000
64	A	69	VAL	0	0.044	0.026	23.174	0.017	0.017	0.000	0.000	0.000	0.000
65	A	70	ASN	0	0.032	0.008	26.312	0.017	0.017	0.000	0.000	0.000	0.000
66	A	71	ARG	1	0.851	0.930	27.899	-0.100	-0.100	0.000	0.000	0.000	0.000
67	A	72	ASN	0	-0.055	-0.054	27.000	0.009	0.009	0.000	0.000	0.000	0.000
68	A	73	LEU	0	0.024	0.023	23.361	0.014	0.014	0.000	0.000	0.000	0.000
69	A	74	VAL	0	-0.039	-0.025	26.344	0.006	0.006	0.000	0.000	0.000	0.000
70	A	75	ARG	1	0.898	0.948	29.438	-0.104	-0.104	0.000	0.000	0.000	0.000
71	A	76	ILE	0	-0.029	0.014	24.130	0.013	0.013	0.000	0.000	0.000	0.000
72	A	77	PRO	0	-0.030	-0.013	28.528	-0.014	-0.014	0.000	0.000	0.000	0.000
73	A	78	GLN	0	0.026	0.019	29.111	0.007	0.007	0.000	0.000	0.000	0.000
74	A	79	GLN	0	-0.050	-0.038	28.546	0.015	0.015	0.000	0.000	0.000	0.000
75	A	80	GLN	0	-0.051	-0.030	30.480	-0.008	-0.008	0.000	0.000	0.000	0.000
76	A	81	PRO	0	-0.007	-0.004	31.870	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	82	ALA	0	0.062	0.031	27.656	0.013	0.013	0.000	0.000	0.000	0.000
78	A	83	PRO	0	-0.063	-0.017	24.433	-0.008	-0.008	0.000	0.000	0.000	0.000
79	A	84	ALA	0	-0.001	-0.011	25.048	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	85	GLU	-1	-0.942	-0.967	18.657	0.331	0.331	0.000	0.000	0.000	0.000
81	A	86	ILE	0	0.008	0.019	19.705	0.003	0.003	0.000	0.000	0.000	0.000
82	A	87	THR	0	0.037	0.031	18.244	0.024	0.024	0.000	0.000	0.000	0.000
83	A	88	PRO	0	-0.017	-0.012	13.925	-0.016	-0.016	0.000	0.000	0.000	0.000
84	A	89	SER	0	0.034	0.005	16.328	0.035	0.035	0.000	0.000	0.000	0.000
85	A	90	TYR	0	0.012	-0.009	16.940	0.081	0.081	0.000	0.000	0.000	0.000
86	A	91	ALA	0	0.017	0.011	17.048	0.090	0.090	0.000	0.000	0.000	0.000
87	A	92	LEU	0	0.032	0.025	13.168	0.075	0.075	0.000	0.000	0.000	0.000
88	A	93	GLY	0	0.027	0.016	12.741	0.126	0.126	0.000	0.000	0.000	0.000
89	A	94	LYS	1	0.852	0.901	12.334	-0.838	-0.838	0.000	0.000	0.000	0.000
90	A	95	VAL	0	0.011	0.014	12.170	0.168	0.168	0.000	0.000	0.000	0.000
91	A	96	LEU	0	0.010	-0.001	8.394	0.185	0.185	0.000	0.000	0.000	0.000
92	A	97	GLN	0	0.010	0.012	8.012	0.509	0.509	0.000	0.000	0.000	0.000
93	A	98	ASP	-1	-0.765	-0.860	9.457	1.839	1.839	0.000	0.000	0.000	0.000
94	A	99	ALA	0	0.034	0.031	7.884	0.202	0.202	0.000	0.000	0.000	0.000
95	A	100	ALA	0	0.003	0.000	5.102	0.297	0.342	-0.001	-0.004	-0.039	0.000
96	A	101	LYS	1	0.791	0.881	5.664	-0.099	-0.099	0.000	0.000	0.000	0.000
97	A	102	ILE	0	0.042	0.018	8.500	-0.081	-0.081	0.000	0.000	0.000	0.000
98	A	103	GLN	0	0.011	0.017	2.406	2.214	4.538	1.689	-1.769	-2.244	0.019
99	A	104	LYS	1	0.835	0.908	2.469	-24.852	-22.952	0.727	-1.138	-1.489	0.016
100	A	105	GLN	0	-0.036	-0.018	7.531	-0.641	-0.641	0.000	0.000	0.000	0.000
101	A	106	GLN	0	0.039	0.015	10.386	-0.195	-0.195	0.000	0.000	0.000	0.000
102	A	107	LYS	1	0.879	0.951	8.824	-0.747	-0.747	0.000	0.000	0.000	0.000
103	A	108	ASP	-1	-0.762	-0.853	6.745	-0.859	-0.859	0.000	0.000	0.000	0.000
104	A	109	SER	0	0.008	0.006	4.003	1.512	1.831	-0.001	-0.120	-0.197	0.000
105	A	110	PHE	0	-0.061	-0.025	2.027	-14.847	-14.008	5.180	-2.669	-3.351	-0.033
106	A	111	ILE	0	-0.038	-0.014	2.607	1.087	3.047	0.639	-0.698	-1.901	0.001
107	A	112	ALA	0	0.045	0.011	4.923	-0.819	-0.827	-0.001	-0.008	0.017	0.000
108	A	113	GLN	0	-0.041	-0.050	8.491	0.554	0.554	0.000	0.000	0.000	0.000
109	A	114	ASP	-1	-0.762	-0.854	11.308	-0.238	-0.238	0.000	0.000	0.000	0.000
110	A	115	HIS	0	-0.008	0.001	7.455	0.341	0.341	0.000	0.000	0.000	0.000
111	A	116	ILE	0	0.016	0.003	7.830	0.268	0.268	0.000	0.000	0.000	0.000
112	A	117	LEU	0	-0.001	0.013	10.865	0.066	0.066	0.000	0.000	0.000	0.000
113	A	118	PHE	0	-0.009	-0.023	13.280	0.046	0.046	0.000	0.000	0.000	0.000
114	A	119	ALA	0	-0.027	-0.008	11.600	0.043	0.043	0.000	0.000	0.000	0.000
115	A	120	LEU	0	-0.021	-0.008	13.681	-0.009	-0.009	0.000	0.000	0.000	0.000
116	A	121	PHE	0	0.032	0.014	16.113	-0.026	-0.026	0.000	0.000	0.000	0.000
117	A	122	ASN	0	-0.038	-0.020	15.643	-0.111	-0.111	0.000	0.000	0.000	0.000
118	A	123	ASP	-1	-0.822	-0.895	18.152	0.480	0.480	0.000	0.000	0.000	0.000
119	A	124	SER	0	0.001	-0.010	19.911	-0.040	-0.040	0.000	0.000	0.000	0.000
120	A	125	SER	0	-0.083	-0.053	21.542	-0.049	-0.049	0.000	0.000	0.000	0.000
121	A	126	ILE	0	0.025	0.012	18.763	-0.045	-0.045	0.000	0.000	0.000	0.000
122	A	127	GLN	0	-0.013	-0.018	21.676	-0.062	-0.062	0.000	0.000	0.000	0.000
123	A	128	GLN	0	-0.059	-0.036	24.675	-0.021	-0.021	0.000	0.000	0.000	0.000
124	A	129	ILE	0	0.010	-0.002	24.215	-0.025	-0.025	0.000	0.000	0.000	0.000
125	A	130	PHE	0	0.030	0.000	21.332	-0.022	-0.022	0.000	0.000	0.000	0.000
126	A	131	LYS	1	0.907	0.964	26.337	-0.225	-0.225	0.000	0.000	0.000	0.000
127	A	132	GLU	-1	-0.857	-0.911	29.579	0.138	0.138	0.000	0.000	0.000	0.000
128	A	133	ALA	0	-0.054	-0.010	28.390	-0.015	-0.015	0.000	0.000	0.000	0.000
129	A	134	GLN	0	-0.069	-0.031	30.476	-0.017	-0.017	0.000	0.000	0.000	0.000
130	A	135	VAL	0	-0.007	-0.002	26.048	-0.010	-0.010	0.000	0.000	0.000	0.000
131	A	136	ASP	-1	-0.830	-0.912	27.581	0.206	0.206	0.000	0.000	0.000	0.000
132	A	137	ILE	0	0.020	0.004	21.779	-0.010	-0.010	0.000	0.000	0.000	0.000
133	A	138	GLU	-1	-0.815	-0.887	23.110	0.353	0.353	0.000	0.000	0.000	0.000
134	A	139	ALA	0	0.005	0.005	24.436	-0.011	-0.011	0.000	0.000	0.000	0.000
135	A	140	ILE	0	-0.006	0.000	21.071	-0.023	-0.023	0.000	0.000	0.000	0.000
136	A	141	LYS	1	0.789	0.876	19.243	-0.414	-0.414	0.000	0.000	0.000	0.000
137	A	142	GLN	0	-0.038	-0.034	20.566	0.018	0.018	0.000	0.000	0.000	0.000
138	A	143	GLN	0	-0.038	-0.042	22.549	-0.048	-0.048	0.000	0.000	0.000	0.000
139	A	144	ALA	0	0.006	0.004	17.423	-0.046	-0.046	0.000	0.000	0.000	0.000
140	A	145	LEU	0	-0.047	-0.022	17.139	-0.051	-0.051	0.000	0.000	0.000	0.000
141	A	146	GLU	-1	-0.867	-0.911	19.327	-0.036	-0.036	0.000	0.000	0.000	0.000
142	A	147	LEU	0	-0.067	-0.017	18.258	-0.037	-0.037	0.000	0.000	0.000	0.000
143	A	148	ARG	1	0.841	0.906	13.397	0.425	0.425	0.000	0.000	0.000	0.000
144	A	149	GLY	0	0.047	0.031	17.472	-0.072	-0.072	0.000	0.000	0.000	0.000
145	A	150	ASN	0	-0.071	-0.048	17.302	0.024	0.024	0.000	0.000	0.000	0.000
146	A	151	THR	0	-0.049	-0.023	14.119	-0.057	-0.057	0.000	0.000	0.000	0.000
147	A	152	ARG	1	0.807	0.891	9.356	0.487	0.487	0.000	0.000	0.000	0.000
148	A	153	ILE	0	0.019	-0.005	8.178	-0.121	-0.121	0.000	0.000	0.000	0.000
149	A	154	ASP	-1	-0.880	-0.947	7.101	-2.488	-2.488	0.000	0.000	0.000	0.000
150	A	155	SER	0	-0.020	-0.028	7.881	-0.664	-0.664	0.000	0.000	0.000	0.000
151	A	156	ARG	1	0.791	0.869	4.309	3.240	3.325	-0.001	-0.012	-0.072	0.000
152	A	157	GLY	0	0.111	0.065	7.979	0.279	0.279	0.000	0.000	0.000	0.000
153	A	158	ALA	0	0.009	0.026	10.748	0.325	0.325	0.000	0.000	0.000	0.000
154	A	159	ASP	-1	-0.742	-0.818	10.641	-1.124	-1.124	0.000	0.000	0.000	0.000
155	A	160	THR	0	-0.039	-0.032	12.904	0.180	0.180	0.000	0.000	0.000	0.000
156	A	161	ASN	0	0.041	0.015	16.376	0.052	0.052	0.000	0.000	0.000	0.000
157	A	162	THR	0	0.027	0.037	18.601	0.090	0.090	0.000	0.000	0.000	0.000

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