FMO DATABASE

FMODB ID: QYR6Y

Calculation Name: 5L33-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5L33

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-20

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	106
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-927123.076157
FMO2-HF: Nuclear repulsion	882604.572788
FMO2-HF: Total energy	-44518.50337
FMO2-MP2: Total energy	-44648.746774

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:-1:HIS)

Summations of interaction energy for fragment #1(A:-1:HIS)

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.
-3.075	0.374	0.122	-1.199	-2.372	0

Interaction energy analysis for fragmet #1(A:-1:HIS)

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 : -0.019

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].
3	A	1	PRO	0	0.009	0.006	3.362	-3.007	0.258	0.123	-1.187	-2.201
4	A	2	GLU	-1	-0.905	-0.964	4.291	-0.695	-0.511	-0.001	-0.012	-0.171
5	A	3	GLU	-1	-0.898	-0.948	6.447	-0.637	-0.637	0.000	0.000	0.000
6	A	4	GLU	-1	-0.812	-0.884	7.864	-0.952	-0.952	0.000	0.000	0.000
7	A	5	LYS	1	0.963	0.977	6.094	-0.273	-0.273	0.000	0.000	0.000
8	A	6	ALA	0	0.017	0.009	9.049	0.326	0.326	0.000	0.000	0.000
9	A	7	ALA	0	0.014	0.002	11.867	0.154	0.154	0.000	0.000	0.000
10	A	8	ARG	1	0.966	0.972	9.166	-0.708	-0.708	0.000	0.000	0.000
11	A	9	LEU	0	-0.025	-0.008	10.851	0.142	0.142	0.000	0.000	0.000
12	A	10	PHE	0	0.028	0.013	13.700	0.014	0.014	0.000	0.000	0.000
13	A	11	ILE	0	-0.011	-0.010	15.428	0.009	0.009	0.000	0.000	0.000
14	A	12	GLU	-1	-0.876	-0.941	13.908	0.940	0.940	0.000	0.000	0.000
15	A	13	ALA	0	-0.023	-0.014	16.248	0.008	0.008	0.000	0.000	0.000
16	A	14	LEU	0	-0.049	-0.020	19.136	-0.021	-0.021	0.000	0.000	0.000
17	A	15	GLU	-1	-0.869	-0.929	16.545	0.524	0.524	0.000	0.000	0.000
18	A	16	LYS	1	0.838	0.923	17.212	-0.746	-0.746	0.000	0.000	0.000
19	A	17	GLY	0	0.036	0.033	21.100	-0.014	-0.014	0.000	0.000	0.000
20	A	18	ASP	-1	-0.880	-0.954	21.038	0.356	0.356	0.000	0.000	0.000
21	A	19	PRO	0	-0.018	-0.027	22.200	-0.010	-0.010	0.000	0.000	0.000
22	A	20	GLU	-1	-0.948	-0.971	22.553	0.162	0.162	0.000	0.000	0.000
23	A	21	LEU	0	-0.017	0.005	15.666	-0.013	-0.013	0.000	0.000	0.000
24	A	22	MET	0	0.030	0.012	18.639	-0.045	-0.045	0.000	0.000	0.000
25	A	23	ARG	1	0.912	0.958	20.380	-0.149	-0.149	0.000	0.000	0.000
26	A	24	LYS	1	0.879	0.937	16.795	-0.185	-0.185	0.000	0.000	0.000
27	A	25	VAL	0	-0.031	0.003	15.265	-0.048	-0.048	0.000	0.000	0.000
28	A	26	ILE	0	-0.032	0.001	16.939	-0.099	-0.099	0.000	0.000	0.000
29	A	27	SER	0	-0.033	-0.024	19.139	-0.029	-0.029	0.000	0.000	0.000
30	A	28	PRO	0	0.007	-0.012	21.423	0.010	0.010	0.000	0.000	0.000
31	A	29	ASP	-1	-0.900	-0.952	22.981	-0.294	-0.294	0.000	0.000	0.000
32	A	30	THR	0	-0.032	-0.024	20.981	-0.014	-0.014	0.000	0.000	0.000
33	A	31	ARG	1	0.908	0.955	23.453	0.194	0.194	0.000	0.000	0.000
34	A	32	MET	0	-0.007	-0.001	24.814	-0.024	-0.024	0.000	0.000	0.000
35	A	33	GLU	-1	-0.836	-0.897	26.496	-0.093	-0.093	0.000	0.000	0.000
36	A	34	ASP	-1	-0.770	-0.875	28.334	-0.008	-0.008	0.000	0.000	0.000
37	A	35	ASN	0	0.012	-0.007	30.296	0.002	0.002	0.000	0.000	0.000
38	A	36	GLY	0	-0.058	-0.035	33.225	0.008	0.008	0.000	0.000	0.000
39	A	37	ARG	1	0.880	0.949	32.375	-0.006	-0.006	0.000	0.000	0.000
40	A	38	GLU	-1	-0.962	-0.980	31.387	-0.117	-0.117	0.000	0.000	0.000
41	A	39	PHE	0	-0.002	-0.005	28.519	0.017	0.017	0.000	0.000	0.000
42	A	40	THR	0	-0.099	-0.057	27.745	-0.029	-0.029	0.000	0.000	0.000
43	A	41	GLY	0	0.058	0.029	25.601	0.016	0.016	0.000	0.000	0.000
44	A	42	ASP	-1	-0.898	-0.964	26.278	-0.001	-0.001	0.000	0.000	0.000
45	A	43	GLU	-1	-0.814	-0.899	27.772	-0.035	-0.035	0.000	0.000	0.000
46	A	44	VAL	0	-0.025	-0.016	23.450	0.014	0.014	0.000	0.000	0.000
47	A	45	VAL	0	-0.019	-0.014	24.086	0.025	0.025	0.000	0.000	0.000
48	A	46	GLU	-1	-0.963	-0.989	26.305	0.041	0.041	0.000	0.000	0.000
49	A	47	TYR	0	-0.049	-0.038	26.153	0.017	0.017	0.000	0.000	0.000
50	A	48	VAL	0	0.014	0.004	23.387	0.012	0.012	0.000	0.000	0.000
51	A	49	LYS	1	0.925	0.965	26.636	-0.067	-0.067	0.000	0.000	0.000
52	A	50	GLU	-1	-0.902	-0.961	29.438	0.090	0.090	0.000	0.000	0.000
53	A	51	ILE	0	-0.064	-0.010	25.578	0.000	0.000	0.000	0.000	0.000
54	A	52	GLN	0	0.014	0.005	27.206	-0.009	-0.009	0.000	0.000	0.000
55	A	53	LYS	1	0.864	0.945	29.041	-0.076	-0.076	0.000	0.000	0.000
56	A	54	ARG	1	0.742	0.837	30.800	-0.090	-0.090	0.000	0.000	0.000
57	A	55	GLY	0	0.036	0.036	30.614	-0.004	-0.004	0.000	0.000	0.000
58	A	56	GLU	-1	-0.845	-0.885	28.439	0.097	0.097	0.000	0.000	0.000
59	A	57	GLN	0	0.004	-0.005	25.308	0.008	0.008	0.000	0.000	0.000
60	A	58	TRP	0	0.004	-0.003	22.437	-0.031	-0.031	0.000	0.000	0.000
61	A	59	HIS	0	0.010	0.003	20.591	0.065	0.065	0.000	0.000	0.000
62	A	60	LEU	0	-0.030	-0.010	13.906	-0.074	-0.074	0.000	0.000	0.000
63	A	61	ARG	1	0.849	0.942	17.906	-0.056	-0.056	0.000	0.000	0.000
64	A	62	ARG	1	0.837	0.910	15.703	0.014	0.014	0.000	0.000	0.000
65	A	63	TYR	0	-0.042	-0.054	9.285	0.158	0.158	0.000	0.000	0.000
66	A	64	THR	0	-0.023	-0.028	14.455	-0.016	-0.016	0.000	0.000	0.000
67	A	65	LYS	1	0.876	0.965	12.711	1.069	1.069	0.000	0.000	0.000
68	A	66	GLU	-1	-0.848	-0.889	15.733	-0.387	-0.387	0.000	0.000	0.000
69	A	67	GLY	0	0.022	0.015	19.187	0.022	0.022	0.000	0.000	0.000
70	A	68	ASN	0	-0.038	-0.042	16.990	-0.136	-0.136	0.000	0.000	0.000
71	A	69	SER	0	-0.035	-0.015	17.630	0.013	0.013	0.000	0.000	0.000
72	A	70	TRP	0	-0.008	-0.015	10.284	0.013	0.013	0.000	0.000	0.000
73	A	71	ARG	1	0.941	0.975	16.845	0.323	0.323	0.000	0.000	0.000
74	A	72	PHE	0	-0.008	-0.019	13.705	0.002	0.002	0.000	0.000	0.000
75	A	73	GLU	-1	-0.829	-0.914	18.608	-0.042	-0.042	0.000	0.000	0.000
76	A	74	VAL	0	0.007	-0.015	19.702	0.047	0.047	0.000	0.000	0.000
77	A	75	GLN	0	-0.058	-0.028	21.876	-0.032	-0.032	0.000	0.000	0.000
78	A	76	VAL	0	0.020	0.003	24.485	0.029	0.029	0.000	0.000	0.000
79	A	77	ASP	-1	-0.815	-0.910	27.058	0.168	0.168	0.000	0.000	0.000
80	A	78	ASN	0	0.006	-0.024	29.748	0.014	0.014	0.000	0.000	0.000
81	A	79	ASN	0	-0.054	-0.011	32.818	-0.004	-0.004	0.000	0.000	0.000
82	A	80	GLY	0	-0.009	-0.003	34.787	-0.008	-0.008	0.000	0.000	0.000
83	A	81	GLN	0	-0.066	-0.017	34.367	-0.005	-0.005	0.000	0.000	0.000
84	A	82	THR	0	-0.024	-0.013	28.771	0.006	0.006	0.000	0.000	0.000
85	A	83	GLU	-1	-0.878	-0.919	29.691	0.028	0.028	0.000	0.000	0.000
86	A	84	GLN	0	-0.055	-0.036	25.439	0.018	0.018	0.000	0.000	0.000
87	A	85	TRP	0	-0.019	-0.036	25.572	-0.021	-0.021	0.000	0.000	0.000
88	A	86	GLU	-1	-0.939	-0.967	23.240	-0.147	-0.147	0.000	0.000	0.000
89	A	87	VAL	0	0.010	0.001	20.750	-0.003	-0.003	0.000	0.000	0.000
90	A	88	GLN	0	0.058	0.035	20.600	-0.027	-0.027	0.000	0.000	0.000
91	A	89	ILE	0	0.003	-0.002	17.090	0.006	0.006	0.000	0.000	0.000
92	A	90	GLU	-1	-0.948	-0.981	17.891	-0.516	-0.516	0.000	0.000	0.000
93	A	91	VAL	0	0.016	0.011	12.528	0.055	0.055	0.000	0.000	0.000
94	A	92	ARG	1	0.841	0.917	15.290	0.524	0.524	0.000	0.000	0.000
95	A	93	ASN	0	-0.020	-0.017	14.629	-0.006	-0.006	0.000	0.000	0.000
96	A	94	GLY	0	0.059	0.029	11.801	0.036	0.036	0.000	0.000	0.000
97	A	95	ARG	1	0.934	0.984	12.680	0.517	0.517	0.000	0.000	0.000
98	A	96	ILE	0	0.029	0.018	15.514	-0.053	-0.053	0.000	0.000	0.000
99	A	97	LYS	1	0.925	0.984	17.814	0.391	0.391	0.000	0.000	0.000
100	A	98	ARG	1	0.950	0.960	20.500	0.304	0.304	0.000	0.000	0.000
101	A	99	VAL	0	0.011	0.010	20.646	-0.038	-0.038	0.000	0.000	0.000
102	A	100	THR	0	-0.048	-0.024	23.034	0.008	0.008	0.000	0.000	0.000
103	A	101	ILE	0	-0.004	0.010	24.711	-0.004	-0.004	0.000	0.000	0.000
104	A	102	THR	0	0.056	0.025	26.738	-0.001	-0.001	0.000	0.000	0.000
105	A	103	HIS	1	0.854	0.924	28.141	0.009	0.009	0.000	0.000	0.000
106	A	104	VAL	0	0.018	0.029	30.719	0.005	0.005	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-1:HIS)