FMO DATABASE

FMODB ID: R86L8

Calculation Name: 5WYG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5WYG

Chain ID: A

ChEMBL ID:

UniProt ID: P0CL62

Base Structure: X-ray

Registration Date: 2023-09-23

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	105
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-735510.897183
FMO2-HF: Nuclear repulsion	697114.063763
FMO2-HF: Total energy	-38396.83342
FMO2-MP2: Total energy	-38510.312982

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:2:ALA)

Summations of interaction energy for fragment #1(A:2:ALA)

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.
-26.664	-29.22	20.392	-7.293	-10.544	0.023

Interaction energy analysis for fragmet #1(A:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : 0.008

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	4	PRO	0	-0.094	-0.051	2.278	-1.592	-0.392	1.613	-1.095	-1.718	0.002
4	A	5	ARG	1	0.968	0.987	4.833	0.030	0.053	-0.001	-0.012	-0.010	0.000
5	A	6	ARG	1	0.800	0.863	7.669	0.589	0.589	0.000	0.000	0.000	0.000
6	A	7	GLY	0	-0.026	-0.021	10.701	-0.012	-0.012	0.000	0.000	0.000	0.000
7	A	8	ASP	-1	-0.750	-0.844	8.676	0.268	0.268	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.100	-0.048	11.657	-0.002	-0.002	0.000	0.000	0.000	0.000
9	A	10	TRP	0	0.029	0.001	6.359	0.348	0.348	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.009	0.002	11.311	-0.198	-0.198	0.000	0.000	0.000	0.000
11	A	12	VAL	0	-0.009	-0.009	10.971	0.246	0.246	0.000	0.000	0.000	0.000
12	A	13	SER	0	0.018	0.011	12.802	-0.184	-0.184	0.000	0.000	0.000	0.000
13	A	14	LEU	0	-0.053	-0.020	14.834	-0.061	-0.061	0.000	0.000	0.000	0.000
14	A	23	GLY	0	0.037	0.015	21.232	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	24	LYS	1	0.893	0.938	20.436	-0.318	-0.318	0.000	0.000	0.000	0.000
16	A	25	HIS	0	0.141	0.084	15.885	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	26	ARG	1	0.868	0.922	16.612	-0.454	-0.454	0.000	0.000	0.000	0.000
18	A	27	PRO	0	0.076	0.053	15.318	0.083	0.083	0.000	0.000	0.000	0.000
19	A	28	ALA	0	-0.033	-0.018	12.884	-0.073	-0.073	0.000	0.000	0.000	0.000
20	A	29	VAL	0	0.017	0.012	12.933	0.071	0.071	0.000	0.000	0.000	0.000
21	A	30	VAL	0	0.022	0.022	7.599	0.031	0.031	0.000	0.000	0.000	0.000
22	A	31	VAL	0	-0.034	-0.033	10.684	-0.095	-0.095	0.000	0.000	0.000	0.000
23	A	32	SER	0	0.016	0.022	8.485	0.035	0.035	0.000	0.000	0.000	0.000
24	A	33	VAL	0	-0.025	-0.014	9.905	0.008	0.008	0.000	0.000	0.000	0.000
25	A	34	ASP	-1	-0.749	-0.874	6.638	-1.109	-1.109	0.000	0.000	0.000	0.000
26	A	35	GLU	-1	-0.908	-0.960	6.032	-1.249	-1.249	0.000	0.000	0.000	0.000
27	A	36	LEU	0	-0.070	-0.035	7.947	0.115	0.115	0.000	0.000	0.000	0.000
28	A	37	LEU	0	-0.086	-0.020	2.287	-0.439	0.103	0.961	-0.484	-1.020	-0.002
29	A	38	THR	0	-0.060	-0.057	3.803	0.099	0.286	0.006	-0.078	-0.115	0.000
30	A	39	GLY	0	-0.014	-0.026	2.218	0.190	-0.384	4.179	-2.250	-1.355	0.002
31	A	40	ILE	0	-0.042	0.006	2.950	2.519	0.469	-0.022	2.405	-0.334	-0.003
32	A	41	ASP	-1	-0.849	-0.948	5.042	2.933	2.933	0.000	0.000	0.000	0.000
33	A	42	ASP	-1	-0.928	-0.971	5.889	0.101	0.101	0.000	0.000	0.000	0.000
34	A	43	GLU	-1	-0.771	-0.860	2.533	-6.122	-4.529	1.148	-1.141	-1.600	-0.016
35	A	44	LEU	0	-0.039	-0.037	7.254	0.408	0.408	0.000	0.000	0.000	0.000
36	A	45	VAL	0	0.058	0.049	5.048	-0.167	-0.167	0.000	0.000	0.000	0.000
37	A	46	VAL	0	-0.007	-0.017	7.830	0.091	0.091	0.000	0.000	0.000	0.000
38	A	47	VAL	0	0.029	0.010	10.122	-0.016	-0.016	0.000	0.000	0.000	0.000
39	A	48	VAL	0	0.003	-0.005	12.624	-0.044	-0.044	0.000	0.000	0.000	0.000
40	A	49	PRO	0	-0.006	0.001	16.079	0.035	0.035	0.000	0.000	0.000	0.000
41	A	50	VAL	0	0.009	0.010	17.346	-0.056	-0.056	0.000	0.000	0.000	0.000
42	A	51	SER	0	-0.047	-0.023	19.499	0.016	0.016	0.000	0.000	0.000	0.000
43	A	52	SER	0	0.069	0.042	22.938	-0.013	-0.013	0.000	0.000	0.000	0.000
44	A	53	SER	0	-0.007	-0.010	25.532	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	54	ARG	1	0.915	0.958	25.279	-0.153	-0.153	0.000	0.000	0.000	0.000
46	A	55	SER	0	0.082	0.048	28.409	0.002	0.002	0.000	0.000	0.000	0.000
47	A	56	ARG	1	1.025	1.013	28.401	-0.055	-0.055	0.000	0.000	0.000	0.000
48	A	57	THR	0	-0.050	-0.030	28.614	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	58	PRO	0	0.053	0.014	28.434	0.004	0.004	0.000	0.000	0.000	0.000
50	A	59	LEU	0	0.023	0.028	26.310	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	60	ARG	1	0.789	0.899	24.546	-0.086	-0.086	0.000	0.000	0.000	0.000
52	A	61	PRO	0	0.083	0.038	23.114	0.002	0.002	0.000	0.000	0.000	0.000
53	A	62	PRO	0	-0.032	-0.017	23.910	0.015	0.015	0.000	0.000	0.000	0.000
54	A	63	VAL	0	-0.009	-0.008	19.361	-0.010	-0.010	0.000	0.000	0.000	0.000
55	A	64	ALA	0	0.047	0.024	22.548	0.010	0.010	0.000	0.000	0.000	0.000
56	A	65	PRO	0	0.063	0.013	22.410	0.013	0.013	0.000	0.000	0.000	0.000
57	A	66	SER	0	-0.009	-0.007	22.102	0.016	0.016	0.000	0.000	0.000	0.000
58	A	67	GLU	-1	-0.769	-0.848	18.862	0.088	0.088	0.000	0.000	0.000	0.000
59	A	68	GLY	0	0.038	0.027	17.295	0.027	0.027	0.000	0.000	0.000	0.000
60	A	69	VAL	0	-0.067	-0.023	18.358	0.051	0.051	0.000	0.000	0.000	0.000
61	A	70	ALA	0	0.016	-0.002	20.827	-0.021	-0.021	0.000	0.000	0.000	0.000
62	A	71	ALA	0	0.014	0.007	23.780	-0.022	-0.022	0.000	0.000	0.000	0.000
63	A	72	ASP	-1	-0.883	-0.938	24.613	0.146	0.146	0.000	0.000	0.000	0.000
64	A	73	SER	0	-0.040	-0.031	22.495	0.014	0.014	0.000	0.000	0.000	0.000
65	A	74	VAL	0	-0.070	-0.031	23.898	-0.020	-0.020	0.000	0.000	0.000	0.000
66	A	75	ALA	0	0.080	0.044	19.657	0.027	0.027	0.000	0.000	0.000	0.000
67	A	76	VAL	0	-0.051	-0.034	20.727	-0.033	-0.033	0.000	0.000	0.000	0.000
68	A	77	CYS	0	0.016	0.013	20.351	0.005	0.005	0.000	0.000	0.000	0.000
69	A	78	ARG	1	0.966	0.981	21.114	-0.066	-0.066	0.000	0.000	0.000	0.000
70	A	79	GLY	0	-0.032	-0.015	21.185	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	80	VAL	0	0.012	0.012	16.209	0.043	0.043	0.000	0.000	0.000	0.000
72	A	81	ARG	1	0.845	0.918	14.763	-0.252	-0.252	0.000	0.000	0.000	0.000
73	A	82	ALA	0	0.060	0.040	12.425	0.020	0.020	0.000	0.000	0.000	0.000
74	A	83	VAL	0	-0.084	-0.055	9.578	0.006	0.006	0.000	0.000	0.000	0.000
75	A	84	ALA	0	0.052	0.040	9.173	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	85	ARG	1	0.891	0.934	1.929	-23.381	-26.858	12.508	-4.638	-4.392	0.040
77	A	86	ALA	0	0.050	0.027	6.048	0.997	0.997	0.000	0.000	0.000	0.000
78	A	87	ARG	1	0.799	0.889	7.849	-0.757	-0.757	0.000	0.000	0.000	0.000
79	A	88	LEU	0	-0.026	-0.002	6.092	-0.479	-0.479	0.000	0.000	0.000	0.000
80	A	89	VAL	0	-0.015	-0.003	7.713	0.848	0.848	0.000	0.000	0.000	0.000
81	A	90	GLU	-1	-0.894	-0.959	9.594	1.202	1.202	0.000	0.000	0.000	0.000
82	A	91	ARG	1	0.863	0.919	9.084	-0.506	-0.506	0.000	0.000	0.000	0.000
83	A	92	LEU	0	-0.026	-0.020	10.950	-0.125	-0.125	0.000	0.000	0.000	0.000
84	A	93	GLY	0	0.007	-0.010	13.544	-0.089	-0.089	0.000	0.000	0.000	0.000
85	A	94	ALA	0	-0.010	0.005	13.315	0.030	0.030	0.000	0.000	0.000	0.000
86	A	95	LEU	0	-0.011	-0.002	15.237	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	96	LYS	1	0.866	0.927	17.930	-0.108	-0.108	0.000	0.000	0.000	0.000
88	A	97	PRO	0	0.064	0.012	19.869	0.004	0.004	0.000	0.000	0.000	0.000
89	A	98	ALA	0	-0.048	-0.020	20.861	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	99	THR	0	-0.036	-0.042	20.567	-0.008	-0.008	0.000	0.000	0.000	0.000
91	A	100	MET	0	0.029	0.035	15.462	0.026	0.026	0.000	0.000	0.000	0.000
92	A	101	ARG	1	1.025	1.019	19.468	0.064	0.064	0.000	0.000	0.000	0.000
93	A	102	ALA	0	-0.026	0.006	22.489	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	103	ILE	0	0.022	-0.005	17.960	0.006	0.006	0.000	0.000	0.000	0.000
95	A	104	GLU	-1	-0.816	-0.885	18.520	-0.128	-0.128	0.000	0.000	0.000	0.000
96	A	105	ASN	0	-0.035	-0.012	21.093	-0.006	-0.006	0.000	0.000	0.000	0.000
97	A	106	ALA	0	0.013	0.000	23.310	0.002	0.002	0.000	0.000	0.000	0.000
98	A	107	LEU	0	-0.019	-0.018	18.040	0.006	0.006	0.000	0.000	0.000	0.000
99	A	108	THR	0	0.015	-0.009	22.258	-0.008	-0.008	0.000	0.000	0.000	0.000
100	A	109	LEU	0	-0.019	-0.008	24.505	0.001	0.001	0.000	0.000	0.000	0.000
101	A	110	ILE	0	-0.100	-0.056	23.525	0.006	0.006	0.000	0.000	0.000	0.000
102	A	111	LEU	0	-0.035	-0.015	20.325	0.005	0.005	0.000	0.000	0.000	0.000
103	A	112	GLY	0	-0.006	0.012	25.063	-0.008	-0.008	0.000	0.000	0.000	0.000
104	A	113	LEU	0	-0.031	-0.009	22.156	-0.006	-0.006	0.000	0.000	0.000	0.000
105	A	114	PRO	0	-0.004	0.000	26.657	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)