FMO DATABASE

FMODB ID: 6YK4Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-735739.401427
FMO2-HF: Nuclear repulsion	697342.979715
FMO2-HF: Total energy	-38396.421712
FMO2-MP2: Total energy	-38509.979477

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.
-21.683	-26.354	27.23	-9.373	-13.186	0.001

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 : -0.024 / 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	4	PRO	0	-0.091	-0.038	2.084	-0.996	-0.751	4.322	-2.240	-2.327	-0.002
4	A	5	ARG	1	1.028	1.025	4.714	-0.186	-0.190	-0.001	-0.015	0.020	0.000
5	A	6	ARG	1	0.820	0.879	7.437	0.577	0.577	0.000	0.000	0.000	0.000
6	A	7	GLY	0	-0.044	-0.034	10.049	-0.007	-0.007	0.000	0.000	0.000	0.000
7	A	8	ASP	-1	-0.816	-0.915	9.133	0.147	0.147	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.092	-0.050	11.536	0.024	0.024	0.000	0.000	0.000	0.000
9	A	10	TRP	0	0.040	0.014	6.177	0.271	0.271	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.004	-0.004	11.106	-0.168	-0.168	0.000	0.000	0.000	0.000
11	A	12	VAL	0	0.000	-0.004	10.847	0.208	0.208	0.000	0.000	0.000	0.000
12	A	13	SER	0	0.035	0.014	12.470	-0.175	-0.175	0.000	0.000	0.000	0.000
13	A	14	LEU	0	-0.068	-0.028	14.520	-0.067	-0.067	0.000	0.000	0.000	0.000
14	A	23	GLY	0	0.030	0.004	21.221	-0.006	-0.006	0.000	0.000	0.000	0.000
15	A	24	LYS	1	0.892	0.942	20.156	-0.291	-0.291	0.000	0.000	0.000	0.000
16	A	25	HIS	0	0.143	0.089	16.244	0.013	0.013	0.000	0.000	0.000	0.000
17	A	26	ARG	1	0.858	0.914	16.232	-0.431	-0.431	0.000	0.000	0.000	0.000
18	A	27	PRO	0	0.079	0.042	14.930	0.068	0.068	0.000	0.000	0.000	0.000
19	A	28	ALA	0	-0.028	-0.004	12.696	-0.065	-0.065	0.000	0.000	0.000	0.000
20	A	29	VAL	0	0.012	0.017	12.740	0.068	0.068	0.000	0.000	0.000	0.000
21	A	30	VAL	0	0.027	0.029	7.429	0.016	0.016	0.000	0.000	0.000	0.000
22	A	31	VAL	0	-0.022	-0.024	10.655	-0.079	-0.079	0.000	0.000	0.000	0.000
23	A	32	SER	0	0.006	0.010	8.034	0.023	0.023	0.000	0.000	0.000	0.000
24	A	33	VAL	0	-0.009	-0.006	9.372	0.007	0.007	0.000	0.000	0.000	0.000
25	A	34	ASP	-1	-0.775	-0.897	6.538	-0.998	-0.998	0.000	0.000	0.000	0.000
26	A	35	GLU	-1	-0.939	-0.968	6.202	-1.160	-1.160	0.000	0.000	0.000	0.000
27	A	36	LEU	0	-0.070	-0.041	7.358	0.078	0.078	0.000	0.000	0.000	0.000
28	A	37	LEU	0	-0.072	-0.014	1.984	0.570	-1.080	5.424	-1.679	-2.096	-0.004
29	A	38	THR	0	-0.036	-0.036	4.028	-0.180	0.000	0.003	-0.056	-0.127	0.000
30	A	39	GLY	0	-0.059	-0.036	2.146	0.094	-1.470	7.844	-4.080	-2.200	0.005
31	A	40	ILE	0	-0.016	0.007	3.009	5.388	1.555	0.071	4.216	-0.454	-0.003
32	A	41	ASP	-1	-0.871	-0.956	4.394	2.694	2.930	-0.001	-0.029	-0.206	0.000
33	A	42	ASP	-1	-0.984	-1.000	5.826	0.082	0.082	0.000	0.000	0.000	0.000
34	A	43	GLU	-1	-0.759	-0.859	2.434	-6.385	-4.966	1.440	-1.166	-1.693	-0.017
35	A	44	LEU	0	-0.046	-0.039	6.928	0.413	0.413	0.000	0.000	0.000	0.000
36	A	45	VAL	0	0.051	0.021	4.895	-0.186	-0.186	0.000	0.000	0.000	0.000
37	A	46	VAL	0	-0.012	-0.007	7.967	0.123	0.123	0.000	0.000	0.000	0.000
38	A	47	VAL	0	0.022	0.009	10.088	-0.019	-0.019	0.000	0.000	0.000	0.000
39	A	48	VAL	0	0.004	-0.006	12.566	-0.036	-0.036	0.000	0.000	0.000	0.000
40	A	49	PRO	0	-0.031	-0.011	16.010	0.033	0.033	0.000	0.000	0.000	0.000
41	A	50	VAL	0	0.036	0.025	17.232	-0.051	-0.051	0.000	0.000	0.000	0.000
42	A	51	SER	0	-0.074	-0.036	19.224	0.025	0.025	0.000	0.000	0.000	0.000
43	A	52	SER	0	0.088	0.049	22.476	-0.011	-0.011	0.000	0.000	0.000	0.000
44	A	53	SER	0	-0.017	-0.003	25.151	-0.014	-0.014	0.000	0.000	0.000	0.000
45	A	54	ARG	1	0.915	0.959	25.213	-0.135	-0.135	0.000	0.000	0.000	0.000
46	A	55	SER	0	0.087	0.046	28.023	0.001	0.001	0.000	0.000	0.000	0.000
47	A	56	ARG	1	1.014	1.009	28.419	-0.047	-0.047	0.000	0.000	0.000	0.000
48	A	57	THR	0	-0.050	-0.031	28.549	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	58	PRO	0	0.071	0.024	28.464	0.004	0.004	0.000	0.000	0.000	0.000
50	A	59	LEU	0	0.038	0.030	26.055	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	60	ARG	1	0.759	0.889	24.507	-0.077	-0.077	0.000	0.000	0.000	0.000
52	A	61	PRO	0	0.068	0.034	22.968	0.003	0.003	0.000	0.000	0.000	0.000
53	A	62	PRO	0	-0.020	-0.029	23.804	0.013	0.013	0.000	0.000	0.000	0.000
54	A	63	VAL	0	0.013	0.009	19.326	-0.010	-0.010	0.000	0.000	0.000	0.000
55	A	64	ALA	0	0.014	0.004	22.608	0.008	0.008	0.000	0.000	0.000	0.000
56	A	65	PRO	0	0.071	0.022	22.061	0.010	0.010	0.000	0.000	0.000	0.000
57	A	66	SER	0	-0.010	-0.005	21.879	0.012	0.012	0.000	0.000	0.000	0.000
58	A	67	GLU	-1	-0.820	-0.895	18.763	0.066	0.066	0.000	0.000	0.000	0.000
59	A	68	GLY	0	0.044	0.024	17.201	0.020	0.020	0.000	0.000	0.000	0.000
60	A	69	VAL	0	-0.064	-0.013	18.260	0.044	0.044	0.000	0.000	0.000	0.000
61	A	70	ALA	0	0.025	0.004	20.336	-0.017	-0.017	0.000	0.000	0.000	0.000
62	A	71	ALA	0	-0.008	-0.010	23.256	-0.020	-0.020	0.000	0.000	0.000	0.000
63	A	72	ASP	-1	-0.880	-0.933	24.304	0.120	0.120	0.000	0.000	0.000	0.000
64	A	73	SER	0	-0.040	-0.032	22.238	0.015	0.015	0.000	0.000	0.000	0.000
65	A	74	VAL	0	-0.081	-0.028	23.628	-0.021	-0.021	0.000	0.000	0.000	0.000
66	A	75	ALA	0	0.066	0.039	19.597	0.026	0.026	0.000	0.000	0.000	0.000
67	A	76	VAL	0	-0.082	-0.058	20.620	-0.029	-0.029	0.000	0.000	0.000	0.000
68	A	77	CYS	0	0.064	0.038	20.164	0.008	0.008	0.000	0.000	0.000	0.000
69	A	78	ARG	1	0.965	0.980	21.025	-0.060	-0.060	0.000	0.000	0.000	0.000
70	A	79	GLY	0	-0.062	-0.032	20.919	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	80	VAL	0	-0.005	0.006	16.066	0.036	0.036	0.000	0.000	0.000	0.000
72	A	81	ARG	1	0.916	0.957	14.733	-0.241	-0.241	0.000	0.000	0.000	0.000
73	A	82	ALA	0	0.043	0.032	12.317	0.032	0.032	0.000	0.000	0.000	0.000
74	A	83	VAL	0	-0.081	-0.047	9.429	-0.010	-0.010	0.000	0.000	0.000	0.000
75	A	84	ALA	0	0.077	0.044	9.029	-0.030	-0.030	0.000	0.000	0.000	0.000
76	A	85	ARG	1	0.993	1.005	2.057	-21.259	-20.959	8.128	-4.324	-4.103	0.022
77	A	86	ALA	0	0.042	0.026	5.843	0.761	0.761	0.000	0.000	0.000	0.000
78	A	87	ARG	1	0.793	0.895	8.116	-0.787	-0.787	0.000	0.000	0.000	0.000
79	A	88	LEU	0	-0.034	-0.012	5.876	-0.426	-0.426	0.000	0.000	0.000	0.000
80	A	89	VAL	0	-0.027	-0.011	7.675	0.583	0.583	0.000	0.000	0.000	0.000
81	A	90	GLU	-1	-0.898	-0.958	9.612	1.092	1.092	0.000	0.000	0.000	0.000
82	A	91	ARG	1	0.933	0.981	9.171	-0.493	-0.493	0.000	0.000	0.000	0.000
83	A	92	LEU	0	-0.030	-0.025	10.680	-0.081	-0.081	0.000	0.000	0.000	0.000
84	A	93	GLY	0	-0.019	-0.018	13.411	-0.070	-0.070	0.000	0.000	0.000	0.000
85	A	94	ALA	0	-0.001	0.017	13.262	0.025	0.025	0.000	0.000	0.000	0.000
86	A	95	LEU	0	-0.038	-0.019	15.156	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	96	LYS	1	0.938	0.962	17.696	-0.085	-0.085	0.000	0.000	0.000	0.000
88	A	97	PRO	0	0.061	0.012	19.657	0.002	0.002	0.000	0.000	0.000	0.000
89	A	98	ALA	0	-0.035	-0.016	20.683	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	99	THR	0	-0.017	-0.020	20.607	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	100	MET	0	0.028	0.034	14.850	0.023	0.023	0.000	0.000	0.000	0.000
92	A	101	ARG	1	1.003	1.012	19.219	0.063	0.063	0.000	0.000	0.000	0.000
93	A	102	ALA	0	-0.034	-0.008	22.109	0.001	0.001	0.000	0.000	0.000	0.000
94	A	103	ILE	0	0.008	-0.015	17.678	0.006	0.006	0.000	0.000	0.000	0.000
95	A	104	GLU	-1	-0.819	-0.885	18.001	-0.137	-0.137	0.000	0.000	0.000	0.000
96	A	105	ASN	0	0.007	0.010	20.604	-0.010	-0.010	0.000	0.000	0.000	0.000
97	A	106	ALA	0	-0.011	-0.012	23.185	0.001	0.001	0.000	0.000	0.000	0.000
98	A	107	LEU	0	0.000	-0.021	17.198	0.008	0.008	0.000	0.000	0.000	0.000
99	A	108	THR	0	0.014	0.011	21.956	-0.009	-0.009	0.000	0.000	0.000	0.000
100	A	109	LEU	0	-0.034	-0.012	23.975	0.002	0.002	0.000	0.000	0.000	0.000
101	A	110	ILE	0	-0.099	-0.053	23.496	0.005	0.005	0.000	0.000	0.000	0.000
102	A	111	LEU	0	-0.040	-0.022	19.877	0.005	0.005	0.000	0.000	0.000	0.000
103	A	112	GLY	0	-0.004	0.020	24.527	-0.007	-0.007	0.000	0.000	0.000	0.000
104	A	113	LEU	0	-0.034	-0.015	21.434	-0.008	-0.008	0.000	0.000	0.000	0.000
105	A	114	PRO	0	-0.004	-0.001	25.892	0.006	0.006	0.000	0.000	0.000	0.000

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