FMO DATABASE

FMODB ID: ZVKZN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-735408.610445
FMO2-HF: Nuclear repulsion	697011.884296
FMO2-HF: Total energy	-38396.726149
FMO2-MP2: Total energy	-38510.252994

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.
-18.109	-18.785	20.051	-7.506	-11.867	-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 : -0.031 / q_NPA : -0.024

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	-0.096	-0.047	2.091	-1.446	-0.685	3.688	-2.224	-2.225	-0.001
4	A	5	ARG	1	0.990	1.004	4.786	-0.078	-0.078	-0.001	-0.014	0.014	0.000
5	A	6	ARG	1	0.812	0.868	7.502	0.526	0.526	0.000	0.000	0.000	0.000
6	A	7	GLY	0	-0.035	-0.027	10.066	-0.001	-0.001	0.000	0.000	0.000	0.000
7	A	8	ASP	-1	-0.754	-0.858	8.875	0.215	0.215	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.093	-0.045	11.546	0.013	0.013	0.000	0.000	0.000	0.000
9	A	10	TRP	0	0.031	0.000	6.120	0.255	0.255	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.001	0.002	11.083	-0.160	-0.160	0.000	0.000	0.000	0.000
11	A	12	VAL	0	-0.004	-0.007	10.774	0.186	0.186	0.000	0.000	0.000	0.000
12	A	13	SER	0	0.029	0.017	12.440	-0.139	-0.139	0.000	0.000	0.000	0.000
13	A	14	LEU	0	-0.073	-0.039	14.485	-0.062	-0.062	0.000	0.000	0.000	0.000
14	A	23	GLY	0	0.029	0.008	21.142	-0.006	-0.006	0.000	0.000	0.000	0.000
15	A	24	LYS	1	0.896	0.947	20.157	-0.258	-0.258	0.000	0.000	0.000	0.000
16	A	25	HIS	0	0.148	0.091	15.889	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	26	ARG	1	0.864	0.918	16.205	-0.380	-0.380	0.000	0.000	0.000	0.000
18	A	27	PRO	0	0.074	0.047	14.899	0.065	0.065	0.000	0.000	0.000	0.000
19	A	28	ALA	0	-0.022	-0.012	12.717	-0.062	-0.062	0.000	0.000	0.000	0.000
20	A	29	VAL	0	0.009	0.017	12.743	0.063	0.063	0.000	0.000	0.000	0.000
21	A	30	VAL	0	0.027	0.029	7.401	0.010	0.010	0.000	0.000	0.000	0.000
22	A	31	VAL	0	-0.025	-0.026	10.624	-0.068	-0.068	0.000	0.000	0.000	0.000
23	A	32	SER	0	0.007	0.015	7.842	0.021	0.021	0.000	0.000	0.000	0.000
24	A	33	VAL	0	-0.010	-0.008	9.335	0.010	0.010	0.000	0.000	0.000	0.000
25	A	34	ASP	-1	-0.755	-0.880	6.601	-0.955	-0.955	0.000	0.000	0.000	0.000
26	A	35	GLU	-1	-0.923	-0.964	6.284	-1.079	-1.079	0.000	0.000	0.000	0.000
27	A	36	LEU	0	-0.067	-0.038	7.361	0.068	0.068	0.000	0.000	0.000	0.000
28	A	37	LEU	0	-0.083	-0.019	2.094	0.109	-0.825	4.283	-1.319	-2.029	-0.003
29	A	38	THR	0	-0.027	-0.048	4.028	-0.053	0.094	0.003	-0.054	-0.096	0.000
30	A	39	GLY	0	-0.056	-0.037	2.230	-0.102	-1.363	7.255	-3.856	-2.137	0.005
31	A	40	ILE	0	-0.027	0.004	3.041	4.870	1.392	0.058	3.863	-0.443	-0.003
32	A	41	ASP	-1	-0.867	-0.961	4.265	2.178	2.434	-0.001	-0.040	-0.215	0.000
33	A	42	ASP	-1	-0.970	-0.990	5.785	-0.042	-0.042	0.000	0.000	0.000	0.000
34	A	43	GLU	-1	-0.762	-0.840	2.496	-6.303	-4.798	1.342	-1.195	-1.651	-0.016
35	A	44	LEU	0	-0.045	-0.038	6.811	0.361	0.361	0.000	0.000	0.000	0.000
36	A	45	VAL	0	0.055	0.025	4.960	-0.172	-0.172	0.000	0.000	0.000	0.000
37	A	46	VAL	0	-0.015	-0.006	7.769	0.120	0.120	0.000	0.000	0.000	0.000
38	A	47	VAL	0	0.023	0.007	10.032	-0.014	-0.014	0.000	0.000	0.000	0.000
39	A	48	VAL	0	0.004	-0.004	12.606	-0.033	-0.033	0.000	0.000	0.000	0.000
40	A	49	PRO	0	-0.022	-0.008	16.032	0.032	0.032	0.000	0.000	0.000	0.000
41	A	50	VAL	0	0.024	0.020	17.188	-0.046	-0.046	0.000	0.000	0.000	0.000
42	A	51	SER	0	-0.057	-0.030	19.229	0.018	0.018	0.000	0.000	0.000	0.000
43	A	52	SER	0	0.097	0.048	22.474	-0.009	-0.009	0.000	0.000	0.000	0.000
44	A	53	SER	0	-0.013	-0.001	25.141	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	54	ARG	1	0.898	0.954	25.112	-0.118	-0.118	0.000	0.000	0.000	0.000
46	A	55	SER	0	0.092	0.051	28.029	0.001	0.001	0.000	0.000	0.000	0.000
47	A	56	ARG	1	1.017	1.011	28.427	-0.041	-0.041	0.000	0.000	0.000	0.000
48	A	57	THR	0	-0.044	-0.031	28.646	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	58	PRO	0	0.066	0.023	28.489	0.003	0.003	0.000	0.000	0.000	0.000
50	A	59	LEU	0	0.030	0.024	26.090	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	60	ARG	1	0.774	0.898	24.532	-0.065	-0.065	0.000	0.000	0.000	0.000
52	A	61	PRO	0	0.071	0.032	23.097	0.005	0.005	0.000	0.000	0.000	0.000
53	A	62	PRO	0	-0.020	-0.025	23.826	0.012	0.012	0.000	0.000	0.000	0.000
54	A	63	VAL	0	-0.003	-0.005	19.345	-0.010	-0.010	0.000	0.000	0.000	0.000
55	A	64	ALA	0	0.026	0.010	22.615	0.007	0.007	0.000	0.000	0.000	0.000
56	A	65	PRO	0	0.074	0.024	22.052	0.010	0.010	0.000	0.000	0.000	0.000
57	A	66	SER	0	-0.003	0.003	21.857	0.012	0.012	0.000	0.000	0.000	0.000
58	A	67	GLU	-1	-0.781	-0.855	18.835	0.063	0.063	0.000	0.000	0.000	0.000
59	A	68	GLY	0	0.048	0.027	17.178	0.018	0.018	0.000	0.000	0.000	0.000
60	A	69	VAL	0	-0.070	-0.016	18.236	0.040	0.040	0.000	0.000	0.000	0.000
61	A	70	ALA	0	0.026	0.005	20.312	-0.015	-0.015	0.000	0.000	0.000	0.000
62	A	71	ALA	0	-0.001	-0.004	23.223	-0.018	-0.018	0.000	0.000	0.000	0.000
63	A	72	ASP	-1	-0.881	-0.929	24.288	0.113	0.113	0.000	0.000	0.000	0.000
64	A	73	SER	0	-0.039	-0.039	22.220	0.013	0.013	0.000	0.000	0.000	0.000
65	A	74	VAL	0	-0.082	-0.031	23.642	-0.019	-0.019	0.000	0.000	0.000	0.000
66	A	75	ALA	0	0.066	0.040	19.621	0.023	0.023	0.000	0.000	0.000	0.000
67	A	76	VAL	0	-0.080	-0.055	20.640	-0.026	-0.026	0.000	0.000	0.000	0.000
68	A	77	CYS	0	0.064	0.035	20.065	0.006	0.006	0.000	0.000	0.000	0.000
69	A	78	ARG	1	0.974	0.985	20.882	-0.045	-0.045	0.000	0.000	0.000	0.000
70	A	79	GLY	0	-0.058	-0.028	20.951	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	80	VAL	0	0.011	0.017	15.871	0.033	0.033	0.000	0.000	0.000	0.000
72	A	81	ARG	1	0.879	0.931	14.790	-0.186	-0.186	0.000	0.000	0.000	0.000
73	A	82	ALA	0	0.038	0.030	12.110	0.029	0.029	0.000	0.000	0.000	0.000
74	A	83	VAL	0	-0.069	-0.043	9.586	0.000	0.000	0.000	0.000	0.000	0.000
75	A	84	ALA	0	0.073	0.042	8.890	-0.035	-0.035	0.000	0.000	0.000	0.000
76	A	85	ARG	1	0.971	0.994	2.184	-16.106	-13.778	3.424	-2.667	-3.085	0.017
77	A	86	ALA	0	0.057	0.038	5.844	0.721	0.721	0.000	0.000	0.000	0.000
78	A	87	ARG	1	0.794	0.890	8.036	-0.638	-0.638	0.000	0.000	0.000	0.000
79	A	88	LEU	0	-0.033	-0.009	5.926	-0.358	-0.358	0.000	0.000	0.000	0.000
80	A	89	VAL	0	-0.039	-0.017	7.614	0.565	0.565	0.000	0.000	0.000	0.000
81	A	90	GLU	-1	-0.895	-0.959	9.576	1.004	1.004	0.000	0.000	0.000	0.000
82	A	91	ARG	1	0.850	0.918	9.103	-0.472	-0.472	0.000	0.000	0.000	0.000
83	A	92	LEU	0	-0.030	-0.021	10.632	-0.074	-0.074	0.000	0.000	0.000	0.000
84	A	93	GLY	0	0.007	-0.006	13.375	-0.065	-0.065	0.000	0.000	0.000	0.000
85	A	94	ALA	0	-0.006	0.009	13.249	0.023	0.023	0.000	0.000	0.000	0.000
86	A	95	LEU	0	-0.026	-0.008	15.156	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	96	LYS	1	0.870	0.919	17.710	-0.084	-0.084	0.000	0.000	0.000	0.000
88	A	97	PRO	0	0.067	0.014	19.700	0.000	0.000	0.000	0.000	0.000	0.000
89	A	98	ALA	0	-0.037	-0.015	20.729	-0.006	-0.006	0.000	0.000	0.000	0.000
90	A	99	THR	0	-0.023	-0.042	20.540	-0.007	-0.007	0.000	0.000	0.000	0.000
91	A	100	MET	0	0.035	0.036	14.799	0.021	0.021	0.000	0.000	0.000	0.000
92	A	101	ARG	1	1.009	1.018	19.211	0.059	0.059	0.000	0.000	0.000	0.000
93	A	102	ALA	0	-0.029	0.002	22.102	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	103	ILE	0	0.010	-0.010	17.619	0.004	0.004	0.000	0.000	0.000	0.000
95	A	104	GLU	-1	-0.806	-0.881	17.796	-0.134	-0.134	0.000	0.000	0.000	0.000
96	A	105	ASN	0	-0.039	-0.019	20.553	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	106	ALA	0	-0.008	-0.008	23.080	0.001	0.001	0.000	0.000	0.000	0.000
98	A	107	LEU	0	0.001	-0.014	17.278	0.006	0.006	0.000	0.000	0.000	0.000
99	A	108	THR	0	0.020	0.003	21.854	-0.009	-0.009	0.000	0.000	0.000	0.000
100	A	109	LEU	0	-0.029	-0.010	23.889	0.002	0.002	0.000	0.000	0.000	0.000
101	A	110	ILE	0	-0.101	-0.053	23.364	0.005	0.005	0.000	0.000	0.000	0.000
102	A	111	LEU	0	-0.037	-0.020	19.707	0.004	0.004	0.000	0.000	0.000	0.000
103	A	112	GLY	0	-0.005	0.019	24.398	-0.007	-0.007	0.000	0.000	0.000	0.000
104	A	113	LEU	0	-0.039	-0.016	21.277	-0.008	-0.008	0.000	0.000	0.000	0.000
105	A	114	PRO	0	0.002	0.001	25.822	0.007	0.007	0.000	0.000	0.000	0.000

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