FMO DATABASE

FMODB ID: 728JK

Calculation Name: 4DYW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DYW

Chain ID: A

ChEMBL ID:

UniProt ID: Q3JWU2

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:

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	129
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1089060.236901
FMO2-HF: Nuclear repulsion	1039290.129773
FMO2-HF: Total energy	-49770.107128
FMO2-MP2: Total energy	-49915.674085

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:5:GLU)

Summations of interaction energy for fragment #1(A:5:GLU)

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.
58.937	62.217	-0.042	-1.927	-1.311	0

Interaction energy analysis for fragmet #1(A:5:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.952 / q_NPA : -0.977

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	7	PRO	0	-0.008	0.009	3.842	-3.371	-0.091	-0.042	-1.927	-1.311
4	A	8	ARG	1	0.931	0.979	6.693	-27.601	-27.601	0.000	0.000	0.000
5	A	9	VAL	0	0.017	0.007	8.912	-1.315	-1.315	0.000	0.000	0.000
6	A	10	GLY	0	0.013	0.003	12.542	-0.047	-0.047	0.000	0.000	0.000
7	A	11	CYS	0	-0.072	-0.035	15.354	-0.490	-0.490	0.000	0.000	0.000
8	A	12	GLY	0	0.082	0.028	19.130	0.104	0.104	0.000	0.000	0.000
9	A	13	ALA	0	-0.008	0.002	22.095	-0.163	-0.163	0.000	0.000	0.000
10	A	14	ALA	0	0.014	0.014	25.876	-0.047	-0.047	0.000	0.000	0.000
11	A	15	ILE	0	0.014	0.001	28.201	-0.224	-0.224	0.000	0.000	0.000
12	A	16	VAL	0	0.008	-0.006	31.376	-0.113	-0.113	0.000	0.000	0.000
13	A	17	ARG	1	0.924	0.972	34.360	-7.901	-7.901	0.000	0.000	0.000
14	A	18	ASP	-1	-0.932	-0.965	38.059	7.176	7.176	0.000	0.000	0.000
15	A	19	GLY	0	-0.003	-0.003	38.189	-0.085	-0.085	0.000	0.000	0.000
16	A	20	ARG	1	0.921	0.959	36.475	-7.226	-7.226	0.000	0.000	0.000
17	A	21	ILE	0	0.008	-0.002	28.944	0.063	0.063	0.000	0.000	0.000
18	A	22	LEU	0	-0.031	-0.009	31.281	-0.091	-0.091	0.000	0.000	0.000
19	A	23	LEU	0	-0.036	-0.004	27.556	0.355	0.355	0.000	0.000	0.000
20	A	24	ILE	0	0.023	-0.002	25.514	-0.387	-0.387	0.000	0.000	0.000
21	A	25	LYS	1	0.858	0.937	26.432	-9.432	-9.432	0.000	0.000	0.000
22	A	26	ARG	1	0.936	0.973	17.880	-14.133	-14.133	0.000	0.000	0.000
23	A	27	LYS	1	0.842	0.905	24.285	-10.135	-10.135	0.000	0.000	0.000
24	A	28	ARG	1	0.800	0.881	20.344	-12.238	-12.238	0.000	0.000	0.000
25	A	29	ALA	0	-0.016	0.010	17.162	0.053	0.053	0.000	0.000	0.000
26	A	30	PRO	0	0.074	0.030	13.804	-0.182	-0.182	0.000	0.000	0.000
27	A	31	GLU	-1	-0.779	-0.916	16.453	13.422	13.422	0.000	0.000	0.000
28	A	32	ALA	0	-0.020	-0.002	19.337	-0.447	-0.447	0.000	0.000	0.000
29	A	33	GLY	0	-0.010	-0.016	21.886	-0.175	-0.175	0.000	0.000	0.000
30	A	34	CYS	0	-0.078	-0.018	22.652	-0.364	-0.364	0.000	0.000	0.000
31	A	35	TRP	0	0.023	-0.002	24.736	0.064	0.064	0.000	0.000	0.000
32	A	36	GLY	0	-0.005	-0.020	23.739	0.199	0.199	0.000	0.000	0.000
33	A	37	LEU	0	-0.005	-0.004	23.141	-0.339	-0.339	0.000	0.000	0.000
34	A	38	PRO	0	0.024	0.031	23.221	0.360	0.360	0.000	0.000	0.000
35	A	39	GLY	0	0.009	-0.014	21.198	-0.015	-0.015	0.000	0.000	0.000
36	A	40	GLY	0	0.012	0.018	17.937	-0.073	-0.073	0.000	0.000	0.000
37	A	41	LYS	1	0.827	0.904	13.828	-16.298	-16.298	0.000	0.000	0.000
38	A	42	VAL	0	0.018	0.008	14.864	-0.934	-0.934	0.000	0.000	0.000
39	A	43	ASP	-1	-0.852	-0.904	14.389	17.706	17.706	0.000	0.000	0.000
40	A	44	TRP	0	-0.011	-0.022	12.670	0.220	0.220	0.000	0.000	0.000
41	A	45	LEU	0	-0.034	-0.026	15.385	-0.840	-0.840	0.000	0.000	0.000
42	A	46	GLU	-1	-0.751	-0.831	17.915	12.897	12.897	0.000	0.000	0.000
43	A	47	PRO	0	-0.013	-0.012	19.044	0.407	0.407	0.000	0.000	0.000
44	A	48	VAL	0	0.085	0.035	19.232	-0.132	-0.132	0.000	0.000	0.000
45	A	49	GLU	-1	-0.836	-0.909	20.569	11.133	11.133	0.000	0.000	0.000
46	A	50	ARG	1	0.832	0.900	22.020	-12.917	-12.917	0.000	0.000	0.000
47	A	51	ALA	0	0.010	0.012	19.616	-0.174	-0.174	0.000	0.000	0.000
48	A	52	VAL	0	0.010	0.003	21.652	-0.128	-0.128	0.000	0.000	0.000
49	A	53	CYS	0	-0.068	-0.042	23.654	-0.357	-0.357	0.000	0.000	0.000
50	A	54	ARG	1	0.751	0.851	19.160	-14.066	-14.066	0.000	0.000	0.000
51	A	55	GLU	-1	-0.840	-0.900	19.727	14.018	14.018	0.000	0.000	0.000
52	A	56	ILE	0	-0.022	-0.017	23.583	-0.216	-0.216	0.000	0.000	0.000
53	A	57	GLU	-1	-0.949	-0.966	26.738	9.081	9.081	0.000	0.000	0.000
54	A	58	GLU	-1	-0.891	-0.960	23.128	12.137	12.137	0.000	0.000	0.000
55	A	59	GLU	-1	-0.832	-0.894	23.059	12.166	12.166	0.000	0.000	0.000
56	A	60	LEU	0	-0.052	-0.042	27.227	-0.276	-0.276	0.000	0.000	0.000
57	A	61	GLY	0	-0.020	0.000	30.451	-0.355	-0.355	0.000	0.000	0.000
58	A	62	ILE	0	-0.066	-0.015	31.641	-0.302	-0.302	0.000	0.000	0.000
59	A	63	ALA	0	0.087	0.043	31.364	0.311	0.311	0.000	0.000	0.000
60	A	64	LEU	0	-0.011	-0.021	28.153	-0.280	-0.280	0.000	0.000	0.000
61	A	65	GLU	-1	-0.824	-0.900	31.995	7.923	7.923	0.000	0.000	0.000
62	A	66	ARG	1	0.766	0.862	33.546	-8.066	-8.066	0.000	0.000	0.000
63	A	67	ALA	0	0.037	0.033	28.916	-0.095	-0.095	0.000	0.000	0.000
64	A	68	THR	0	0.018	0.011	29.904	0.027	0.027	0.000	0.000	0.000
65	A	69	LEU	0	-0.039	-0.016	23.407	0.065	0.065	0.000	0.000	0.000
66	A	70	LEU	0	-0.047	-0.011	26.072	-0.327	-0.327	0.000	0.000	0.000
67	A	71	CYS	0	-0.011	0.000	23.713	-0.035	-0.035	0.000	0.000	0.000
68	A	72	VAL	0	-0.003	-0.019	17.728	0.185	0.185	0.000	0.000	0.000
69	A	73	VAL	0	0.012	0.025	16.855	-0.096	-0.096	0.000	0.000	0.000
70	A	74	ASP	-1	-0.871	-0.930	14.394	18.424	18.424	0.000	0.000	0.000
71	A	75	HIS	0	-0.041	-0.029	12.067	-1.296	-1.296	0.000	0.000	0.000
72	A	76	ILE	0	0.011	0.002	10.097	1.595	1.595	0.000	0.000	0.000
73	A	77	ASP	-1	-0.837	-0.907	9.996	17.045	17.045	0.000	0.000	0.000
74	A	78	ALA	0	0.015	-0.007	8.615	1.264	1.264	0.000	0.000	0.000
75	A	79	ALA	0	-0.048	-0.017	9.245	1.102	1.102	0.000	0.000	0.000
76	A	80	ASN	0	-0.085	-0.060	10.860	-0.114	-0.114	0.000	0.000	0.000
77	A	81	GLY	0	-0.026	0.005	6.672	0.703	0.703	0.000	0.000	0.000
78	A	82	GLU	-1	-0.911	-0.955	5.741	24.229	24.229	0.000	0.000	0.000
79	A	83	HIS	0	0.013	-0.007	6.574	-1.444	-1.444	0.000	0.000	0.000
80	A	84	TRP	0	-0.065	-0.033	8.123	2.200	2.200	0.000	0.000	0.000
81	A	85	VAL	0	0.024	0.020	10.935	-0.859	-0.859	0.000	0.000	0.000
82	A	86	ALA	0	-0.001	-0.009	13.636	0.229	0.229	0.000	0.000	0.000
83	A	87	PRO	0	-0.017	-0.001	16.837	-0.702	-0.702	0.000	0.000	0.000
84	A	88	VAL	0	0.004	0.010	20.199	-0.024	-0.024	0.000	0.000	0.000
85	A	89	TYR	0	-0.041	-0.047	22.501	-0.062	-0.062	0.000	0.000	0.000
86	A	90	LEU	0	-0.009	0.005	26.464	-0.048	-0.048	0.000	0.000	0.000
87	A	91	ALA	0	0.035	0.008	29.840	-0.069	-0.069	0.000	0.000	0.000
88	A	92	HIS	0	0.042	0.022	32.326	-0.041	-0.041	0.000	0.000	0.000
89	A	93	ALA	0	-0.068	-0.046	35.388	-0.265	-0.265	0.000	0.000	0.000
90	A	94	PHE	0	0.003	0.005	34.111	0.254	0.254	0.000	0.000	0.000
91	A	95	SER	0	0.010	0.002	35.941	-0.227	-0.227	0.000	0.000	0.000
92	A	96	GLY	0	0.019	0.008	36.171	0.202	0.202	0.000	0.000	0.000
93	A	97	GLU	-1	-0.920	-0.981	37.996	7.552	7.552	0.000	0.000	0.000
94	A	98	PRO	0	-0.061	-0.005	33.734	0.125	0.125	0.000	0.000	0.000
95	A	99	ARG	1	0.950	0.969	33.656	-8.914	-8.914	0.000	0.000	0.000
96	A	100	VAL	0	0.017	0.005	29.534	0.246	0.246	0.000	0.000	0.000
97	A	101	VAL	0	-0.060	-0.019	29.569	-0.303	-0.303	0.000	0.000	0.000
98	A	102	GLU	-1	-0.803	-0.886	24.913	11.851	11.851	0.000	0.000	0.000
99	A	103	PRO	0	-0.022	-0.022	27.898	0.218	0.218	0.000	0.000	0.000
100	A	104	ASP	-1	-0.839	-0.901	25.740	10.746	10.746	0.000	0.000	0.000
101	A	105	ARG	1	0.757	0.862	21.651	-12.230	-12.230	0.000	0.000	0.000
102	A	106	HIS	0	-0.014	-0.021	23.255	0.014	0.014	0.000	0.000	0.000
103	A	107	GLU	-1	-0.824	-0.898	27.100	9.536	9.536	0.000	0.000	0.000
104	A	108	ALA	0	-0.050	-0.014	29.948	-0.338	-0.338	0.000	0.000	0.000
105	A	109	LEU	0	0.015	0.007	30.336	0.321	0.321	0.000	0.000	0.000
106	A	110	GLY	0	-0.005	0.006	32.408	-0.276	-0.276	0.000	0.000	0.000
107	A	111	TRP	0	0.007	0.012	33.380	0.254	0.254	0.000	0.000	0.000
108	A	112	PHE	0	0.013	-0.002	32.492	-0.170	-0.170	0.000	0.000	0.000
109	A	113	ALA	0	0.038	0.033	35.350	0.112	0.112	0.000	0.000	0.000
110	A	114	LEU	0	-0.008	-0.022	32.784	0.119	0.119	0.000	0.000	0.000
111	A	115	ASP	-1	-0.944	-0.970	34.679	7.602	7.602	0.000	0.000	0.000
112	A	116	ASP	-1	-0.978	-0.983	36.575	7.477	7.477	0.000	0.000	0.000
113	A	117	LEU	0	-0.042	-0.002	30.466	0.107	0.107	0.000	0.000	0.000
114	A	118	PRO	0	0.008	0.019	30.453	-0.080	-0.080	0.000	0.000	0.000
115	A	119	GLN	0	-0.038	-0.019	29.334	0.469	0.469	0.000	0.000	0.000
116	A	120	PRO	0	0.004	-0.009	25.350	-0.195	-0.195	0.000	0.000	0.000
117	A	121	LEU	0	0.036	0.014	25.518	0.076	0.076	0.000	0.000	0.000
118	A	122	THR	0	0.016	0.015	20.263	0.061	0.061	0.000	0.000	0.000
119	A	123	HIS	0	-0.033	-0.045	16.850	-0.909	-0.909	0.000	0.000	0.000
120	A	124	ALA	0	0.022	0.003	18.608	-0.254	-0.254	0.000	0.000	0.000
121	A	125	THR	0	0.013	-0.003	20.280	-0.345	-0.345	0.000	0.000	0.000
122	A	126	ARG	1	0.871	0.947	20.861	-12.551	-12.551	0.000	0.000	0.000
123	A	127	ILE	0	0.055	0.032	19.430	-0.244	-0.244	0.000	0.000	0.000
124	A	128	ALA	0	0.000	-0.004	23.515	-0.282	-0.282	0.000	0.000	0.000
125	A	129	LEU	0	-0.026	-0.032	25.211	-0.378	-0.378	0.000	0.000	0.000
126	A	130	GLU	-1	-0.959	-0.971	25.539	10.681	10.681	0.000	0.000	0.000
127	A	131	GLN	0	-0.079	-0.027	26.413	-0.210	-0.210	0.000	0.000	0.000
128	A	132	VAL	0	-0.053	-0.021	29.125	-0.298	-0.298	0.000	0.000	0.000
129	A	133	THR	0	-0.023	0.000	31.591	-0.333	-0.333	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:GLU)