FMO DATABASE

FMODB ID: 3Q15L

Calculation Name: 4DOX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DOX

Chain ID: A

ChEMBL ID:

UniProt ID: P16596

Base Structure: X-ray

Registration Date: 2023-06-20

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	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	164
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1445937.571594
FMO2-HF: Nuclear repulsion	1383956.540582
FMO2-HF: Total energy	-61981.031011
FMO2-MP2: Total energy	-62160.687422

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:11:ILE)

Summations of interaction energy for fragment #1(A:11:ILE)

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.
-3.644	-0.01	1.949	-2.011	-3.572	-0.01

Interaction energy analysis for fragmet #1(A:11:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : -0.028

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	13	PHE	0	0.016	0.007	3.019	-2.244	0.269	0.064	-1.146	-1.432	0.000
4	A	14	PRO	0	-0.010	0.004	2.650	-1.759	-0.679	1.882	-0.949	-2.013	-0.010
5	A	15	ALA	0	0.003	-0.003	3.765	0.369	0.410	0.003	0.084	-0.127	0.000
6	A	16	ILE	0	0.012	0.013	6.282	-0.016	-0.016	0.000	0.000	0.000	0.000
7	A	17	THR	0	0.003	0.006	9.767	0.068	0.068	0.000	0.000	0.000	0.000
8	A	18	GLN	0	0.041	-0.004	12.044	0.046	0.046	0.000	0.000	0.000	0.000
9	A	19	GLU	-1	-0.812	-0.895	15.443	-0.309	-0.309	0.000	0.000	0.000	0.000
10	A	20	GLN	0	0.049	0.037	11.034	-0.018	-0.018	0.000	0.000	0.000	0.000
11	A	21	MET	0	-0.057	-0.035	14.125	0.020	0.020	0.000	0.000	0.000	0.000
12	A	22	SER	0	-0.038	-0.008	16.548	0.034	0.034	0.000	0.000	0.000	0.000
13	A	23	SER	0	-0.070	-0.055	17.599	0.018	0.018	0.000	0.000	0.000	0.000
14	A	24	ILE	0	-0.012	0.010	14.937	0.015	0.015	0.000	0.000	0.000	0.000
15	A	25	LYS	1	0.833	0.908	18.495	0.175	0.175	0.000	0.000	0.000	0.000
16	A	26	VAL	0	0.010	-0.005	19.146	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	27	ASP	-1	-0.894	-0.934	22.052	-0.088	-0.088	0.000	0.000	0.000	0.000
18	A	28	PRO	0	-0.011	-0.013	25.426	0.002	0.002	0.000	0.000	0.000	0.000
19	A	29	THR	0	0.008	0.012	24.504	0.002	0.002	0.000	0.000	0.000	0.000
20	A	30	SER	0	0.017	-0.005	27.665	0.008	0.008	0.000	0.000	0.000	0.000
21	A	31	ASN	0	0.025	0.015	28.797	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	32	LEU	0	0.012	0.004	30.429	0.001	0.001	0.000	0.000	0.000	0.000
23	A	33	LEU	0	0.040	0.031	33.408	0.002	0.002	0.000	0.000	0.000	0.000
24	A	34	PRO	0	-0.017	-0.001	33.456	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	35	SER	0	-0.003	-0.018	30.337	0.001	0.001	0.000	0.000	0.000	0.000
26	A	36	GLN	0	0.051	0.016	31.881	0.004	0.004	0.000	0.000	0.000	0.000
27	A	37	GLU	-1	-0.794	-0.879	30.259	-0.067	-0.067	0.000	0.000	0.000	0.000
28	A	38	GLN	0	0.002	0.029	33.108	0.005	0.005	0.000	0.000	0.000	0.000
29	A	39	LEU	0	0.034	0.024	35.576	0.003	0.003	0.000	0.000	0.000	0.000
30	A	40	LYS	1	0.934	0.980	36.697	0.050	0.050	0.000	0.000	0.000	0.000
31	A	41	SER	0	-0.024	-0.006	36.246	0.001	0.001	0.000	0.000	0.000	0.000
32	A	42	VAL	0	0.002	0.004	38.910	0.002	0.002	0.000	0.000	0.000	0.000
33	A	43	SER	0	0.000	-0.015	41.198	0.001	0.001	0.000	0.000	0.000	0.000
34	A	44	THR	0	-0.033	-0.037	40.933	0.000	0.000	0.000	0.000	0.000	0.000
35	A	45	LEU	0	0.015	-0.002	41.260	0.001	0.001	0.000	0.000	0.000	0.000
36	A	46	MET	0	-0.026	0.000	44.654	0.002	0.002	0.000	0.000	0.000	0.000
37	A	47	VAL	0	0.002	0.010	46.749	0.001	0.001	0.000	0.000	0.000	0.000
38	A	48	ALA	0	-0.056	-0.027	46.508	0.001	0.001	0.000	0.000	0.000	0.000
39	A	49	ALA	0	-0.030	-0.019	48.472	0.001	0.001	0.000	0.000	0.000	0.000
40	A	50	LYS	1	0.918	0.967	50.585	0.027	0.027	0.000	0.000	0.000	0.000
41	A	51	VAL	0	0.014	0.019	50.106	0.001	0.001	0.000	0.000	0.000	0.000
42	A	52	PRO	0	0.038	0.012	51.101	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	53	ALA	0	0.046	0.011	48.458	0.000	0.000	0.000	0.000	0.000	0.000
44	A	54	ALA	0	-0.027	-0.013	48.955	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	55	SER	0	0.007	0.005	51.377	0.001	0.001	0.000	0.000	0.000	0.000
46	A	56	VAL	0	-0.010	-0.001	45.955	0.001	0.001	0.000	0.000	0.000	0.000
47	A	57	THR	0	0.036	0.011	46.423	0.000	0.000	0.000	0.000	0.000	0.000
48	A	58	THR	0	0.021	0.004	48.062	0.001	0.001	0.000	0.000	0.000	0.000
49	A	59	VAL	0	0.020	0.012	51.027	0.001	0.001	0.000	0.000	0.000	0.000
50	A	60	ALA	0	-0.020	-0.008	46.410	0.001	0.001	0.000	0.000	0.000	0.000
51	A	61	LEU	0	0.008	-0.010	47.886	0.001	0.001	0.000	0.000	0.000	0.000
52	A	62	GLU	-1	-0.780	-0.846	50.177	-0.014	-0.014	0.000	0.000	0.000	0.000
53	A	63	LEU	0	-0.018	0.002	46.888	0.001	0.001	0.000	0.000	0.000	0.000
54	A	64	VAL	0	0.016	-0.007	46.223	0.001	0.001	0.000	0.000	0.000	0.000
55	A	65	ASN	0	0.034	0.017	48.888	0.002	0.002	0.000	0.000	0.000	0.000
56	A	66	PHE	0	0.047	0.021	51.494	0.001	0.001	0.000	0.000	0.000	0.000
57	A	67	CYS	0	-0.029	-0.024	47.941	0.001	0.001	0.000	0.000	0.000	0.000
58	A	68	TYR	0	-0.055	-0.023	50.025	0.001	0.001	0.000	0.000	0.000	0.000
59	A	69	ASP	-1	-0.755	-0.835	51.173	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	70	ASN	0	-0.083	-0.035	52.619	0.002	0.002	0.000	0.000	0.000	0.000
61	A	71	GLY	0	0.026	0.032	48.685	0.001	0.001	0.000	0.000	0.000	0.000
62	A	72	SER	0	-0.001	-0.055	44.553	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	73	SER	0	0.001	0.000	43.931	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	74	ALA	0	0.006	-0.007	41.483	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	75	TYR	0	0.016	0.004	43.584	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	76	THR	0	0.009	0.015	47.063	0.001	0.001	0.000	0.000	0.000	0.000
67	A	77	THR	0	-0.029	-0.012	49.270	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	78	VAL	0	-0.023	-0.012	49.098	0.000	0.000	0.000	0.000	0.000	0.000
69	A	79	THR	0	-0.032	-0.011	52.274	0.000	0.000	0.000	0.000	0.000	0.000
70	A	80	GLY	0	0.051	0.032	55.792	0.000	0.000	0.000	0.000	0.000	0.000
71	A	81	PRO	0	-0.012	-0.014	56.572	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	82	SER	0	-0.007	-0.005	54.409	0.000	0.000	0.000	0.000	0.000	0.000
73	A	83	SER	0	-0.057	-0.073	55.964	0.000	0.000	0.000	0.000	0.000	0.000
74	A	84	ILE	0	-0.046	-0.021	54.305	0.000	0.000	0.000	0.000	0.000	0.000
75	A	85	PRO	0	0.023	-0.008	57.380	0.000	0.000	0.000	0.000	0.000	0.000
76	A	86	GLU	-1	-0.908	-0.951	57.777	-0.016	-0.016	0.000	0.000	0.000	0.000
77	A	87	ILE	0	-0.053	0.000	52.083	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	88	SER	0	0.006	-0.008	54.421	0.001	0.001	0.000	0.000	0.000	0.000
79	A	89	LEU	0	0.025	-0.002	52.185	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	90	ALA	0	0.047	0.024	50.581	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	91	GLN	0	0.015	0.037	49.608	0.000	0.000	0.000	0.000	0.000	0.000
82	A	92	LEU	0	0.018	0.019	48.261	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	93	ALA	0	0.027	0.003	46.191	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	94	SER	0	-0.061	-0.040	44.913	0.000	0.000	0.000	0.000	0.000	0.000
85	A	95	ILE	0	-0.007	-0.003	44.038	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	96	VAL	0	-0.021	-0.009	41.279	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	97	LYS	1	0.894	0.950	40.316	0.011	0.011	0.000	0.000	0.000	0.000
88	A	98	ALA	0	-0.008	0.004	39.409	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	99	SER	0	-0.064	-0.030	37.203	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	100	GLY	0	0.036	0.016	34.894	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	101	THR	0	-0.057	-0.032	34.627	0.002	0.002	0.000	0.000	0.000	0.000
92	A	102	SER	0	-0.008	-0.011	36.697	0.001	0.001	0.000	0.000	0.000	0.000
93	A	103	LEU	0	0.054	0.015	39.189	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	104	ARG	1	0.901	0.963	39.967	0.000	0.000	0.000	0.000	0.000	0.000
95	A	105	LYS	1	0.830	0.922	31.947	0.025	0.025	0.000	0.000	0.000	0.000
96	A	106	PHE	0	0.044	0.007	38.626	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	107	CYS	0	-0.027	-0.017	40.975	0.000	0.000	0.000	0.000	0.000	0.000
98	A	108	ARG	1	0.769	0.851	37.338	0.006	0.006	0.000	0.000	0.000	0.000
99	A	109	TYR	0	0.007	-0.003	37.699	0.000	0.000	0.000	0.000	0.000	0.000
100	A	110	PHE	0	0.028	0.003	40.518	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	111	ALA	0	0.003	0.017	43.373	0.001	0.001	0.000	0.000	0.000	0.000
102	A	112	PRO	0	0.020	0.009	43.122	0.001	0.001	0.000	0.000	0.000	0.000
103	A	113	ILE	0	-0.025	0.001	46.091	0.001	0.001	0.000	0.000	0.000	0.000
104	A	114	ILE	0	0.002	-0.003	47.924	0.001	0.001	0.000	0.000	0.000	0.000
105	A	115	TRP	0	0.022	0.008	48.647	0.001	0.001	0.000	0.000	0.000	0.000
106	A	116	ASN	0	-0.012	-0.007	50.491	0.002	0.002	0.000	0.000	0.000	0.000
107	A	117	LEU	0	-0.037	-0.016	52.204	0.000	0.000	0.000	0.000	0.000	0.000
108	A	118	ARG	1	0.718	0.821	53.611	0.006	0.006	0.000	0.000	0.000	0.000
109	A	119	THR	0	0.021	-0.005	52.481	0.001	0.001	0.000	0.000	0.000	0.000
110	A	120	ASP	-1	-0.868	-0.919	55.123	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	121	LYS	1	0.859	0.952	57.314	0.006	0.006	0.000	0.000	0.000	0.000
112	A	122	MET	0	-0.018	-0.018	58.439	0.000	0.000	0.000	0.000	0.000	0.000
113	A	123	ALA	0	0.031	0.026	56.628	0.000	0.000	0.000	0.000	0.000	0.000
114	A	124	PRO	0	0.020	0.026	53.128	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	125	ALA	0	0.001	-0.010	55.651	0.001	0.001	0.000	0.000	0.000	0.000
116	A	126	ASN	0	-0.039	-0.024	55.505	0.001	0.001	0.000	0.000	0.000	0.000
117	A	127	TRP	0	-0.007	-0.017	55.636	0.001	0.001	0.000	0.000	0.000	0.000
118	A	128	GLU	-1	-0.926	-0.972	56.657	0.006	0.006	0.000	0.000	0.000	0.000
119	A	129	ALA	0	-0.013	0.001	57.908	0.001	0.001	0.000	0.000	0.000	0.000
120	A	130	SER	0	-0.051	-0.013	53.121	0.001	0.001	0.000	0.000	0.000	0.000
121	A	131	GLY	0	0.023	0.014	53.411	0.000	0.000	0.000	0.000	0.000	0.000
122	A	132	TYR	0	-0.021	-0.011	49.176	0.001	0.001	0.000	0.000	0.000	0.000
123	A	133	LYS	1	0.899	0.922	55.284	-0.011	-0.011	0.000	0.000	0.000	0.000
124	A	134	PRO	0	0.058	0.021	57.527	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	135	SER	0	-0.062	-0.057	57.479	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	136	ALA	0	-0.008	-0.004	53.171	0.000	0.000	0.000	0.000	0.000	0.000
127	A	137	LYS	1	0.900	0.952	53.616	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	138	PHE	0	0.022	0.020	53.624	0.000	0.000	0.000	0.000	0.000	0.000
129	A	139	ALA	0	0.029	0.016	49.179	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	140	ALA	0	-0.011	0.010	49.518	0.001	0.001	0.000	0.000	0.000	0.000
131	A	141	PHE	0	0.018	0.005	46.669	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	142	ASP	-1	-0.750	-0.852	45.262	-0.002	-0.002	0.000	0.000	0.000	0.000
133	A	143	PHE	0	-0.022	-0.025	42.832	0.000	0.000	0.000	0.000	0.000	0.000
134	A	144	PHE	0	0.041	0.035	43.580	-0.002	-0.002	0.000	0.000	0.000	0.000
135	A	145	ASP	-1	-0.784	-0.856	39.569	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	146	GLY	0	0.005	-0.024	39.912	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	147	VAL	0	-0.069	-0.026	41.272	-0.002	-0.002	0.000	0.000	0.000	0.000
138	A	148	GLU	-1	-0.777	-0.873	42.356	0.000	0.000	0.000	0.000	0.000	0.000
139	A	149	ASN	0	-0.024	-0.001	35.676	-0.002	-0.002	0.000	0.000	0.000	0.000
140	A	150	PRO	0	0.026	0.003	35.769	-0.002	-0.002	0.000	0.000	0.000	0.000
141	A	151	ALA	0	-0.008	0.002	34.317	-0.003	-0.003	0.000	0.000	0.000	0.000
142	A	152	ALA	0	-0.041	-0.011	36.372	-0.002	-0.002	0.000	0.000	0.000	0.000
143	A	153	MET	0	-0.027	-0.011	39.529	0.000	0.000	0.000	0.000	0.000	0.000
144	A	154	GLN	0	0.008	-0.006	40.669	0.004	0.004	0.000	0.000	0.000	0.000
145	A	155	PRO	0	-0.009	-0.003	44.171	-0.001	-0.001	0.000	0.000	0.000	0.000
146	A	156	PRO	0	0.005	-0.006	47.599	0.000	0.000	0.000	0.000	0.000	0.000
147	A	157	SER	0	-0.063	-0.038	49.307	0.000	0.000	0.000	0.000	0.000	0.000
148	A	158	GLY	0	0.032	0.036	47.388	0.001	0.001	0.000	0.000	0.000	0.000
149	A	159	LEU	0	-0.001	-0.006	45.864	0.000	0.000	0.000	0.000	0.000	0.000
150	A	160	THR	0	-0.029	-0.016	49.561	0.000	0.000	0.000	0.000	0.000	0.000
151	A	161	ARG	1	0.730	0.816	52.016	0.001	0.001	0.000	0.000	0.000	0.000
152	A	162	SER	0	0.020	-0.002	46.630	-0.001	-0.001	0.000	0.000	0.000	0.000
153	A	163	PRO	0	-0.042	-0.011	46.633	0.001	0.001	0.000	0.000	0.000	0.000
154	A	164	THR	0	-0.011	-0.029	49.390	0.001	0.001	0.000	0.000	0.000	0.000
155	A	165	GLN	0	0.066	0.021	45.076	-0.001	-0.001	0.000	0.000	0.000	0.000
156	A	166	GLU	-1	-0.789	-0.835	49.212	0.011	0.011	0.000	0.000	0.000	0.000
157	A	167	GLU	-1	-0.721	-0.817	50.333	0.003	0.003	0.000	0.000	0.000	0.000
158	A	168	ARG	1	0.851	0.904	44.311	-0.005	-0.005	0.000	0.000	0.000	0.000
159	A	169	ILE	0	-0.016	-0.002	46.251	0.001	0.001	0.000	0.000	0.000	0.000
160	A	170	ALA	0	0.004	0.019	47.840	0.001	0.001	0.000	0.000	0.000	0.000
161	A	171	ASN	0	-0.011	-0.008	44.961	0.001	0.001	0.000	0.000	0.000	0.000
162	A	172	ALA	0	0.003	0.008	43.348	0.001	0.001	0.000	0.000	0.000	0.000
163	A	173	THR	0	-0.096	-0.071	44.407	0.001	0.001	0.000	0.000	0.000	0.000
164	A	174	ASN	0	-0.096	-0.034	45.124	-0.001	-0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:11:ILE)