FMO DATABASE

FMODB ID: J35Z9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1439430.020624
FMO2-HF: Nuclear repulsion	1377449.372981
FMO2-HF: Total energy	-61980.647643
FMO2-MP2: Total energy	-62160.334637

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.
-3.135	0.028	2.095	-1.596	-3.662	-0.009

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 : -0.024 / 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	0.022	0.002	3.223	-1.911	0.074	0.111	-0.750	-1.347	0.001
4	A	14	PRO	0	-0.003	0.005	2.663	-1.733	-0.540	1.979	-1.044	-2.127	-0.010
5	A	15	ALA	0	0.002	-0.007	3.671	0.496	0.481	0.005	0.198	-0.188	0.000
6	A	16	ILE	0	0.006	0.011	5.805	-0.013	-0.013	0.000	0.000	0.000	0.000
7	A	17	THR	0	0.014	0.011	9.398	0.083	0.083	0.000	0.000	0.000	0.000
8	A	18	GLN	0	0.049	-0.003	11.710	0.036	0.036	0.000	0.000	0.000	0.000
9	A	19	GLU	-1	-0.845	-0.919	15.181	-0.330	-0.330	0.000	0.000	0.000	0.000
10	A	20	GLN	0	0.053	0.034	10.664	-0.014	-0.014	0.000	0.000	0.000	0.000
11	A	21	MET	0	-0.015	-0.009	13.810	0.014	0.014	0.000	0.000	0.000	0.000
12	A	22	SER	0	-0.057	-0.014	16.297	0.034	0.034	0.000	0.000	0.000	0.000
13	A	23	SER	0	-0.057	-0.052	17.684	0.015	0.015	0.000	0.000	0.000	0.000
14	A	24	ILE	0	-0.015	0.019	14.702	0.011	0.011	0.000	0.000	0.000	0.000
15	A	25	LYS	1	0.836	0.904	18.476	0.221	0.221	0.000	0.000	0.000	0.000
16	A	26	VAL	0	-0.002	0.000	19.179	-0.005	-0.005	0.000	0.000	0.000	0.000
17	A	27	ASP	-1	-0.901	-0.929	22.103	-0.119	-0.119	0.000	0.000	0.000	0.000
18	A	28	PRO	0	-0.012	-0.022	25.045	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	29	THR	0	0.019	0.017	23.925	0.003	0.003	0.000	0.000	0.000	0.000
20	A	30	SER	0	0.030	0.004	27.133	0.009	0.009	0.000	0.000	0.000	0.000
21	A	31	ASN	0	0.003	0.001	28.419	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	32	LEU	0	-0.022	-0.018	30.239	0.005	0.005	0.000	0.000	0.000	0.000
23	A	33	LEU	0	0.031	0.020	33.093	0.003	0.003	0.000	0.000	0.000	0.000
24	A	34	PRO	0	-0.053	-0.014	33.072	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	35	SER	0	0.009	-0.020	30.035	0.001	0.001	0.000	0.000	0.000	0.000
26	A	36	GLN	0	0.063	0.024	31.515	0.006	0.006	0.000	0.000	0.000	0.000
27	A	37	GLU	-1	-0.820	-0.895	29.757	-0.095	-0.095	0.000	0.000	0.000	0.000
28	A	38	GLN	0	0.029	0.015	32.607	0.006	0.006	0.000	0.000	0.000	0.000
29	A	39	LEU	0	0.028	0.018	35.056	0.004	0.004	0.000	0.000	0.000	0.000
30	A	40	LYS	1	0.935	0.968	36.347	0.067	0.067	0.000	0.000	0.000	0.000
31	A	41	SER	0	-0.006	0.009	36.063	0.002	0.002	0.000	0.000	0.000	0.000
32	A	42	VAL	0	0.003	0.014	38.719	0.003	0.003	0.000	0.000	0.000	0.000
33	A	43	SER	0	0.022	0.002	41.228	0.002	0.002	0.000	0.000	0.000	0.000
34	A	44	THR	0	-0.051	-0.040	40.590	0.001	0.001	0.000	0.000	0.000	0.000
35	A	45	LEU	0	0.020	-0.006	41.110	0.002	0.002	0.000	0.000	0.000	0.000
36	A	46	MET	0	-0.032	0.002	44.433	0.002	0.002	0.000	0.000	0.000	0.000
37	A	47	VAL	0	0.006	0.007	46.458	0.002	0.002	0.000	0.000	0.000	0.000
38	A	48	ALA	0	-0.045	-0.014	46.486	0.002	0.002	0.000	0.000	0.000	0.000
39	A	49	ALA	0	-0.053	-0.027	48.407	0.001	0.001	0.000	0.000	0.000	0.000
40	A	50	LYS	1	0.891	0.937	50.403	0.036	0.036	0.000	0.000	0.000	0.000
41	A	51	VAL	0	0.052	0.051	50.005	0.002	0.002	0.000	0.000	0.000	0.000
42	A	52	PRO	0	0.016	-0.002	51.041	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	53	ALA	0	0.051	0.012	48.445	0.000	0.000	0.000	0.000	0.000	0.000
44	A	54	ALA	0	-0.017	-0.013	49.063	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	55	SER	0	0.020	0.014	51.172	0.000	0.000	0.000	0.000	0.000	0.000
46	A	56	VAL	0	0.009	0.007	45.852	0.001	0.001	0.000	0.000	0.000	0.000
47	A	57	THR	0	0.027	0.011	46.294	0.000	0.000	0.000	0.000	0.000	0.000
48	A	58	THR	0	0.038	0.008	47.923	0.001	0.001	0.000	0.000	0.000	0.000
49	A	59	VAL	0	0.009	0.021	50.798	0.001	0.001	0.000	0.000	0.000	0.000
50	A	60	ALA	0	-0.005	0.000	46.158	0.001	0.001	0.000	0.000	0.000	0.000
51	A	61	LEU	0	-0.008	-0.025	47.725	0.001	0.001	0.000	0.000	0.000	0.000
52	A	62	GLU	-1	-0.773	-0.838	49.845	-0.024	-0.024	0.000	0.000	0.000	0.000
53	A	63	LEU	0	-0.033	-0.007	46.619	0.001	0.001	0.000	0.000	0.000	0.000
54	A	64	VAL	0	-0.010	-0.017	46.003	0.001	0.001	0.000	0.000	0.000	0.000
55	A	65	ASN	0	0.044	0.019	48.642	0.002	0.002	0.000	0.000	0.000	0.000
56	A	66	PHE	0	0.040	0.029	51.130	0.001	0.001	0.000	0.000	0.000	0.000
57	A	67	CYS	0	-0.032	-0.027	47.582	0.001	0.001	0.000	0.000	0.000	0.000
58	A	68	TYR	0	-0.031	-0.006	49.698	0.001	0.001	0.000	0.000	0.000	0.000
59	A	69	ASP	-1	-0.781	-0.847	50.806	-0.013	-0.013	0.000	0.000	0.000	0.000
60	A	70	ASN	0	-0.072	-0.045	52.417	0.002	0.002	0.000	0.000	0.000	0.000
61	A	71	GLY	0	0.023	0.041	48.485	0.001	0.001	0.000	0.000	0.000	0.000
62	A	72	SER	0	-0.016	-0.062	44.392	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	73	SER	0	-0.018	-0.006	43.620	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	74	ALA	0	-0.015	-0.022	41.296	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	75	TYR	0	0.015	-0.009	43.429	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	76	THR	0	0.017	0.027	46.752	0.001	0.001	0.000	0.000	0.000	0.000
67	A	77	THR	0	-0.041	-0.017	49.105	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	78	VAL	0	0.006	0.008	49.003	0.001	0.001	0.000	0.000	0.000	0.000
69	A	79	THR	0	-0.029	-0.016	52.201	0.000	0.000	0.000	0.000	0.000	0.000
70	A	80	GLY	0	0.050	0.028	55.854	0.000	0.000	0.000	0.000	0.000	0.000
71	A	81	PRO	0	-0.011	-0.010	56.470	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	82	SER	0	0.000	-0.008	54.370	0.000	0.000	0.000	0.000	0.000	0.000
73	A	83	SER	0	-0.069	-0.081	55.842	0.000	0.000	0.000	0.000	0.000	0.000
74	A	84	ILE	0	-0.049	-0.023	54.172	0.000	0.000	0.000	0.000	0.000	0.000
75	A	85	PRO	0	0.012	-0.004	57.323	0.000	0.000	0.000	0.000	0.000	0.000
76	A	86	GLU	-1	-0.926	-0.976	58.042	-0.025	-0.025	0.000	0.000	0.000	0.000
77	A	87	ILE	0	-0.039	0.006	51.890	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	88	SER	0	-0.015	-0.010	54.493	0.001	0.001	0.000	0.000	0.000	0.000
79	A	89	LEU	0	0.052	0.007	52.216	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	90	ALA	0	0.026	0.010	50.534	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	91	GLN	0	0.038	0.043	49.572	0.000	0.000	0.000	0.000	0.000	0.000
82	A	92	LEU	0	0.031	0.024	48.212	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	93	ALA	0	0.033	0.014	46.177	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	94	SER	0	-0.059	-0.032	44.740	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	95	ILE	0	0.000	0.006	43.826	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	96	VAL	0	-0.021	-0.016	41.155	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	97	LYS	1	0.897	0.949	40.261	0.025	0.025	0.000	0.000	0.000	0.000
88	A	98	ALA	0	-0.018	0.008	39.340	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	99	SER	0	-0.079	-0.041	37.280	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	100	GLY	0	0.025	0.011	34.905	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	101	THR	0	-0.048	-0.015	34.680	0.001	0.001	0.000	0.000	0.000	0.000
92	A	102	SER	0	0.003	-0.006	36.310	0.002	0.002	0.000	0.000	0.000	0.000
93	A	103	LEU	0	0.062	0.012	38.786	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	104	ARG	1	0.896	0.946	39.714	0.018	0.018	0.000	0.000	0.000	0.000
95	A	105	LYS	1	0.887	0.956	31.840	0.050	0.050	0.000	0.000	0.000	0.000
96	A	106	PHE	0	0.058	0.016	38.383	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	107	CYS	0	-0.028	-0.016	40.603	0.000	0.000	0.000	0.000	0.000	0.000
98	A	108	ARG	1	0.775	0.866	36.937	0.028	0.028	0.000	0.000	0.000	0.000
99	A	109	TYR	0	0.009	-0.001	37.456	0.001	0.001	0.000	0.000	0.000	0.000
100	A	110	PHE	0	0.024	0.007	40.274	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	111	ALA	0	0.012	0.022	43.174	0.002	0.002	0.000	0.000	0.000	0.000
102	A	112	PRO	0	0.011	0.012	42.813	0.002	0.002	0.000	0.000	0.000	0.000
103	A	113	ILE	0	0.005	0.011	45.863	0.001	0.001	0.000	0.000	0.000	0.000
104	A	114	ILE	0	-0.004	0.001	47.664	0.001	0.001	0.000	0.000	0.000	0.000
105	A	115	TRP	0	0.002	0.001	48.319	0.002	0.002	0.000	0.000	0.000	0.000
106	A	116	ASN	0	-0.019	-0.012	50.135	0.002	0.002	0.000	0.000	0.000	0.000
107	A	117	LEU	0	-0.041	-0.017	51.828	0.001	0.001	0.000	0.000	0.000	0.000
108	A	118	ARG	1	0.721	0.826	53.537	0.017	0.017	0.000	0.000	0.000	0.000
109	A	119	THR	0	0.015	-0.006	52.126	0.002	0.002	0.000	0.000	0.000	0.000
110	A	120	ASP	-1	-0.870	-0.918	54.830	-0.012	-0.012	0.000	0.000	0.000	0.000
111	A	121	LYS	1	0.876	0.956	57.382	0.016	0.016	0.000	0.000	0.000	0.000
112	A	122	MET	0	-0.020	-0.017	58.208	0.000	0.000	0.000	0.000	0.000	0.000
113	A	123	ALA	0	0.022	0.013	56.435	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	124	PRO	0	0.022	0.027	52.826	0.000	0.000	0.000	0.000	0.000	0.000
115	A	125	ALA	0	0.013	-0.002	55.378	0.001	0.001	0.000	0.000	0.000	0.000
116	A	126	ASN	0	-0.048	-0.025	55.208	0.001	0.001	0.000	0.000	0.000	0.000
117	A	127	TRP	0	0.001	-0.017	55.191	0.001	0.001	0.000	0.000	0.000	0.000
118	A	128	GLU	-1	-0.955	-0.987	56.258	-0.003	-0.003	0.000	0.000	0.000	0.000
119	A	129	ALA	0	0.012	0.018	57.622	0.001	0.001	0.000	0.000	0.000	0.000
120	A	130	SER	0	-0.044	-0.012	52.611	0.000	0.000	0.000	0.000	0.000	0.000
121	A	131	GLY	0	0.011	-0.005	53.001	0.000	0.000	0.000	0.000	0.000	0.000
122	A	132	TYR	0	-0.024	0.004	48.997	0.000	0.000	0.000	0.000	0.000	0.000
123	A	133	LYS	1	0.922	0.944	55.313	0.000	0.000	0.000	0.000	0.000	0.000
124	A	134	PRO	0	0.069	0.015	57.065	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	135	SER	0	-0.060	-0.055	57.054	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	136	ALA	0	0.015	0.017	52.635	0.000	0.000	0.000	0.000	0.000	0.000
127	A	137	LYS	1	0.907	0.953	53.114	0.006	0.006	0.000	0.000	0.000	0.000
128	A	138	PHE	0	-0.014	0.004	53.297	0.000	0.000	0.000	0.000	0.000	0.000
129	A	139	ALA	0	0.025	0.012	49.000	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	140	ALA	0	-0.023	0.011	49.019	0.000	0.000	0.000	0.000	0.000	0.000
131	A	141	PHE	0	0.032	0.012	46.432	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	142	ASP	-1	-0.747	-0.851	44.869	-0.018	-0.018	0.000	0.000	0.000	0.000
133	A	143	PHE	0	-0.016	-0.020	42.578	-0.001	-0.001	0.000	0.000	0.000	0.000
134	A	144	PHE	0	0.053	0.043	43.541	-0.002	-0.002	0.000	0.000	0.000	0.000
135	A	145	ASP	-1	-0.809	-0.870	39.277	-0.023	-0.023	0.000	0.000	0.000	0.000
136	A	146	GLY	0	0.016	-0.019	39.841	-0.002	-0.002	0.000	0.000	0.000	0.000
137	A	147	VAL	0	-0.070	-0.034	41.021	-0.002	-0.002	0.000	0.000	0.000	0.000
138	A	148	GLU	-1	-0.802	-0.897	41.762	-0.016	-0.016	0.000	0.000	0.000	0.000
139	A	149	ASN	0	-0.017	-0.005	35.081	-0.003	-0.003	0.000	0.000	0.000	0.000
140	A	150	PRO	0	0.029	0.002	35.617	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	151	ALA	0	-0.005	0.004	34.164	-0.002	-0.002	0.000	0.000	0.000	0.000
142	A	152	ALA	0	-0.055	-0.019	36.238	-0.002	-0.002	0.000	0.000	0.000	0.000
143	A	153	MET	0	-0.030	-0.010	39.209	0.001	0.001	0.000	0.000	0.000	0.000
144	A	154	GLN	0	0.010	-0.011	40.670	0.005	0.005	0.000	0.000	0.000	0.000
145	A	155	PRO	0	-0.029	-0.013	44.148	-0.001	-0.001	0.000	0.000	0.000	0.000
146	A	156	PRO	0	0.016	0.001	47.369	-0.001	-0.001	0.000	0.000	0.000	0.000
147	A	157	SER	0	-0.051	-0.024	49.242	0.000	0.000	0.000	0.000	0.000	0.000
148	A	158	GLY	0	0.031	0.029	47.250	0.001	0.001	0.000	0.000	0.000	0.000
149	A	159	LEU	0	-0.009	-0.015	45.468	0.001	0.001	0.000	0.000	0.000	0.000
150	A	160	THR	0	-0.020	-0.007	49.287	0.000	0.000	0.000	0.000	0.000	0.000
151	A	161	ARG	1	0.723	0.812	51.630	0.013	0.013	0.000	0.000	0.000	0.000
152	A	162	SER	0	0.021	0.008	46.440	-0.002	-0.002	0.000	0.000	0.000	0.000
153	A	163	PRO	0	-0.033	-0.010	46.157	0.001	0.001	0.000	0.000	0.000	0.000
154	A	164	THR	0	-0.013	-0.024	49.119	0.001	0.001	0.000	0.000	0.000	0.000
155	A	165	GLN	0	0.080	0.022	44.584	-0.002	-0.002	0.000	0.000	0.000	0.000
156	A	166	GLU	-1	-0.811	-0.859	48.684	-0.001	-0.001	0.000	0.000	0.000	0.000
157	A	167	GLU	-1	-0.714	-0.818	49.952	-0.009	-0.009	0.000	0.000	0.000	0.000
158	A	168	ARG	1	0.837	0.894	43.659	0.010	0.010	0.000	0.000	0.000	0.000
159	A	169	ILE	0	-0.027	-0.016	45.757	0.000	0.000	0.000	0.000	0.000	0.000
160	A	170	ALA	0	-0.006	0.007	47.224	0.001	0.001	0.000	0.000	0.000	0.000
161	A	171	ASN	0	-0.035	-0.012	44.597	0.000	0.000	0.000	0.000	0.000	0.000
162	A	172	ALA	0	0.010	0.011	42.840	0.000	0.000	0.000	0.000	0.000	0.000
163	A	173	THR	0	-0.129	-0.071	43.869	0.001	0.001	0.000	0.000	0.000	0.000
164	A	174	ASN	0	-0.011	0.002	43.982	0.000	0.000	0.000	0.000	0.000	0.000

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