FMO DATABASE

FMODB ID: 82JJY

Calculation Name: 4DOX-A-Xray321

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	166
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1443866.985459
FMO2-HF: Nuclear repulsion	1381716.224547
FMO2-HF: Total energy	-62150.760912
FMO2-MP2: Total energy	-62331.034098

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:10:ACE )

Summations of interaction energy for fragment #1(A:10:ACE )

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.
1.358	2.07	-0.004	-0.306	-0.403	0

Interaction energy analysis for fragmet #1(A:10:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : -0.004

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	12	ALA	0	-0.022	0.010	3.878	1.102	1.814	-0.004	-0.306	-0.403
4	A	13	PHE	0	0.018	0.000	6.547	0.334	0.334	0.000	0.000	0.000
5	A	14	PRO	0	0.005	0.008	8.903	-0.201	-0.201	0.000	0.000	0.000
6	A	15	ALA	0	0.004	-0.006	9.767	0.090	0.090	0.000	0.000	0.000
7	A	16	ILE	0	0.019	0.014	12.404	0.053	0.053	0.000	0.000	0.000
8	A	17	THR	0	0.001	0.003	15.958	0.008	0.008	0.000	0.000	0.000
9	A	18	GLN	0	0.065	0.003	18.054	0.002	0.002	0.000	0.000	0.000
10	A	19	GLU	-1	-0.938	-0.957	21.562	-0.110	-0.110	0.000	0.000	0.000
11	A	20	GLN	0	0.072	0.034	16.308	-0.016	-0.016	0.000	0.000	0.000
12	A	21	MET	0	-0.003	-0.006	20.588	-0.001	-0.001	0.000	0.000	0.000
13	A	22	SER	0	-0.066	-0.026	22.820	0.012	0.012	0.000	0.000	0.000
14	A	23	SER	0	-0.067	-0.037	23.939	0.008	0.008	0.000	0.000	0.000
15	A	24	ILE	0	-0.011	0.014	21.088	0.008	0.008	0.000	0.000	0.000
16	A	25	LYS	1	0.911	0.948	24.787	0.092	0.092	0.000	0.000	0.000
17	A	26	VAL	0	-0.015	-0.002	25.839	-0.003	-0.003	0.000	0.000	0.000
18	A	27	ASP	-1	-0.897	-0.933	28.447	-0.071	-0.071	0.000	0.000	0.000
19	A	28	PRO	0	-0.025	-0.029	31.165	-0.003	-0.003	0.000	0.000	0.000
20	A	29	THR	0	0.018	0.023	29.453	0.005	0.005	0.000	0.000	0.000
21	A	30	SER	0	0.032	0.001	32.782	0.001	0.001	0.000	0.000	0.000
22	A	31	ASN	0	-0.008	0.001	32.579	0.003	0.003	0.000	0.000	0.000
23	A	32	LEU	0	-0.003	-0.011	34.952	0.004	0.004	0.000	0.000	0.000
24	A	33	LEU	0	0.013	0.007	38.140	0.004	0.004	0.000	0.000	0.000
25	A	34	PRO	0	-0.058	-0.015	38.199	-0.001	-0.001	0.000	0.000	0.000
26	A	35	SER	0	0.062	0.030	35.668	0.000	0.000	0.000	0.000	0.000
27	A	36	GLN	0	0.081	0.036	37.256	0.002	0.002	0.000	0.000	0.000
28	A	37	GLU	-1	-0.885	-0.959	35.433	-0.047	-0.047	0.000	0.000	0.000
29	A	38	GLN	0	0.022	0.018	37.129	0.002	0.002	0.000	0.000	0.000
30	A	39	LEU	0	0.031	0.017	40.325	0.003	0.003	0.000	0.000	0.000
31	A	40	LYS	1	0.961	0.979	41.920	0.031	0.031	0.000	0.000	0.000
32	A	41	SER	0	0.001	0.011	41.354	0.003	0.003	0.000	0.000	0.000
33	A	42	VAL	0	-0.005	0.011	44.012	0.002	0.002	0.000	0.000	0.000
34	A	43	SER	0	0.012	-0.006	46.623	0.002	0.002	0.000	0.000	0.000
35	A	44	THR	0	-0.057	-0.025	46.070	0.001	0.001	0.000	0.000	0.000
36	A	45	LEU	0	0.022	-0.012	46.076	0.002	0.002	0.000	0.000	0.000
37	A	46	MET	0	-0.043	-0.002	49.560	0.001	0.001	0.000	0.000	0.000
38	A	47	VAL	0	0.005	0.008	51.881	0.001	0.001	0.000	0.000	0.000
39	A	48	ALA	0	-0.034	-0.011	51.742	0.001	0.001	0.000	0.000	0.000
40	A	49	ALA	0	-0.054	-0.025	53.606	0.001	0.001	0.000	0.000	0.000
41	A	50	LYS	1	0.894	0.937	55.433	0.013	0.013	0.000	0.000	0.000
42	A	51	VAL	0	0.049	0.052	55.407	0.000	0.000	0.000	0.000	0.000
43	A	52	PRO	0	0.011	-0.008	56.584	0.000	0.000	0.000	0.000	0.000
44	A	53	ALA	0	0.060	0.014	54.259	-0.001	-0.001	0.000	0.000	0.000
45	A	54	ALA	0	-0.022	-0.013	54.980	-0.001	-0.001	0.000	0.000	0.000
46	A	55	SER	0	0.016	0.009	57.134	0.000	0.000	0.000	0.000	0.000
47	A	56	VAL	0	0.008	0.011	51.614	0.000	0.000	0.000	0.000	0.000
48	A	57	THR	0	0.024	0.008	52.169	0.000	0.000	0.000	0.000	0.000
49	A	58	THR	0	0.047	0.009	53.660	0.000	0.000	0.000	0.000	0.000
50	A	59	VAL	0	0.017	0.026	56.008	0.000	0.000	0.000	0.000	0.000
51	A	60	ALA	0	0.007	0.005	51.595	0.000	0.000	0.000	0.000	0.000
52	A	61	LEU	0	-0.012	-0.023	53.274	0.000	0.000	0.000	0.000	0.000
53	A	62	GLU	-1	-0.783	-0.851	55.195	-0.016	-0.016	0.000	0.000	0.000
54	A	63	LEU	0	-0.021	-0.002	51.200	0.000	0.000	0.000	0.000	0.000
55	A	64	VAL	0	-0.020	-0.022	51.233	0.000	0.000	0.000	0.000	0.000
56	A	65	ASN	0	0.053	0.029	53.632	-0.001	-0.001	0.000	0.000	0.000
57	A	66	PHE	0	0.031	0.021	55.439	0.000	0.000	0.000	0.000	0.000
58	A	67	CYS	0	-0.021	-0.018	52.116	0.000	0.000	0.000	0.000	0.000
59	A	68	TYR	0	-0.040	-0.004	54.148	0.000	0.000	0.000	0.000	0.000
60	A	69	ASP	-1	-0.791	-0.869	55.442	-0.018	-0.018	0.000	0.000	0.000
61	A	70	ASN	0	-0.065	-0.040	56.681	0.001	0.001	0.000	0.000	0.000
62	A	71	GLY	0	0.022	0.039	52.580	0.000	0.000	0.000	0.000	0.000
63	A	72	SER	0	-0.050	-0.080	48.605	0.000	0.000	0.000	0.000	0.000
64	A	73	SER	0	-0.009	-0.006	47.419	-0.001	-0.001	0.000	0.000	0.000
65	A	74	ALA	0	-0.014	-0.023	44.928	0.001	0.001	0.000	0.000	0.000
66	A	75	TYR	0	-0.006	-0.019	46.973	0.001	0.001	0.000	0.000	0.000
67	A	76	THR	0	0.009	0.029	50.160	0.001	0.001	0.000	0.000	0.000
68	A	77	THR	0	-0.040	-0.024	52.813	0.000	0.000	0.000	0.000	0.000
69	A	78	VAL	0	0.007	0.012	53.302	0.000	0.000	0.000	0.000	0.000
70	A	79	THR	0	-0.028	-0.013	56.330	0.001	0.001	0.000	0.000	0.000
71	A	80	GLY	0	0.041	0.021	60.053	-0.001	-0.001	0.000	0.000	0.000
72	A	81	PRO	0	-0.005	-0.008	61.013	0.000	0.000	0.000	0.000	0.000
73	A	82	SER	0	0.011	0.012	59.375	-0.001	-0.001	0.000	0.000	0.000
74	A	83	SER	0	-0.076	-0.075	61.345	0.001	0.001	0.000	0.000	0.000
75	A	84	ILE	0	-0.054	-0.023	59.612	0.000	0.000	0.000	0.000	0.000
76	A	85	PRO	0	0.010	-0.007	62.529	0.000	0.000	0.000	0.000	0.000
77	A	86	GLU	-1	-0.961	-1.000	62.328	-0.010	-0.010	0.000	0.000	0.000
78	A	87	ILE	0	-0.006	0.030	56.918	0.000	0.000	0.000	0.000	0.000
79	A	88	SER	0	-0.022	-0.002	58.854	0.000	0.000	0.000	0.000	0.000
80	A	89	LEU	0	0.059	0.009	56.839	-0.001	-0.001	0.000	0.000	0.000
81	A	90	ALA	0	0.012	0.003	55.105	-0.001	-0.001	0.000	0.000	0.000
82	A	91	GLN	0	0.037	0.011	53.898	0.000	0.000	0.000	0.000	0.000
83	A	92	LEU	0	0.046	0.030	52.923	-0.001	-0.001	0.000	0.000	0.000
84	A	93	ALA	0	0.034	0.016	50.759	-0.001	-0.001	0.000	0.000	0.000
85	A	94	SER	0	-0.056	-0.028	49.161	-0.001	-0.001	0.000	0.000	0.000
86	A	95	ILE	0	0.005	0.012	48.211	-0.001	-0.001	0.000	0.000	0.000
87	A	96	VAL	0	-0.027	-0.019	45.836	-0.001	-0.001	0.000	0.000	0.000
88	A	97	LYS	1	0.925	0.956	44.604	0.016	0.016	0.000	0.000	0.000
89	A	98	ALA	0	-0.013	0.009	43.610	0.000	0.000	0.000	0.000	0.000
90	A	99	SER	0	-0.082	-0.032	42.280	-0.001	-0.001	0.000	0.000	0.000
91	A	100	GLY	0	0.037	0.017	39.345	-0.002	-0.002	0.000	0.000	0.000
92	A	101	THR	0	-0.053	-0.018	39.055	-0.002	-0.002	0.000	0.000	0.000
93	A	102	SER	0	0.012	-0.001	40.900	0.002	0.002	0.000	0.000	0.000
94	A	103	LEU	0	0.055	0.007	43.102	-0.001	-0.001	0.000	0.000	0.000
95	A	104	ARG	1	0.896	0.934	43.780	0.026	0.026	0.000	0.000	0.000
96	A	105	LYS	1	0.896	0.956	36.751	0.040	0.040	0.000	0.000	0.000
97	A	106	PHE	0	0.044	0.015	43.121	-0.001	-0.001	0.000	0.000	0.000
98	A	107	CYS	0	-0.032	-0.021	45.594	0.000	0.000	0.000	0.000	0.000
99	A	108	ARG	1	0.821	0.896	41.552	0.036	0.036	0.000	0.000	0.000
100	A	109	TYR	0	0.009	0.001	43.544	0.000	0.000	0.000	0.000	0.000
101	A	110	PHE	0	0.019	0.009	45.630	0.000	0.000	0.000	0.000	0.000
102	A	111	ALA	0	0.017	0.023	48.392	0.001	0.001	0.000	0.000	0.000
103	A	112	PRO	0	0.017	0.014	48.283	0.002	0.002	0.000	0.000	0.000
104	A	113	ILE	0	0.006	0.013	51.328	0.001	0.001	0.000	0.000	0.000
105	A	114	ILE	0	-0.008	-0.002	52.978	0.001	0.001	0.000	0.000	0.000
106	A	115	TRP	0	-0.009	-0.002	53.467	0.001	0.001	0.000	0.000	0.000
107	A	116	ASN	0	-0.015	-0.016	55.377	0.000	0.000	0.000	0.000	0.000
108	A	117	LEU	0	-0.054	-0.020	57.334	0.001	0.001	0.000	0.000	0.000
109	A	118	ARG	1	0.731	0.834	58.619	0.020	0.020	0.000	0.000	0.000
110	A	119	THR	0	0.018	0.001	57.151	0.001	0.001	0.000	0.000	0.000
111	A	120	ASP	-1	-0.883	-0.927	59.916	-0.021	-0.021	0.000	0.000	0.000
112	A	121	LYS	1	0.893	0.957	63.057	0.020	0.020	0.000	0.000	0.000
113	A	122	MET	0	-0.024	-0.026	63.217	0.001	0.001	0.000	0.000	0.000
114	A	123	ALA	0	0.017	0.011	61.117	-0.001	-0.001	0.000	0.000	0.000
115	A	124	PRO	0	0.016	0.025	57.275	0.001	0.001	0.000	0.000	0.000
116	A	125	ALA	0	0.018	0.000	59.832	0.000	0.000	0.000	0.000	0.000
117	A	126	ASN	0	-0.035	-0.011	59.288	0.001	0.001	0.000	0.000	0.000
118	A	127	TRP	0	0.010	-0.015	59.198	0.000	0.000	0.000	0.000	0.000
119	A	128	GLU	-1	-0.965	-0.982	60.074	-0.015	-0.015	0.000	0.000	0.000
120	A	129	ALA	0	0.007	0.011	61.214	0.000	0.000	0.000	0.000	0.000
121	A	130	SER	0	-0.039	-0.011	56.128	0.000	0.000	0.000	0.000	0.000
122	A	131	GLY	0	0.008	-0.008	56.470	0.000	0.000	0.000	0.000	0.000
123	A	132	TYR	0	-0.023	0.006	52.729	-0.001	-0.001	0.000	0.000	0.000
124	A	133	LYS	1	0.966	0.980	59.043	0.021	0.021	0.000	0.000	0.000
125	A	134	PRO	0	0.037	0.001	61.076	-0.001	-0.001	0.000	0.000	0.000
126	A	135	SER	0	-0.023	-0.020	61.525	0.000	0.000	0.000	0.000	0.000
127	A	136	ALA	0	-0.002	0.013	56.620	-0.001	-0.001	0.000	0.000	0.000
128	A	137	LYS	1	0.944	0.975	57.370	0.017	0.017	0.000	0.000	0.000
129	A	138	PHE	0	-0.017	0.002	58.056	0.000	0.000	0.000	0.000	0.000
130	A	139	ALA	0	0.031	0.021	53.401	-0.001	-0.001	0.000	0.000	0.000
131	A	140	ALA	0	-0.030	0.003	53.314	-0.001	-0.001	0.000	0.000	0.000
132	A	141	PHE	0	0.022	0.005	51.413	0.001	0.001	0.000	0.000	0.000
133	A	142	ASP	-1	-0.745	-0.831	48.765	-0.025	-0.025	0.000	0.000	0.000
134	A	143	PHE	0	-0.012	-0.018	47.149	-0.001	-0.001	0.000	0.000	0.000
135	A	144	PHE	0	0.044	0.036	48.120	-0.001	-0.001	0.000	0.000	0.000
136	A	145	ASP	-1	-0.821	-0.885	43.971	-0.036	-0.036	0.000	0.000	0.000
137	A	146	GLY	0	-0.001	-0.026	44.717	-0.002	-0.002	0.000	0.000	0.000
138	A	147	VAL	0	-0.069	-0.034	46.060	-0.001	-0.001	0.000	0.000	0.000
139	A	148	GLU	-1	-0.822	-0.922	46.761	-0.036	-0.036	0.000	0.000	0.000
140	A	149	ASN	0	-0.008	-0.003	40.308	-0.004	-0.004	0.000	0.000	0.000
141	A	150	PRO	0	0.026	0.002	41.302	0.002	0.002	0.000	0.000	0.000
142	A	151	ALA	0	-0.004	0.004	39.970	0.000	0.000	0.000	0.000	0.000
143	A	152	ALA	0	-0.057	-0.020	42.046	0.001	0.001	0.000	0.000	0.000
144	A	153	MET	0	-0.042	-0.021	44.841	0.000	0.000	0.000	0.000	0.000
145	A	154	GLN	0	0.002	-0.010	46.322	0.002	0.002	0.000	0.000	0.000
146	A	155	PRO	0	-0.033	-0.010	50.052	0.001	0.001	0.000	0.000	0.000
147	A	156	PRO	0	0.020	-0.001	53.409	-0.001	-0.001	0.000	0.000	0.000
148	A	157	SER	0	-0.050	-0.021	55.374	0.000	0.000	0.000	0.000	0.000
149	A	158	GLY	0	0.026	0.026	53.159	0.000	0.000	0.000	0.000	0.000
150	A	159	LEU	0	-0.006	-0.017	50.950	0.001	0.001	0.000	0.000	0.000
151	A	160	THR	0	-0.021	-0.007	54.941	0.000	0.000	0.000	0.000	0.000
152	A	161	ARG	1	0.731	0.844	57.063	0.025	0.025	0.000	0.000	0.000
153	A	162	SER	0	0.035	0.019	51.933	-0.001	-0.001	0.000	0.000	0.000
154	A	163	PRO	0	-0.028	-0.004	51.058	0.001	0.001	0.000	0.000	0.000
155	A	164	THR	0	0.018	0.009	54.046	-0.001	-0.001	0.000	0.000	0.000
156	A	165	GLN	0	0.053	0.009	49.197	-0.001	-0.001	0.000	0.000	0.000
157	A	166	GLU	-1	-0.867	-0.939	52.965	-0.022	-0.022	0.000	0.000	0.000
158	A	167	GLU	-1	-0.736	-0.860	54.447	-0.025	-0.025	0.000	0.000	0.000
159	A	168	ARG	1	0.852	0.917	48.389	0.034	0.034	0.000	0.000	0.000
160	A	169	ILE	0	-0.020	-0.011	49.854	-0.001	-0.001	0.000	0.000	0.000
161	A	170	ALA	0	-0.011	-0.004	51.006	0.000	0.000	0.000	0.000	0.000
162	A	171	ASN	0	-0.025	-0.002	48.669	-0.001	-0.001	0.000	0.000	0.000
163	A	172	ALA	0	0.031	0.023	46.539	0.000	0.000	0.000	0.000	0.000
164	A	173	THR	0	-0.134	-0.075	47.337	0.000	0.000	0.000	0.000	0.000
165	A	174	ASN	0	-0.037	-0.025	49.358	0.002	0.002	0.000	0.000	0.000
166	A	175	NME	0	0.007	0.023	45.902	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:10:ACE )