FMO DATABASE

FMODB ID: N1YMQ

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	OptH
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	-1438897.897157
FMO2-HF: Nuclear repulsion	1376918.03041
FMO2-HF: Total energy	-61979.866748
FMO2-MP2: Total energy	-62159.612503

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.
-2.873	-0.211	2.894	-1.748	-3.809	-0.011

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 : -0.013 / q_NPA : -0.026

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	0.018	0.001	3.029	-1.849	0.158	0.146	-0.769	-1.385	0.001
4	A	14	PRO	0	0.002	0.006	2.477	-1.577	-0.967	2.746	-1.113	-2.243	-0.012
5	A	15	ALA	0	0.002	-0.007	3.712	0.512	0.557	0.002	0.134	-0.181	0.000
6	A	16	ILE	0	0.021	0.015	5.699	-0.011	-0.011	0.000	0.000	0.000	0.000
7	A	17	THR	0	0.000	0.003	9.352	0.094	0.094	0.000	0.000	0.000	0.000
8	A	18	GLN	0	0.064	0.003	11.717	0.030	0.030	0.000	0.000	0.000	0.000
9	A	19	GLU	-1	-0.938	-0.957	15.137	-0.334	-0.334	0.000	0.000	0.000	0.000
10	A	20	GLN	0	0.072	0.033	10.781	-0.005	-0.005	0.000	0.000	0.000	0.000
11	A	21	MET	0	-0.002	-0.006	13.958	0.011	0.011	0.000	0.000	0.000	0.000
12	A	22	SER	0	-0.068	-0.026	16.252	0.036	0.036	0.000	0.000	0.000	0.000
13	A	23	SER	0	-0.066	-0.037	18.143	0.020	0.020	0.000	0.000	0.000	0.000
14	A	24	ILE	0	-0.011	0.013	14.712	0.007	0.007	0.000	0.000	0.000	0.000
15	A	25	LYS	1	0.911	0.948	18.434	0.237	0.237	0.000	0.000	0.000	0.000
16	A	26	VAL	0	-0.015	-0.002	19.357	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	27	ASP	-1	-0.897	-0.932	22.002	-0.131	-0.131	0.000	0.000	0.000	0.000
18	A	28	PRO	0	-0.025	-0.029	24.936	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	29	THR	0	0.018	0.022	23.735	0.003	0.003	0.000	0.000	0.000	0.000
20	A	30	SER	0	0.033	0.002	27.021	0.011	0.011	0.000	0.000	0.000	0.000
21	A	31	ASN	0	-0.007	0.001	28.208	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	32	LEU	0	-0.003	-0.011	30.135	0.005	0.005	0.000	0.000	0.000	0.000
23	A	33	LEU	0	0.012	0.007	32.976	0.004	0.004	0.000	0.000	0.000	0.000
24	A	34	PRO	0	-0.055	-0.012	32.998	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	35	SER	0	0.057	0.028	30.108	0.002	0.002	0.000	0.000	0.000	0.000
26	A	36	GLN	0	0.083	0.036	31.468	0.007	0.007	0.000	0.000	0.000	0.000
27	A	37	GLU	-1	-0.887	-0.959	29.550	-0.114	-0.114	0.000	0.000	0.000	0.000
28	A	38	GLN	0	0.021	0.017	32.404	0.006	0.006	0.000	0.000	0.000	0.000
29	A	39	LEU	0	0.032	0.017	35.057	0.005	0.005	0.000	0.000	0.000	0.000
30	A	40	LYS	1	0.961	0.978	36.193	0.078	0.078	0.000	0.000	0.000	0.000
31	A	41	SER	0	-0.002	0.010	36.132	0.002	0.002	0.000	0.000	0.000	0.000
32	A	42	VAL	0	-0.002	0.012	38.749	0.004	0.004	0.000	0.000	0.000	0.000
33	A	43	SER	0	0.010	-0.006	41.351	0.002	0.002	0.000	0.000	0.000	0.000
34	A	44	THR	0	-0.055	-0.025	40.543	0.002	0.002	0.000	0.000	0.000	0.000
35	A	45	LEU	0	0.019	-0.013	41.131	0.002	0.002	0.000	0.000	0.000	0.000
36	A	46	MET	0	-0.038	0.000	44.479	0.002	0.002	0.000	0.000	0.000	0.000
37	A	47	VAL	0	0.005	0.007	46.484	0.002	0.002	0.000	0.000	0.000	0.000
38	A	48	ALA	0	-0.038	-0.013	46.623	0.002	0.002	0.000	0.000	0.000	0.000
39	A	49	ALA	0	-0.053	-0.025	48.467	0.002	0.002	0.000	0.000	0.000	0.000
40	A	50	LYS	1	0.897	0.938	50.453	0.043	0.043	0.000	0.000	0.000	0.000
41	A	51	VAL	0	0.047	0.053	49.994	0.002	0.002	0.000	0.000	0.000	0.000
42	A	52	PRO	0	0.010	-0.008	51.061	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	53	ALA	0	0.060	0.014	48.403	0.000	0.000	0.000	0.000	0.000	0.000
44	A	54	ALA	0	-0.022	-0.014	49.048	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	55	SER	0	0.018	0.011	51.137	0.001	0.001	0.000	0.000	0.000	0.000
46	A	56	VAL	0	0.008	0.011	45.803	0.001	0.001	0.000	0.000	0.000	0.000
47	A	57	THR	0	0.022	0.008	46.330	0.000	0.000	0.000	0.000	0.000	0.000
48	A	58	THR	0	0.047	0.008	47.872	0.001	0.001	0.000	0.000	0.000	0.000
49	A	59	VAL	0	0.018	0.026	50.694	0.001	0.001	0.000	0.000	0.000	0.000
50	A	60	ALA	0	0.005	0.004	46.198	0.001	0.001	0.000	0.000	0.000	0.000
51	A	61	LEU	0	-0.014	-0.024	47.759	0.001	0.001	0.000	0.000	0.000	0.000
52	A	62	GLU	-1	-0.783	-0.851	49.778	-0.029	-0.029	0.000	0.000	0.000	0.000
53	A	63	LEU	0	-0.025	-0.002	46.449	0.001	0.001	0.000	0.000	0.000	0.000
54	A	64	VAL	0	-0.014	-0.020	46.064	0.001	0.001	0.000	0.000	0.000	0.000
55	A	65	ASN	0	0.052	0.029	48.569	0.002	0.002	0.000	0.000	0.000	0.000
56	A	66	PHE	0	0.032	0.020	50.951	0.001	0.001	0.000	0.000	0.000	0.000
57	A	67	CYS	0	-0.020	-0.018	47.541	0.001	0.001	0.000	0.000	0.000	0.000
58	A	68	TYR	0	-0.040	-0.005	49.622	0.002	0.002	0.000	0.000	0.000	0.000
59	A	69	ASP	-1	-0.788	-0.868	50.706	-0.018	-0.018	0.000	0.000	0.000	0.000
60	A	70	ASN	0	-0.066	-0.041	52.395	0.002	0.002	0.000	0.000	0.000	0.000
61	A	71	GLY	0	0.021	0.039	48.398	0.001	0.001	0.000	0.000	0.000	0.000
62	A	72	SER	0	-0.046	-0.078	44.220	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	73	SER	0	-0.011	-0.007	43.552	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	74	ALA	0	-0.017	-0.024	41.281	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	75	TYR	0	-0.003	-0.019	43.401	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	76	THR	0	0.007	0.029	46.729	0.002	0.002	0.000	0.000	0.000	0.000
67	A	77	THR	0	-0.041	-0.025	49.067	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	78	VAL	0	0.006	0.012	48.991	0.001	0.001	0.000	0.000	0.000	0.000
69	A	79	THR	0	-0.027	-0.013	52.178	0.000	0.000	0.000	0.000	0.000	0.000
70	A	80	GLY	0	0.043	0.022	55.835	0.000	0.000	0.000	0.000	0.000	0.000
71	A	81	PRO	0	-0.007	-0.008	56.457	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	82	SER	0	0.011	0.012	54.422	0.000	0.000	0.000	0.000	0.000	0.000
73	A	83	SER	0	-0.076	-0.075	55.997	0.001	0.001	0.000	0.000	0.000	0.000
74	A	84	ILE	0	-0.054	-0.023	54.276	0.000	0.000	0.000	0.000	0.000	0.000
75	A	85	PRO	0	0.010	-0.008	57.325	0.000	0.000	0.000	0.000	0.000	0.000
76	A	86	GLU	-1	-0.962	-1.000	57.835	-0.031	-0.031	0.000	0.000	0.000	0.000
77	A	87	ILE	0	-0.005	0.031	51.961	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	88	SER	0	-0.023	-0.002	54.439	0.001	0.001	0.000	0.000	0.000	0.000
79	A	89	LEU	0	0.056	0.009	52.183	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	90	ALA	0	0.018	0.005	50.526	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	91	GLN	0	0.033	0.010	49.585	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	92	LEU	0	0.046	0.031	48.217	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	93	ALA	0	0.034	0.016	46.175	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	94	SER	0	-0.055	-0.028	44.745	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	95	ILE	0	0.004	0.012	43.857	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	96	VAL	0	-0.023	-0.018	41.097	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	97	LYS	1	0.922	0.955	40.266	0.034	0.034	0.000	0.000	0.000	0.000
88	A	98	ALA	0	-0.016	0.008	39.371	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	99	SER	0	-0.076	-0.030	37.309	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	100	GLY	0	0.035	0.017	34.935	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	101	THR	0	-0.050	-0.016	34.687	0.000	0.000	0.000	0.000	0.000	0.000
92	A	102	SER	0	0.009	-0.002	36.297	0.003	0.003	0.000	0.000	0.000	0.000
93	A	103	LEU	0	0.057	0.008	38.757	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	104	ARG	1	0.890	0.931	39.520	0.027	0.027	0.000	0.000	0.000	0.000
95	A	105	LYS	1	0.896	0.956	32.318	0.061	0.061	0.000	0.000	0.000	0.000
96	A	106	PHE	0	0.049	0.017	38.309	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	107	CYS	0	-0.030	-0.021	40.543	0.001	0.001	0.000	0.000	0.000	0.000
98	A	108	ARG	1	0.818	0.895	36.981	0.038	0.038	0.000	0.000	0.000	0.000
99	A	109	TYR	0	0.005	-0.001	37.699	0.001	0.001	0.000	0.000	0.000	0.000
100	A	110	PHE	0	0.025	0.011	40.175	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	111	ALA	0	0.012	0.021	43.058	0.002	0.002	0.000	0.000	0.000	0.000
102	A	112	PRO	0	0.015	0.013	42.697	0.003	0.003	0.000	0.000	0.000	0.000
103	A	113	ILE	0	0.009	0.014	45.721	0.002	0.002	0.000	0.000	0.000	0.000
104	A	114	ILE	0	-0.009	-0.002	47.695	0.002	0.002	0.000	0.000	0.000	0.000
105	A	115	TRP	0	-0.006	-0.001	48.123	0.002	0.002	0.000	0.000	0.000	0.000
106	A	116	ASN	0	-0.018	-0.018	49.991	0.002	0.002	0.000	0.000	0.000	0.000
107	A	117	LEU	0	-0.050	-0.019	51.755	0.001	0.001	0.000	0.000	0.000	0.000
108	A	118	ARG	1	0.730	0.834	53.415	0.021	0.021	0.000	0.000	0.000	0.000
109	A	119	THR	0	0.018	0.001	51.838	0.002	0.002	0.000	0.000	0.000	0.000
110	A	120	ASP	-1	-0.883	-0.927	54.674	-0.015	-0.015	0.000	0.000	0.000	0.000
111	A	121	LYS	1	0.894	0.957	57.562	0.020	0.020	0.000	0.000	0.000	0.000
112	A	122	MET	0	-0.023	-0.024	58.067	0.000	0.000	0.000	0.000	0.000	0.000
113	A	123	ALA	0	0.019	0.013	56.288	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	124	PRO	0	0.013	0.024	52.678	0.000	0.000	0.000	0.000	0.000	0.000
115	A	125	ALA	0	0.017	-0.001	55.254	0.001	0.001	0.000	0.000	0.000	0.000
116	A	126	ASN	0	-0.034	-0.011	55.180	0.002	0.002	0.000	0.000	0.000	0.000
117	A	127	TRP	0	0.011	-0.015	55.069	0.001	0.001	0.000	0.000	0.000	0.000
118	A	128	GLU	-1	-0.964	-0.982	56.115	-0.006	-0.006	0.000	0.000	0.000	0.000
119	A	129	ALA	0	0.007	0.012	57.494	0.001	0.001	0.000	0.000	0.000	0.000
120	A	130	SER	0	-0.041	-0.012	52.397	0.000	0.000	0.000	0.000	0.000	0.000
121	A	131	GLY	0	0.008	-0.008	52.868	0.001	0.001	0.000	0.000	0.000	0.000
122	A	132	TYR	0	-0.022	0.007	48.745	0.001	0.001	0.000	0.000	0.000	0.000
123	A	133	LYS	1	0.966	0.981	55.148	0.002	0.002	0.000	0.000	0.000	0.000
124	A	134	PRO	0	0.038	0.001	56.888	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	135	SER	0	-0.024	-0.021	57.114	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	136	ALA	0	-0.004	0.013	52.333	0.000	0.000	0.000	0.000	0.000	0.000
127	A	137	LYS	1	0.947	0.975	52.939	0.009	0.009	0.000	0.000	0.000	0.000
128	A	138	PHE	0	-0.020	0.002	53.101	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	139	ALA	0	0.027	0.020	48.893	-0.002	-0.002	0.000	0.000	0.000	0.000
130	A	140	ALA	0	-0.022	0.005	48.863	0.000	0.000	0.000	0.000	0.000	0.000
131	A	141	PHE	0	0.019	0.005	46.410	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	142	ASP	-1	-0.748	-0.833	44.659	-0.025	-0.025	0.000	0.000	0.000	0.000
133	A	143	PHE	0	-0.011	-0.017	42.435	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	144	PHE	0	0.043	0.035	43.409	-0.002	-0.002	0.000	0.000	0.000	0.000
135	A	145	ASP	-1	-0.821	-0.886	39.223	-0.030	-0.030	0.000	0.000	0.000	0.000
136	A	146	GLY	0	-0.002	-0.025	39.679	-0.002	-0.002	0.000	0.000	0.000	0.000
137	A	147	VAL	0	-0.071	-0.036	40.877	-0.002	-0.002	0.000	0.000	0.000	0.000
138	A	148	GLU	-1	-0.821	-0.921	41.494	-0.020	-0.020	0.000	0.000	0.000	0.000
139	A	149	ASN	0	-0.006	-0.002	34.921	-0.004	-0.004	0.000	0.000	0.000	0.000
140	A	150	PRO	0	0.028	0.003	35.422	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	151	ALA	0	-0.004	0.004	34.027	-0.002	-0.002	0.000	0.000	0.000	0.000
142	A	152	ALA	0	-0.060	-0.021	36.098	-0.003	-0.003	0.000	0.000	0.000	0.000
143	A	153	MET	0	-0.039	-0.021	39.083	0.001	0.001	0.000	0.000	0.000	0.000
144	A	154	GLN	0	0.003	-0.009	40.382	0.005	0.005	0.000	0.000	0.000	0.000
145	A	155	PRO	0	-0.033	-0.010	44.011	-0.001	-0.001	0.000	0.000	0.000	0.000
146	A	156	PRO	0	0.021	-0.002	47.223	-0.001	-0.001	0.000	0.000	0.000	0.000
147	A	157	SER	0	-0.051	-0.022	49.107	0.000	0.000	0.000	0.000	0.000	0.000
148	A	158	GLY	0	0.026	0.026	47.080	0.001	0.001	0.000	0.000	0.000	0.000
149	A	159	LEU	0	-0.007	-0.017	45.324	0.001	0.001	0.000	0.000	0.000	0.000
150	A	160	THR	0	-0.021	-0.007	49.112	0.000	0.000	0.000	0.000	0.000	0.000
151	A	161	ARG	1	0.732	0.845	51.431	0.016	0.016	0.000	0.000	0.000	0.000
152	A	162	SER	0	0.034	0.019	46.491	-0.002	-0.002	0.000	0.000	0.000	0.000
153	A	163	PRO	0	-0.027	-0.004	45.952	0.001	0.001	0.000	0.000	0.000	0.000
154	A	164	THR	0	0.018	0.009	48.970	0.001	0.001	0.000	0.000	0.000	0.000
155	A	165	GLN	0	0.053	0.009	44.782	-0.002	-0.002	0.000	0.000	0.000	0.000
156	A	166	GLU	-1	-0.869	-0.939	48.566	-0.004	-0.004	0.000	0.000	0.000	0.000
157	A	167	GLU	-1	-0.737	-0.860	49.739	-0.013	-0.013	0.000	0.000	0.000	0.000
158	A	168	ARG	1	0.852	0.917	43.629	0.014	0.014	0.000	0.000	0.000	0.000
159	A	169	ILE	0	-0.017	-0.010	45.559	0.000	0.000	0.000	0.000	0.000	0.000
160	A	170	ALA	0	-0.013	-0.006	47.057	0.001	0.001	0.000	0.000	0.000	0.000
161	A	171	ASN	0	-0.028	-0.004	44.320	-0.001	-0.001	0.000	0.000	0.000	0.000
162	A	172	ALA	0	0.021	0.017	42.655	0.000	0.000	0.000	0.000	0.000	0.000
163	A	173	THR	0	-0.136	-0.068	43.691	0.001	0.001	0.000	0.000	0.000	0.000
164	A	174	ASN	0	-0.011	0.000	43.901	-0.001	-0.001	0.000	0.000	0.000	0.000

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