FMO DATABASE

FMODB ID: 494GN

Calculation Name: 3DO8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DO8

Chain ID: A

ChEMBL ID:

UniProt ID: O28077

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	135
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1263695.14749
FMO2-HF: Nuclear repulsion	1209159.691221
FMO2-HF: Total energy	-54535.456269
FMO2-MP2: Total energy	-54693.807268

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:1:MET)

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

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.
-22.542	-14.163	27.944	-11.204	-25.122	-0.095

Interaction energy analysis for fragmet #1(A:1:MET)

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 : 0.012

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	3	VAL	0	-0.025	-0.027	3.482	-3.016	-0.681	0.193	-1.023	-1.505	0.008
4	A	4	ALA	0	-0.013	0.007	4.046	1.765	2.793	0.110	-0.351	-0.787	-0.003
5	A	5	LEU	0	0.031	0.011	6.126	-0.722	-0.722	0.000	0.000	0.000	0.000
6	A	6	GLY	0	-0.001	0.002	9.054	0.134	0.134	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.007	0.001	11.693	-0.088	-0.088	0.000	0.000	0.000	0.000
8	A	8	THR	0	-0.030	-0.019	15.173	0.012	0.012	0.000	0.000	0.000	0.000
9	A	9	PHE	0	-0.006	-0.009	12.750	-0.033	-0.033	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.772	-0.824	18.294	0.071	0.071	0.000	0.000	0.000	0.000
11	A	11	PRO	0	0.036	-0.002	21.939	0.001	0.001	0.000	0.000	0.000	0.000
12	A	12	LEU	0	-0.001	0.000	16.239	0.012	0.012	0.000	0.000	0.000	0.000
13	A	13	HIS	0	0.064	0.023	20.201	-0.023	-0.023	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.795	-0.908	20.222	0.024	0.024	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.071	0.025	20.491	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	16	HIS	0	0.062	0.020	16.545	0.002	0.002	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.853	0.928	15.745	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.868	0.950	16.330	-0.041	-0.041	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.000	0.012	13.787	-0.011	-0.011	0.000	0.000	0.000	0.000
20	A	20	ILE	0	0.014	0.000	11.314	0.039	0.039	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.743	-0.833	11.651	-0.058	-0.058	0.000	0.000	0.000	0.000
22	A	22	VAL	0	-0.006	0.001	13.059	-0.030	-0.030	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.016	0.003	8.540	-0.038	-0.038	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.006	0.000	8.565	0.018	0.018	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.814	0.905	9.631	-0.015	-0.015	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.048	-0.014	9.957	-0.044	-0.044	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.004	-0.020	6.624	-0.112	-0.112	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.055	0.048	6.381	-0.257	-0.257	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.909	0.936	5.691	0.927	0.927	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.861	-0.920	2.506	-9.240	-5.049	3.995	-3.333	-4.854	-0.041
31	A	31	ILE	0	-0.022	-0.022	2.515	3.247	2.575	5.469	-0.710	-4.087	-0.012
32	A	32	THR	0	0.000	-0.027	2.418	-0.193	-1.014	6.367	-0.919	-4.628	-0.019
33	A	33	ILE	0	-0.027	-0.013	4.333	-0.210	-0.192	0.010	0.189	-0.217	0.001
34	A	34	GLY	0	0.002	-0.012	7.881	-0.197	-0.197	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.026	-0.007	10.171	-0.091	-0.091	0.000	0.000	0.000	0.000
36	A	36	THR	0	0.007	0.017	13.509	-0.008	-0.008	0.000	0.000	0.000	0.000
37	A	37	SER	0	0.036	0.005	16.278	-0.043	-0.043	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.799	-0.905	18.278	0.117	0.117	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.923	0.962	21.722	-0.128	-0.128	0.000	0.000	0.000	0.000
40	A	40	MET	0	0.013	0.013	17.708	0.004	0.004	0.000	0.000	0.000	0.000
41	A	41	ALA	0	-0.020	-0.007	20.673	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.979	0.976	21.812	-0.106	-0.106	0.000	0.000	0.000	0.000
43	A	43	ALA	0	-0.011	0.021	23.781	-0.008	-0.008	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.922	0.978	19.357	-0.175	-0.175	0.000	0.000	0.000	0.000
45	A	45	ILE	0	0.033	0.018	23.612	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	46	ARG	1	0.993	0.993	26.621	-0.052	-0.052	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.118	-0.076	23.870	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.003	-0.032	26.172	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.028	0.000	22.784	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	50	PRO	0	0.045	0.024	22.646	0.013	0.013	0.000	0.000	0.000	0.000
51	A	51	PHE	0	0.051	-0.003	13.551	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.002	0.001	17.758	0.002	0.002	0.000	0.000	0.000	0.000
53	A	53	ILE	0	0.025	0.018	18.434	-0.012	-0.012	0.000	0.000	0.000	0.000
54	A	54	ARG	1	0.783	0.884	17.887	-0.157	-0.157	0.000	0.000	0.000	0.000
55	A	55	ALA	0	0.017	0.006	13.952	0.004	0.004	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.773	-0.880	14.565	-0.061	-0.061	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.049	-0.022	16.889	-0.029	-0.029	0.000	0.000	0.000	0.000
58	A	58	VAL	0	-0.024	-0.007	11.794	-0.015	-0.015	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.864	0.928	11.432	0.073	0.073	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.895	0.932	13.461	-0.012	-0.012	0.000	0.000	0.000	0.000
61	A	61	TYR	0	-0.058	-0.030	14.722	-0.018	-0.018	0.000	0.000	0.000	0.000
62	A	62	VAL	0	0.028	0.001	9.899	0.003	0.003	0.000	0.000	0.000	0.000
63	A	63	MET	0	0.033	0.042	13.371	-0.025	-0.025	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.885	0.941	14.769	0.035	0.035	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.867	0.931	16.302	0.053	0.053	0.000	0.000	0.000	0.000
66	A	66	TYR	0	-0.038	-0.053	12.417	0.031	0.031	0.000	0.000	0.000	0.000
67	A	67	GLY	0	0.040	0.052	13.609	-0.033	-0.033	0.000	0.000	0.000	0.000
68	A	68	PHE	0	-0.015	-0.023	7.043	-0.078	-0.078	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.828	-0.915	10.699	-0.148	-0.148	0.000	0.000	0.000	0.000
70	A	70	PRO	0	-0.053	-0.024	6.870	-0.151	-0.151	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.728	-0.847	2.494	-2.667	-1.848	1.024	-0.511	-1.333	-0.010
72	A	72	ILE	0	-0.051	-0.031	6.108	0.426	0.426	0.000	0.000	0.000	0.000
73	A	73	VAL	0	0.022	0.020	6.497	-0.052	-0.052	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.882	0.944	9.233	-0.142	-0.142	0.000	0.000	0.000	0.000
75	A	75	ILE	0	-0.009	0.013	11.283	0.042	0.042	0.000	0.000	0.000	0.000
76	A	76	THR	0	-0.005	-0.028	13.242	-0.050	-0.050	0.000	0.000	0.000	0.000
77	A	77	ASN	0	0.034	0.012	13.423	-0.051	-0.051	0.000	0.000	0.000	0.000
78	A	78	PRO	0	0.034	-0.004	15.112	0.043	0.043	0.000	0.000	0.000	0.000
79	A	79	TYR	0	0.081	0.050	12.639	0.002	0.002	0.000	0.000	0.000	0.000
80	A	80	GLY	0	-0.030	0.013	10.762	0.086	0.086	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.934	0.966	3.285	-1.944	-1.633	0.005	-0.069	-0.247	0.000
82	A	82	THR	0	-0.026	-0.026	7.336	0.012	0.012	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.012	0.005	8.393	-0.149	-0.149	0.000	0.000	0.000	0.000
84	A	84	ASP	-1	-0.909	-0.938	8.735	0.760	0.760	0.000	0.000	0.000	0.000
85	A	85	VAL	0	0.027	0.010	2.616	-0.686	-0.067	0.862	-0.347	-1.133	0.002
86	A	86	ASP	-1	-0.832	-0.877	4.098	-0.770	-0.377	-0.001	-0.130	-0.263	0.000
87	A	87	PHE	0	0.011	-0.008	1.980	-8.470	-8.627	9.910	-3.955	-5.798	-0.021
88	A	88	GLU	-1	-0.800	-0.877	4.036	-0.683	-0.368	0.000	-0.045	-0.270	0.000
89	A	89	TYR	0	-0.032	-0.032	6.407	0.540	0.540	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.014	-0.001	6.875	0.317	0.317	0.000	0.000	0.000	0.000
91	A	91	VAL	0	-0.007	-0.001	9.195	-0.135	-0.135	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.038	-0.022	11.747	0.085	0.085	0.000	0.000	0.000	0.000
93	A	93	SER	0	0.042	0.030	14.667	-0.035	-0.035	0.000	0.000	0.000	0.000
94	A	94	PRO	0	0.008	-0.017	18.297	0.003	0.003	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.882	-0.937	20.789	0.106	0.106	0.000	0.000	0.000	0.000
96	A	96	THR	0	-0.043	-0.026	15.784	0.016	0.016	0.000	0.000	0.000	0.000
97	A	97	TYR	0	0.028	0.018	16.620	0.019	0.019	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.864	-0.934	17.923	0.072	0.072	0.000	0.000	0.000	0.000
99	A	99	MET	0	-0.045	-0.020	15.485	-0.014	-0.014	0.000	0.000	0.000	0.000
100	A	100	ALA	0	0.016	0.005	13.847	0.012	0.012	0.000	0.000	0.000	0.000
101	A	101	LEU	0	0.022	0.013	14.774	-0.026	-0.026	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.914	0.969	17.415	-0.106	-0.106	0.000	0.000	0.000	0.000
103	A	103	ILE	0	-0.007	-0.013	10.814	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	104	ASN	0	0.047	0.014	12.672	-0.032	-0.032	0.000	0.000	0.000	0.000
105	A	105	GLN	0	-0.014	0.003	14.656	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	106	LYS	1	0.829	0.882	15.995	-0.116	-0.116	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.761	0.845	7.428	0.119	0.119	0.000	0.000	0.000	0.000
108	A	108	GLU	-1	-0.842	-0.905	13.961	-0.024	-0.024	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.833	-0.897	16.556	0.096	0.096	0.000	0.000	0.000	0.000
110	A	110	LEU	0	-0.043	-0.019	14.894	0.007	0.007	0.000	0.000	0.000	0.000
111	A	111	GLY	0	0.014	0.031	15.817	0.016	0.016	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.786	0.888	8.091	-0.362	-0.362	0.000	0.000	0.000	0.000
113	A	113	ARG	1	0.932	0.959	5.912	0.625	0.625	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.849	0.911	10.189	0.005	0.005	0.000	0.000	0.000	0.000
115	A	115	ILE	0	-0.037	-0.009	7.458	-0.069	-0.069	0.000	0.000	0.000	0.000
116	A	116	THR	0	0.030	0.023	9.875	0.177	0.177	0.000	0.000	0.000	0.000
117	A	117	ILE	0	-0.033	-0.016	11.172	0.035	0.035	0.000	0.000	0.000	0.000
118	A	118	VAL	0	0.013	0.006	12.543	-0.027	-0.027	0.000	0.000	0.000	0.000
119	A	119	LYS	1	0.857	0.916	14.475	0.020	0.020	0.000	0.000	0.000	0.000
120	A	120	VAL	0	0.007	-0.005	15.769	-0.025	-0.025	0.000	0.000	0.000	0.000
121	A	121	ASP	-1	-0.767	-0.878	18.498	0.054	0.054	0.000	0.000	0.000	0.000
122	A	122	TRP	0	-0.069	-0.057	17.902	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	123	MET	0	-0.068	-0.032	21.917	-0.004	-0.004	0.000	0.000	0.000	0.000
124	A	124	MET	0	0.030	0.047	23.087	-0.007	-0.007	0.000	0.000	0.000	0.000
125	A	132	SER	0	0.029	0.024	30.416	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	133	SER	0	-0.002	-0.032	26.075	0.007	0.007	0.000	0.000	0.000	0.000
127	A	134	THR	0	0.048	0.035	26.226	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	135	ARG	1	0.936	0.965	25.734	0.031	0.031	0.000	0.000	0.000	0.000
129	A	136	ILE	0	0.040	0.018	19.848	-0.003	-0.003	0.000	0.000	0.000	0.000
130	A	137	LYS	1	0.930	0.964	22.066	0.071	0.071	0.000	0.000	0.000	0.000
131	A	138	ARG	1	0.776	0.884	17.566	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	139	GLY	0	0.056	0.033	16.118	-0.002	-0.002	0.000	0.000	0.000	0.000
133	A	140	GLU	-1	-0.896	-0.957	11.045	-0.363	-0.363	0.000	0.000	0.000	0.000
134	A	141	ILE	0	-0.015	-0.022	14.999	0.017	0.017	0.000	0.000	0.000	0.000
135	A	142	ASP	-1	-0.968	-0.966	15.823	-0.210	-0.210	0.000	0.000	0.000	0.000

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