FMO DATABASE

FMODB ID: 9G7Z2

Calculation Name: 2DM9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DM9

Chain ID: A

ChEMBL ID:

UniProt ID: O57724

Base Structure: X-ray

Registration Date: 2023-03-13

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	118
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-946929.849839
FMO2-HF: Nuclear repulsion	899703.070355
FMO2-HF: Total energy	-47226.779484
FMO2-MP2: Total energy	-47363.79353

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:81:GLU)

Summations of interaction energy for fragment #1(A:81:GLU)

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.
-6.4510000000001	0.17599999999993	18.906	-12.101	-13.431	0.121

Interaction energy analysis for fragmet #1(A:81:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.783 / q_NPA : -0.904

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	83	ILE	0	0.067	0.033	1.755	-32.448	-34.219	16.020	-7.010	-7.240	0.067
4	A	84	SER	0	-0.013	-0.023	2.649	-15.253	-12.802	0.843	-1.145	-2.149	-0.003
5	A	85	SER	0	-0.040	-0.023	4.587	-6.734	-6.450	-0.001	-0.068	-0.215	0.000
6	A	86	VAL	0	0.028	-0.001	6.126	-5.066	-5.066	0.000	0.000	0.000	0.000
7	A	87	LEU	0	0.004	0.002	6.395	-4.332	-4.332	0.000	0.000	0.000	0.000
8	A	88	GLU	-1	-0.916	-0.942	7.763	23.236	23.236	0.000	0.000	0.000	0.000
9	A	89	GLU	-1	-0.839	-0.891	10.699	18.868	18.868	0.000	0.000	0.000	0.000
10	A	90	VAL	0	-0.027	-0.011	11.950	-1.683	-1.683	0.000	0.000	0.000	0.000
11	A	91	LYS	1	0.941	0.952	10.800	-24.407	-24.407	0.000	0.000	0.000	0.000
12	A	92	ARG	1	0.816	0.873	10.878	-22.845	-22.845	0.000	0.000	0.000	0.000
13	A	93	ARG	1	0.840	0.916	16.730	-15.960	-15.960	0.000	0.000	0.000	0.000
14	A	94	LEU	0	-0.007	-0.028	16.027	-0.870	-0.870	0.000	0.000	0.000	0.000
15	A	95	GLU	-1	-0.999	-0.983	18.991	14.226	14.226	0.000	0.000	0.000	0.000
16	A	96	THR	0	-0.079	-0.045	20.845	-0.713	-0.713	0.000	0.000	0.000	0.000
17	A	97	MET	0	-0.086	0.008	20.148	-0.421	-0.421	0.000	0.000	0.000	0.000
18	A	98	SER	0	0.003	0.010	23.777	-0.436	-0.436	0.000	0.000	0.000	0.000
19	A	99	GLU	-1	-0.789	-0.892	26.138	10.432	10.432	0.000	0.000	0.000	0.000
20	A	100	ASP	-1	-0.812	-0.903	27.376	10.077	10.077	0.000	0.000	0.000	0.000
21	A	101	GLU	-1	-0.816	-0.896	23.548	13.268	13.268	0.000	0.000	0.000	0.000
22	A	102	TYR	0	0.026	-0.020	19.835	0.691	0.691	0.000	0.000	0.000	0.000
23	A	103	PHE	0	-0.007	-0.013	23.852	0.336	0.336	0.000	0.000	0.000	0.000
24	A	104	GLU	-1	-0.800	-0.891	26.153	10.789	10.789	0.000	0.000	0.000	0.000
25	A	105	SER	0	-0.023	-0.005	20.257	0.486	0.486	0.000	0.000	0.000	0.000
26	A	106	VAL	0	-0.038	-0.018	22.305	0.318	0.318	0.000	0.000	0.000	0.000
27	A	107	LYS	1	0.756	0.859	23.913	-10.219	-10.219	0.000	0.000	0.000	0.000
28	A	108	ALA	0	-0.011	-0.006	23.026	-0.256	-0.256	0.000	0.000	0.000	0.000
29	A	109	LEU	0	-0.024	-0.008	18.300	0.051	0.051	0.000	0.000	0.000	0.000
30	A	110	LEU	0	0.029	0.017	21.942	0.106	0.106	0.000	0.000	0.000	0.000
31	A	111	LYS	1	0.806	0.903	25.034	-10.915	-10.915	0.000	0.000	0.000	0.000
32	A	112	GLU	-1	-0.834	-0.868	19.833	15.843	15.843	0.000	0.000	0.000	0.000
33	A	113	ALA	0	0.054	0.027	22.053	-0.213	-0.213	0.000	0.000	0.000	0.000
34	A	114	ILE	0	0.025	0.003	23.776	-0.316	-0.316	0.000	0.000	0.000	0.000
35	A	115	LYS	1	0.896	0.949	27.199	-10.984	-10.984	0.000	0.000	0.000	0.000
36	A	116	GLU	-1	-0.966	-0.970	22.297	13.639	13.639	0.000	0.000	0.000	0.000
37	A	117	LEU	0	0.002	0.003	25.352	-0.255	-0.255	0.000	0.000	0.000	0.000
38	A	118	ASN	0	-0.044	-0.020	27.899	-0.599	-0.599	0.000	0.000	0.000	0.000
39	A	119	GLU	-1	-0.824	-0.912	31.133	9.339	9.339	0.000	0.000	0.000	0.000
40	A	120	LYS	1	0.843	0.929	32.645	-8.815	-8.815	0.000	0.000	0.000	0.000
41	A	121	LYS	1	0.775	0.874	34.171	-8.537	-8.537	0.000	0.000	0.000	0.000
42	A	122	VAL	0	-0.007	0.011	28.823	0.117	0.117	0.000	0.000	0.000	0.000
43	A	123	ARG	1	0.742	0.862	27.671	-10.503	-10.503	0.000	0.000	0.000	0.000
44	A	124	VAL	0	0.005	-0.006	24.464	0.428	0.428	0.000	0.000	0.000	0.000
45	A	125	MET	0	-0.014	0.018	22.535	-0.402	-0.402	0.000	0.000	0.000	0.000
46	A	126	SER	0	-0.002	-0.035	20.403	0.631	0.631	0.000	0.000	0.000	0.000
47	A	127	ASN	0	0.018	0.023	18.995	-1.136	-1.136	0.000	0.000	0.000	0.000
48	A	128	GLU	-1	-0.899	-0.971	21.721	10.417	10.417	0.000	0.000	0.000	0.000
49	A	129	LYS	1	0.876	0.935	23.939	-11.106	-11.106	0.000	0.000	0.000	0.000
50	A	130	THR	0	0.030	0.026	21.571	-0.361	-0.361	0.000	0.000	0.000	0.000
51	A	131	LEU	0	0.004	0.017	24.663	-0.334	-0.334	0.000	0.000	0.000	0.000
52	A	132	GLY	0	0.027	0.013	27.174	-0.412	-0.412	0.000	0.000	0.000	0.000
53	A	133	LEU	0	-0.051	-0.014	26.122	-0.368	-0.368	0.000	0.000	0.000	0.000
54	A	134	ILE	0	0.013	-0.002	25.669	-0.279	-0.279	0.000	0.000	0.000	0.000
55	A	135	ALA	0	-0.027	-0.013	29.826	-0.301	-0.301	0.000	0.000	0.000	0.000
56	A	136	SER	0	-0.078	-0.051	32.506	-0.370	-0.370	0.000	0.000	0.000	0.000
57	A	137	ARG	1	0.760	0.870	30.941	-10.066	-10.066	0.000	0.000	0.000	0.000
58	A	138	ILE	0	0.038	0.028	32.833	0.069	0.069	0.000	0.000	0.000	0.000
59	A	139	GLU	-1	-0.800	-0.898	34.425	8.068	8.068	0.000	0.000	0.000	0.000
60	A	140	GLU	-1	-0.811	-0.888	32.403	9.647	9.647	0.000	0.000	0.000	0.000
61	A	141	ILE	0	-0.006	-0.002	29.834	0.138	0.138	0.000	0.000	0.000	0.000
62	A	142	LYS	1	0.827	0.892	32.662	-8.188	-8.188	0.000	0.000	0.000	0.000
63	A	143	SER	0	-0.062	-0.044	35.727	-0.211	-0.211	0.000	0.000	0.000	0.000
64	A	144	GLU	-1	-0.866	-0.927	31.218	10.018	10.018	0.000	0.000	0.000	0.000
65	A	145	LEU	0	-0.078	-0.050	30.299	0.236	0.236	0.000	0.000	0.000	0.000
66	A	146	GLY	0	0.043	0.030	33.990	0.035	0.035	0.000	0.000	0.000	0.000
67	A	147	ASP	-1	-0.946	-0.980	35.776	8.279	8.279	0.000	0.000	0.000	0.000
68	A	148	VAL	0	-0.041	-0.011	31.441	0.000	0.000	0.000	0.000	0.000	0.000
69	A	149	SER	0	-0.045	-0.015	34.820	-0.168	-0.168	0.000	0.000	0.000	0.000
70	A	150	ILE	0	-0.001	-0.016	29.835	0.199	0.199	0.000	0.000	0.000	0.000
71	A	151	GLU	-1	-0.861	-0.911	31.813	9.113	9.113	0.000	0.000	0.000	0.000
72	A	152	LEU	0	-0.037	-0.027	29.247	0.381	0.381	0.000	0.000	0.000	0.000
73	A	153	GLY	0	0.047	0.012	27.511	-0.291	-0.291	0.000	0.000	0.000	0.000
74	A	154	GLU	-1	-0.930	-0.966	24.327	11.451	11.451	0.000	0.000	0.000	0.000
75	A	155	THR	0	-0.019	-0.018	24.103	0.320	0.320	0.000	0.000	0.000	0.000
76	A	156	VAL	0	-0.050	-0.028	19.202	0.032	0.032	0.000	0.000	0.000	0.000
77	A	157	ASP	-1	-0.952	-0.977	15.718	17.062	17.062	0.000	0.000	0.000	0.000
78	A	158	THR	0	-0.034	-0.042	14.818	0.492	0.492	0.000	0.000	0.000	0.000
79	A	159	MET	0	-0.046	-0.013	11.028	-1.206	-1.206	0.000	0.000	0.000	0.000
80	A	160	GLY	0	-0.007	-0.014	15.680	-0.837	-0.837	0.000	0.000	0.000	0.000
81	A	161	GLY	0	0.038	0.038	16.551	1.023	1.023	0.000	0.000	0.000	0.000
82	A	162	VAL	0	-0.048	-0.027	18.817	-0.652	-0.652	0.000	0.000	0.000	0.000
83	A	163	ILE	0	-0.001	0.015	18.453	0.582	0.582	0.000	0.000	0.000	0.000
84	A	164	VAL	0	0.000	-0.012	20.756	-0.697	-0.697	0.000	0.000	0.000	0.000
85	A	165	GLU	-1	-0.830	-0.915	23.729	12.247	12.247	0.000	0.000	0.000	0.000
86	A	166	THR	0	0.001	-0.016	26.131	-0.199	-0.199	0.000	0.000	0.000	0.000
87	A	167	GLU	-1	-0.780	-0.872	29.744	8.614	8.614	0.000	0.000	0.000	0.000
88	A	168	ASP	-1	-0.795	-0.871	31.606	9.824	9.824	0.000	0.000	0.000	0.000
89	A	169	GLY	0	0.034	0.024	27.983	-0.028	-0.028	0.000	0.000	0.000	0.000
90	A	170	ARG	1	0.669	0.822	27.220	-9.584	-9.584	0.000	0.000	0.000	0.000
91	A	171	ILE	0	-0.026	-0.023	25.330	0.261	0.261	0.000	0.000	0.000	0.000
92	A	172	ARG	1	0.921	0.956	18.083	-15.326	-15.326	0.000	0.000	0.000	0.000
93	A	173	ILE	0	-0.019	0.003	19.754	0.450	0.450	0.000	0.000	0.000	0.000
94	A	174	ASP	-1	-0.798	-0.892	16.016	17.472	17.472	0.000	0.000	0.000	0.000
95	A	175	ASN	0	-0.017	-0.027	16.276	2.078	2.078	0.000	0.000	0.000	0.000
96	A	176	THR	0	0.023	0.017	14.412	0.122	0.122	0.000	0.000	0.000	0.000
97	A	177	PHE	0	0.006	-0.015	12.960	0.860	0.860	0.000	0.000	0.000	0.000
98	A	178	GLU	-1	-0.779	-0.874	9.601	23.315	23.315	0.000	0.000	0.000	0.000
99	A	179	ALA	0	0.068	0.039	9.456	2.769	2.769	0.000	0.000	0.000	0.000
100	A	180	ARG	1	0.766	0.845	11.484	-17.775	-17.775	0.000	0.000	0.000	0.000
101	A	181	MET	0	-0.019	0.007	6.486	0.644	0.644	0.000	0.000	0.000	0.000
102	A	182	GLU	-1	-0.935	-0.982	6.382	37.271	37.271	0.000	0.000	0.000	0.000
103	A	183	ARG	1	0.815	0.900	7.472	-20.492	-20.492	0.000	0.000	0.000	0.000
104	A	184	PHE	0	0.015	0.015	9.587	-1.961	-1.961	0.000	0.000	0.000	0.000
105	A	185	GLU	-1	-0.825	-0.881	3.864	56.503	56.898	0.003	-0.106	-0.291	0.001
106	A	186	GLY	0	0.080	0.034	6.971	0.166	0.166	0.000	0.000	0.000	0.000
107	A	187	GLU	-1	-0.918	-0.947	9.637	20.438	20.438	0.000	0.000	0.000	0.000
108	A	188	ILE	0	0.011	0.015	7.241	-1.699	-1.699	0.000	0.000	0.000	0.000
109	A	189	ARG	1	0.810	0.880	2.223	-97.935	-92.667	2.041	-3.772	-3.536	0.056
110	A	190	SER	0	-0.013	-0.019	9.191	-3.335	-3.335	0.000	0.000	0.000	0.000
111	A	191	THR	0	-0.091	-0.047	12.030	-3.322	-3.322	0.000	0.000	0.000	0.000
112	A	192	ILE	0	0.010	-0.003	8.171	-1.684	-1.684	0.000	0.000	0.000	0.000
113	A	193	ALA	0	0.010	-0.002	12.243	-1.775	-1.775	0.000	0.000	0.000	0.000
114	A	194	LYS	1	0.911	0.952	14.197	-21.034	-21.034	0.000	0.000	0.000	0.000
115	A	195	VAL	0	-0.050	-0.018	14.860	-1.337	-1.337	0.000	0.000	0.000	0.000
116	A	196	LEU	0	-0.054	-0.016	12.540	-0.840	-0.840	0.000	0.000	0.000	0.000
117	A	197	PHE	0	-0.037	-0.021	14.881	-0.838	-0.838	0.000	0.000	0.000	0.000
118	A	198	GLY	0	-0.027	0.003	19.481	-0.599	-0.599	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:81:GLU)