FMO DATABASE

FMODB ID: 3QZLL

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

Total energy (hartree)

FMO2-HF: Electronic energy	-942649.958199
FMO2-HF: Nuclear repulsion	895423.859315
FMO2-HF: Total energy	-47226.098884
FMO2-MP2: Total energy	-47362.973922

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.
51.52	60.008	7.452	-6.294	-9.645	0.017

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 : -0.888 / q_NPA : -0.956

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	0.107	0.051	2.120	-23.463	-17.095	3.768	-4.342	-5.794	0.024
4	A	84	SER	0	-0.035	-0.025	1.852	-13.904	-12.727	3.680	-1.725	-3.131	-0.008
5	A	85	SER	0	-0.009	0.004	3.781	-7.464	-6.822	0.006	-0.190	-0.458	0.001
6	A	86	VAL	0	0.024	-0.003	5.454	-4.351	-4.351	0.000	0.000	0.000	0.000
7	A	87	LEU	0	0.016	0.001	6.232	-3.681	-3.681	0.000	0.000	0.000	0.000
8	A	88	GLU	-1	-0.994	-1.000	6.740	24.800	24.800	0.000	0.000	0.000	0.000
9	A	89	GLU	-1	-0.898	-0.942	9.949	16.822	16.822	0.000	0.000	0.000	0.000
10	A	90	VAL	0	-0.021	-0.003	11.182	-1.600	-1.600	0.000	0.000	0.000	0.000
11	A	91	LYS	1	0.980	0.973	10.202	-24.352	-24.352	0.000	0.000	0.000	0.000
12	A	92	ARG	1	0.882	0.945	10.807	-21.389	-21.389	0.000	0.000	0.000	0.000
13	A	93	ARG	1	0.912	0.966	15.841	-15.890	-15.890	0.000	0.000	0.000	0.000
14	A	94	LEU	0	-0.032	-0.031	15.586	-0.800	-0.800	0.000	0.000	0.000	0.000
15	A	95	GLU	-1	-0.992	-0.972	18.521	13.684	13.684	0.000	0.000	0.000	0.000
16	A	96	THR	0	-0.064	-0.037	20.301	-0.720	-0.720	0.000	0.000	0.000	0.000
17	A	97	MET	0	-0.054	0.012	19.508	-0.406	-0.406	0.000	0.000	0.000	0.000
18	A	98	SER	0	0.017	0.015	23.307	-0.156	-0.156	0.000	0.000	0.000	0.000
19	A	99	GLU	-1	-0.868	-0.970	25.599	10.470	10.470	0.000	0.000	0.000	0.000
20	A	100	ASP	-1	-0.852	-0.926	27.188	9.803	9.803	0.000	0.000	0.000	0.000
21	A	101	GLU	-1	-0.905	-0.950	23.507	12.671	12.671	0.000	0.000	0.000	0.000
22	A	102	TYR	0	0.021	-0.031	19.431	0.603	0.603	0.000	0.000	0.000	0.000
23	A	103	PHE	0	0.003	-0.009	23.537	0.372	0.372	0.000	0.000	0.000	0.000
24	A	104	GLU	-1	-0.840	-0.920	25.518	10.607	10.607	0.000	0.000	0.000	0.000
25	A	105	SER	0	-0.056	-0.018	19.375	0.272	0.272	0.000	0.000	0.000	0.000
26	A	106	VAL	0	-0.005	-0.005	22.371	0.211	0.211	0.000	0.000	0.000	0.000
27	A	107	LYS	1	0.807	0.903	23.649	-10.108	-10.108	0.000	0.000	0.000	0.000
28	A	108	ALA	0	-0.019	-0.004	23.031	-0.154	-0.154	0.000	0.000	0.000	0.000
29	A	109	LEU	0	-0.023	-0.012	18.091	0.156	0.156	0.000	0.000	0.000	0.000
30	A	110	LEU	0	0.042	0.016	22.095	0.099	0.099	0.000	0.000	0.000	0.000
31	A	111	LYS	1	0.837	0.931	25.026	-10.714	-10.714	0.000	0.000	0.000	0.000
32	A	112	GLU	-1	-0.862	-0.919	20.515	15.176	15.176	0.000	0.000	0.000	0.000
33	A	113	ALA	0	0.038	0.021	22.550	-0.086	-0.086	0.000	0.000	0.000	0.000
34	A	114	ILE	0	0.005	-0.009	24.299	-0.293	-0.293	0.000	0.000	0.000	0.000
35	A	115	LYS	1	0.894	0.936	27.761	-10.976	-10.976	0.000	0.000	0.000	0.000
36	A	116	GLU	-1	-0.968	-0.963	22.956	13.658	13.658	0.000	0.000	0.000	0.000
37	A	117	LEU	0	-0.037	-0.024	25.461	-0.221	-0.221	0.000	0.000	0.000	0.000
38	A	118	ASN	0	-0.053	-0.015	28.130	-0.457	-0.457	0.000	0.000	0.000	0.000
39	A	119	GLU	-1	-0.903	-0.954	30.775	9.574	9.574	0.000	0.000	0.000	0.000
40	A	120	LYS	1	0.893	0.935	33.187	-8.493	-8.493	0.000	0.000	0.000	0.000
41	A	121	LYS	1	0.886	0.955	34.297	-8.607	-8.607	0.000	0.000	0.000	0.000
42	A	122	VAL	0	-0.006	0.008	28.682	0.149	0.149	0.000	0.000	0.000	0.000
43	A	123	ARG	1	0.869	0.938	27.543	-10.829	-10.829	0.000	0.000	0.000	0.000
44	A	124	VAL	0	-0.026	-0.018	24.422	0.440	0.440	0.000	0.000	0.000	0.000
45	A	125	MET	0	0.019	0.022	22.088	-0.444	-0.444	0.000	0.000	0.000	0.000
46	A	126	SER	0	0.001	-0.039	20.277	0.554	0.554	0.000	0.000	0.000	0.000
47	A	127	ASN	0	0.025	0.040	18.386	-1.111	-1.111	0.000	0.000	0.000	0.000
48	A	128	GLU	-1	-0.904	-0.975	21.187	10.744	10.744	0.000	0.000	0.000	0.000
49	A	129	LYS	1	0.946	0.980	23.267	-11.604	-11.604	0.000	0.000	0.000	0.000
50	A	130	THR	0	-0.001	0.002	21.667	-0.328	-0.328	0.000	0.000	0.000	0.000
51	A	131	LEU	0	-0.001	0.006	24.305	-0.348	-0.348	0.000	0.000	0.000	0.000
52	A	132	GLY	0	0.022	0.016	26.626	-0.423	-0.423	0.000	0.000	0.000	0.000
53	A	133	LEU	0	-0.022	-0.017	25.672	-0.379	-0.379	0.000	0.000	0.000	0.000
54	A	134	ILE	0	-0.003	-0.002	25.418	-0.292	-0.292	0.000	0.000	0.000	0.000
55	A	135	ALA	0	-0.022	-0.014	29.519	-0.312	-0.312	0.000	0.000	0.000	0.000
56	A	136	SER	0	-0.053	-0.021	32.209	-0.398	-0.398	0.000	0.000	0.000	0.000
57	A	137	ARG	1	0.825	0.923	30.725	-10.088	-10.088	0.000	0.000	0.000	0.000
58	A	138	ILE	0	0.047	0.030	32.922	0.068	0.068	0.000	0.000	0.000	0.000
59	A	139	GLU	-1	-0.873	-0.959	34.416	7.940	7.940	0.000	0.000	0.000	0.000
60	A	140	GLU	-1	-0.841	-0.915	32.320	9.474	9.474	0.000	0.000	0.000	0.000
61	A	141	ILE	0	-0.020	-0.012	29.697	0.122	0.122	0.000	0.000	0.000	0.000
62	A	142	LYS	1	0.878	0.939	32.818	-8.078	-8.078	0.000	0.000	0.000	0.000
63	A	143	SER	0	-0.034	-0.010	35.887	-0.214	-0.214	0.000	0.000	0.000	0.000
64	A	144	GLU	-1	-0.908	-0.957	31.460	9.869	9.869	0.000	0.000	0.000	0.000
65	A	145	LEU	0	-0.099	-0.061	30.369	0.281	0.281	0.000	0.000	0.000	0.000
66	A	146	GLY	0	0.044	0.030	34.333	0.032	0.032	0.000	0.000	0.000	0.000
67	A	147	ASP	-1	-0.917	-0.964	36.642	8.196	8.196	0.000	0.000	0.000	0.000
68	A	148	VAL	0	-0.082	-0.023	31.655	-0.043	-0.043	0.000	0.000	0.000	0.000
69	A	149	SER	0	-0.045	-0.018	35.061	-0.235	-0.235	0.000	0.000	0.000	0.000
70	A	150	ILE	0	-0.008	-0.016	29.865	0.186	0.186	0.000	0.000	0.000	0.000
71	A	151	GLU	-1	-0.953	-0.959	31.517	8.934	8.934	0.000	0.000	0.000	0.000
72	A	152	LEU	0	-0.037	-0.031	28.486	0.394	0.394	0.000	0.000	0.000	0.000
73	A	153	GLY	0	0.059	0.018	27.094	-0.284	-0.284	0.000	0.000	0.000	0.000
74	A	154	GLU	-1	-0.966	-0.974	24.094	11.775	11.775	0.000	0.000	0.000	0.000
75	A	155	THR	0	-0.023	-0.025	23.356	0.353	0.353	0.000	0.000	0.000	0.000
76	A	156	VAL	0	-0.023	-0.015	18.385	0.085	0.085	0.000	0.000	0.000	0.000
77	A	157	ASP	-1	-0.972	-0.989	14.430	18.568	18.568	0.000	0.000	0.000	0.000
78	A	158	THR	0	-0.027	-0.025	14.318	0.713	0.713	0.000	0.000	0.000	0.000
79	A	159	MET	0	-0.027	-0.018	10.438	-1.218	-1.218	0.000	0.000	0.000	0.000
80	A	160	GLY	0	-0.009	-0.024	15.084	-1.032	-1.032	0.000	0.000	0.000	0.000
81	A	161	GLY	0	0.024	0.039	16.346	1.019	1.019	0.000	0.000	0.000	0.000
82	A	162	VAL	0	-0.043	-0.017	18.586	-0.667	-0.667	0.000	0.000	0.000	0.000
83	A	163	ILE	0	0.001	0.014	17.483	0.654	0.654	0.000	0.000	0.000	0.000
84	A	164	VAL	0	0.005	0.004	20.747	-0.697	-0.697	0.000	0.000	0.000	0.000
85	A	165	GLU	-1	-0.848	-0.922	23.857	12.688	12.688	0.000	0.000	0.000	0.000
86	A	166	THR	0	0.006	-0.008	25.986	-0.224	-0.224	0.000	0.000	0.000	0.000
87	A	167	GLU	-1	-0.855	-0.937	29.386	8.954	8.954	0.000	0.000	0.000	0.000
88	A	168	ASP	-1	-0.863	-0.934	31.189	10.099	10.099	0.000	0.000	0.000	0.000
89	A	169	GLY	0	0.037	0.029	27.770	-0.035	-0.035	0.000	0.000	0.000	0.000
90	A	170	ARG	1	0.777	0.908	26.805	-9.887	-9.887	0.000	0.000	0.000	0.000
91	A	171	ILE	0	-0.023	-0.014	24.606	0.373	0.373	0.000	0.000	0.000	0.000
92	A	172	ARG	1	1.009	0.999	17.742	-16.022	-16.022	0.000	0.000	0.000	0.000
93	A	173	ILE	0	-0.018	-0.004	20.372	0.547	0.547	0.000	0.000	0.000	0.000
94	A	174	ASP	-1	-0.844	-0.914	15.052	19.875	19.875	0.000	0.000	0.000	0.000
95	A	175	ASN	0	-0.011	-0.036	16.720	1.853	1.853	0.000	0.000	0.000	0.000
96	A	176	THR	0	0.005	0.001	14.045	0.006	0.006	0.000	0.000	0.000	0.000
97	A	177	PHE	0	-0.012	-0.019	12.632	0.636	0.636	0.000	0.000	0.000	0.000
98	A	178	GLU	-1	-0.761	-0.866	9.365	23.706	23.706	0.000	0.000	0.000	0.000
99	A	179	ALA	0	0.057	0.039	9.287	3.076	3.076	0.000	0.000	0.000	0.000
100	A	180	ARG	1	0.823	0.900	11.572	-17.041	-17.041	0.000	0.000	0.000	0.000
101	A	181	MET	0	-0.021	-0.004	7.014	-0.108	-0.108	0.000	0.000	0.000	0.000
102	A	182	GLU	-1	-0.958	-0.983	6.397	42.012	42.012	0.000	0.000	0.000	0.000
103	A	183	ARG	1	0.857	0.933	8.290	-20.457	-20.457	0.000	0.000	0.000	0.000
104	A	184	PHE	0	-0.019	0.003	10.753	-1.747	-1.747	0.000	0.000	0.000	0.000
105	A	185	GLU	-1	-0.901	-0.944	4.964	46.829	46.947	-0.001	-0.002	-0.115	0.000
106	A	186	GLY	0	0.052	0.010	8.052	-0.065	-0.065	0.000	0.000	0.000	0.000
107	A	187	GLU	-1	-0.937	-0.971	10.703	18.842	18.842	0.000	0.000	0.000	0.000
108	A	188	ILE	0	0.007	0.006	8.096	-1.531	-1.531	0.000	0.000	0.000	0.000
109	A	189	ARG	1	0.929	0.955	4.212	-55.123	-54.940	-0.001	-0.035	-0.147	0.000
110	A	190	SER	0	-0.004	0.003	10.236	-2.419	-2.419	0.000	0.000	0.000	0.000
111	A	191	THR	0	-0.051	-0.023	13.134	-2.267	-2.267	0.000	0.000	0.000	0.000
112	A	192	ILE	0	0.002	0.001	8.805	-1.214	-1.214	0.000	0.000	0.000	0.000
113	A	193	ALA	0	0.011	0.003	13.124	-1.158	-1.158	0.000	0.000	0.000	0.000
114	A	194	LYS	1	0.940	0.973	15.369	-17.829	-17.829	0.000	0.000	0.000	0.000
115	A	195	VAL	0	-0.051	-0.020	15.226	-1.025	-1.025	0.000	0.000	0.000	0.000
116	A	196	LEU	0	-0.059	-0.019	13.254	-0.725	-0.725	0.000	0.000	0.000	0.000
117	A	197	PHE	0	-0.037	-0.024	16.259	-0.772	-0.772	0.000	0.000	0.000	0.000
118	A	198	GLY	0	-0.026	0.007	20.427	-0.546	-0.546	0.000	0.000	0.000	0.000

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