FMO DATABASE

FMODB ID: LJGY9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-944246.189736
FMO2-HF: Nuclear repulsion	897019.462265
FMO2-HF: Total energy	-47226.727471
FMO2-MP2: Total energy	-47363.665594

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.
29.612	34.76	14.616	-8.49	-11.275	0.051

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 : -0.877 / q_NPA : -0.934

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

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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	0.063	0.023	1.859	-35.205	-32.560	10.818	-6.106	-7.358	0.063
4	A	84	SER	0	0.026	0.003	1.879	-12.693	-11.329	3.794	-2.018	-3.140	-0.013
5	A	85	SER	0	-0.045	-0.018	3.859	-8.072	-7.552	0.004	-0.148	-0.377	0.000
6	A	86	VAL	0	0.021	-0.004	5.540	-5.148	-5.148	0.000	0.000	0.000	0.000
7	A	87	LEU	0	0.023	0.007	6.015	-4.140	-4.140	0.000	0.000	0.000	0.000
8	A	88	GLU	-1	-0.962	-0.984	6.931	23.609	23.609	0.000	0.000	0.000	0.000
9	A	89	GLU	-1	-0.845	-0.903	9.988	17.667	17.667	0.000	0.000	0.000	0.000
10	A	90	VAL	0	-0.033	-0.008	11.333	-1.669	-1.669	0.000	0.000	0.000	0.000
11	A	91	LYS	1	0.964	0.964	10.117	-24.497	-24.497	0.000	0.000	0.000	0.000
12	A	92	ARG	1	0.822	0.903	10.461	-22.708	-22.708	0.000	0.000	0.000	0.000
13	A	93	ARG	1	0.870	0.931	15.970	-15.969	-15.969	0.000	0.000	0.000	0.000
14	A	94	LEU	0	-0.029	-0.032	15.487	-0.837	-0.837	0.000	0.000	0.000	0.000
15	A	95	GLU	-1	-0.988	-0.972	18.575	13.922	13.922	0.000	0.000	0.000	0.000
16	A	96	THR	0	-0.053	-0.034	20.316	-0.704	-0.704	0.000	0.000	0.000	0.000
17	A	97	MET	0	-0.080	0.009	19.698	-0.434	-0.434	0.000	0.000	0.000	0.000
18	A	98	SER	0	0.013	0.013	23.379	-0.331	-0.331	0.000	0.000	0.000	0.000
19	A	99	GLU	-1	-0.771	-0.894	25.638	10.442	10.442	0.000	0.000	0.000	0.000
20	A	100	ASP	-1	-0.820	-0.905	27.199	9.886	9.886	0.000	0.000	0.000	0.000
21	A	101	GLU	-1	-0.861	-0.919	23.116	13.042	13.042	0.000	0.000	0.000	0.000
22	A	102	TYR	0	0.027	-0.024	19.393	0.575	0.575	0.000	0.000	0.000	0.000
23	A	103	PHE	0	0.001	-0.010	23.560	0.370	0.370	0.000	0.000	0.000	0.000
24	A	104	GLU	-1	-0.808	-0.892	25.878	10.640	10.640	0.000	0.000	0.000	0.000
25	A	105	SER	0	-0.017	-0.002	20.045	0.480	0.480	0.000	0.000	0.000	0.000
26	A	106	VAL	0	-0.056	-0.023	22.415	0.229	0.229	0.000	0.000	0.000	0.000
27	A	107	LYS	1	0.781	0.868	23.637	-10.116	-10.116	0.000	0.000	0.000	0.000
28	A	108	ALA	0	-0.021	-0.007	23.140	-0.165	-0.165	0.000	0.000	0.000	0.000
29	A	109	LEU	0	-0.021	-0.008	18.164	0.102	0.102	0.000	0.000	0.000	0.000
30	A	110	LEU	0	0.034	0.014	22.117	0.076	0.076	0.000	0.000	0.000	0.000
31	A	111	LYS	1	0.803	0.905	24.994	-10.789	-10.789	0.000	0.000	0.000	0.000
32	A	112	GLU	-1	-0.824	-0.862	20.481	15.537	15.537	0.000	0.000	0.000	0.000
33	A	113	ALA	0	0.048	0.026	22.468	-0.090	-0.090	0.000	0.000	0.000	0.000
34	A	114	ILE	0	0.008	-0.004	24.268	-0.294	-0.294	0.000	0.000	0.000	0.000
35	A	115	LYS	1	0.900	0.939	27.737	-10.881	-10.881	0.000	0.000	0.000	0.000
36	A	116	GLU	-1	-0.962	-0.968	22.727	13.624	13.624	0.000	0.000	0.000	0.000
37	A	117	LEU	0	-0.027	-0.013	25.962	-0.231	-0.231	0.000	0.000	0.000	0.000
38	A	118	ASN	0	-0.068	-0.027	28.394	-0.530	-0.530	0.000	0.000	0.000	0.000
39	A	119	GLU	-1	-0.847	-0.910	31.720	9.495	9.495	0.000	0.000	0.000	0.000
40	A	120	LYS	1	0.885	0.933	33.292	-8.719	-8.719	0.000	0.000	0.000	0.000
41	A	121	LYS	1	0.795	0.888	34.484	-8.551	-8.551	0.000	0.000	0.000	0.000
42	A	122	VAL	0	-0.008	0.006	28.858	0.141	0.141	0.000	0.000	0.000	0.000
43	A	123	ARG	1	0.768	0.874	27.832	-10.542	-10.542	0.000	0.000	0.000	0.000
44	A	124	VAL	0	-0.017	-0.016	24.538	0.434	0.434	0.000	0.000	0.000	0.000
45	A	125	MET	0	0.007	0.019	22.448	-0.396	-0.396	0.000	0.000	0.000	0.000
46	A	126	SER	0	0.002	-0.041	20.462	0.569	0.569	0.000	0.000	0.000	0.000
47	A	127	ASN	0	0.027	0.043	18.511	-1.112	-1.112	0.000	0.000	0.000	0.000
48	A	128	GLU	-1	-0.902	-0.973	21.467	10.651	10.651	0.000	0.000	0.000	0.000
49	A	129	LYS	1	0.879	0.930	23.348	-11.259	-11.259	0.000	0.000	0.000	0.000
50	A	130	THR	0	0.002	-0.005	21.743	-0.319	-0.319	0.000	0.000	0.000	0.000
51	A	131	LEU	0	-0.003	0.006	24.341	-0.336	-0.336	0.000	0.000	0.000	0.000
52	A	132	GLY	0	0.026	0.019	26.781	-0.416	-0.416	0.000	0.000	0.000	0.000
53	A	133	LEU	0	-0.036	-0.014	25.846	-0.383	-0.383	0.000	0.000	0.000	0.000
54	A	134	ILE	0	0.004	-0.001	25.342	-0.275	-0.275	0.000	0.000	0.000	0.000
55	A	135	ALA	0	-0.029	-0.012	29.504	-0.304	-0.304	0.000	0.000	0.000	0.000
56	A	136	SER	0	-0.068	-0.042	32.218	-0.380	-0.380	0.000	0.000	0.000	0.000
57	A	137	ARG	1	0.770	0.877	30.752	-10.087	-10.087	0.000	0.000	0.000	0.000
58	A	138	ILE	0	0.049	0.029	32.816	0.078	0.078	0.000	0.000	0.000	0.000
59	A	139	GLU	-1	-0.808	-0.902	34.341	7.996	7.996	0.000	0.000	0.000	0.000
60	A	140	GLU	-1	-0.823	-0.903	32.141	9.559	9.559	0.000	0.000	0.000	0.000
61	A	141	ILE	0	-0.015	-0.011	29.575	0.125	0.125	0.000	0.000	0.000	0.000
62	A	142	LYS	1	0.823	0.896	32.798	-8.087	-8.087	0.000	0.000	0.000	0.000
63	A	143	SER	0	-0.057	-0.029	35.858	-0.217	-0.217	0.000	0.000	0.000	0.000
64	A	144	GLU	-1	-0.857	-0.922	31.369	9.934	9.934	0.000	0.000	0.000	0.000
65	A	145	LEU	0	-0.076	-0.049	30.643	0.258	0.258	0.000	0.000	0.000	0.000
66	A	146	GLY	0	0.042	0.029	34.342	0.023	0.023	0.000	0.000	0.000	0.000
67	A	147	ASP	-1	-0.915	-0.963	36.540	8.170	8.170	0.000	0.000	0.000	0.000
68	A	148	VAL	0	-0.076	-0.019	31.667	-0.042	-0.042	0.000	0.000	0.000	0.000
69	A	149	SER	0	-0.043	-0.015	35.049	-0.229	-0.229	0.000	0.000	0.000	0.000
70	A	150	ILE	0	-0.007	-0.017	29.733	0.179	0.179	0.000	0.000	0.000	0.000
71	A	151	GLU	-1	-0.868	-0.910	31.738	9.046	9.046	0.000	0.000	0.000	0.000
72	A	152	LEU	0	-0.026	-0.025	29.006	0.362	0.362	0.000	0.000	0.000	0.000
73	A	153	GLY	0	0.060	0.020	27.378	-0.297	-0.297	0.000	0.000	0.000	0.000
74	A	154	GLU	-1	-0.953	-0.969	24.275	11.532	11.532	0.000	0.000	0.000	0.000
75	A	155	THR	0	-0.022	-0.020	23.695	0.330	0.330	0.000	0.000	0.000	0.000
76	A	156	VAL	0	-0.033	-0.023	18.762	0.090	0.090	0.000	0.000	0.000	0.000
77	A	157	ASP	-1	-0.964	-0.976	15.257	17.415	17.415	0.000	0.000	0.000	0.000
78	A	158	THR	0	-0.036	-0.030	14.540	0.741	0.741	0.000	0.000	0.000	0.000
79	A	159	MET	0	-0.029	-0.014	10.465	-1.154	-1.154	0.000	0.000	0.000	0.000
80	A	160	GLY	0	-0.014	-0.021	15.140	-0.965	-0.965	0.000	0.000	0.000	0.000
81	A	161	GLY	0	0.024	0.037	16.317	0.978	0.978	0.000	0.000	0.000	0.000
82	A	162	VAL	0	-0.044	-0.018	18.507	-0.673	-0.673	0.000	0.000	0.000	0.000
83	A	163	ILE	0	-0.006	0.013	17.869	0.672	0.672	0.000	0.000	0.000	0.000
84	A	164	VAL	0	-0.001	-0.001	20.966	-0.672	-0.672	0.000	0.000	0.000	0.000
85	A	165	GLU	-1	-0.835	-0.910	24.110	12.278	12.278	0.000	0.000	0.000	0.000
86	A	166	THR	0	-0.015	-0.026	26.232	-0.213	-0.213	0.000	0.000	0.000	0.000
87	A	167	GLU	-1	-0.776	-0.873	29.639	8.715	8.715	0.000	0.000	0.000	0.000
88	A	168	ASP	-1	-0.813	-0.882	31.567	9.966	9.966	0.000	0.000	0.000	0.000
89	A	169	GLY	0	0.040	0.031	28.071	-0.044	-0.044	0.000	0.000	0.000	0.000
90	A	170	ARG	1	0.694	0.836	27.249	-9.717	-9.717	0.000	0.000	0.000	0.000
91	A	171	ILE	0	-0.019	-0.015	25.450	0.355	0.355	0.000	0.000	0.000	0.000
92	A	172	ARG	1	0.953	0.962	17.607	-15.883	-15.883	0.000	0.000	0.000	0.000
93	A	173	ILE	0	-0.025	-0.002	20.534	0.533	0.533	0.000	0.000	0.000	0.000
94	A	174	ASP	-1	-0.816	-0.896	16.018	18.265	18.265	0.000	0.000	0.000	0.000
95	A	175	ASN	0	-0.005	-0.025	16.790	1.931	1.931	0.000	0.000	0.000	0.000
96	A	176	THR	0	0.014	0.013	14.282	0.088	0.088	0.000	0.000	0.000	0.000
97	A	177	PHE	0	0.012	-0.012	12.591	0.760	0.760	0.000	0.000	0.000	0.000
98	A	178	GLU	-1	-0.770	-0.875	9.410	23.416	23.416	0.000	0.000	0.000	0.000
99	A	179	ALA	0	0.055	0.031	9.261	2.880	2.880	0.000	0.000	0.000	0.000
100	A	180	ARG	1	0.776	0.839	11.547	-16.726	-16.726	0.000	0.000	0.000	0.000
101	A	181	MET	0	-0.019	-0.001	7.304	0.082	0.082	0.000	0.000	0.000	0.000
102	A	182	GLU	-1	-0.956	-0.980	6.672	39.084	39.084	0.000	0.000	0.000	0.000
103	A	183	ARG	1	0.839	0.913	8.075	-19.871	-19.871	0.000	0.000	0.000	0.000
104	A	184	PHE	0	-0.020	0.004	10.405	-1.702	-1.702	0.000	0.000	0.000	0.000
105	A	185	GLU	-1	-0.802	-0.873	4.657	51.134	51.283	-0.001	-0.006	-0.141	0.000
106	A	186	GLY	0	0.066	0.018	7.695	0.171	0.171	0.000	0.000	0.000	0.000
107	A	187	GLU	-1	-0.929	-0.957	10.469	19.437	19.437	0.000	0.000	0.000	0.000
108	A	188	ILE	0	0.004	0.003	7.627	-1.664	-1.664	0.000	0.000	0.000	0.000
109	A	189	ARG	1	0.841	0.893	3.802	-61.665	-61.195	0.001	-0.212	-0.259	0.001
110	A	190	SER	0	-0.024	-0.016	9.923	-2.689	-2.689	0.000	0.000	0.000	0.000
111	A	191	THR	0	-0.063	-0.033	12.612	-2.478	-2.478	0.000	0.000	0.000	0.000
112	A	192	ILE	0	0.007	0.004	8.549	-1.424	-1.424	0.000	0.000	0.000	0.000
113	A	193	ALA	0	0.008	0.002	12.756	-1.303	-1.303	0.000	0.000	0.000	0.000
114	A	194	LYS	1	0.932	0.965	15.115	-18.894	-18.894	0.000	0.000	0.000	0.000
115	A	195	VAL	0	-0.045	-0.016	15.320	-1.094	-1.094	0.000	0.000	0.000	0.000
116	A	196	LEU	0	-0.060	-0.015	13.241	-0.790	-0.790	0.000	0.000	0.000	0.000
117	A	197	PHE	0	-0.034	-0.026	16.062	-0.801	-0.801	0.000	0.000	0.000	0.000
118	A	198	GLY	0	-0.025	0.008	20.231	-0.586	-0.586	0.000	0.000	0.000	0.000

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