FMO DATABASE

FMODB ID: 9Y6V2

Calculation Name: 2DM9-A-Xray310

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	119
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-946455.082324
FMO2-HF: Nuclear repulsion	899077.956737
FMO2-HF: Total energy	-47377.125587
FMO2-MP2: Total energy	-47514.425617

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:80:ACE )

Summations of interaction energy for fragment #1(A:80:ACE )

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.
2.581	3.335	-0.005	-0.338	-0.411	0

Interaction energy analysis for fragmet #1(A:80:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.014

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].
3	A	82	ILE	0	-0.013	0.001	3.846	1.295	2.006	-0.005	-0.331	-0.375
4	A	83	ILE	0	0.109	0.054	6.802	0.350	0.350	0.000	0.000	0.000
5	A	84	SER	0	-0.031	-0.024	4.924	0.350	0.393	0.000	-0.007	-0.036
6	A	85	SER	0	-0.015	0.001	5.278	0.349	0.349	0.000	0.000	0.000
7	A	86	VAL	0	0.031	0.001	7.077	0.140	0.140	0.000	0.000	0.000
8	A	87	LEU	0	0.016	0.001	10.223	0.083	0.083	0.000	0.000	0.000
9	A	88	GLU	-1	-0.999	-1.003	7.396	0.566	0.566	0.000	0.000	0.000
10	A	89	GLU	-1	-0.897	-0.941	11.377	0.073	0.073	0.000	0.000	0.000
11	A	90	VAL	0	-0.016	-0.001	13.888	0.007	0.007	0.000	0.000	0.000
12	A	91	LYS	1	0.975	0.971	11.456	-0.041	-0.041	0.000	0.000	0.000
13	A	92	ARG	1	0.881	0.945	11.520	-0.131	-0.131	0.000	0.000	0.000
14	A	93	ARG	1	0.914	0.967	17.190	0.027	0.027	0.000	0.000	0.000
15	A	94	LEU	0	-0.031	-0.031	18.516	-0.002	-0.002	0.000	0.000	0.000
16	A	95	GLU	-1	-0.994	-0.972	19.808	0.091	0.091	0.000	0.000	0.000
17	A	96	THR	0	-0.065	-0.038	21.664	0.000	0.000	0.000	0.000	0.000
18	A	97	MET	0	-0.054	0.012	22.787	-0.006	-0.006	0.000	0.000	0.000
19	A	98	SER	0	0.016	0.014	25.738	0.000	0.000	0.000	0.000	0.000
20	A	99	GLU	-1	-0.869	-0.971	28.699	-0.009	-0.009	0.000	0.000	0.000
21	A	100	ASP	-1	-0.853	-0.926	30.607	-0.014	-0.014	0.000	0.000	0.000
22	A	101	GLU	-1	-0.900	-0.949	26.834	-0.019	-0.019	0.000	0.000	0.000
23	A	102	TYR	0	0.019	-0.033	23.373	-0.009	-0.009	0.000	0.000	0.000
24	A	103	PHE	0	0.003	-0.008	27.395	-0.008	-0.008	0.000	0.000	0.000
25	A	104	GLU	-1	-0.838	-0.920	29.753	-0.034	-0.034	0.000	0.000	0.000
26	A	105	SER	0	-0.056	-0.018	23.948	-0.008	-0.008	0.000	0.000	0.000
27	A	106	VAL	0	-0.004	-0.005	27.106	-0.007	-0.007	0.000	0.000	0.000
28	A	107	LYS	1	0.799	0.899	28.386	0.026	0.026	0.000	0.000	0.000
29	A	108	ALA	0	-0.014	-0.002	28.277	-0.002	-0.002	0.000	0.000	0.000
30	A	109	LEU	0	-0.020	-0.011	23.351	-0.005	-0.005	0.000	0.000	0.000
31	A	110	LEU	0	0.038	0.013	27.619	-0.004	-0.004	0.000	0.000	0.000
32	A	111	LYS	1	0.838	0.932	30.445	0.043	0.043	0.000	0.000	0.000
33	A	112	GLU	-1	-0.861	-0.918	26.574	-0.103	-0.103	0.000	0.000	0.000
34	A	113	ALA	0	0.037	0.021	28.322	-0.001	-0.001	0.000	0.000	0.000
35	A	114	ILE	0	0.002	-0.010	30.185	0.002	0.002	0.000	0.000	0.000
36	A	115	LYS	1	0.895	0.937	33.701	0.055	0.055	0.000	0.000	0.000
37	A	116	GLU	-1	-0.966	-0.962	29.563	-0.098	-0.098	0.000	0.000	0.000
38	A	117	LEU	0	-0.039	-0.025	31.766	0.001	0.001	0.000	0.000	0.000
39	A	118	ASN	0	-0.052	-0.014	34.576	0.005	0.005	0.000	0.000	0.000
40	A	119	GLU	-1	-0.903	-0.955	37.141	-0.051	-0.051	0.000	0.000	0.000
41	A	120	LYS	1	0.891	0.934	39.088	0.040	0.040	0.000	0.000	0.000
42	A	121	LYS	1	0.884	0.956	39.944	0.038	0.038	0.000	0.000	0.000
43	A	122	VAL	0	-0.005	0.008	34.310	-0.002	-0.002	0.000	0.000	0.000
44	A	123	ARG	1	0.867	0.938	32.651	0.052	0.052	0.000	0.000	0.000
45	A	124	VAL	0	-0.023	-0.017	29.547	-0.005	-0.005	0.000	0.000	0.000
46	A	125	MET	0	0.018	0.022	26.867	0.006	0.006	0.000	0.000	0.000
47	A	126	SER	0	-0.001	-0.040	24.818	-0.005	-0.005	0.000	0.000	0.000
48	A	127	ASN	0	0.025	0.041	21.845	0.009	0.009	0.000	0.000	0.000
49	A	128	GLU	-1	-0.901	-0.974	24.881	-0.006	-0.006	0.000	0.000	0.000
50	A	129	LYS	1	0.942	0.979	26.305	0.003	0.003	0.000	0.000	0.000
51	A	130	THR	0	-0.001	0.002	25.380	0.000	0.000	0.000	0.000	0.000
52	A	131	LEU	0	-0.002	0.006	28.111	0.000	0.000	0.000	0.000	0.000
53	A	132	GLY	0	0.024	0.017	30.697	0.001	0.001	0.000	0.000	0.000
54	A	133	LEU	0	-0.020	-0.017	29.185	0.002	0.002	0.000	0.000	0.000
55	A	134	ILE	0	-0.005	-0.003	30.062	0.000	0.000	0.000	0.000	0.000
56	A	135	ALA	0	-0.024	-0.014	33.799	0.001	0.001	0.000	0.000	0.000
57	A	136	SER	0	-0.052	-0.021	36.066	0.002	0.002	0.000	0.000	0.000
58	A	137	ARG	1	0.822	0.921	34.154	0.017	0.017	0.000	0.000	0.000
59	A	138	ILE	0	0.049	0.030	37.657	-0.002	-0.002	0.000	0.000	0.000
60	A	139	GLU	-1	-0.873	-0.960	38.915	-0.022	-0.022	0.000	0.000	0.000
61	A	140	GLU	-1	-0.839	-0.913	36.778	-0.023	-0.023	0.000	0.000	0.000
62	A	141	ILE	0	-0.021	-0.012	34.304	-0.002	-0.002	0.000	0.000	0.000
63	A	142	LYS	1	0.879	0.939	37.782	0.022	0.022	0.000	0.000	0.000
64	A	143	SER	0	-0.036	-0.011	41.022	0.000	0.000	0.000	0.000	0.000
65	A	144	GLU	-1	-0.909	-0.957	36.635	-0.034	-0.034	0.000	0.000	0.000
66	A	145	LEU	0	-0.097	-0.061	36.002	-0.004	-0.004	0.000	0.000	0.000
67	A	146	GLY	0	0.046	0.031	39.875	0.000	0.000	0.000	0.000	0.000
68	A	147	ASP	-1	-0.920	-0.965	42.412	-0.034	-0.034	0.000	0.000	0.000
69	A	148	VAL	0	-0.081	-0.023	37.232	0.000	0.000	0.000	0.000	0.000
70	A	149	SER	0	-0.045	-0.018	40.590	0.003	0.003	0.000	0.000	0.000
71	A	150	ILE	0	-0.011	-0.016	34.856	-0.002	-0.002	0.000	0.000	0.000
72	A	151	GLU	-1	-0.953	-0.960	36.710	-0.030	-0.030	0.000	0.000	0.000
73	A	152	LEU	0	-0.038	-0.030	32.973	-0.004	-0.004	0.000	0.000	0.000
74	A	153	GLY	0	0.060	0.018	31.893	0.001	0.001	0.000	0.000	0.000
75	A	154	GLU	-1	-0.967	-0.975	28.496	-0.049	-0.049	0.000	0.000	0.000
76	A	155	THR	0	-0.023	-0.025	26.926	-0.004	-0.004	0.000	0.000	0.000
77	A	156	VAL	0	-0.024	-0.015	22.672	-0.002	-0.002	0.000	0.000	0.000
78	A	157	ASP	-1	-0.974	-0.989	17.504	-0.058	-0.058	0.000	0.000	0.000
79	A	158	THR	0	-0.028	-0.025	18.447	-0.013	-0.013	0.000	0.000	0.000
80	A	159	MET	0	-0.025	-0.017	13.366	0.025	0.025	0.000	0.000	0.000
81	A	160	GLY	0	-0.009	-0.023	18.491	0.017	0.017	0.000	0.000	0.000
82	A	161	GLY	0	0.025	0.040	20.905	-0.018	-0.018	0.000	0.000	0.000
83	A	162	VAL	0	-0.045	-0.017	23.345	0.010	0.010	0.000	0.000	0.000
84	A	163	ILE	0	-0.001	0.014	22.636	-0.011	-0.011	0.000	0.000	0.000
85	A	164	VAL	0	0.011	0.005	26.190	0.010	0.010	0.000	0.000	0.000
86	A	165	GLU	-1	-0.851	-0.923	29.718	-0.075	-0.075	0.000	0.000	0.000
87	A	166	THR	0	0.009	-0.007	31.791	0.004	0.004	0.000	0.000	0.000
88	A	167	GLU	-1	-0.853	-0.936	35.143	-0.038	-0.038	0.000	0.000	0.000
89	A	168	ASP	-1	-0.867	-0.935	37.398	-0.054	-0.054	0.000	0.000	0.000
90	A	169	GLY	0	0.039	0.030	33.576	0.000	0.000	0.000	0.000	0.000
91	A	170	ARG	1	0.776	0.907	32.892	0.054	0.054	0.000	0.000	0.000
92	A	171	ILE	0	-0.021	-0.014	31.297	-0.005	-0.005	0.000	0.000	0.000
93	A	172	ARG	1	1.008	0.998	23.572	0.112	0.112	0.000	0.000	0.000
94	A	173	ILE	0	-0.016	-0.003	26.515	-0.008	-0.008	0.000	0.000	0.000
95	A	174	ASP	-1	-0.849	-0.916	20.805	-0.151	-0.151	0.000	0.000	0.000
96	A	175	ASN	0	-0.009	-0.035	22.677	-0.027	-0.027	0.000	0.000	0.000
97	A	176	THR	0	-0.001	-0.001	19.444	0.004	0.004	0.000	0.000	0.000
98	A	177	PHE	0	-0.005	-0.017	17.362	-0.013	-0.013	0.000	0.000	0.000
99	A	178	GLU	-1	-0.762	-0.865	14.343	-0.162	-0.162	0.000	0.000	0.000
100	A	179	ALA	0	0.056	0.039	15.029	-0.051	-0.051	0.000	0.000	0.000
101	A	180	ARG	1	0.821	0.899	17.610	0.110	0.110	0.000	0.000	0.000
102	A	181	MET	0	-0.017	-0.002	12.583	-0.003	-0.003	0.000	0.000	0.000
103	A	182	GLU	-1	-0.957	-0.982	13.065	-0.472	-0.472	0.000	0.000	0.000
104	A	183	ARG	1	0.854	0.932	14.820	0.172	0.172	0.000	0.000	0.000
105	A	184	PHE	0	-0.022	0.002	17.162	0.022	0.022	0.000	0.000	0.000
106	A	185	GLU	-1	-0.902	-0.945	11.859	-0.560	-0.560	0.000	0.000	0.000
107	A	186	GLY	0	0.052	0.009	14.506	-0.008	-0.008	0.000	0.000	0.000
108	A	187	GLU	-1	-0.938	-0.971	17.100	-0.146	-0.146	0.000	0.000	0.000
109	A	188	ILE	0	0.002	0.003	11.498	0.025	0.025	0.000	0.000	0.000
110	A	189	ARG	1	0.925	0.953	9.158	0.798	0.798	0.000	0.000	0.000
111	A	190	SER	0	-0.002	0.004	14.852	0.039	0.039	0.000	0.000	0.000
112	A	191	THR	0	-0.048	-0.020	16.098	0.037	0.037	0.000	0.000	0.000
113	A	192	ILE	0	-0.012	-0.007	11.138	0.021	0.021	0.000	0.000	0.000
114	A	193	ALA	0	0.002	-0.004	15.394	0.023	0.023	0.000	0.000	0.000
115	A	194	LYS	1	0.977	0.993	18.321	0.130	0.130	0.000	0.000	0.000
116	A	195	VAL	0	-0.067	-0.025	16.431	0.017	0.017	0.000	0.000	0.000
117	A	196	LEU	0	-0.085	-0.037	15.003	0.014	0.014	0.000	0.000	0.000
118	A	197	PHE	0	-0.088	-0.054	18.680	0.011	0.011	0.000	0.000	0.000
119	A	198	GLY	-1	-0.935	-0.940	22.390	-0.079	-0.079	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:80:ACE )