FMO DATABASE

FMODB ID: VQN11

Calculation Name: 2D2A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D2A

Chain ID: A

ChEMBL ID:

UniProt ID: P77667

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	114
LigandResidueName
LigandFragmentNumber	0
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-832071.138696
FMO2-HF: Nuclear repulsion	788219.184674
FMO2-HF: Total energy	-43851.954023
FMO2-MP2: Total energy	-43978.788144

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:9:ASN)

Summations of interaction energy for fragment #1(A:9:ASN)

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.
-1.577	1.594	0.082	-1.38	-1.872	-0.003

Interaction energy analysis for fragmet #1(A:9:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.031

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	11	GLN	0	0.003	-0.027	4.103	-2.717	-0.491	-0.007	-1.133	-1.085	-0.004
4	A	12	ASP	-1	-0.866	-0.911	5.870	2.418	2.418	0.000	0.000	0.000	0.000
5	A	13	PHE	0	-0.050	-0.045	3.397	-0.231	0.630	0.090	-0.244	-0.707	0.001
6	A	14	ALA	0	-0.081	-0.026	8.510	-0.338	-0.338	0.000	0.000	0.000	0.000
7	A	15	TRP	0	-0.008	0.013	5.131	-0.173	-0.173	0.000	0.000	0.000	0.000
8	A	16	GLN	0	-0.074	-0.019	11.771	0.011	0.011	0.000	0.000	0.000	0.000
9	A	17	GLY	0	0.000	-0.013	14.069	0.041	0.041	0.000	0.000	0.000	0.000
10	A	18	LEU	0	-0.076	-0.040	13.955	-0.089	-0.089	0.000	0.000	0.000	0.000
11	A	19	THR	0	0.013	-0.010	17.627	0.037	0.037	0.000	0.000	0.000	0.000
12	A	20	LEU	0	0.039	0.046	21.291	-0.028	-0.028	0.000	0.000	0.000	0.000
13	A	21	THR	0	0.009	0.002	24.412	0.025	0.025	0.000	0.000	0.000	0.000
14	A	22	PRO	0	0.071	0.012	27.298	0.003	0.003	0.000	0.000	0.000	0.000
15	A	23	ALA	0	0.031	0.030	30.624	0.007	0.007	0.000	0.000	0.000	0.000
16	A	24	ALA	0	-0.010	-0.005	26.716	0.002	0.002	0.000	0.000	0.000	0.000
17	A	25	ALA	0	0.046	0.017	28.367	0.003	0.003	0.000	0.000	0.000	0.000
18	A	26	ILE	0	-0.019	-0.006	29.402	0.011	0.011	0.000	0.000	0.000	0.000
19	A	27	HIS	1	0.901	0.947	30.592	0.146	0.146	0.000	0.000	0.000	0.000
20	A	28	ILE	0	0.001	0.022	25.493	0.001	0.001	0.000	0.000	0.000	0.000
21	A	29	ARG	1	0.915	0.940	30.216	0.046	0.046	0.000	0.000	0.000	0.000
22	A	30	GLU	-1	-0.941	-0.964	32.953	-0.081	-0.081	0.000	0.000	0.000	0.000
23	A	31	LEU	0	-0.114	-0.068	30.469	0.002	0.002	0.000	0.000	0.000	0.000
24	A	32	VAL	0	0.048	0.008	30.752	0.003	0.003	0.000	0.000	0.000	0.000
25	A	33	ALA	0	-0.043	0.028	33.434	0.007	0.007	0.000	0.000	0.000	0.000
26	A	34	LYS	1	0.844	0.906	36.859	0.100	0.100	0.000	0.000	0.000	0.000
27	A	35	GLN	0	-0.004	-0.005	34.241	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	36	PRO	0	0.084	0.067	34.682	0.003	0.003	0.000	0.000	0.000	0.000
29	A	37	GLY	0	-0.040	-0.046	33.814	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	38	MET	0	-0.058	-0.004	28.880	0.000	0.000	0.000	0.000	0.000	0.000
31	A	39	VAL	0	-0.025	-0.009	26.496	0.010	0.010	0.000	0.000	0.000	0.000
32	A	40	GLY	0	-0.028	-0.021	26.117	0.012	0.012	0.000	0.000	0.000	0.000
33	A	41	VAL	0	0.010	0.024	23.169	-0.007	-0.007	0.000	0.000	0.000	0.000
34	A	42	ARG	1	0.854	0.898	17.408	0.254	0.254	0.000	0.000	0.000	0.000
35	A	43	LEU	0	-0.013	-0.001	16.973	-0.020	-0.020	0.000	0.000	0.000	0.000
36	A	44	GLY	0	0.024	0.021	16.002	-0.011	-0.011	0.000	0.000	0.000	0.000
37	A	45	VAL	0	-0.041	-0.038	12.425	0.021	0.021	0.000	0.000	0.000	0.000
38	A	46	LYS	1	0.921	0.992	15.589	0.544	0.544	0.000	0.000	0.000	0.000
39	A	47	GLN	0	0.076	0.027	13.226	0.092	0.092	0.000	0.000	0.000	0.000
40	A	48	THR	0	-0.057	-0.035	16.779	0.140	0.140	0.000	0.000	0.000	0.000
41	A	49	GLY	0	0.059	0.031	18.680	-0.069	-0.069	0.000	0.000	0.000	0.000
42	A	50	CYS	0	-0.029	-0.006	19.185	0.016	0.016	0.000	0.000	0.000	0.000
43	A	51	ALA	0	-0.004	-0.009	13.631	-0.018	-0.018	0.000	0.000	0.000	0.000
44	A	52	GLY	0	0.011	0.002	14.074	-0.166	-0.166	0.000	0.000	0.000	0.000
45	A	53	PHE	0	0.006	-0.018	11.065	-0.134	-0.134	0.000	0.000	0.000	0.000
46	A	54	GLY	0	-0.058	0.005	15.897	0.069	0.069	0.000	0.000	0.000	0.000
47	A	55	TYR	0	0.073	0.026	15.954	-0.079	-0.079	0.000	0.000	0.000	0.000
48	A	56	VAL	0	-0.036	-0.040	19.139	0.035	0.035	0.000	0.000	0.000	0.000
49	A	57	LEU	0	0.024	0.022	20.458	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	58	ASP	-1	-0.895	-0.941	22.814	-0.237	-0.237	0.000	0.000	0.000	0.000
51	A	59	SER	0	0.020	0.010	24.490	0.020	0.020	0.000	0.000	0.000	0.000
52	A	60	VAL	0	-0.030	0.002	23.119	-0.013	-0.013	0.000	0.000	0.000	0.000
53	A	61	SER	0	-0.016	-0.038	26.085	0.008	0.008	0.000	0.000	0.000	0.000
54	A	62	GLU	-1	-0.975	-0.981	24.837	-0.012	-0.012	0.000	0.000	0.000	0.000
55	A	63	PRO	0	-0.039	-0.012	21.891	-0.021	-0.021	0.000	0.000	0.000	0.000
56	A	64	ASP	-1	-0.792	-0.882	17.573	0.036	0.036	0.000	0.000	0.000	0.000
57	A	65	LYS	1	0.787	0.860	17.871	-0.040	-0.040	0.000	0.000	0.000	0.000
58	A	66	ASP	-1	-0.842	-0.926	13.530	-0.009	-0.009	0.000	0.000	0.000	0.000
59	A	67	ASP	-1	-0.792	-0.877	14.507	-0.117	-0.117	0.000	0.000	0.000	0.000
60	A	68	LEU	0	-0.038	-0.012	12.357	0.083	0.083	0.000	0.000	0.000	0.000
61	A	69	LEU	0	0.000	-0.011	16.798	-0.078	-0.078	0.000	0.000	0.000	0.000
62	A	70	PHE	0	0.016	0.008	14.849	0.035	0.035	0.000	0.000	0.000	0.000
63	A	71	GLU	-1	-0.965	-1.007	20.883	0.021	0.021	0.000	0.000	0.000	0.000
64	A	72	HIS	0	0.020	0.032	24.589	0.013	0.013	0.000	0.000	0.000	0.000
65	A	73	ASP	-1	-0.915	-0.956	26.774	-0.051	-0.051	0.000	0.000	0.000	0.000
66	A	74	GLY	0	-0.021	-0.019	29.563	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	75	ALA	0	-0.057	-0.025	27.925	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	76	LYS	1	0.968	0.966	24.518	-0.031	-0.031	0.000	0.000	0.000	0.000
69	A	77	LEU	0	0.027	0.042	19.322	-0.022	-0.022	0.000	0.000	0.000	0.000
70	A	78	PHE	0	-0.023	-0.020	19.524	0.030	0.030	0.000	0.000	0.000	0.000
71	A	79	VAL	0	0.002	-0.025	13.606	-0.065	-0.065	0.000	0.000	0.000	0.000
72	A	80	PRO	0	0.072	0.041	13.535	0.061	0.061	0.000	0.000	0.000	0.000
73	A	81	LEU	0	0.074	0.046	9.453	-0.153	-0.153	0.000	0.000	0.000	0.000
74	A	82	GLN	0	-0.073	-0.030	6.182	0.468	0.468	0.000	0.000	0.000	0.000
75	A	83	ALA	0	-0.044	-0.048	9.492	-0.480	-0.480	0.000	0.000	0.000	0.000
76	A	84	MET	0	0.005	0.032	8.450	-0.234	-0.234	0.000	0.000	0.000	0.000
77	A	85	PRO	0	-0.039	-0.033	4.603	-0.247	-0.163	-0.001	-0.003	-0.080	0.000
78	A	86	PHE	0	-0.020	0.021	6.444	-0.199	-0.199	0.000	0.000	0.000	0.000
79	A	87	ILE	0	-0.070	-0.040	9.195	0.239	0.239	0.000	0.000	0.000	0.000
80	A	88	ASP	-1	-0.746	-0.886	9.830	0.016	0.016	0.000	0.000	0.000	0.000
81	A	89	GLY	0	-0.013	-0.021	11.722	-0.091	-0.091	0.000	0.000	0.000	0.000
82	A	90	THR	0	-0.087	-0.032	15.062	0.015	0.015	0.000	0.000	0.000	0.000
83	A	91	GLU	-1	-0.954	-0.952	17.164	-0.175	-0.175	0.000	0.000	0.000	0.000
84	A	92	VAL	0	-0.014	-0.032	20.493	-0.033	-0.033	0.000	0.000	0.000	0.000
85	A	93	ASP	-1	-0.735	-0.850	22.726	-0.161	-0.161	0.000	0.000	0.000	0.000
86	A	94	PHE	0	-0.134	-0.103	26.311	-0.013	-0.013	0.000	0.000	0.000	0.000
87	A	95	VAL	0	-0.004	0.029	29.420	0.010	0.010	0.000	0.000	0.000	0.000
88	A	96	ARG	1	0.975	0.955	32.369	0.115	0.115	0.000	0.000	0.000	0.000
89	A	97	GLU	-1	-0.922	-0.959	35.674	-0.127	-0.127	0.000	0.000	0.000	0.000
90	A	98	GLY	0	-0.026	-0.010	38.498	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	99	LEU	0	-0.050	-0.037	39.753	0.002	0.002	0.000	0.000	0.000	0.000
92	A	100	ASN	0	-0.021	0.013	34.168	-0.013	-0.013	0.000	0.000	0.000	0.000
93	A	101	GLN	0	-0.021	-0.031	34.022	0.010	0.010	0.000	0.000	0.000	0.000
94	A	102	ILE	0	-0.049	-0.034	28.161	-0.011	-0.011	0.000	0.000	0.000	0.000
95	A	103	PHE	0	0.092	0.056	25.424	0.016	0.016	0.000	0.000	0.000	0.000
96	A	104	LYS	1	0.944	0.987	25.155	0.260	0.260	0.000	0.000	0.000	0.000
97	A	105	PHE	0	-0.022	-0.038	19.681	0.017	0.017	0.000	0.000	0.000	0.000
98	A	106	HIS	0	0.077	0.072	20.878	-0.046	-0.046	0.000	0.000	0.000	0.000
99	A	107	ASN	0	0.087	0.021	13.150	0.055	0.055	0.000	0.000	0.000	0.000
100	A	108	PRO	0	0.006	0.003	15.210	0.009	0.009	0.000	0.000	0.000	0.000
101	A	109	LYS	1	0.916	0.963	9.542	0.942	0.942	0.000	0.000	0.000	0.000
102	A	110	ALA	0	-0.001	-0.003	15.201	-0.060	-0.060	0.000	0.000	0.000	0.000
103	A	111	GLN	0	-0.015	0.013	17.271	-0.011	-0.011	0.000	0.000	0.000	0.000
104	A	112	ASN	0	-0.080	-0.071	18.840	-0.083	-0.083	0.000	0.000	0.000	0.000
105	A	113	GLU	-1	-0.873	-0.911	22.184	-0.461	-0.461	0.000	0.000	0.000	0.000
106	A	114	CYS	0	0.031	0.104	23.211	0.015	0.015	0.000	0.000	0.000	0.000
107	A	115	GLY	0	-0.080	-0.114	25.057	0.031	0.031	0.000	0.000	0.000	0.000
108	A	116	CYM	-1	-0.879	-0.931	27.516	-0.387	-0.387	0.000	0.000	0.000	0.000
109	A	117	GLY	0	-0.071	-0.029	29.140	-0.005	-0.005	0.000	0.000	0.000	0.000
110	A	118	GLU	-1	-1.001	-1.038	30.444	-0.310	-0.310	0.000	0.000	0.000	0.000
111	A	119	SER	0	-0.048	-0.022	29.536	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	120	PHE	0	-0.007	-0.016	31.707	0.008	0.008	0.000	0.000	0.000	0.000
113	A	121	GLY	0	0.035	0.049	32.189	0.002	0.002	0.000	0.000	0.000	0.000
114	A	122	VAL	0	0.012	-0.003	33.018	0.017	0.017	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:9:ASN)