FMO DATABASE

FMODB ID: M3K4Z

Calculation Name: 2FDQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FDQ

Chain ID: A

ChEMBL ID:

UniProt ID: P82934

Base Structure: X-ray

Registration Date: 2023-06-21

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	86
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-596040.801023
FMO2-HF: Nuclear repulsion	561243.955885
FMO2-HF: Total energy	-34796.845137
FMO2-MP2: Total energy	-34898.418318

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:1:SER)

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

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.
-15.545	-8.59	2.115	-4.321	-4.746	-0.034

Interaction energy analysis for fragmet #1(A:1:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.072 / q_NPA : 0.028

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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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	3	ALA	0	0.045	0.031	3.819	-3.247	-2.105	0.004	-0.463	-0.683	0.001
4	A	4	GLU	-1	-0.878	-0.944	2.570	-5.927	-2.599	2.066	-2.713	-2.680	-0.028
5	A	5	PHE	0	0.011	-0.002	4.425	0.267	0.522	-0.001	-0.084	-0.170	0.000
6	A	6	ASP	-1	-0.883	-0.967	5.923	0.943	0.943	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.870	0.948	7.469	0.529	0.529	0.000	0.000	0.000	0.000
8	A	8	ALA	0	0.088	0.037	7.776	0.157	0.157	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.016	-0.001	9.706	0.173	0.173	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.913	-0.978	11.780	-0.079	-0.079	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.946	-0.967	11.199	-0.592	-0.592	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.008	-0.014	13.439	0.079	0.079	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.831	0.931	15.240	0.202	0.202	0.000	0.000	0.000	0.000
14	A	14	ASN	0	-0.060	-0.018	17.776	0.057	0.057	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.050	-0.038	17.077	0.013	0.013	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.891	0.954	20.110	0.206	0.206	0.000	0.000	0.000	0.000
17	A	17	THR	0	-0.003	0.009	23.245	0.023	0.023	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.904	0.953	23.342	0.172	0.172	0.000	0.000	0.000	0.000
19	A	19	PRO	0	0.011	0.017	20.676	0.012	0.012	0.000	0.000	0.000	0.000
20	A	20	ALA	0	-0.002	-0.008	23.025	0.026	0.026	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.902	-0.975	22.928	-0.268	-0.268	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.833	-0.928	22.147	-0.335	-0.335	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.705	-0.796	19.245	-0.403	-0.403	0.000	0.000	0.000	0.000
24	A	24	MET	0	-0.042	0.000	18.311	-0.045	-0.045	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.013	-0.018	18.636	-0.037	-0.037	0.000	0.000	0.000	0.000
26	A	26	PHE	0	0.089	0.031	12.711	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	27	ILE	0	0.070	0.062	13.568	-0.078	-0.078	0.000	0.000	0.000	0.000
28	A	28	TYR	0	-0.032	-0.024	14.256	-0.043	-0.043	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.059	-0.037	15.393	-0.056	-0.056	0.000	0.000	0.000	0.000
30	A	30	HIS	1	0.892	0.930	11.179	0.871	0.871	0.000	0.000	0.000	0.000
31	A	31	TYR	0	0.068	0.046	11.217	-0.064	-0.064	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.893	0.955	11.809	0.258	0.258	0.000	0.000	0.000	0.000
33	A	33	GLN	0	0.011	0.009	11.994	0.107	0.107	0.000	0.000	0.000	0.000
34	A	34	ALA	0	-0.039	-0.037	7.817	-0.016	-0.016	0.000	0.000	0.000	0.000
35	A	35	THR	0	-0.074	-0.028	8.697	0.136	0.136	0.000	0.000	0.000	0.000
36	A	36	VAL	0	-0.111	-0.038	11.154	0.135	0.135	0.000	0.000	0.000	0.000
37	A	37	GLY	0	-0.004	-0.002	13.387	0.062	0.062	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.810	-0.903	14.294	-0.399	-0.399	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.054	-0.030	17.135	0.046	0.046	0.000	0.000	0.000	0.000
40	A	40	ASN	0	0.008	0.000	19.795	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	41	THR	0	-0.017	-0.010	22.016	0.017	0.017	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.881	-0.940	24.667	-0.103	-0.103	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.763	0.871	27.545	0.159	0.159	0.000	0.000	0.000	0.000
44	A	44	PRO	0	-0.009	0.004	27.219	0.011	0.011	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.042	0.010	30.258	0.000	0.000	0.000	0.000	0.000	0.000
46	A	46	MET	0	-0.017	-0.017	33.962	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	47	LEU	0	-0.001	-0.005	36.171	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.857	-0.928	30.089	-0.132	-0.132	0.000	0.000	0.000	0.000
49	A	49	PHE	0	0.030	-0.006	30.759	-0.009	-0.009	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.999	1.018	26.899	0.136	0.136	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.048	0.027	26.594	-0.018	-0.018	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.899	0.934	26.065	0.106	0.106	0.000	0.000	0.000	0.000
53	A	53	ALA	0	0.004	0.031	26.269	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.920	0.940	22.083	0.220	0.220	0.000	0.000	0.000	0.000
55	A	55	TRP	0	0.008	0.003	21.777	-0.034	-0.034	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.738	-0.850	22.593	-0.216	-0.216	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.026	0.013	20.294	-0.018	-0.018	0.000	0.000	0.000	0.000
58	A	58	TRP	0	-0.013	-0.004	16.052	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.003	0.001	18.867	-0.011	-0.011	0.000	0.000	0.000	0.000
60	A	60	GLN	0	-0.133	-0.073	20.939	0.023	0.023	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.070	-0.036	14.246	-0.042	-0.042	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.970	0.987	16.300	0.187	0.187	0.000	0.000	0.000	0.000
63	A	63	GLY	0	-0.060	-0.024	17.129	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	64	THR	0	-0.021	-0.010	11.442	-0.043	-0.043	0.000	0.000	0.000	0.000
65	A	65	SER	0	0.028	0.029	8.920	-0.040	-0.040	0.000	0.000	0.000	0.000
66	A	66	LYS	1	1.035	0.986	7.661	-0.129	-0.129	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.842	-0.929	3.405	-9.365	-7.645	0.025	-0.957	-0.788	-0.007
68	A	68	ASP	-1	-0.898	-0.932	5.522	-2.315	-2.315	0.000	0.000	0.000	0.000
69	A	69	ALA	0	-0.070	-0.027	8.062	-0.094	-0.094	0.000	0.000	0.000	0.000
70	A	70	MET	0	-0.010	-0.007	4.119	-0.079	0.198	0.019	-0.071	-0.224	0.000
71	A	71	LYS	1	0.970	1.010	4.692	1.871	1.959	-0.001	-0.005	-0.081	0.000
72	A	72	SER	0	-0.074	-0.040	5.500	0.665	0.665	0.000	0.000	0.000	0.000
73	A	73	TYR	0	-0.030	-0.005	7.568	0.368	0.368	0.000	0.000	0.000	0.000
74	A	74	ILE	0	0.045	0.009	3.671	0.250	0.395	0.003	-0.028	-0.120	0.000
75	A	75	ASP	-1	-0.839	-0.907	7.767	-1.389	-1.389	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.888	0.951	9.714	0.856	0.856	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.015	0.021	9.877	0.167	0.167	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.842	-0.948	9.992	-0.656	-0.656	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-1.025	-1.008	12.782	-0.435	-0.435	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.026	-0.035	15.320	0.089	0.089	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.798	0.917	12.571	0.642	0.642	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.862	0.936	15.723	0.522	0.522	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.835	0.914	19.271	0.370	0.370	0.000	0.000	0.000	0.000
84	A	84	TYR	0	-0.048	-0.062	20.495	0.032	0.032	0.000	0.000	0.000	0.000
85	A	85	GLY	0	0.034	0.029	20.676	0.031	0.031	0.000	0.000	0.000	0.000
86	A	86	ILE	0	-0.024	-0.015	17.313	0.013	0.013	0.000	0.000	0.000	0.000

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