FMO DATABASE

FMODB ID: 6YRQZ

Calculation Name: 2PD2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2PD2

Chain ID: A

ChEMBL ID:

UniProt ID: Q976P3

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:

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	108
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-861410.678412
FMO2-HF: Nuclear repulsion	819598.028524
FMO2-HF: Total energy	-41812.649888
FMO2-MP2: Total energy	-41936.54893

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:MET)

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

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.
-5.472	-0.415	8.164	-4.083	-9.137	-0.014

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : 0.000

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	3	VAL	0	-0.007	0.005	2.603	-0.597	1.632	0.410	-0.860	-1.779	0.001
4	A	4	VAL	0	-0.018	-0.006	4.900	-0.065	-0.021	-0.001	-0.008	-0.035	0.000
5	A	5	VAL	0	0.001	-0.016	8.524	0.094	0.094	0.000	0.000	0.000	0.000
6	A	6	GLN	0	0.028	0.030	10.563	0.059	0.059	0.000	0.000	0.000	0.000
7	A	7	ILE	0	-0.005	-0.004	14.173	-0.036	-0.036	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.927	0.961	17.135	0.064	0.064	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.842	-0.906	20.584	-0.083	-0.083	0.000	0.000	0.000	0.000
10	A	10	PHE	0	0.032	-0.010	22.456	-0.025	-0.025	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.843	-0.928	24.531	-0.151	-0.151	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.797	0.889	21.007	0.110	0.110	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.011	0.008	19.970	-0.038	-0.038	0.000	0.000	0.000	0.000
14	A	14	PRO	0	0.048	0.027	19.661	-0.048	-0.048	0.000	0.000	0.000	0.000
15	A	15	GLN	0	0.021	0.003	19.796	-0.061	-0.061	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.021	0.034	16.276	-0.057	-0.057	0.000	0.000	0.000	0.000
17	A	17	LEU	0	0.048	0.009	15.094	-0.091	-0.091	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.917	0.960	15.628	0.351	0.351	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.028	-0.022	13.251	-0.070	-0.070	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.008	0.008	10.615	-0.157	-0.157	0.000	0.000	0.000	0.000
21	A	21	ILE	0	-0.005	0.001	10.903	-0.232	-0.232	0.000	0.000	0.000	0.000
22	A	22	ASN	0	-0.046	-0.035	11.996	-0.095	-0.095	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.021	0.015	5.195	-0.048	-0.048	0.000	0.000	0.000	0.000
24	A	24	TYR	0	-0.014	-0.019	7.398	-0.441	-0.441	0.000	0.000	0.000	0.000
25	A	25	ASN	0	-0.058	-0.045	8.362	-0.155	-0.155	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.972	-0.965	7.780	-1.915	-1.915	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.027	-0.003	2.187	-1.727	-1.198	2.585	-0.683	-2.431	-0.005
28	A	28	LYS	1	0.929	0.963	5.186	1.203	1.257	-0.001	-0.004	-0.049	0.000
29	A	29	ASP	-1	-0.923	-0.978	4.380	-3.124	-2.837	-0.001	-0.031	-0.255	0.000
30	A	30	ALA	0	0.000	0.019	2.460	-4.470	-1.973	0.777	-1.628	-1.646	-0.011
31	A	31	GLU	-1	-0.860	-0.906	3.136	4.054	5.104	0.017	-0.173	-0.895	-0.001
32	A	32	ILE	0	0.001	-0.013	4.763	0.162	0.166	-0.001	-0.018	0.016	0.000
33	A	33	GLH	0	-0.022	-0.025	7.633	0.391	0.391	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.017	-0.011	10.424	0.013	0.013	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.014	-0.003	12.760	0.062	0.062	0.000	0.000	0.000	0.000
36	A	36	LEU	0	0.000	-0.001	15.469	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	37	HIS	0	0.046	-0.001	18.237	0.035	0.035	0.000	0.000	0.000	0.000
38	A	38	GLN	0	-0.004	-0.010	21.377	-0.017	-0.017	0.000	0.000	0.000	0.000
39	A	39	SER	0	0.029	0.014	24.517	-0.011	-0.011	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.038	0.019	20.875	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	41	ILE	0	-0.020	0.009	22.547	-0.021	-0.021	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.922	0.963	23.724	0.074	0.074	0.000	0.000	0.000	0.000
43	A	43	ALA	0	-0.019	0.006	22.077	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.006	-0.001	19.811	-0.020	-0.020	0.000	0.000	0.000	0.000
45	A	45	LEU	0	0.026	0.023	23.888	0.011	0.011	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.837	0.896	27.264	0.068	0.068	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.918	-0.961	29.201	-0.120	-0.120	0.000	0.000	0.000	0.000
48	A	48	SER	0	-0.043	-0.017	24.829	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	49	ASP	-1	-0.860	-0.933	27.616	-0.175	-0.175	0.000	0.000	0.000	0.000
50	A	50	THR	0	-0.079	-0.053	22.218	-0.022	-0.022	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.835	0.916	22.713	0.145	0.145	0.000	0.000	0.000	0.000
52	A	52	SER	0	0.032	0.014	22.966	-0.021	-0.021	0.000	0.000	0.000	0.000
53	A	53	ILE	0	0.004	0.002	18.453	-0.028	-0.028	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.018	0.005	18.584	-0.058	-0.058	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.830	-0.914	18.484	-0.249	-0.249	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.843	-0.900	17.280	-0.632	-0.632	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.007	-0.006	13.242	-0.065	-0.065	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.001	0.001	14.218	-0.057	-0.057	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.920	0.972	15.595	0.348	0.348	0.000	0.000	0.000	0.000
60	A	60	LYS	1	0.760	0.873	12.264	0.778	0.778	0.000	0.000	0.000	0.000
61	A	61	ASN	0	-0.046	-0.025	9.865	-0.079	-0.079	0.000	0.000	0.000	0.000
62	A	62	ILE	0	-0.006	0.018	9.903	-0.033	-0.033	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.031	-0.011	11.238	0.153	0.153	0.000	0.000	0.000	0.000
64	A	64	ILE	0	0.002	0.004	13.226	-0.025	-0.025	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.004	-0.014	15.765	0.059	0.059	0.000	0.000	0.000	0.000
66	A	66	GLY	0	0.046	0.020	17.568	-0.019	-0.019	0.000	0.000	0.000	0.000
67	A	67	CYM	-1	-0.883	-0.819	20.704	0.066	0.066	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.722	-0.848	22.259	0.016	0.016	0.000	0.000	0.000	0.000
69	A	69	ASN	0	0.005	-0.011	25.290	-0.009	-0.009	0.000	0.000	0.000	0.000
70	A	70	SER	0	0.017	-0.071	23.899	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	71	ILE	0	-0.008	-0.001	24.705	-0.010	-0.010	0.000	0.000	0.000	0.000
72	A	72	ARG	1	0.837	0.897	27.778	-0.046	-0.046	0.000	0.000	0.000	0.000
73	A	73	SER	0	-0.037	-0.017	28.890	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	74	GLN	0	-0.057	-0.023	28.139	-0.014	-0.014	0.000	0.000	0.000	0.000
75	A	75	ASN	0	-0.050	-0.020	31.159	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.002	0.009	28.011	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	77	SER	0	0.012	-0.020	31.772	0.012	0.012	0.000	0.000	0.000	0.000
78	A	78	HIS	0	0.032	0.005	28.147	-0.021	-0.021	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.864	-0.904	29.433	-0.039	-0.039	0.000	0.000	0.000	0.000
80	A	80	GLN	0	-0.008	-0.016	31.166	-0.008	-0.008	0.000	0.000	0.000	0.000
81	A	81	LEU	0	0.002	0.023	25.134	-0.013	-0.013	0.000	0.000	0.000	0.000
82	A	82	ILE	0	-0.010	-0.002	23.231	0.005	0.005	0.000	0.000	0.000	0.000
83	A	83	PRO	0	0.004	-0.012	24.542	0.009	0.009	0.000	0.000	0.000	0.000
84	A	84	GLY	0	0.020	0.015	21.693	-0.020	-0.020	0.000	0.000	0.000	0.000
85	A	85	ILE	0	0.011	0.020	19.971	-0.020	-0.020	0.000	0.000	0.000	0.000
86	A	86	LYS	1	0.868	0.942	17.233	0.160	0.160	0.000	0.000	0.000	0.000
87	A	87	ILE	0	0.028	0.017	20.365	-0.018	-0.018	0.000	0.000	0.000	0.000
88	A	88	VAL	0	0.008	0.017	18.178	0.029	0.029	0.000	0.000	0.000	0.000
89	A	89	THR	0	0.014	-0.011	21.522	-0.012	-0.012	0.000	0.000	0.000	0.000
90	A	90	SER	0	0.018	-0.005	22.216	-0.014	-0.014	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.075	-0.004	19.087	0.020	0.020	0.000	0.000	0.000	0.000
92	A	92	VAL	0	0.011	-0.003	17.778	0.017	0.017	0.000	0.000	0.000	0.000
93	A	93	GLY	0	0.014	0.007	18.337	0.040	0.040	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.783	-0.877	14.950	0.322	0.322	0.000	0.000	0.000	0.000
95	A	95	ILE	0	-0.012	-0.007	13.346	0.066	0.066	0.000	0.000	0.000	0.000
96	A	96	VAL	0	-0.011	-0.002	13.555	0.094	0.094	0.000	0.000	0.000	0.000
97	A	97	ARG	1	0.903	0.949	15.136	-0.225	-0.225	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.840	0.931	10.588	-0.535	-0.535	0.000	0.000	0.000	0.000
99	A	99	GLN	0	-0.008	-0.008	10.552	0.253	0.253	0.000	0.000	0.000	0.000
100	A	100	SER	0	-0.101	-0.047	11.624	0.159	0.159	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.862	-0.923	11.363	0.848	0.848	0.000	0.000	0.000	0.000
102	A	102	GLY	0	-0.019	-0.008	8.667	0.208	0.208	0.000	0.000	0.000	0.000
103	A	103	TRP	0	-0.084	-0.043	6.518	0.815	0.815	0.000	0.000	0.000	0.000
104	A	104	ILE	0	0.036	0.002	2.889	0.330	-1.307	4.379	-0.678	-2.063	0.002
105	A	105	TYR	0	-0.018	-0.018	6.282	-0.742	-0.742	0.000	0.000	0.000	0.000
106	A	106	LEU	0	0.020	0.019	8.082	0.015	0.015	0.000	0.000	0.000	0.000
107	A	107	ALA	0	-0.024	-0.009	9.992	-0.056	-0.056	0.000	0.000	0.000	0.000
108	A	108	LEU	0	-0.019	-0.011	11.945	-0.010	-0.010	0.000	0.000	0.000	0.000

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