FMO DATABASE

FMODB ID: 2N51R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-860135.550899
FMO2-HF: Nuclear repulsion	818323.306292
FMO2-HF: Total energy	-41812.244606
FMO2-MP2: Total energy	-41936.137674

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.
-5.989	-1.165	9.251	-4.309	-9.763	-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 : 0.019 / q_NPA : 0.003

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	0.005	0.016	2.596	-0.525	1.704	0.460	-0.873	-1.816	0.001
4	A	4	VAL	0	-0.017	-0.007	4.789	-0.032	0.022	-0.001	-0.010	-0.042	0.000
5	A	5	VAL	0	0.010	-0.013	8.495	0.105	0.105	0.000	0.000	0.000	0.000
6	A	6	GLN	0	0.000	0.005	10.493	0.079	0.079	0.000	0.000	0.000	0.000
7	A	7	ILE	0	-0.010	-0.002	14.103	-0.035	-0.035	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.941	0.966	17.080	0.125	0.125	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.891	-0.944	20.524	-0.127	-0.127	0.000	0.000	0.000	0.000
10	A	10	PHE	0	0.015	-0.019	22.423	-0.027	-0.027	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.857	-0.930	24.504	-0.192	-0.192	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.908	0.953	20.996	0.171	0.171	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.018	0.013	19.977	-0.045	-0.045	0.000	0.000	0.000	0.000
14	A	14	PRO	0	0.045	0.025	19.652	-0.055	-0.055	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.031	-0.035	19.374	-0.056	-0.056	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.019	0.026	16.231	-0.062	-0.062	0.000	0.000	0.000	0.000
17	A	17	LEU	0	0.052	0.009	14.979	-0.106	-0.106	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.958	0.992	15.378	0.413	0.413	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.026	-0.013	12.916	-0.078	-0.078	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.009	0.010	10.637	-0.175	-0.175	0.000	0.000	0.000	0.000
21	A	21	ILE	0	-0.007	0.002	10.672	-0.247	-0.247	0.000	0.000	0.000	0.000
22	A	22	ASN	0	-0.041	-0.034	11.909	-0.096	-0.096	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.016	0.015	4.844	-0.042	-0.042	0.000	0.000	0.000	0.000
24	A	24	TYR	0	-0.020	-0.023	7.234	-0.443	-0.443	0.000	0.000	0.000	0.000
25	A	25	ASN	0	-0.051	-0.043	8.368	-0.141	-0.141	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.969	-0.963	7.761	-1.913	-1.913	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.028	0.000	2.159	-1.851	-1.314	3.164	-0.799	-2.902	-0.006
28	A	28	LYS	1	0.937	0.961	5.199	1.117	1.172	-0.001	-0.004	-0.050	0.000
29	A	29	ASP	-1	-0.927	-0.974	4.401	-3.011	-2.729	-0.001	-0.028	-0.253	0.000
30	A	30	ALA	0	-0.012	0.010	2.432	-4.601	-2.128	0.820	-1.634	-1.659	-0.010
31	A	31	GLU	-1	-0.896	-0.944	3.102	3.481	4.547	0.021	-0.169	-0.917	-0.001
32	A	32	ILE	0	-0.006	-0.012	4.707	0.151	0.155	-0.001	-0.018	0.015	0.000
33	A	33	GLH	0	-0.044	-0.066	7.551	0.416	0.416	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.024	-0.014	10.326	0.007	0.007	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.008	0.002	12.676	0.076	0.076	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.009	-0.008	15.371	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	37	HIS	0	0.027	0.008	18.342	0.034	0.034	0.000	0.000	0.000	0.000
38	A	38	GLN	0	-0.008	-0.014	21.288	-0.029	-0.029	0.000	0.000	0.000	0.000
39	A	39	SER	0	0.046	0.017	24.437	-0.012	-0.012	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.017	0.012	20.802	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	41	ILE	0	-0.006	0.013	22.565	-0.023	-0.023	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.959	0.981	23.646	0.120	0.120	0.000	0.000	0.000	0.000
43	A	43	ALA	0	-0.021	0.004	22.010	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.006	-0.005	19.785	-0.021	-0.021	0.000	0.000	0.000	0.000
45	A	45	LEU	0	0.031	0.026	23.819	0.012	0.012	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.865	0.923	27.205	0.098	0.098	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.914	-0.954	29.140	-0.152	-0.152	0.000	0.000	0.000	0.000
48	A	48	SER	0	-0.031	0.000	24.823	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	49	ASP	-1	-0.843	-0.924	27.758	-0.209	-0.209	0.000	0.000	0.000	0.000
50	A	50	THR	0	-0.097	-0.058	22.145	-0.023	-0.023	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.866	0.937	22.689	0.173	0.173	0.000	0.000	0.000	0.000
52	A	52	SER	0	0.049	0.021	22.940	-0.015	-0.015	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.017	-0.006	18.548	-0.031	-0.031	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.015	0.004	18.569	-0.065	-0.065	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.863	-0.948	18.457	-0.308	-0.308	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.878	-0.927	17.470	-0.677	-0.677	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.014	-0.014	13.385	-0.072	-0.072	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.003	0.007	14.196	-0.068	-0.068	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.918	0.970	15.564	0.390	0.390	0.000	0.000	0.000	0.000
60	A	60	LYS	1	0.783	0.895	12.238	0.854	0.854	0.000	0.000	0.000	0.000
61	A	61	ASN	0	-0.033	-0.018	9.637	-0.069	-0.069	0.000	0.000	0.000	0.000
62	A	62	ILE	0	-0.005	0.020	9.876	-0.060	-0.060	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.026	-0.008	11.185	0.173	0.173	0.000	0.000	0.000	0.000
64	A	64	ILE	0	0.004	0.007	13.169	-0.036	-0.036	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.008	-0.018	15.470	0.069	0.069	0.000	0.000	0.000	0.000
66	A	66	GLY	0	0.047	0.020	17.461	-0.020	-0.020	0.000	0.000	0.000	0.000
67	A	67	CYM	-1	-0.905	-0.849	20.600	0.018	0.018	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.764	-0.884	22.148	-0.019	-0.019	0.000	0.000	0.000	0.000
69	A	69	ASN	0	0.018	-0.006	25.013	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	70	SER	0	0.027	-0.056	23.955	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	71	ILE	0	0.001	0.005	24.840	-0.008	-0.008	0.000	0.000	0.000	0.000
72	A	72	ARG	1	0.858	0.918	27.678	-0.015	-0.015	0.000	0.000	0.000	0.000
73	A	73	SER	0	-0.050	-0.014	28.718	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	74	GLN	0	-0.047	-0.023	28.001	-0.008	-0.008	0.000	0.000	0.000	0.000
75	A	75	ASN	0	-0.047	-0.014	31.072	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	76	LEU	0	0.003	0.009	27.867	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	77	SER	0	0.012	0.000	31.680	0.010	0.010	0.000	0.000	0.000	0.000
78	A	78	HIS	0	0.057	0.009	28.165	-0.022	-0.022	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.917	-0.941	29.363	-0.068	-0.068	0.000	0.000	0.000	0.000
80	A	80	GLN	0	-0.029	-0.043	30.990	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	81	LEU	0	0.006	0.024	25.209	-0.014	-0.014	0.000	0.000	0.000	0.000
82	A	82	ILE	0	-0.015	-0.007	23.217	0.008	0.008	0.000	0.000	0.000	0.000
83	A	83	PRO	0	-0.006	-0.018	24.491	0.006	0.006	0.000	0.000	0.000	0.000
84	A	84	GLY	0	0.017	0.011	21.641	-0.021	-0.021	0.000	0.000	0.000	0.000
85	A	85	ILE	0	-0.010	0.009	19.915	-0.026	-0.026	0.000	0.000	0.000	0.000
86	A	86	LYS	1	0.904	0.963	17.435	0.207	0.207	0.000	0.000	0.000	0.000
87	A	87	ILE	0	0.036	0.023	20.297	-0.021	-0.021	0.000	0.000	0.000	0.000
88	A	88	VAL	0	-0.002	0.014	18.014	0.028	0.028	0.000	0.000	0.000	0.000
89	A	89	THR	0	0.003	-0.017	21.391	-0.011	-0.011	0.000	0.000	0.000	0.000
90	A	90	SER	0	0.031	0.004	22.090	-0.012	-0.012	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.067	-0.002	18.968	0.016	0.016	0.000	0.000	0.000	0.000
92	A	92	VAL	0	0.007	-0.004	17.661	0.009	0.009	0.000	0.000	0.000	0.000
93	A	93	GLY	0	0.010	0.002	18.218	0.039	0.039	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.820	-0.868	14.695	0.217	0.217	0.000	0.000	0.000	0.000
95	A	95	ILE	0	-0.015	-0.008	13.265	0.061	0.061	0.000	0.000	0.000	0.000
96	A	96	VAL	0	-0.015	-0.007	13.434	0.086	0.086	0.000	0.000	0.000	0.000
97	A	97	ARG	1	0.975	0.985	15.009	-0.181	-0.181	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.908	0.979	10.514	-0.428	-0.428	0.000	0.000	0.000	0.000
99	A	99	GLN	0	-0.011	-0.007	10.429	0.274	0.274	0.000	0.000	0.000	0.000
100	A	100	SER	0	-0.106	-0.052	11.501	0.175	0.175	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.904	-0.955	11.400	0.752	0.752	0.000	0.000	0.000	0.000
102	A	102	GLY	0	-0.030	-0.011	8.666	0.224	0.224	0.000	0.000	0.000	0.000
103	A	103	TRP	0	-0.082	-0.039	6.379	0.732	0.732	0.000	0.000	0.000	0.000
104	A	104	ILE	0	0.042	0.002	2.803	0.524	-1.352	4.790	-0.774	-2.139	0.002
105	A	105	TYR	0	-0.028	-0.030	6.196	-0.764	-0.764	0.000	0.000	0.000	0.000
106	A	106	LEU	0	0.017	0.022	8.134	0.020	0.020	0.000	0.000	0.000	0.000
107	A	107	ALA	0	-0.021	-0.007	9.960	-0.048	-0.048	0.000	0.000	0.000	0.000
108	A	108	LEU	0	-0.032	-0.018	11.970	-0.002	-0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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