FMO DATABASE

FMODB ID: N8VMQ

Calculation Name: 2PD2-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2PD2

Chain ID: A

ChEMBL ID:

UniProt ID: Q976P3

Base Structure: X-ray

Registration Date: 2025-10-04

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	108
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-860656.866703
FMO2-HF: Nuclear repulsion	818844.202653
FMO2-HF: Total energy	-41812.66405
FMO2-MP2: Total energy	-41936.496893

3D Structure Molmil

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.
-152.655	-145.961	15.477	-9.56	-12.611	-0.099

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 : 1 / q_Mulliken : 0.828 / q_NPA : 0.906

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	0.004	0.010	2.675	4.163	6.430	0.341	-0.837	-1.772	-0.003
4	A	4	VAL	0	-0.010	0.003	4.931	1.870	1.908	-0.001	-0.007	-0.029	0.000
27	A	27	ILE	0	-0.035	-0.018	2.209	-4.982	-4.470	2.757	-0.788	-2.482	-0.009
28	A	28	LYS	1	0.962	0.979	4.986	30.807	30.871	-0.001	-0.005	-0.058	0.000
29	A	29	ASP	-1	-0.899	-0.963	3.907	-54.718	-53.911	0.003	-0.297	-0.513	-0.001
30	A	30	ALA	0	-0.020	0.005	1.897	-46.696	-44.237	9.175	-6.836	-4.797	-0.081
31	A	31	GLU	-1	-0.853	-0.907	3.101	-43.482	-42.173	0.025	-0.257	-1.078	-0.003
32	A	32	ILE	0	0.012	0.001	4.596	1.232	1.281	-0.001	-0.018	-0.029	0.000
104	A	104	ILE	0	0.020	-0.001	3.036	3.788	2.977	3.179	-0.515	-1.853	-0.002
5	A	5	VAL	0	0.015	-0.001	8.672	0.839	0.839	0.000	0.000	0.000	0.000
6	A	6	GLN	0	0.011	0.006	10.748	0.776	0.776	0.000	0.000	0.000	0.000
7	A	7	ILE	0	0.023	0.005	14.449	0.038	0.038	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.880	0.939	17.294	15.245	15.245	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.787	-0.867	20.860	-12.171	-12.171	0.000	0.000	0.000	0.000
10	A	10	PHE	0	0.008	-0.023	22.447	-0.382	-0.382	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.854	-0.932	24.641	-11.679	-11.679	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.856	0.914	20.912	12.555	12.555	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.033	0.029	19.943	-0.742	-0.742	0.000	0.000	0.000	0.000
14	A	14	PRO	0	0.033	0.009	19.647	-0.791	-0.791	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.049	-0.029	19.647	-0.428	-0.428	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.040	0.041	16.137	-0.841	-0.841	0.000	0.000	0.000	0.000
17	A	17	LEU	0	0.037	0.006	14.938	-1.407	-1.407	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.949	0.980	15.308	13.946	13.946	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.019	-0.018	13.203	-0.617	-0.617	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.005	-0.001	10.351	-1.905	-1.905	0.000	0.000	0.000	0.000
21	A	21	ILE	0	0.006	0.003	10.585	-2.098	-2.098	0.000	0.000	0.000	0.000
22	A	22	ASN	0	-0.044	-0.030	11.759	-0.585	-0.585	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.013	0.007	5.288	-0.887	-0.887	0.000	0.000	0.000	0.000
24	A	24	TYR	0	-0.012	-0.019	6.892	-3.337	-3.337	0.000	0.000	0.000	0.000
25	A	25	ASN	0	-0.048	-0.030	8.273	-1.207	-1.207	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.969	-0.955	7.919	-28.362	-28.362	0.000	0.000	0.000	0.000
33	A	33	GLU	0	-0.034	-0.045	7.535	2.860	2.860	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.003	-0.007	10.277	-0.187	-0.187	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.019	-0.001	12.746	1.227	1.227	0.000	0.000	0.000	0.000
36	A	36	LEU	0	0.006	0.007	15.569	0.329	0.329	0.000	0.000	0.000	0.000
37	A	37	HIS	0	0.035	-0.006	18.643	0.102	0.102	0.000	0.000	0.000	0.000
38	A	38	GLN	0	-0.018	-0.015	21.448	-0.063	-0.063	0.000	0.000	0.000	0.000
39	A	39	SER	0	0.011	0.003	24.602	0.215	0.215	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.027	0.005	20.839	0.242	0.242	0.000	0.000	0.000	0.000
41	A	41	ILE	0	-0.035	0.002	22.478	-0.313	-0.313	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.940	0.977	23.552	10.446	10.446	0.000	0.000	0.000	0.000
43	A	43	ALA	0	-0.006	0.009	21.785	0.230	0.230	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.008	-0.004	19.591	-0.146	-0.146	0.000	0.000	0.000	0.000
45	A	45	LEU	0	0.029	0.026	23.632	0.080	0.080	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.829	0.897	27.187	10.324	10.324	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.882	-0.941	29.067	-10.146	-10.146	0.000	0.000	0.000	0.000
48	A	48	SER	0	-0.033	-0.002	24.808	0.177	0.177	0.000	0.000	0.000	0.000
49	A	49	ASP	-1	-0.861	-0.933	27.313	-10.747	-10.747	0.000	0.000	0.000	0.000
50	A	50	THR	0	-0.062	-0.044	22.184	-0.420	-0.420	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.815	0.893	22.330	11.077	11.077	0.000	0.000	0.000	0.000
52	A	52	SER	0	0.024	0.008	22.506	-0.658	-0.658	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.001	0.002	18.051	-0.525	-0.525	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.018	0.009	18.153	-1.190	-1.190	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.830	-0.910	18.176	-13.712	-13.712	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.841	-0.899	16.878	-19.025	-19.025	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.002	-0.005	12.843	-1.207	-1.207	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.000	-0.001	13.763	-1.465	-1.465	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.901	0.956	15.336	15.489	15.489	0.000	0.000	0.000	0.000
60	A	60	LYS	1	0.783	0.881	11.744	20.319	20.319	0.000	0.000	0.000	0.000
61	A	61	ASN	0	-0.056	-0.023	9.511	-0.663	-0.663	0.000	0.000	0.000	0.000
62	A	62	ILE	0	-0.005	0.009	9.426	-2.373	-2.373	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.023	-0.011	10.875	2.732	2.732	0.000	0.000	0.000	0.000
64	A	64	ILE	0	0.013	0.009	12.851	-0.210	-0.210	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.025	-0.017	15.136	0.971	0.971	0.000	0.000	0.000	0.000
66	A	66	GLY	0	0.055	0.025	17.674	0.029	0.029	0.000	0.000	0.000	0.000
67	A	67	CYS	-1	-0.909	-0.859	20.724	-13.055	-13.055	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.741	-0.862	22.370	-10.708	-10.708	0.000	0.000	0.000	0.000
69	A	69	ASN	0	-0.024	-0.036	25.007	0.825	0.825	0.000	0.000	0.000	0.000
70	A	70	SER	0	0.032	-0.019	24.010	0.408	0.408	0.000	0.000	0.000	0.000
71	A	71	ILE	0	-0.004	0.004	24.672	0.251	0.251	0.000	0.000	0.000	0.000
72	A	72	ARG	1	0.847	0.904	27.804	10.632	10.632	0.000	0.000	0.000	0.000
73	A	73	SER	0	-0.038	-0.030	28.841	0.267	0.267	0.000	0.000	0.000	0.000
74	A	74	GLN	0	-0.042	-0.023	28.180	0.272	0.272	0.000	0.000	0.000	0.000
75	A	75	ASN	0	-0.053	-0.021	31.146	0.222	0.222	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.004	0.010	28.026	0.092	0.092	0.000	0.000	0.000	0.000
77	A	77	SER	0	0.012	-0.001	31.775	-0.023	-0.023	0.000	0.000	0.000	0.000
78	A	78	HIS	0	0.064	0.016	28.157	-0.238	-0.238	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.903	-0.939	29.165	-9.927	-9.927	0.000	0.000	0.000	0.000
80	A	80	GLN	0	-0.003	-0.007	30.983	-0.060	-0.060	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.004	0.015	25.045	-0.146	-0.146	0.000	0.000	0.000	0.000
82	A	82	ILE	0	-0.010	-0.003	22.664	0.250	0.250	0.000	0.000	0.000	0.000
83	A	83	PRO	0	0.000	-0.017	24.064	-0.312	-0.312	0.000	0.000	0.000	0.000
84	A	84	GLY	0	0.015	0.016	21.228	-0.383	-0.383	0.000	0.000	0.000	0.000
85	A	85	ILE	0	0.010	0.018	19.557	-1.143	-1.143	0.000	0.000	0.000	0.000
86	A	86	LYS	1	0.867	0.941	17.033	18.230	18.230	0.000	0.000	0.000	0.000
87	A	87	ILE	0	0.022	0.014	20.165	-0.073	-0.073	0.000	0.000	0.000	0.000
88	A	88	VAL	0	0.007	0.011	18.250	-0.089	-0.089	0.000	0.000	0.000	0.000
89	A	89	THR	0	0.005	-0.010	21.552	0.188	0.188	0.000	0.000	0.000	0.000
90	A	90	SER	0	0.044	0.001	22.262	0.385	0.385	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.035	-0.012	18.931	-0.550	-0.550	0.000	0.000	0.000	0.000
92	A	92	VAL	0	0.012	0.004	17.788	-0.790	-0.790	0.000	0.000	0.000	0.000
93	A	93	GLY	0	0.025	0.008	18.526	-0.348	-0.348	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.823	-0.892	15.064	-19.477	-19.477	0.000	0.000	0.000	0.000
95	A	95	ILE	0	0.008	-0.003	13.381	-0.998	-0.998	0.000	0.000	0.000	0.000
96	A	96	VAL	0	-0.012	0.008	13.780	-0.887	-0.887	0.000	0.000	0.000	0.000
97	A	97	ARG	1	0.934	0.983	15.388	15.474	15.474	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.875	0.941	10.569	23.980	23.980	0.000	0.000	0.000	0.000
99	A	99	GLN	0	-0.006	-0.006	10.949	-1.552	-1.552	0.000	0.000	0.000	0.000
100	A	100	SER	0	-0.087	-0.046	11.996	0.099	0.099	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.893	-0.940	11.543	-22.576	-22.576	0.000	0.000	0.000	0.000
102	A	102	GLY	0	-0.013	-0.003	9.376	-1.869	-1.869	0.000	0.000	0.000	0.000
103	A	103	TRP	0	-0.086	-0.053	6.522	-5.031	-5.031	0.000	0.000	0.000	0.000
105	A	105	TYR	0	-0.021	-0.020	6.374	-0.737	-0.737	0.000	0.000	0.000	0.000
106	A	106	LEU	0	-0.004	0.009	8.310	0.284	0.284	0.000	0.000	0.000	0.000
107	A	107	ALA	0	-0.017	-0.020	10.108	0.535	0.535	0.000	0.000	0.000	0.000
108	A	108	LEU	-1	-0.905	-0.939	12.312	-15.818	-15.818	0.000	0.000	0.000	0.000

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