FMO DATABASE

FMODB ID: 7YL7K

Calculation Name: 2D8C-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2D8C

Chain ID: A

ChEMBL ID:

UniProt ID: Q8VCQ6

Base Structure: SolutionNMR

Registration Date: 2025-10-03

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	97
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-669984.828119
FMO2-HF: Nuclear repulsion	630325.011651
FMO2-HF: Total energy	-39659.816469
FMO2-MP2: Total energy	-39770.971405

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:GLY)

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

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.
-59.121	-58.054	-0.011	-0.494	-0.563	-0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.870 / q_NPA : 0.920

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	SER	0	0.065	0.038	3.850	3.046	4.113	-0.011	-0.494	-0.563	-0.002
4	A	4	GLY	0	-0.030	-0.009	4.896	-2.058	-2.058	0.000	0.000	0.000	0.000
5	A	5	SER	0	0.016	-0.004	5.443	3.338	3.338	0.000	0.000	0.000	0.000
6	A	6	SER	0	0.022	0.018	9.289	-1.035	-1.035	0.000	0.000	0.000	0.000
7	A	7	GLY	0	-0.010	0.003	11.939	0.924	0.924	0.000	0.000	0.000	0.000
8	A	8	MET	0	-0.067	-0.037	14.611	1.369	1.369	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.023	0.019	14.229	-0.977	-0.977	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.024	-0.005	18.133	0.860	0.860	0.000	0.000	0.000	0.000
11	A	11	ALA	0	0.028	0.013	21.842	-0.134	-0.134	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.901	0.956	24.398	10.540	10.540	0.000	0.000	0.000	0.000
13	A	13	THR	0	0.007	-0.026	27.566	0.389	0.389	0.000	0.000	0.000	0.000
14	A	14	MET	0	-0.001	0.000	26.269	-0.564	-0.564	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.825	0.916	29.819	9.805	9.805	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.903	-0.938	31.601	-9.539	-9.539	0.000	0.000	0.000	0.000
17	A	17	VAL	0	0.034	-0.001	27.770	0.038	0.038	0.000	0.000	0.000	0.000
18	A	18	VAL	0	0.032	0.020	29.984	-0.173	-0.173	0.000	0.000	0.000	0.000
19	A	19	TYR	0	-0.045	-0.029	31.865	-0.041	-0.041	0.000	0.000	0.000	0.000
20	A	20	TRP	0	-0.017	-0.001	24.281	-0.347	-0.347	0.000	0.000	0.000	0.000
21	A	21	SER	0	0.029	0.006	25.542	0.009	0.009	0.000	0.000	0.000	0.000
22	A	22	PRO	0	0.051	0.009	24.312	-0.287	-0.287	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.910	0.965	20.051	13.577	13.577	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.956	0.995	20.156	12.292	12.292	0.000	0.000	0.000	0.000
25	A	25	VAL	0	0.010	0.002	21.491	-0.235	-0.235	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.054	0.032	17.109	-0.224	-0.224	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.931	-0.971	16.782	-17.801	-17.801	0.000	0.000	0.000	0.000
28	A	28	TRP	0	0.007	-0.009	17.596	-0.577	-0.577	0.000	0.000	0.000	0.000
29	A	29	LEU	0	0.026	0.028	17.753	0.147	0.147	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.046	-0.021	12.725	-0.616	-0.616	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.894	-0.948	14.649	-17.002	-17.002	0.000	0.000	0.000	0.000
32	A	32	ASN	0	-0.049	-0.032	16.989	0.294	0.294	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.030	-0.011	14.233	0.221	0.221	0.000	0.000	0.000	0.000
34	A	34	MET	0	-0.018	0.000	15.202	0.316	0.316	0.000	0.000	0.000	0.000
35	A	35	PRO	0	0.002	-0.016	11.853	0.398	0.398	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.871	-0.917	14.301	-16.081	-16.081	0.000	0.000	0.000	0.000
37	A	37	TYR	0	0.057	0.000	16.538	0.915	0.915	0.000	0.000	0.000	0.000
38	A	38	CYS	0	-0.045	-0.025	14.949	0.715	0.715	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.911	-0.951	15.591	-17.723	-17.723	0.000	0.000	0.000	0.000
40	A	40	PRO	0	-0.045	-0.020	18.540	0.616	0.616	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.008	-0.009	20.991	0.725	0.725	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.922	-0.947	19.764	-14.138	-14.138	0.000	0.000	0.000	0.000
43	A	43	HIS	0	-0.097	-0.054	21.096	0.230	0.230	0.000	0.000	0.000	0.000
44	A	44	PHE	0	0.007	0.011	24.300	0.572	0.572	0.000	0.000	0.000	0.000
45	A	45	THR	0	0.000	-0.009	25.464	-0.273	-0.273	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.027	0.004	27.663	-0.076	-0.076	0.000	0.000	0.000	0.000
47	A	47	GLN	0	0.040	0.016	28.533	0.093	0.093	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.920	-0.950	29.221	-9.805	-9.805	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.009	-0.005	24.101	-0.034	-0.034	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.018	-0.010	28.086	0.014	0.014	0.000	0.000	0.000	0.000
51	A	51	ASN	0	-0.089	-0.039	30.794	0.410	0.410	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.030	0.011	26.890	0.100	0.100	0.000	0.000	0.000	0.000
53	A	53	THR	0	0.046	0.017	30.985	0.117	0.117	0.000	0.000	0.000	0.000
54	A	54	GLN	0	0.028	0.000	31.436	-0.370	-0.370	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.940	-0.983	32.516	-8.234	-8.234	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.893	-0.941	30.678	-9.283	-9.283	0.000	0.000	0.000	0.000
57	A	57	PHE	0	0.063	0.049	25.070	-0.179	-0.179	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.870	0.940	29.258	8.549	8.549	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.797	0.893	30.851	9.308	9.308	0.000	0.000	0.000	0.000
60	A	60	PRO	0	0.002	0.020	28.033	-0.274	-0.274	0.000	0.000	0.000	0.000
61	A	61	PRO	0	0.027	0.003	24.874	0.349	0.349	0.000	0.000	0.000	0.000
62	A	62	LEU	0	0.014	0.010	23.768	-0.523	-0.523	0.000	0.000	0.000	0.000
63	A	63	TYR	0	0.015	0.006	25.542	0.296	0.296	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.884	0.939	23.424	11.885	11.885	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.020	0.019	20.044	-0.189	-0.189	0.000	0.000	0.000	0.000
66	A	66	SER	0	-0.019	-0.017	20.360	-0.547	-0.547	0.000	0.000	0.000	0.000
67	A	67	SER	0	-0.035	-0.026	21.853	0.640	0.640	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.884	-0.925	22.540	-12.731	-12.731	0.000	0.000	0.000	0.000
69	A	69	ASN	0	-0.034	-0.033	25.252	0.270	0.270	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.059	0.021	25.550	0.329	0.329	0.000	0.000	0.000	0.000
71	A	71	GLN	0	0.006	0.009	26.533	-0.023	-0.023	0.000	0.000	0.000	0.000
72	A	72	ARG	1	0.893	0.940	19.346	14.295	14.295	0.000	0.000	0.000	0.000
73	A	73	LEU	0	0.022	0.007	22.189	-0.138	-0.138	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.015	-0.010	24.416	0.226	0.226	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.918	-0.942	27.098	-10.511	-10.511	0.000	0.000	0.000	0.000
76	A	76	MET	0	-0.012	-0.013	22.624	0.133	0.133	0.000	0.000	0.000	0.000
77	A	77	ILE	0	-0.013	-0.019	25.527	0.003	0.003	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.985	-0.990	27.929	-8.857	-8.857	0.000	0.000	0.000	0.000
79	A	79	THR	0	0.009	-0.005	28.057	0.403	0.403	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.025	-0.018	25.934	0.210	0.210	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.918	0.963	30.353	9.544	9.544	0.000	0.000	0.000	0.000
82	A	82	MET	0	-0.037	0.000	32.642	0.300	0.300	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.844	-0.910	31.275	-9.777	-9.777	0.000	0.000	0.000	0.000
84	A	84	HIS	0	-0.020	0.007	35.007	0.241	0.241	0.000	0.000	0.000	0.000
85	A	85	HIS	0	-0.029	-0.010	36.758	0.086	0.086	0.000	0.000	0.000	0.000
86	A	86	MET	0	-0.014	-0.014	36.087	0.106	0.106	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.968	-0.977	40.386	-6.792	-6.792	0.000	0.000	0.000	0.000
88	A	88	ALA	0	0.000	0.008	41.298	0.059	0.059	0.000	0.000	0.000	0.000
89	A	89	HIS	0	0.005	0.003	42.415	0.210	0.210	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.987	0.977	45.607	6.219	6.219	0.000	0.000	0.000	0.000
91	A	91	ASN	0	-0.075	-0.038	48.297	0.086	0.086	0.000	0.000	0.000	0.000
92	A	92	SER	0	0.011	0.000	46.918	-0.141	-0.141	0.000	0.000	0.000	0.000
93	A	93	GLY	0	0.038	0.013	48.540	0.083	0.083	0.000	0.000	0.000	0.000
94	A	94	PRO	0	-0.038	0.007	46.298	0.108	0.108	0.000	0.000	0.000	0.000
95	A	95	SER	0	-0.013	-0.024	49.331	0.041	0.041	0.000	0.000	0.000	0.000
96	A	96	SER	0	-0.061	-0.034	49.899	0.094	0.094	0.000	0.000	0.000	0.000
97	A	97	GLY	-1	-0.905	-0.930	45.226	-6.955	-6.955	0.000	0.000	0.000	0.000

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