FMO DATABASE

FMODB ID: M836Z

Calculation Name: 2X3D-D-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2X3D

Chain ID: D

ChEMBL ID:

UniProt ID: Q97ZR0

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	91
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-601568.527077
FMO2-HF: Nuclear repulsion	565686.287759
FMO2-HF: Total energy	-35882.239318
FMO2-MP2: Total energy	-35983.216114

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:0:GLY)

Summations of interaction energy for fragment #1(A:0: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.
-98.76	-95.435	0.199	-1.631	-1.892	-0.013

Interaction energy analysis for fragmet #1(A:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.836 / q_NPA : 0.901

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	2	ALA	0	0.035	0.036	3.685	8.301	10.324	-0.011	-0.887	-1.124	-0.005
85	A	84	ASN	0	-0.020	-0.048	2.911	-13.604	-12.302	0.210	-0.744	-0.768	-0.008
4	A	3	ILE	0	0.062	0.031	5.712	1.015	1.015	0.000	0.000	0.000	0.000
5	A	4	ARG	1	0.767	0.877	6.815	34.287	34.287	0.000	0.000	0.000	0.000
6	A	5	ARG	1	0.789	0.854	10.702	18.526	18.526	0.000	0.000	0.000	0.000
7	A	6	LEU	0	-0.026	-0.010	14.410	-0.663	-0.663	0.000	0.000	0.000	0.000
8	A	7	VAL	0	0.020	0.012	17.013	0.429	0.429	0.000	0.000	0.000	0.000
9	A	8	LEU	0	-0.039	-0.025	19.813	-0.120	-0.120	0.000	0.000	0.000	0.000
10	A	9	ASP	-1	-0.835	-0.900	23.056	-10.532	-10.532	0.000	0.000	0.000	0.000
11	A	10	VAL	0	-0.034	-0.029	25.401	-0.198	-0.198	0.000	0.000	0.000	0.000
12	A	11	LEU	0	0.057	0.040	28.236	0.302	0.302	0.000	0.000	0.000	0.000
13	A	12	LYS	1	0.894	0.938	31.318	9.261	9.261	0.000	0.000	0.000	0.000
14	A	13	PRO	0	0.042	0.021	33.334	0.283	0.283	0.000	0.000	0.000	0.000
15	A	14	ILE	0	-0.026	-0.002	36.443	-0.147	-0.147	0.000	0.000	0.000	0.000
16	A	15	ARG	1	0.903	0.944	38.564	7.479	7.479	0.000	0.000	0.000	0.000
17	A	16	GLY	0	0.015	0.006	36.910	-0.057	-0.057	0.000	0.000	0.000	0.000
18	A	17	THR	0	-0.009	-0.030	31.077	0.283	0.283	0.000	0.000	0.000	0.000
19	A	18	SER	0	-0.052	-0.052	33.931	-0.041	-0.041	0.000	0.000	0.000	0.000
20	A	19	ILE	0	0.079	0.014	30.464	-0.244	-0.244	0.000	0.000	0.000	0.000
21	A	20	VAL	0	0.002	0.011	29.461	-0.384	-0.384	0.000	0.000	0.000	0.000
22	A	21	ASP	-1	-0.858	-0.898	29.355	-10.158	-10.158	0.000	0.000	0.000	0.000
23	A	22	LEU	0	0.009	0.007	26.580	-0.352	-0.352	0.000	0.000	0.000	0.000
24	A	23	ALA	0	0.029	0.008	25.219	-0.579	-0.579	0.000	0.000	0.000	0.000
25	A	24	GLU	-1	-0.868	-0.909	24.417	-11.945	-11.945	0.000	0.000	0.000	0.000
26	A	25	ARG	1	0.855	0.923	24.673	10.361	10.361	0.000	0.000	0.000	0.000
27	A	26	ILE	0	0.081	0.020	20.326	-0.594	-0.594	0.000	0.000	0.000	0.000
28	A	27	SER	0	-0.101	-0.067	20.240	-0.791	-0.791	0.000	0.000	0.000	0.000
29	A	28	LYS	1	0.796	0.883	20.618	12.326	12.326	0.000	0.000	0.000	0.000
30	A	29	LEU	0	-0.005	0.011	17.630	-0.091	-0.091	0.000	0.000	0.000	0.000
31	A	30	ASP	-1	-0.900	-0.953	13.825	-20.519	-20.519	0.000	0.000	0.000	0.000
32	A	31	GLY	0	-0.029	-0.018	12.132	-0.898	-0.898	0.000	0.000	0.000	0.000
33	A	32	VAL	0	-0.053	-0.021	12.784	-0.934	-0.934	0.000	0.000	0.000	0.000
34	A	33	GLU	-1	-0.920	-0.943	12.121	-25.153	-25.153	0.000	0.000	0.000	0.000
35	A	34	GLY	0	-0.020	-0.011	16.587	1.115	1.115	0.000	0.000	0.000	0.000
36	A	35	VAL	0	-0.007	-0.007	18.908	-0.589	-0.589	0.000	0.000	0.000	0.000
37	A	36	ASN	0	-0.062	-0.027	21.698	0.779	0.779	0.000	0.000	0.000	0.000
38	A	37	ILE	0	0.021	0.019	24.510	-0.243	-0.243	0.000	0.000	0.000	0.000
39	A	38	SER	0	-0.016	-0.010	27.153	0.394	0.394	0.000	0.000	0.000	0.000
40	A	39	VAL	0	-0.024	-0.013	29.945	-0.107	-0.107	0.000	0.000	0.000	0.000
41	A	40	THR	0	-0.052	-0.036	30.683	-0.019	-0.019	0.000	0.000	0.000	0.000
42	A	41	ASP	-1	-0.893	-0.935	33.501	-8.865	-8.865	0.000	0.000	0.000	0.000
43	A	42	MET	0	-0.036	-0.026	36.185	-0.207	-0.207	0.000	0.000	0.000	0.000
44	A	43	ASP	-1	-0.882	-0.909	38.738	-7.818	-7.818	0.000	0.000	0.000	0.000
45	A	44	VAL	0	-0.053	-0.051	41.508	0.031	0.031	0.000	0.000	0.000	0.000
46	A	45	GLU	-1	-0.976	-0.993	41.207	-7.523	-7.523	0.000	0.000	0.000	0.000
47	A	46	THR	0	-0.049	-0.013	36.653	-0.224	-0.224	0.000	0.000	0.000	0.000
48	A	47	MET	0	-0.018	-0.016	34.274	0.134	0.134	0.000	0.000	0.000	0.000
49	A	48	GLY	0	0.080	0.059	32.710	-0.240	-0.240	0.000	0.000	0.000	0.000
50	A	49	LEU	0	-0.039	-0.035	28.989	0.114	0.114	0.000	0.000	0.000	0.000
51	A	50	MET	0	0.057	0.045	25.444	-0.333	-0.333	0.000	0.000	0.000	0.000
52	A	51	ILE	0	-0.034	-0.027	22.348	0.050	0.050	0.000	0.000	0.000	0.000
53	A	52	ILE	0	0.009	0.003	19.836	-0.485	-0.485	0.000	0.000	0.000	0.000
54	A	53	ILE	0	-0.008	-0.008	16.568	0.302	0.302	0.000	0.000	0.000	0.000
55	A	54	GLU	-1	-0.822	-0.913	15.054	-19.115	-19.115	0.000	0.000	0.000	0.000
56	A	55	GLY	0	0.046	0.024	12.963	0.986	0.986	0.000	0.000	0.000	0.000
57	A	56	THR	0	-0.073	-0.055	7.181	-3.999	-3.999	0.000	0.000	0.000	0.000
58	A	57	SER	0	-0.101	-0.051	6.763	-0.606	-0.606	0.000	0.000	0.000	0.000
59	A	58	LEU	0	0.014	0.026	8.549	1.775	1.775	0.000	0.000	0.000	0.000
60	A	59	ASN	0	0.015	-0.005	12.227	-0.705	-0.705	0.000	0.000	0.000	0.000
61	A	60	PHE	0	0.024	0.004	13.951	1.453	1.453	0.000	0.000	0.000	0.000
62	A	61	ASP	-1	-0.883	-0.940	16.306	-16.498	-16.498	0.000	0.000	0.000	0.000
63	A	62	ASP	-1	-0.925	-0.963	17.221	-16.872	-16.872	0.000	0.000	0.000	0.000
64	A	63	ILE	0	-0.004	-0.001	16.391	0.885	0.885	0.000	0.000	0.000	0.000
65	A	64	ARG	1	0.938	0.977	20.107	14.619	14.619	0.000	0.000	0.000	0.000
66	A	65	LYS	1	0.909	0.965	21.389	15.120	15.120	0.000	0.000	0.000	0.000
67	A	66	MET	0	0.028	0.026	22.998	0.579	0.579	0.000	0.000	0.000	0.000
68	A	67	LEU	0	-0.013	-0.014	23.066	0.580	0.580	0.000	0.000	0.000	0.000
69	A	68	GLU	-1	-0.929	-0.968	25.910	-11.773	-11.773	0.000	0.000	0.000	0.000
70	A	69	GLU	-1	-0.981	-0.992	26.774	-11.709	-11.709	0.000	0.000	0.000	0.000
71	A	70	GLU	-1	-0.879	-0.907	28.410	-10.309	-10.309	0.000	0.000	0.000	0.000
72	A	71	GLY	0	-0.043	-0.018	30.599	0.260	0.260	0.000	0.000	0.000	0.000
73	A	72	CYS	0	-0.102	-0.051	28.381	0.297	0.297	0.000	0.000	0.000	0.000
74	A	73	ALA	0	0.010	0.000	28.900	-0.169	-0.169	0.000	0.000	0.000	0.000
75	A	74	ILE	0	-0.043	-0.022	22.235	0.003	0.003	0.000	0.000	0.000	0.000
76	A	75	HIS	0	-0.056	-0.015	26.458	0.131	0.131	0.000	0.000	0.000	0.000
77	A	76	SER	0	-0.037	-0.052	25.539	0.003	0.003	0.000	0.000	0.000	0.000
78	A	77	ILE	0	-0.039	-0.026	18.656	-0.362	-0.362	0.000	0.000	0.000	0.000
79	A	78	ASP	-1	-0.855	-0.893	21.549	-12.577	-12.577	0.000	0.000	0.000	0.000
80	A	79	GLU	-1	-0.880	-0.939	17.414	-16.470	-16.470	0.000	0.000	0.000	0.000
81	A	80	VAL	0	-0.025	-0.008	13.122	-0.432	-0.432	0.000	0.000	0.000	0.000
82	A	81	VAL	0	0.002	0.026	11.576	-0.403	-0.403	0.000	0.000	0.000	0.000
83	A	82	SER	0	0.020	0.000	7.960	-2.976	-2.976	0.000	0.000	0.000	0.000
84	A	83	GLY	0	-0.002	0.007	5.151	1.381	1.381	0.000	0.000	0.000	0.000
86	A	85	ARG	1	0.942	0.976	5.446	23.952	23.952	0.000	0.000	0.000	0.000
87	A	86	ILE	0	0.095	0.055	9.276	-0.992	-0.992	0.000	0.000	0.000	0.000
88	A	87	ILE	0	-0.124	-0.065	12.163	0.444	0.444	0.000	0.000	0.000	0.000
89	A	88	GLU	-1	-0.779	-0.885	14.514	-16.173	-16.173	0.000	0.000	0.000	0.000
90	A	89	GLY	0	0.029	0.027	18.092	-0.158	-0.158	0.000	0.000	0.000	0.000
91	A	90	LYS	0	-0.023	-0.004	20.829	-0.045	-0.045	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)