FMO DATABASE

FMODB ID: Y7J32

Calculation Name: 3DEX-H-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3DEX

Chain ID: H

ChEMBL ID:

UniProt ID: Q82LK9

Base Structure: X-ray

Registration Date: 2025-10-06

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	82
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-587771.493081
FMO2-HF: Nuclear repulsion	554261.683828
FMO2-HF: Total energy	-33509.809252
FMO2-MP2: Total energy	-33608.669427

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(H:10:PRO)

Summations of interaction energy for fragment #1(H:10:PRO)

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.
-80.746	-74.568	1.979	-3.677	-4.479	-0.032

Interaction energy analysis for fragmet #1(H:10:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.857 / q_NPA : 0.907

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

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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	H	12	THR	0	-0.031	-0.020	2.790	7.459	9.518	0.031	-0.850	-1.240	-0.003
4	H	13	HIS	1	0.838	0.922	5.318	43.722	43.869	-0.001	-0.010	-0.135	0.000
32	H	42	THR	0	0.045	0.033	3.203	-5.160	-4.670	0.014	-0.196	-0.308	-0.001
33	H	43	GLU	-1	-0.827	-0.925	2.597	-61.065	-57.571	1.936	-2.638	-2.792	-0.028
34	H	44	LEU	0	-0.030	-0.025	3.697	-2.310	-2.322	-0.001	0.017	-0.004	0.000
5	H	14	ARG	1	0.913	0.946	7.694	20.295	20.295	0.000	0.000	0.000	0.000
6	H	15	VAL	0	0.019	0.019	10.924	1.195	1.195	0.000	0.000	0.000	0.000
7	H	16	GLN	0	-0.030	-0.019	13.233	0.680	0.680	0.000	0.000	0.000	0.000
8	H	17	ILE	0	0.015	0.023	16.926	0.494	0.494	0.000	0.000	0.000	0.000
9	H	18	GLU	-1	-0.894	-0.941	19.721	-12.376	-12.376	0.000	0.000	0.000	0.000
10	H	19	TYR	0	0.020	-0.002	23.233	0.506	0.506	0.000	0.000	0.000	0.000
11	H	20	CYS	0	-0.090	0.001	26.206	0.574	0.574	0.000	0.000	0.000	0.000
12	H	21	THR	0	0.017	0.008	29.915	0.075	0.075	0.000	0.000	0.000	0.000
13	H	22	GLN	0	0.034	0.004	31.046	0.025	0.025	0.000	0.000	0.000	0.000
14	H	24	ARG	1	0.950	0.981	32.434	9.119	9.119	0.000	0.000	0.000	0.000
15	H	25	TRP	0	-0.027	-0.025	28.014	-0.183	-0.183	0.000	0.000	0.000	0.000
16	H	26	LEU	0	0.065	0.046	25.049	-0.336	-0.336	0.000	0.000	0.000	0.000
17	H	27	PRO	0	0.019	0.009	25.347	-0.489	-0.489	0.000	0.000	0.000	0.000
18	H	28	ARG	1	0.958	0.986	25.295	10.173	10.173	0.000	0.000	0.000	0.000
19	H	29	ALA	0	0.037	0.013	22.633	-0.434	-0.434	0.000	0.000	0.000	0.000
20	H	30	ALA	0	0.009	0.004	20.937	-0.734	-0.734	0.000	0.000	0.000	0.000
21	H	31	TRP	0	-0.028	-0.016	20.512	-0.455	-0.455	0.000	0.000	0.000	0.000
22	H	32	LEU	0	0.022	0.009	18.278	-0.556	-0.556	0.000	0.000	0.000	0.000
23	H	33	ALA	0	0.033	-0.001	16.790	-0.942	-0.942	0.000	0.000	0.000	0.000
24	H	34	GLN	0	0.003	0.010	15.674	-0.909	-0.909	0.000	0.000	0.000	0.000
25	H	35	GLU	-1	-0.855	-0.917	16.136	-15.912	-15.912	0.000	0.000	0.000	0.000
26	H	36	LEU	0	-0.005	-0.003	13.293	-0.809	-0.809	0.000	0.000	0.000	0.000
27	H	37	LEU	0	0.011	-0.004	11.084	-1.760	-1.760	0.000	0.000	0.000	0.000
28	H	38	THR	0	-0.042	-0.026	11.334	-1.369	-1.369	0.000	0.000	0.000	0.000
29	H	39	THR	0	-0.054	-0.023	12.236	0.526	0.526	0.000	0.000	0.000	0.000
30	H	40	PHE	0	-0.042	-0.029	8.099	-0.506	-0.506	0.000	0.000	0.000	0.000
31	H	41	GLU	-1	-0.925	-0.940	6.964	-35.960	-35.960	0.000	0.000	0.000	0.000
35	H	45	THR	0	-0.062	-0.020	6.435	-0.635	-0.635	0.000	0.000	0.000	0.000
36	H	46	GLU	-1	-0.853	-0.911	7.794	-19.177	-19.177	0.000	0.000	0.000	0.000
37	H	47	LEU	0	-0.021	-0.005	11.143	-0.268	-0.268	0.000	0.000	0.000	0.000
38	H	48	ALA	0	-0.005	0.007	13.667	1.032	1.032	0.000	0.000	0.000	0.000
39	H	49	LEU	0	0.003	-0.008	17.084	0.410	0.410	0.000	0.000	0.000	0.000
40	H	50	LYS	1	0.931	0.966	20.519	13.857	13.857	0.000	0.000	0.000	0.000
41	H	51	PRO	0	-0.019	-0.011	23.297	0.228	0.228	0.000	0.000	0.000	0.000
42	H	52	GLY	0	0.071	0.035	27.012	-0.028	-0.028	0.000	0.000	0.000	0.000
43	H	53	THR	0	-0.006	-0.020	28.526	0.156	0.156	0.000	0.000	0.000	0.000
44	H	54	GLY	0	0.056	0.007	32.193	0.155	0.155	0.000	0.000	0.000	0.000
45	H	55	GLY	0	0.008	-0.007	32.947	-0.016	-0.016	0.000	0.000	0.000	0.000
46	H	56	VAL	0	-0.001	0.000	26.871	-0.107	-0.107	0.000	0.000	0.000	0.000
47	H	57	PHE	0	-0.006	-0.026	22.531	0.139	0.139	0.000	0.000	0.000	0.000
48	H	58	VAL	0	-0.015	0.003	22.248	0.181	0.181	0.000	0.000	0.000	0.000
49	H	59	VAL	0	0.010	0.013	17.132	-0.255	-0.255	0.000	0.000	0.000	0.000
50	H	60	ARG	1	0.901	0.936	17.596	14.611	14.611	0.000	0.000	0.000	0.000
51	H	61	VAL	0	0.022	-0.001	11.538	-0.675	-0.675	0.000	0.000	0.000	0.000
52	H	62	ASP	-1	-0.781	-0.870	10.698	-28.815	-28.815	0.000	0.000	0.000	0.000
53	H	63	ASP	-1	-0.932	-0.959	13.643	-17.346	-17.346	0.000	0.000	0.000	0.000
54	H	64	GLU	-1	-0.949	-0.967	16.719	-17.092	-17.092	0.000	0.000	0.000	0.000
55	H	65	VAL	0	-0.068	-0.048	17.893	-0.476	-0.476	0.000	0.000	0.000	0.000
56	H	66	VAL	0	0.004	0.007	16.103	0.094	0.094	0.000	0.000	0.000	0.000
57	H	67	TRP	0	0.012	-0.015	19.493	0.127	0.127	0.000	0.000	0.000	0.000
58	H	68	ASP	-1	-0.810	-0.902	22.173	-11.302	-11.302	0.000	0.000	0.000	0.000
59	H	69	ARG	1	0.954	0.974	25.585	10.248	10.248	0.000	0.000	0.000	0.000
60	H	70	ARG	1	0.762	0.874	28.099	10.988	10.988	0.000	0.000	0.000	0.000
61	H	71	GLU	-1	-0.938	-0.952	27.305	-10.344	-10.344	0.000	0.000	0.000	0.000
62	H	72	GLN	0	0.023	0.008	22.945	0.136	0.136	0.000	0.000	0.000	0.000
63	H	73	GLY	0	0.016	0.029	28.085	0.042	0.042	0.000	0.000	0.000	0.000
64	H	74	PHE	0	-0.057	-0.043	25.903	-0.230	-0.230	0.000	0.000	0.000	0.000
65	H	75	PRO	0	0.007	0.015	22.223	0.033	0.033	0.000	0.000	0.000	0.000
66	H	76	GLU	-1	-0.762	-0.868	23.649	-13.004	-13.004	0.000	0.000	0.000	0.000
67	H	77	PRO	0	0.032	0.015	20.766	-0.469	-0.469	0.000	0.000	0.000	0.000
68	H	78	THR	0	-0.009	-0.034	19.433	-1.013	-1.013	0.000	0.000	0.000	0.000
69	H	79	ALA	0	-0.055	-0.023	19.881	-0.604	-0.604	0.000	0.000	0.000	0.000
70	H	80	VAL	0	0.005	0.006	18.036	-0.501	-0.501	0.000	0.000	0.000	0.000
71	H	81	LYS	1	0.875	0.936	15.380	15.707	15.707	0.000	0.000	0.000	0.000
72	H	82	ARG	1	0.925	0.964	15.079	13.165	13.165	0.000	0.000	0.000	0.000
73	H	83	LEU	0	0.009	0.009	16.026	-0.713	-0.713	0.000	0.000	0.000	0.000
74	H	84	VAL	0	-0.027	-0.021	11.908	-0.471	-0.471	0.000	0.000	0.000	0.000
75	H	85	ARG	1	0.772	0.867	11.483	17.410	17.410	0.000	0.000	0.000	0.000
76	H	86	ASP	-1	-0.837	-0.903	11.835	-19.424	-19.424	0.000	0.000	0.000	0.000
77	H	87	ARG	1	0.893	0.962	12.119	22.081	22.081	0.000	0.000	0.000	0.000
78	H	88	VAL	0	-0.091	-0.055	6.729	-2.440	-2.440	0.000	0.000	0.000	0.000
79	H	89	ALA	0	-0.013	0.001	8.049	-1.544	-1.544	0.000	0.000	0.000	0.000
80	H	90	PRO	0	-0.022	-0.018	9.306	1.894	1.894	0.000	0.000	0.000	0.000
81	H	91	GLU	-1	-0.987	-1.000	12.162	-20.511	-20.511	0.000	0.000	0.000	0.000
82	H	92	LYS	0	0.007	0.024	8.035	11.442	11.442	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(H:10:PRO)