FMO DATABASE

FMODB ID: KVQL3

Calculation Name: 2ZOM-B-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2ZOM

Chain ID: B

ChEMBL ID:

UniProt ID: Q109R6

Base Structure: X-ray

Registration Date: 2025-10-05

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	-797603.540053
FMO2-HF: Nuclear repulsion	756364.810668
FMO2-HF: Total energy	-41238.729385
FMO2-MP2: Total energy	-41361.757146

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:6:THR)

Summations of interaction energy for fragment #1(A:6:THR)

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.
-74.044	-74.934	21.022	-11.48	-8.652	-0.108

Interaction energy analysis for fragmet #1(A:6:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.785 / q_NPA : 0.855

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	8	VAL	0	0.021	0.017	3.867	-3.891	-1.847	-0.026	-1.057	-0.961	-0.002
95	A	100	LEU	0	0.051	0.028	2.897	-0.825	-0.395	0.053	-0.128	-0.355	0.000
99	A	104	GLU	-1	-0.867	-0.920	1.647	-102.750	-106.388	20.996	-10.258	-7.100	-0.106
100	A	105	TRP	0	-0.023	-0.009	4.515	0.688	0.777	-0.001	-0.011	-0.077	0.000
102	A	107	LYS	1	0.930	0.976	3.769	54.286	54.471	0.000	-0.026	-0.159	0.000
4	A	9	PRO	0	0.042	0.031	6.705	1.026	1.026	0.000	0.000	0.000	0.000
5	A	10	SER	0	-0.001	0.000	9.881	0.871	0.871	0.000	0.000	0.000	0.000
6	A	11	ILE	0	0.006	0.005	12.429	0.759	0.759	0.000	0.000	0.000	0.000
7	A	12	VAL	0	-0.013	-0.004	16.064	-0.429	-0.429	0.000	0.000	0.000	0.000
8	A	13	VAL	0	-0.015	-0.013	18.614	0.277	0.277	0.000	0.000	0.000	0.000
9	A	14	TYR	0	-0.029	-0.003	21.498	-0.015	-0.015	0.000	0.000	0.000	0.000
10	A	15	VAL	0	0.070	0.020	24.748	-0.009	-0.009	0.000	0.000	0.000	0.000
11	A	16	THR	0	-0.007	0.020	27.316	-0.157	-0.157	0.000	0.000	0.000	0.000
12	A	17	VAL	0	-0.017	-0.005	29.858	-0.031	-0.031	0.000	0.000	0.000	0.000
13	A	18	PRO	0	0.116	0.078	32.629	0.022	0.022	0.000	0.000	0.000	0.000
14	A	19	ASN	0	0.018	-0.015	35.049	0.082	0.082	0.000	0.000	0.000	0.000
15	A	20	LYS	1	0.984	0.988	33.585	8.526	8.526	0.000	0.000	0.000	0.000
16	A	21	GLU	-1	-0.906	-0.933	32.761	-8.872	-8.872	0.000	0.000	0.000	0.000
17	A	22	ALA	0	0.070	0.047	32.644	-0.242	-0.242	0.000	0.000	0.000	0.000
18	A	23	GLY	0	0.074	0.044	29.473	-0.357	-0.357	0.000	0.000	0.000	0.000
19	A	24	LYS	1	0.906	0.934	28.168	9.564	9.564	0.000	0.000	0.000	0.000
20	A	25	ARG	1	0.829	0.895	28.117	8.805	8.805	0.000	0.000	0.000	0.000
21	A	26	LEU	0	0.055	0.051	26.007	-0.358	-0.358	0.000	0.000	0.000	0.000
22	A	27	ALA	0	0.049	0.027	24.179	-0.519	-0.519	0.000	0.000	0.000	0.000
23	A	28	GLY	0	0.008	0.002	23.373	-0.569	-0.569	0.000	0.000	0.000	0.000
24	A	29	SER	0	-0.025	-0.009	24.151	-0.419	-0.419	0.000	0.000	0.000	0.000
25	A	30	ILE	0	0.019	0.015	20.148	-0.387	-0.387	0.000	0.000	0.000	0.000
26	A	31	ILE	0	0.005	0.006	18.436	-0.708	-0.708	0.000	0.000	0.000	0.000
27	A	32	SER	0	-0.043	-0.030	19.735	-0.425	-0.425	0.000	0.000	0.000	0.000
28	A	33	GLU	-1	-0.931	-0.964	21.646	-12.687	-12.687	0.000	0.000	0.000	0.000
29	A	34	LYS	1	0.934	0.961	16.289	15.082	15.082	0.000	0.000	0.000	0.000
30	A	35	LEU	0	0.021	0.014	16.239	-1.301	-1.301	0.000	0.000	0.000	0.000
31	A	36	ALA	0	-0.013	0.004	15.829	-0.537	-0.537	0.000	0.000	0.000	0.000
32	A	37	ALA	0	-0.029	0.007	12.454	0.269	0.269	0.000	0.000	0.000	0.000
33	A	38	CYS	-1	-0.866	-0.866	14.502	-16.312	-16.312	0.000	0.000	0.000	0.000
34	A	39	VAL	0	0.043	0.015	17.206	-0.012	-0.012	0.000	0.000	0.000	0.000
35	A	40	ASN	0	-0.047	-0.022	19.886	-0.024	-0.024	0.000	0.000	0.000	0.000
36	A	41	ILE	0	0.019	0.013	23.030	0.028	0.028	0.000	0.000	0.000	0.000
37	A	42	VAL	0	-0.010	-0.002	26.639	0.040	0.040	0.000	0.000	0.000	0.000
38	A	43	PRO	0	-0.015	-0.015	29.025	0.156	0.156	0.000	0.000	0.000	0.000
39	A	44	GLY	0	-0.005	-0.006	32.444	0.058	0.058	0.000	0.000	0.000	0.000
40	A	45	ILE	0	-0.030	0.003	31.923	0.066	0.066	0.000	0.000	0.000	0.000
41	A	46	GLU	-1	-0.945	-0.984	35.209	-7.492	-7.492	0.000	0.000	0.000	0.000
42	A	47	SER	0	-0.035	-0.034	35.297	-0.193	-0.193	0.000	0.000	0.000	0.000
43	A	48	VAL	0	-0.019	-0.017	37.676	0.264	0.264	0.000	0.000	0.000	0.000
44	A	49	TYR	0	-0.070	-0.055	38.898	-0.150	-0.150	0.000	0.000	0.000	0.000
45	A	50	TRP	0	-0.033	-0.016	40.910	0.247	0.247	0.000	0.000	0.000	0.000
46	A	51	TRP	0	0.008	-0.016	41.117	-0.213	-0.213	0.000	0.000	0.000	0.000
47	A	52	GLU	-1	-0.877	-0.930	44.810	-6.802	-6.802	0.000	0.000	0.000	0.000
48	A	53	GLY	0	-0.065	-0.031	47.836	0.154	0.154	0.000	0.000	0.000	0.000
49	A	54	LYS	1	0.862	0.926	48.240	6.755	6.755	0.000	0.000	0.000	0.000
50	A	55	VAL	0	0.006	0.000	44.739	-0.136	-0.136	0.000	0.000	0.000	0.000
51	A	56	GLN	0	0.001	0.023	43.082	0.323	0.323	0.000	0.000	0.000	0.000
52	A	57	THR	0	-0.001	-0.022	42.295	-0.052	-0.052	0.000	0.000	0.000	0.000
53	A	58	ASP	-1	-0.842	-0.886	39.615	-7.831	-7.831	0.000	0.000	0.000	0.000
54	A	59	ALA	0	-0.009	0.003	38.895	-0.169	-0.169	0.000	0.000	0.000	0.000
55	A	60	GLU	-1	-0.751	-0.813	34.228	-9.256	-9.256	0.000	0.000	0.000	0.000
56	A	61	GLU	-1	-0.976	-0.998	31.142	-9.731	-9.731	0.000	0.000	0.000	0.000
57	A	62	LEU	0	0.038	0.021	26.933	-0.099	-0.099	0.000	0.000	0.000	0.000
58	A	63	LEU	0	-0.045	-0.019	24.743	-0.239	-0.239	0.000	0.000	0.000	0.000
59	A	64	ILE	0	0.023	0.006	20.665	-0.198	-0.198	0.000	0.000	0.000	0.000
60	A	65	ILE	0	0.010	-0.002	19.108	-0.593	-0.593	0.000	0.000	0.000	0.000
61	A	66	LYS	1	0.744	0.822	14.974	16.463	16.463	0.000	0.000	0.000	0.000
62	A	67	THR	0	0.057	-0.019	13.945	-1.256	-1.256	0.000	0.000	0.000	0.000
63	A	68	ARG	1	0.765	0.857	9.259	27.300	27.300	0.000	0.000	0.000	0.000
64	A	69	GLU	-1	-0.907	-0.969	12.767	-19.639	-19.639	0.000	0.000	0.000	0.000
65	A	70	SER	0	-0.019	-0.024	12.032	0.600	0.600	0.000	0.000	0.000	0.000
66	A	71	LEU	0	-0.019	0.004	14.316	0.686	0.686	0.000	0.000	0.000	0.000
67	A	72	LEU	0	0.004	0.016	16.978	0.766	0.766	0.000	0.000	0.000	0.000
68	A	73	ASP	-1	-0.846	-0.904	19.413	-14.194	-14.194	0.000	0.000	0.000	0.000
69	A	74	ALA	0	0.010	0.006	19.424	0.542	0.542	0.000	0.000	0.000	0.000
70	A	75	LEU	0	-0.034	-0.020	19.583	0.564	0.564	0.000	0.000	0.000	0.000
71	A	76	THR	0	-0.012	-0.023	21.848	0.757	0.757	0.000	0.000	0.000	0.000
72	A	77	GLU	-1	-0.815	-0.916	24.891	-11.461	-11.461	0.000	0.000	0.000	0.000
73	A	78	HIS	1	0.794	0.896	24.097	12.858	12.858	0.000	0.000	0.000	0.000
74	A	79	VAL	0	-0.021	-0.023	25.222	0.358	0.358	0.000	0.000	0.000	0.000
75	A	80	LYS	1	0.848	0.906	27.591	11.496	11.496	0.000	0.000	0.000	0.000
76	A	81	ALA	0	-0.019	0.015	29.376	0.380	0.380	0.000	0.000	0.000	0.000
77	A	82	ASN	0	-0.126	-0.068	28.526	-0.046	-0.046	0.000	0.000	0.000	0.000
78	A	83	HIS	0	-0.044	-0.031	30.325	0.070	0.070	0.000	0.000	0.000	0.000
79	A	84	GLU	-1	-0.941	-0.972	32.756	-8.222	-8.222	0.000	0.000	0.000	0.000
80	A	85	TYR	0	-0.021	-0.051	34.521	0.231	0.231	0.000	0.000	0.000	0.000
81	A	86	ASP	-1	-0.895	-0.950	34.893	-8.527	-8.527	0.000	0.000	0.000	0.000
82	A	87	VAL	0	-0.070	-0.043	34.130	-0.172	-0.172	0.000	0.000	0.000	0.000
83	A	88	PRO	0	-0.026	-0.005	30.292	-0.023	-0.023	0.000	0.000	0.000	0.000
84	A	89	GLU	-1	-0.900	-0.943	29.010	-11.040	-11.040	0.000	0.000	0.000	0.000
85	A	90	VAL	0	-0.014	-0.027	24.561	-0.302	-0.302	0.000	0.000	0.000	0.000
86	A	91	ILE	0	-0.014	0.010	25.385	-0.065	-0.065	0.000	0.000	0.000	0.000
87	A	92	ALA	0	0.008	0.001	19.922	-0.387	-0.387	0.000	0.000	0.000	0.000
88	A	93	LEU	0	0.001	0.000	20.497	0.410	0.410	0.000	0.000	0.000	0.000
89	A	94	PRO	0	-0.001	0.005	16.595	-0.892	-0.892	0.000	0.000	0.000	0.000
90	A	95	ILE	0	-0.010	-0.003	12.255	0.425	0.425	0.000	0.000	0.000	0.000
91	A	96	LYS	1	0.912	0.942	13.356	17.054	17.054	0.000	0.000	0.000	0.000
92	A	97	GLY	0	0.009	0.007	11.651	1.007	1.007	0.000	0.000	0.000	0.000
93	A	98	GLY	0	0.030	0.012	11.448	0.585	0.585	0.000	0.000	0.000	0.000
94	A	99	ASN	0	-0.002	-0.003	9.740	-2.581	-2.581	0.000	0.000	0.000	0.000
96	A	101	LYS	1	1.000	0.998	5.499	26.432	26.432	0.000	0.000	0.000	0.000
97	A	102	TYR	0	0.016	0.009	6.843	-0.838	-0.838	0.000	0.000	0.000	0.000
98	A	103	LEU	0	0.037	0.017	6.403	0.263	0.263	0.000	0.000	0.000	0.000
101	A	106	LEU	0	0.026	0.030	7.854	1.456	1.456	0.000	0.000	0.000	0.000
103	A	108	ASN	0	-0.057	-0.049	4.816	-0.245	-0.245	0.000	0.000	0.000	0.000
104	A	109	SER	0	-0.026	-0.005	8.215	2.730	2.730	0.000	0.000	0.000	0.000
105	A	110	THR	0	-0.032	-0.007	11.059	1.482	1.482	0.000	0.000	0.000	0.000
106	A	111	ARG	1	0.762	0.852	11.419	14.826	14.826	0.000	0.000	0.000	0.000
107	A	112	GLU	-1	-0.833	-0.911	9.431	-30.576	-30.576	0.000	0.000	0.000	0.000
108	A	113	SER	-1	-0.815	-0.859	13.057	-16.677	-16.677	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:6:THR)