FMO DATABASE

FMODB ID: ML6MZ

Calculation Name: 1FMB-A-Xray547

Preferred Name:

Target Type:

Ligand Name: [2-(2-methyl-propane-2-sulfonylmethyl)-3-naphthalen-1-yl-propionyl-valinyl]-phenylalaninol

Ligand 3-letter code: HYB

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1FMB

Chain ID: A

ChEMBL ID:

UniProt ID: P32542

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	104
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-745752.469378
FMO2-HF: Nuclear repulsion	706699.750426
FMO2-HF: Total energy	-39052.718952
FMO2-MP2: Total energy	-39169.140038

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:VAL)

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

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.
89.726	92.698	0.24	-1.205	-2.007	-0.008

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.832 / 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	TYR	0	-0.021	-0.016	2.901	-2.687	0.211	0.241	-1.204	-1.936	-0.008
11	A	11	THR	0	0.014	0.007	4.562	-4.470	-4.396	-0.001	-0.001	-0.071	0.000
4	A	4	ASN	0	0.017	-0.005	5.969	0.679	0.679	0.000	0.000	0.000	0.000
5	A	5	LEU	0	-0.006	-0.002	9.212	2.135	2.135	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.841	-0.893	11.185	-21.188	-21.188	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.909	0.947	10.926	21.459	21.459	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.984	0.989	10.824	15.430	15.430	0.000	0.000	0.000	0.000
9	A	9	PRO	0	0.044	0.038	7.477	-1.165	-1.165	0.000	0.000	0.000	0.000
10	A	10	THR	0	-0.006	0.004	7.634	1.778	1.778	0.000	0.000	0.000	0.000
12	A	12	ILE	0	0.054	0.045	7.003	2.356	2.356	0.000	0.000	0.000	0.000
13	A	13	VAL	0	-0.006	-0.001	8.824	-2.734	-2.734	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.008	0.009	11.300	1.359	1.359	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.069	0.030	14.777	-0.132	-0.132	0.000	0.000	0.000	0.000
16	A	16	ASN	0	0.035	0.004	17.340	0.144	0.144	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.858	-0.933	18.938	-13.596	-13.596	0.000	0.000	0.000	0.000
18	A	18	THR	0	-0.001	0.009	18.861	0.403	0.403	0.000	0.000	0.000	0.000
19	A	19	PRO	0	-0.029	0.002	14.860	-0.702	-0.702	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.006	-0.005	14.195	0.838	0.838	0.000	0.000	0.000	0.000
21	A	21	ASN	0	-0.021	-0.019	10.153	-2.632	-2.632	0.000	0.000	0.000	0.000
22	A	22	VAL	0	-0.019	-0.006	10.488	1.387	1.387	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.012	-0.005	10.325	-2.019	-2.019	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.072	-0.035	5.868	-0.159	-0.159	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.834	-0.929	9.896	-18.786	-18.786	0.000	0.000	0.000	0.000
26	A	26	THR	0	-0.027	-0.026	11.692	0.326	0.326	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.017	0.013	14.241	0.738	0.738	0.000	0.000	0.000	0.000
28	A	28	ALA	0	0.009	0.022	16.604	0.917	0.917	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.820	-0.899	17.345	-14.785	-14.785	0.000	0.000	0.000	0.000
30	A	30	THR	0	-0.072	-0.053	19.165	-0.063	-0.063	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.033	-0.049	16.259	-0.629	-0.629	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.030	-0.004	18.066	0.805	0.805	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.020	-0.009	18.789	-0.744	-0.744	0.000	0.000	0.000	0.000
34	A	34	THR	0	0.052	0.027	19.710	0.681	0.681	0.000	0.000	0.000	0.000
35	A	35	THR	0	0.022	-0.024	22.165	-0.175	-0.175	0.000	0.000	0.000	0.000
36	A	36	ALA	0	0.015	0.006	23.566	0.176	0.176	0.000	0.000	0.000	0.000
37	A	37	HIS	0	-0.033	-0.006	16.832	-0.349	-0.349	0.000	0.000	0.000	0.000
38	A	38	TYR	0	0.054	0.018	21.666	0.051	0.051	0.000	0.000	0.000	0.000
39	A	39	ASN	0	0.022	0.003	24.072	0.171	0.171	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.939	0.971	18.666	13.948	13.948	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.075	-0.005	20.293	-0.193	-0.193	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.916	0.957	21.940	13.123	13.123	0.000	0.000	0.000	0.000
43	A	43	TYR	0	-0.006	0.000	23.998	0.534	0.534	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.856	0.927	24.691	10.398	10.398	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.039	0.030	26.611	0.233	0.233	0.000	0.000	0.000	0.000
46	A	46	ARG	0	-0.004	-0.008	28.184	0.254	0.254	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.894	0.967	29.207	9.116	9.116	0.000	0.000	0.000	0.000
48	A	48	TYR	-1	-0.826	-0.914	29.412	-9.570	-9.570	0.000	0.000	0.000	0.000
49	A	49	GLN	0	0.034	0.004	31.026	-0.491	-0.491	0.000	0.000	0.000	0.000
50	A	50	GLY	0	0.004	0.012	30.250	-0.134	-0.134	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.013	-0.018	30.547	0.271	0.271	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.000	0.007	29.625	0.129	0.129	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.064	-0.029	23.688	-0.324	-0.324	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.061	0.033	26.955	0.338	0.338	0.000	0.000	0.000	0.000
55	A	55	GLY	0	-0.023	-0.021	25.461	-0.578	-0.578	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.015	-0.013	24.394	0.358	0.358	0.000	0.000	0.000	0.000
57	A	57	GLY	0	-0.015	-0.002	27.044	0.294	0.294	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.016	0.024	29.765	0.343	0.343	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.016	-0.023	29.318	-0.581	-0.581	0.000	0.000	0.000	0.000
60	A	60	VAL	0	-0.012	0.001	27.616	0.198	0.198	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.886	-0.943	29.501	-8.902	-8.902	0.000	0.000	0.000	0.000
62	A	62	THR	0	-0.041	-0.027	26.096	-0.205	-0.205	0.000	0.000	0.000	0.000
63	A	63	PHE	0	0.008	0.016	27.907	0.348	0.348	0.000	0.000	0.000	0.000
64	A	64	SER	0	-0.004	0.002	26.325	-0.488	-0.488	0.000	0.000	0.000	0.000
65	A	65	THR	0	-0.016	-0.026	24.202	0.319	0.319	0.000	0.000	0.000	0.000
66	A	66	PRO	0	-0.004	0.021	24.339	-0.564	-0.564	0.000	0.000	0.000	0.000
67	A	67	VAL	0	-0.027	-0.023	19.308	0.014	0.014	0.000	0.000	0.000	0.000
68	A	68	THR	0	-0.037	-0.025	18.836	0.085	0.085	0.000	0.000	0.000	0.000
69	A	69	ILE	0	0.008	0.007	13.201	-0.096	-0.096	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.846	0.921	14.057	15.957	15.957	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.878	0.917	5.679	34.355	34.355	0.000	0.000	0.000	0.000
72	A	72	LYS	1	0.849	0.919	5.381	41.723	41.723	0.000	0.000	0.000	0.000
73	A	73	GLY	0	0.035	0.017	8.331	0.305	0.305	0.000	0.000	0.000	0.000
74	A	74	ARG	1	0.873	0.952	10.442	27.430	27.430	0.000	0.000	0.000	0.000
75	A	75	HIS	0	0.017	-0.020	13.465	0.406	0.406	0.000	0.000	0.000	0.000
76	A	76	ILE	0	0.036	0.026	13.208	0.610	0.610	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.920	0.959	17.187	13.624	13.624	0.000	0.000	0.000	0.000
78	A	78	THR	0	0.043	0.021	18.276	0.212	0.212	0.000	0.000	0.000	0.000
79	A	79	ARG	0	0.011	0.007	21.366	0.489	0.489	0.000	0.000	0.000	0.000
80	A	80	MET	0	-0.047	-0.011	17.301	-0.852	-0.852	0.000	0.000	0.000	0.000
81	A	81	LEU	0	0.063	0.032	21.814	0.694	0.694	0.000	0.000	0.000	0.000
82	A	82	VAL	0	-0.046	-0.029	22.570	-0.624	-0.624	0.000	0.000	0.000	0.000
83	A	83	ALA	0	0.061	0.029	24.290	0.452	0.452	0.000	0.000	0.000	0.000
84	A	84	ASP	-1	-0.843	-0.883	24.725	-10.762	-10.762	0.000	0.000	0.000	0.000
85	A	85	ILE	0	-0.015	-0.003	20.341	0.122	0.122	0.000	0.000	0.000	0.000
86	A	86	PRO	0	-0.019	-0.029	21.141	-0.198	-0.198	0.000	0.000	0.000	0.000
87	A	87	VAL	0	-0.049	-0.025	15.440	-0.376	-0.376	0.000	0.000	0.000	0.000
88	A	88	THR	0	0.025	-0.003	15.524	0.546	0.546	0.000	0.000	0.000	0.000
89	A	89	ILE	0	-0.004	-0.008	14.620	-1.293	-1.293	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.019	-0.018	10.983	0.487	0.487	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.087	0.039	12.875	-0.981	-0.981	0.000	0.000	0.000	0.000
92	A	92	ARG	1	0.852	0.890	14.322	14.538	14.538	0.000	0.000	0.000	0.000
93	A	93	ASP	-1	-0.721	-0.794	15.475	-17.181	-17.181	0.000	0.000	0.000	0.000
94	A	94	ILE	0	0.025	-0.001	12.809	-0.745	-0.745	0.000	0.000	0.000	0.000
95	A	95	LEU	0	-0.065	-0.034	9.096	-2.480	-2.480	0.000	0.000	0.000	0.000
96	A	96	GLN	0	0.008	0.017	11.386	-2.078	-2.078	0.000	0.000	0.000	0.000
97	A	97	ASP	-1	-0.855	-0.913	13.507	-18.752	-18.752	0.000	0.000	0.000	0.000
98	A	98	LEU	0	-0.067	-0.042	8.628	-1.331	-1.331	0.000	0.000	0.000	0.000
99	A	99	GLY	0	-0.017	0.004	9.010	-3.436	-3.436	0.000	0.000	0.000	0.000
100	A	100	ALA	0	-0.100	-0.050	7.449	-4.362	-4.362	0.000	0.000	0.000	0.000
101	A	101	LYS	1	0.954	0.965	8.185	32.632	32.632	0.000	0.000	0.000	0.000
102	A	102	LEU	0	0.016	0.016	8.950	-3.360	-3.360	0.000	0.000	0.000	0.000
103	A	103	VAL	0	-0.061	-0.042	10.078	0.323	0.323	0.000	0.000	0.000	0.000
104	A	104	LEU	-1	-0.892	-0.925	12.593	-19.363	-19.363	0.000	0.000	0.000	0.000

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