FMO DATABASE

FMODB ID: K87N3

Calculation Name: 2P3D-A-Xray547

Preferred Name:

Target Type:

Ligand Name: benzyl [(1s,4s,7s,8r,9r,10s,13s,16s)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate

Ligand 3-letter code: 3TL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2P3D

Chain ID: A

ChEMBL ID:

UniProt ID: Q7SRY5

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	99
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-691857.247861
FMO2-HF: Nuclear repulsion	654139.737761
FMO2-HF: Total energy	-37717.510101
FMO2-MP2: Total energy	-37828.021945

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:PRO)

Summations of interaction energy for fragment #1(A:1: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.
-59.504	-55.25	1.309	-2.04	-3.523	-0.017

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.876 / q_NPA : 0.918

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	ILE	0	0.006	0.006	3.041	-0.041	2.336	0.084	-0.929	-1.533	-0.003
4	A	4	THR	0	0.018	0.010	5.093	3.394	3.406	-0.001	-0.004	-0.006	0.000
11	A	11	VAL	0	-0.003	-0.004	4.652	-3.540	-3.477	-0.001	-0.003	-0.059	0.000
67	A	67	CYS	0	-0.010	-0.010	3.254	-6.284	-5.720	0.336	-0.247	-0.653	-0.003
68	A	68	GLY	0	0.009	0.012	4.471	-7.126	-6.936	-0.001	-0.013	-0.175	0.000
69	A	69	HIS	0	-0.067	-0.029	2.591	-5.853	-4.805	0.892	-0.844	-1.097	-0.011
5	A	5	LEU	0	0.030	-0.001	8.807	-0.072	-0.072	0.000	0.000	0.000	0.000
6	A	6	TRP	0	-0.005	0.007	11.762	1.960	1.960	0.000	0.000	0.000	0.000
7	A	7	LYS	0	0.035	0.034	12.156	1.824	1.824	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.931	0.948	11.987	15.540	15.540	0.000	0.000	0.000	0.000
9	A	9	PRO	0	0.048	0.037	8.132	-0.373	-0.373	0.000	0.000	0.000	0.000
10	A	10	ILE	0	-0.022	-0.012	9.057	-0.371	-0.371	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.029	0.017	7.842	2.199	2.199	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.024	-0.015	8.658	-2.811	-2.811	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.864	0.936	11.402	18.702	18.702	0.000	0.000	0.000	0.000
15	A	15	VAL	0	0.034	0.013	14.010	-0.506	-0.506	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.734	-0.843	16.917	-12.554	-12.554	0.000	0.000	0.000	0.000
17	A	17	GLY	0	-0.034	-0.019	19.089	0.568	0.568	0.000	0.000	0.000	0.000
18	A	18	GLN	0	0.001	0.007	19.185	-0.056	-0.056	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.006	-0.004	13.545	-0.913	-0.913	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.797	0.892	14.439	16.257	16.257	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.909	-0.942	11.697	-22.649	-22.649	0.000	0.000	0.000	0.000
22	A	22	ALA	0	-0.031	-0.021	11.279	1.734	1.734	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.003	0.007	10.328	-2.202	-2.202	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.027	-0.017	5.173	0.100	0.100	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.855	-0.934	9.794	-18.559	-18.559	0.000	0.000	0.000	0.000
26	A	26	THR	0	-0.006	-0.023	11.862	0.491	0.491	0.000	0.000	0.000	0.000
27	A	27	GLY	0	-0.013	-0.002	14.403	0.847	0.847	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.017	0.012	16.479	1.077	1.077	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.844	-0.904	17.011	-15.755	-15.755	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.902	-0.961	18.140	-15.040	-15.040	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.031	-0.021	15.141	-0.893	-0.893	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.034	-0.017	17.117	1.031	1.031	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.008	-0.012	15.925	-0.872	-0.872	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.801	-0.900	19.326	-13.690	-13.690	0.000	0.000	0.000	0.000
35	A	35	ASP	-1	-0.919	-0.966	21.412	-12.014	-12.014	0.000	0.000	0.000	0.000
36	A	36	ILE	0	0.003	0.013	19.100	0.242	0.242	0.000	0.000	0.000	0.000
37	A	37	ASN	0	-0.049	-0.036	23.497	-0.193	-0.193	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.013	0.027	20.413	-0.365	-0.365	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.072	-0.069	24.344	0.697	0.697	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.038	0.017	25.922	-0.231	-0.231	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.916	0.947	28.311	9.932	9.932	0.000	0.000	0.000	0.000
42	A	42	TRP	0	0.066	0.035	27.616	-0.232	-0.232	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.878	0.932	28.586	10.270	10.270	0.000	0.000	0.000	0.000
44	A	44	PRO	0	0.000	-0.011	29.293	-0.306	-0.306	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.918	0.965	26.430	11.613	11.613	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.041	-0.026	28.979	0.184	0.184	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.047	0.045	22.954	0.018	0.018	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.016	-0.001	26.483	0.320	0.320	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.049	0.018	24.637	-0.620	-0.620	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.024	0.011	24.336	0.479	0.479	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.906	0.956	26.771	9.299	9.299	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.004	0.000	29.115	0.434	0.434	0.000	0.000	0.000	0.000
53	A	53	PHE	0	0.028	0.016	28.816	-0.323	-0.323	0.000	0.000	0.000	0.000
54	A	54	VAL	0	0.007	0.019	25.683	0.419	0.419	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.930	0.955	28.280	8.768	8.768	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.014	0.011	24.602	-0.059	-0.059	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.877	0.942	26.579	10.694	10.694	0.000	0.000	0.000	0.000
58	A	58	GLN	0	0.049	0.016	24.063	-0.194	-0.194	0.000	0.000	0.000	0.000
59	A	59	TYR	0	-0.013	-0.010	22.995	0.712	0.712	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.838	-0.915	22.815	-13.037	-13.037	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.937	-0.975	21.110	-12.830	-12.830	0.000	0.000	0.000	0.000
62	A	62	ILE	0	-0.015	0.009	17.906	-0.182	-0.182	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.003	0.001	14.165	-0.799	-0.799	0.000	0.000	0.000	0.000
64	A	64	ILE	0	0.001	-0.001	12.057	0.392	0.392	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.851	-0.908	9.795	-24.561	-24.561	0.000	0.000	0.000	0.000
66	A	66	ILE	0	0.024	0.004	6.775	0.912	0.912	0.000	0.000	0.000	0.000
70	A	70	ARG	1	0.829	0.884	6.769	23.082	23.082	0.000	0.000	0.000	0.000
71	A	71	ALA	0	0.030	0.026	10.492	-0.587	-0.587	0.000	0.000	0.000	0.000
72	A	72	VAL	0	0.003	-0.009	12.419	0.876	0.876	0.000	0.000	0.000	0.000
73	A	73	GLY	0	0.005	0.000	16.259	-0.069	-0.069	0.000	0.000	0.000	0.000
74	A	74	ALA	0	0.000	0.014	18.505	0.294	0.294	0.000	0.000	0.000	0.000
75	A	75	VAL	0	0.000	0.002	17.500	-0.876	-0.876	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.031	-0.011	20.156	1.011	1.011	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.015	0.013	21.463	-0.402	-0.402	0.000	0.000	0.000	0.000
78	A	78	GLY	0	-0.016	-0.017	23.581	0.692	0.692	0.000	0.000	0.000	0.000
79	A	79	PRO	0	0.056	0.046	23.955	-0.470	-0.470	0.000	0.000	0.000	0.000
80	A	80	THR	0	-0.064	-0.041	19.943	0.348	0.348	0.000	0.000	0.000	0.000
81	A	81	PRO	0	-0.029	-0.036	22.001	-0.109	-0.109	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.047	0.034	16.871	-0.249	-0.249	0.000	0.000	0.000	0.000
83	A	83	ASN	0	-0.033	-0.016	14.993	0.885	0.885	0.000	0.000	0.000	0.000
84	A	84	ILE	0	0.003	0.004	14.538	-1.033	-1.033	0.000	0.000	0.000	0.000
85	A	85	ILE	0	0.004	-0.005	9.983	0.699	0.699	0.000	0.000	0.000	0.000
86	A	86	GLY	0	0.115	0.056	12.411	-1.082	-1.082	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.866	0.898	13.774	15.535	15.535	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.007	0.006	14.292	-1.500	-1.500	0.000	0.000	0.000	0.000
89	A	89	MET	0	-0.034	0.003	11.886	-0.121	-0.121	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.018	-0.017	8.692	-2.297	-2.297	0.000	0.000	0.000	0.000
91	A	91	THR	0	-0.024	-0.028	9.262	-2.400	-2.400	0.000	0.000	0.000	0.000
92	A	92	GLN	0	-0.030	-0.009	11.498	-0.627	-0.627	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.049	-0.019	5.701	-0.383	-0.383	0.000	0.000	0.000	0.000
94	A	94	GLY	0	0.019	0.017	6.110	-6.497	-6.497	0.000	0.000	0.000	0.000
95	A	95	CYS	0	-0.082	-0.032	5.791	-4.017	-4.017	0.000	0.000	0.000	0.000
96	A	96	THR	0	0.019	0.004	6.729	4.949	4.949	0.000	0.000	0.000	0.000
97	A	97	LEU	0	-0.040	-0.018	8.300	-2.454	-2.454	0.000	0.000	0.000	0.000
98	A	98	ASN	0	-0.073	-0.044	8.565	2.323	2.323	0.000	0.000	0.000	0.000
99	A	99	PHE	-1	-0.918	-0.939	11.693	-20.028	-20.028	0.000	0.000	0.000	0.000

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