FMO DATABASE

FMODB ID: YR4K2

Calculation Name: 3VC0-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3VC0

Chain ID: A

ChEMBL ID:

UniProt ID: P00615

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	111
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-958473.14742
FMO2-HF: Nuclear repulsion	908212.899974
FMO2-HF: Total energy	-50260.247446
FMO2-MP2: Total energy	-50393.624922

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:ASN)

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

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.
-184.692	-172.925	30.194	-18.653	-23.309	-0.124

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.822 / q_NPA : 0.917

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	VAL	0	0.030	0.012	2.628	2.141	5.005	1.208	-1.591	-2.481	0.012
4	A	4	GLN	0	-0.029	-0.025	1.965	-37.203	-36.475	13.160	-6.218	-7.670	-0.025
5	A	5	PHE	0	0.065	0.044	3.672	5.474	6.204	0.015	-0.270	-0.475	0.001
6	A	6	GLY	0	0.029	0.019	5.212	5.813	5.941	-0.001	-0.007	-0.120	0.000
51	A	52	TYR	0	-0.023	-0.067	4.704	-3.430	-3.344	-0.001	-0.005	-0.080	0.000
62	A	63	SER	0	-0.021	-0.013	2.693	-20.271	-17.753	0.469	-1.355	-1.632	-0.016
63	A	64	LEU	0	-0.001	-0.008	2.677	-11.464	-9.329	0.617	-1.224	-1.529	-0.014
64	A	65	THR	0	-0.025	-0.011	3.647	1.732	2.765	0.018	-0.422	-0.630	-0.002
65	A	66	THR	0	-0.041	-0.022	1.833	-43.886	-45.020	11.792	-5.050	-5.607	-0.057
66	A	67	TYR	0	-0.027	-0.039	2.345	7.553	9.265	2.913	-1.948	-2.677	-0.019
67	A	68	THR	0	0.001	0.007	5.097	0.259	0.262	-0.001	0.000	-0.002	0.000
85	A	88	VAL	0	0.042	0.013	3.886	-0.208	-0.078	0.000	-0.033	-0.097	0.000
87	A	92	ASP	-1	-0.705	-0.794	3.366	-65.074	-64.240	0.005	-0.530	-0.309	-0.004
7	A	7	LYS	0	0.048	0.023	5.346	1.220	1.220	0.000	0.000	0.000	0.000
8	A	8	MET	0	-0.047	-0.009	5.868	3.947	3.947	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.019	0.008	8.826	3.102	3.102	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.960	-0.968	10.953	-18.776	-18.776	0.000	0.000	0.000	0.000
11	A	11	CYS	0	-0.047	-0.016	11.746	1.977	1.977	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.024	-0.010	12.905	1.497	1.497	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.026	-0.009	14.626	1.472	1.472	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.895	0.941	16.725	15.511	15.511	0.000	0.000	0.000	0.000
15	A	15	ASN	0	0.017	-0.002	16.582	0.508	0.508	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.914	0.965	17.590	14.269	14.269	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.853	0.932	17.706	15.315	15.315	0.000	0.000	0.000	0.000
18	A	18	PRO	0	0.036	0.022	15.638	-0.891	-0.891	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.055	0.018	11.053	0.095	0.095	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.013	-0.015	12.114	-0.815	-0.815	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.805	-0.888	13.842	-15.392	-15.392	0.000	0.000	0.000	0.000
22	A	22	PHE	0	0.013	-0.006	13.206	0.871	0.871	0.000	0.000	0.000	0.000
23	A	23	MET	0	-0.071	-0.033	10.408	-1.716	-1.716	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.009	-0.020	14.087	0.245	0.245	0.000	0.000	0.000	0.000
25	A	25	TYR	0	-0.036	-0.033	17.741	0.965	0.965	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.003	-0.002	18.750	-0.550	-0.550	0.000	0.000	0.000	0.000
27	A	27	CYS	0	-0.071	-0.010	20.626	0.424	0.424	0.000	0.000	0.000	0.000
28	A	28	TYR	0	-0.017	-0.021	16.151	-0.233	-0.233	0.000	0.000	0.000	0.000
29	A	29	CYS	0	-0.103	-0.008	13.622	-3.042	-3.042	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.076	0.028	13.699	0.821	0.821	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.789	0.885	8.569	26.002	26.002	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.053	0.051	13.152	1.123	1.123	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.048	0.001	15.554	0.076	0.076	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.127	-0.061	17.790	0.136	0.136	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.077	0.047	21.655	0.028	0.028	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.060	-0.021	23.561	-0.356	-0.356	0.000	0.000	0.000	0.000
37	A	37	PRO	0	-0.006	0.007	21.025	0.095	0.095	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.031	-0.026	22.885	0.545	0.545	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.800	-0.872	22.108	-13.106	-13.106	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.830	-0.918	22.305	-12.982	-12.982	0.000	0.000	0.000	0.000
41	A	41	LEU	0	0.012	0.010	16.733	-0.902	-0.902	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.711	-0.879	17.578	-16.482	-16.482	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.829	0.917	18.277	14.529	14.529	0.000	0.000	0.000	0.000
44	A	44	CYS	0	-0.035	0.009	14.575	1.036	1.036	0.000	0.000	0.000	0.000
45	A	46	GLN	0	0.067	0.052	14.135	-0.809	-0.809	0.000	0.000	0.000	0.000
46	A	47	VAL	0	-0.008	-0.005	14.448	-0.392	-0.392	0.000	0.000	0.000	0.000
47	A	48	HIS	0	-0.089	-0.047	6.743	1.784	1.784	0.000	0.000	0.000	0.000
48	A	49	ASP	-1	-0.818	-0.919	11.229	-24.169	-24.169	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.910	-0.961	12.830	-16.493	-16.493	0.000	0.000	0.000	0.000
50	A	51	CYS	0	-0.086	-0.025	7.521	2.285	2.285	0.000	0.000	0.000	0.000
52	A	53	ALA	0	0.046	0.031	10.263	0.022	0.022	0.000	0.000	0.000	0.000
53	A	54	GLU	-1	-0.849	-0.930	13.580	-16.558	-16.558	0.000	0.000	0.000	0.000
54	A	55	ALA	0	-0.023	-0.022	9.763	0.370	0.370	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.923	-0.962	9.579	-27.507	-27.507	0.000	0.000	0.000	0.000
56	A	57	LYS	1	0.837	0.941	12.428	17.915	17.915	0.000	0.000	0.000	0.000
57	A	58	HIS	1	0.774	0.868	14.714	19.677	19.677	0.000	0.000	0.000	0.000
58	A	59	GLY	0	0.032	0.030	14.304	0.118	0.118	0.000	0.000	0.000	0.000
59	A	60	CYS	0	-0.003	0.007	8.422	-0.397	-0.397	0.000	0.000	0.000	0.000
60	A	61	TYR	0	0.083	0.027	8.097	1.150	1.150	0.000	0.000	0.000	0.000
61	A	62	PRO	0	0.013	0.026	4.975	-6.829	-6.829	0.000	0.000	0.000	0.000
68	A	69	TRP	0	-0.016	-0.020	6.063	1.473	1.473	0.000	0.000	0.000	0.000
69	A	70	GLU	-1	-0.779	-0.855	8.934	-18.845	-18.845	0.000	0.000	0.000	0.000
70	A	72	ARG	1	0.838	0.894	13.414	19.445	19.445	0.000	0.000	0.000	0.000
71	A	73	GLN	0	0.021	0.007	16.990	0.201	0.201	0.000	0.000	0.000	0.000
72	A	74	VAL	0	-0.045	-0.027	18.389	0.417	0.417	0.000	0.000	0.000	0.000
73	A	75	GLY	0	0.035	0.033	16.007	0.032	0.032	0.000	0.000	0.000	0.000
74	A	76	PRO	0	-0.002	-0.008	10.523	0.082	0.082	0.000	0.000	0.000	0.000
75	A	77	TYR	0	-0.023	-0.015	11.987	1.463	1.463	0.000	0.000	0.000	0.000
76	A	78	CYS	0	-0.033	-0.001	5.608	-3.344	-3.344	0.000	0.000	0.000	0.000
77	A	79	ASN	0	-0.077	-0.054	10.513	2.502	2.502	0.000	0.000	0.000	0.000
78	A	80	SER	0	0.041	0.018	8.283	-2.257	-2.257	0.000	0.000	0.000	0.000
79	A	81	LYS	1	0.946	0.980	10.507	20.460	20.460	0.000	0.000	0.000	0.000
80	A	82	THR	0	-0.032	-0.030	9.754	1.741	1.741	0.000	0.000	0.000	0.000
81	A	83	GLN	0	0.035	0.002	10.831	-1.749	-1.749	0.000	0.000	0.000	0.000
82	A	85	GLU	-1	-0.839	-0.907	6.157	-37.262	-37.262	0.000	0.000	0.000	0.000
83	A	86	VAL	0	-0.019	-0.017	7.127	-2.388	-2.388	0.000	0.000	0.000	0.000
84	A	87	PHE	0	-0.020	-0.003	9.823	0.010	0.010	0.000	0.000	0.000	0.000
86	A	90	ALA	0	0.025	0.004	6.471	2.366	2.366	0.000	0.000	0.000	0.000
88	A	93	PHE	0	0.004	-0.020	6.976	3.867	3.867	0.000	0.000	0.000	0.000
89	A	94	ALA	0	-0.035	-0.013	9.814	2.291	2.291	0.000	0.000	0.000	0.000
90	A	95	ALA	0	0.029	0.023	9.755	1.797	1.797	0.000	0.000	0.000	0.000
91	A	96	ALA	0	0.005	0.006	9.655	1.739	1.739	0.000	0.000	0.000	0.000
92	A	97	LYS	1	0.901	0.937	11.609	19.910	19.910	0.000	0.000	0.000	0.000
93	A	99	PHE	0	0.036	-0.020	11.558	0.690	0.690	0.000	0.000	0.000	0.000
94	A	100	ALA	0	-0.077	-0.023	15.908	0.669	0.669	0.000	0.000	0.000	0.000
95	A	101	GLN	0	-0.133	-0.055	17.761	0.761	0.761	0.000	0.000	0.000	0.000
96	A	102	GLU	-1	-0.875	-0.942	19.542	-13.240	-13.240	0.000	0.000	0.000	0.000
97	A	103	ASP	-1	-0.943	-0.964	20.933	-12.186	-12.186	0.000	0.000	0.000	0.000
98	A	104	TYR	0	-0.071	-0.038	18.591	0.244	0.244	0.000	0.000	0.000	0.000
99	A	105	ASN	0	0.024	0.005	22.257	0.676	0.676	0.000	0.000	0.000	0.000
100	A	106	PRO	0	0.027	-0.006	24.656	-0.248	-0.248	0.000	0.000	0.000	0.000
101	A	107	ALA	0	-0.024	-0.005	26.022	-0.129	-0.129	0.000	0.000	0.000	0.000
102	A	108	HIS	1	0.792	0.875	23.655	12.213	12.213	0.000	0.000	0.000	0.000
103	A	109	SER	0	0.040	0.027	21.565	-0.587	-0.587	0.000	0.000	0.000	0.000
104	A	110	ASN	0	-0.051	-0.015	21.641	0.230	0.230	0.000	0.000	0.000	0.000
105	A	111	ILE	0	0.006	0.018	23.104	0.692	0.692	0.000	0.000	0.000	0.000
106	A	112	ASN	0	-0.001	-0.001	23.981	-0.674	-0.674	0.000	0.000	0.000	0.000
107	A	113	THR	0	0.101	0.026	20.740	0.611	0.611	0.000	0.000	0.000	0.000
108	A	114	GLY	0	0.031	0.027	24.155	0.163	0.163	0.000	0.000	0.000	0.000
109	A	115	GLU	-1	-0.949	-0.984	26.461	-9.508	-9.508	0.000	0.000	0.000	0.000
110	A	116	ARG	1	0.790	0.871	26.840	10.262	10.262	0.000	0.000	0.000	0.000
111	A	118	LYS	0	0.047	0.055	24.508	-1.451	-1.451	0.000	0.000	0.000	0.000

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