FMO DATABASE

FMODB ID: VYLG1

Calculation Name: 4LQW-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4LQW

Chain ID: A

ChEMBL ID:

UniProt ID: P12497

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	169
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1769798.552698
FMO2-HF: Nuclear repulsion	1703188.634586
FMO2-HF: Total energy	-66609.918113
FMO2-MP2: Total energy	-66800.59505

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:-4:MET)

Summations of interaction energy for fragment #1(A:-4:MET)

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.
-26.189	-18.161	3.27	-3.425	-7.875	-0.027

Interaction energy analysis for fragmet #1(A:-4:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.816 / q_NPA : 0.904

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	-2	LEU	0	0.003	0.010	2.208	5.127	8.343	2.070	-1.730	-3.556	-0.013
4	A	-1	SER	0	-0.099	-0.056	2.686	4.978	6.096	0.209	-0.421	-0.907	-0.003
5	A	0	LYS	1	0.917	0.939	4.214	32.826	32.918	0.000	-0.036	-0.056	0.000
30	A	25	PHE	0	0.044	0.012	2.338	-1.576	-0.434	0.749	-0.474	-1.417	-0.005
98	A	93	THR	0	-0.002	-0.021	3.489	1.538	1.746	0.001	-0.040	-0.169	0.000
102	A	97	LEU	0	-0.052	-0.012	3.573	-2.220	-1.659	0.164	-0.119	-0.606	-0.001
136	A	131	PHE	0	-0.076	-0.018	3.812	-5.540	-3.849	0.077	-0.605	-1.164	-0.005
6	A	1	GLU	-1	-0.917	-0.954	7.942	-24.541	-24.541	0.000	0.000	0.000	0.000
7	A	2	THR	0	-0.026	-0.014	10.659	0.947	0.947	0.000	0.000	0.000	0.000
8	A	3	ASN	0	-0.062	-0.035	7.022	4.243	4.243	0.000	0.000	0.000	0.000
9	A	4	PRO	0	-0.015	-0.005	10.774	-0.119	-0.119	0.000	0.000	0.000	0.000
10	A	5	VAL	0	0.017	0.006	10.435	-1.822	-1.822	0.000	0.000	0.000	0.000
11	A	6	VAL	0	0.013	0.002	12.483	1.728	1.728	0.000	0.000	0.000	0.000
12	A	7	PHE	0	-0.030	-0.018	13.854	-1.375	-1.375	0.000	0.000	0.000	0.000
13	A	8	PHE	0	0.019	0.002	16.369	0.756	0.756	0.000	0.000	0.000	0.000
14	A	9	ASP	-1	-0.792	-0.849	18.399	-15.018	-15.018	0.000	0.000	0.000	0.000
15	A	10	VAL	0	0.016	-0.003	19.541	0.417	0.417	0.000	0.000	0.000	0.000
16	A	11	CYS	0	-0.025	0.012	22.425	-0.033	-0.033	0.000	0.000	0.000	0.000
17	A	12	ALA	0	0.013	0.014	25.749	-0.010	-0.010	0.000	0.000	0.000	0.000
18	A	13	ASP	-1	-0.832	-0.920	27.403	-9.655	-9.655	0.000	0.000	0.000	0.000
19	A	14	GLY	0	-0.005	0.004	29.757	0.317	0.317	0.000	0.000	0.000	0.000
20	A	15	GLU	-1	-0.861	-0.906	28.247	-10.757	-10.757	0.000	0.000	0.000	0.000
21	A	16	PRO	0	0.011	-0.019	25.941	-0.400	-0.400	0.000	0.000	0.000	0.000
22	A	17	LEU	0	-0.006	-0.001	21.713	-0.132	-0.132	0.000	0.000	0.000	0.000
23	A	18	GLY	0	-0.009	0.008	20.488	-0.521	-0.521	0.000	0.000	0.000	0.000
24	A	19	ARG	1	0.850	0.895	16.666	15.774	15.774	0.000	0.000	0.000	0.000
25	A	20	ILE	0	-0.017	-0.001	13.051	-0.756	-0.756	0.000	0.000	0.000	0.000
26	A	21	THR	0	0.027	0.000	11.987	1.310	1.310	0.000	0.000	0.000	0.000
27	A	22	MET	0	-0.063	-0.019	9.580	-2.034	-2.034	0.000	0.000	0.000	0.000
28	A	23	GLU	-1	-0.744	-0.831	5.955	-41.547	-41.547	0.000	0.000	0.000	0.000
29	A	24	LEU	0	0.004	0.004	7.646	-1.111	-1.111	0.000	0.000	0.000	0.000
31	A	26	SER	0	0.025	0.004	7.833	2.311	2.311	0.000	0.000	0.000	0.000
32	A	27	ASN	0	-0.049	-0.032	6.751	1.723	1.723	0.000	0.000	0.000	0.000
33	A	28	ILE	0	-0.050	-0.019	7.144	-0.161	-0.161	0.000	0.000	0.000	0.000
34	A	29	VAL	0	-0.005	0.013	10.021	1.403	1.403	0.000	0.000	0.000	0.000
35	A	30	PRO	0	0.044	0.026	12.496	-0.014	-0.014	0.000	0.000	0.000	0.000
36	A	31	ARG	1	0.902	0.975	14.568	13.105	13.105	0.000	0.000	0.000	0.000
37	A	32	THR	0	0.000	-0.035	13.638	0.821	0.821	0.000	0.000	0.000	0.000
38	A	33	ALA	0	-0.025	-0.004	11.840	0.123	0.123	0.000	0.000	0.000	0.000
39	A	34	GLU	-1	-0.790	-0.882	13.672	-13.992	-13.992	0.000	0.000	0.000	0.000
40	A	35	ASN	0	-0.002	0.000	17.255	1.072	1.072	0.000	0.000	0.000	0.000
41	A	36	PHE	0	0.043	0.007	14.288	0.393	0.393	0.000	0.000	0.000	0.000
42	A	37	ARG	1	0.794	0.846	15.605	14.851	14.851	0.000	0.000	0.000	0.000
43	A	38	ALA	0	-0.010	0.000	17.011	0.467	0.467	0.000	0.000	0.000	0.000
44	A	39	LEU	0	-0.039	-0.010	19.533	0.584	0.584	0.000	0.000	0.000	0.000
45	A	40	CYS	0	-0.050	-0.018	17.170	0.131	0.131	0.000	0.000	0.000	0.000
46	A	41	THR	0	-0.022	-0.034	19.707	0.323	0.323	0.000	0.000	0.000	0.000
47	A	42	GLY	0	0.006	0.015	22.320	0.489	0.489	0.000	0.000	0.000	0.000
48	A	43	GLU	-1	-0.786	-0.844	22.629	-12.485	-12.485	0.000	0.000	0.000	0.000
49	A	44	LYS	1	0.812	0.900	23.193	12.503	12.503	0.000	0.000	0.000	0.000
50	A	45	GLY	0	0.001	0.010	27.381	0.331	0.331	0.000	0.000	0.000	0.000
51	A	46	PHE	0	-0.037	-0.021	25.242	0.236	0.236	0.000	0.000	0.000	0.000
52	A	47	GLY	0	0.049	0.009	23.593	-0.343	-0.343	0.000	0.000	0.000	0.000
53	A	48	PHE	0	-0.019	-0.008	17.955	0.466	0.466	0.000	0.000	0.000	0.000
54	A	49	LYS	1	0.865	0.932	22.989	11.305	11.305	0.000	0.000	0.000	0.000
55	A	50	ASN	0	-0.040	-0.024	25.627	0.226	0.226	0.000	0.000	0.000	0.000
56	A	51	SER	0	-0.044	-0.021	23.813	0.202	0.202	0.000	0.000	0.000	0.000
57	A	52	ILE	0	0.009	-0.012	24.778	-0.136	-0.136	0.000	0.000	0.000	0.000
58	A	53	PHE	0	-0.002	-0.017	17.156	-0.321	-0.321	0.000	0.000	0.000	0.000
59	A	54	HIS	0	-0.004	0.015	22.610	0.118	0.118	0.000	0.000	0.000	0.000
60	A	55	ARG	1	0.887	0.950	21.376	12.838	12.838	0.000	0.000	0.000	0.000
61	A	56	VAL	0	0.020	0.008	19.835	-0.702	-0.702	0.000	0.000	0.000	0.000
62	A	57	ILE	0	-0.050	-0.009	20.073	0.644	0.644	0.000	0.000	0.000	0.000
63	A	58	PRO	0	0.033	-0.002	18.953	-0.710	-0.710	0.000	0.000	0.000	0.000
64	A	59	ASP	-1	-0.855	-0.895	16.243	-15.500	-15.500	0.000	0.000	0.000	0.000
65	A	60	PHE	0	-0.021	-0.012	15.550	-0.254	-0.254	0.000	0.000	0.000	0.000
66	A	61	VAL	0	-0.009	-0.006	14.544	-1.202	-1.202	0.000	0.000	0.000	0.000
67	A	62	CYS	0	-0.004	0.017	15.655	1.046	1.046	0.000	0.000	0.000	0.000
68	A	63	GLN	0	0.008	0.003	16.620	-0.767	-0.767	0.000	0.000	0.000	0.000
69	A	64	GLY	0	0.043	0.015	18.957	0.532	0.532	0.000	0.000	0.000	0.000
70	A	65	GLY	0	0.042	0.031	20.640	-0.190	-0.190	0.000	0.000	0.000	0.000
71	A	66	ASP	-1	-0.715	-0.853	21.800	-10.420	-10.420	0.000	0.000	0.000	0.000
72	A	67	ILE	0	-0.013	-0.018	23.816	0.297	0.297	0.000	0.000	0.000	0.000
73	A	68	THR	0	-0.068	-0.024	26.578	0.352	0.352	0.000	0.000	0.000	0.000
74	A	69	LYS	1	0.871	0.935	29.199	9.323	9.323	0.000	0.000	0.000	0.000
75	A	70	HIS	0	-0.045	-0.013	27.727	-0.024	-0.024	0.000	0.000	0.000	0.000
76	A	71	ASP	-1	-0.801	-0.884	28.705	-9.583	-9.583	0.000	0.000	0.000	0.000
77	A	72	GLY	0	-0.017	-0.004	25.842	-0.150	-0.150	0.000	0.000	0.000	0.000
78	A	73	THR	0	-0.101	-0.076	26.728	-0.012	-0.012	0.000	0.000	0.000	0.000
79	A	74	GLY	0	-0.016	-0.012	28.173	0.293	0.293	0.000	0.000	0.000	0.000
80	A	75	GLY	0	-0.001	0.009	24.863	-0.430	-0.430	0.000	0.000	0.000	0.000
81	A	76	GLN	0	-0.056	-0.037	24.718	0.513	0.513	0.000	0.000	0.000	0.000
82	A	77	SER	0	-0.011	-0.003	21.973	-0.364	-0.364	0.000	0.000	0.000	0.000
83	A	78	ILE	0	-0.028	-0.032	21.393	0.509	0.509	0.000	0.000	0.000	0.000
84	A	79	TYR	0	-0.062	-0.055	19.361	0.474	0.474	0.000	0.000	0.000	0.000
85	A	80	GLY	0	0.040	0.036	25.504	0.373	0.373	0.000	0.000	0.000	0.000
86	A	81	ASP	-1	-0.897	-0.949	26.024	-10.152	-10.152	0.000	0.000	0.000	0.000
87	A	82	LYS	1	0.914	0.964	24.870	9.549	9.549	0.000	0.000	0.000	0.000
88	A	83	PHE	0	-0.058	-0.022	17.765	0.186	0.186	0.000	0.000	0.000	0.000
89	A	84	GLU	-1	-0.943	-0.982	21.085	-12.161	-12.161	0.000	0.000	0.000	0.000
90	A	85	ASP	-1	-0.820	-0.916	18.205	-14.256	-14.256	0.000	0.000	0.000	0.000
91	A	86	GLU	-1	-0.790	-0.860	15.471	-16.701	-16.701	0.000	0.000	0.000	0.000
92	A	87	ASN	0	0.033	0.009	12.499	-0.654	-0.654	0.000	0.000	0.000	0.000
93	A	88	PHE	0	0.020	0.007	13.272	-0.164	-0.164	0.000	0.000	0.000	0.000
94	A	89	ASP	-1	-0.857	-0.911	10.903	-19.610	-19.610	0.000	0.000	0.000	0.000
95	A	90	VAL	0	-0.031	-0.017	5.452	-1.218	-1.218	0.000	0.000	0.000	0.000
96	A	91	LYS	1	0.822	0.911	7.397	22.787	22.787	0.000	0.000	0.000	0.000
97	A	92	HIS	1	0.839	0.886	7.083	17.510	17.510	0.000	0.000	0.000	0.000
99	A	94	GLY	0	0.021	0.002	5.941	0.462	0.462	0.000	0.000	0.000	0.000
100	A	95	PRO	0	-0.020	0.015	6.712	1.055	1.055	0.000	0.000	0.000	0.000
101	A	96	GLY	0	0.052	0.008	6.899	-3.038	-3.038	0.000	0.000	0.000	0.000
103	A	98	LEU	0	-0.006	0.002	7.308	2.374	2.374	0.000	0.000	0.000	0.000
104	A	99	SER	0	0.022	0.006	9.805	-0.727	-0.727	0.000	0.000	0.000	0.000
105	A	100	MET	0	-0.024	0.006	12.255	0.473	0.473	0.000	0.000	0.000	0.000
106	A	101	ALA	0	-0.041	-0.021	15.789	-0.046	-0.046	0.000	0.000	0.000	0.000
107	A	102	ASN	0	-0.016	-0.018	18.673	0.439	0.439	0.000	0.000	0.000	0.000
108	A	103	GLN	0	-0.035	-0.023	21.644	0.288	0.288	0.000	0.000	0.000	0.000
109	A	104	GLY	0	0.012	0.014	23.101	0.447	0.447	0.000	0.000	0.000	0.000
110	A	105	GLN	0	-0.013	-0.003	22.692	-0.315	-0.315	0.000	0.000	0.000	0.000
111	A	106	ASN	0	-0.002	-0.010	22.395	0.016	0.016	0.000	0.000	0.000	0.000
112	A	107	THR	0	-0.010	-0.012	22.995	0.390	0.390	0.000	0.000	0.000	0.000
113	A	108	ASN	0	-0.017	-0.012	18.745	-0.263	-0.263	0.000	0.000	0.000	0.000
114	A	109	ASN	0	0.059	0.011	20.866	-0.048	-0.048	0.000	0.000	0.000	0.000
115	A	110	SER	0	0.007	-0.009	20.488	-0.192	-0.192	0.000	0.000	0.000	0.000
116	A	111	GLN	0	-0.055	-0.037	19.904	-0.727	-0.727	0.000	0.000	0.000	0.000
117	A	112	PHE	0	-0.004	0.007	15.279	-0.479	-0.479	0.000	0.000	0.000	0.000
118	A	113	VAL	0	-0.002	-0.008	13.052	0.674	0.674	0.000	0.000	0.000	0.000
119	A	114	ILE	0	0.030	0.023	11.037	-1.170	-1.170	0.000	0.000	0.000	0.000
120	A	115	THR	0	-0.043	-0.035	8.831	1.013	1.013	0.000	0.000	0.000	0.000
121	A	116	LEU	0	-0.035	-0.015	11.477	-1.207	-1.207	0.000	0.000	0.000	0.000
122	A	117	LYS	1	0.796	0.881	11.233	15.599	15.599	0.000	0.000	0.000	0.000
123	A	118	LYS	1	0.849	0.919	9.224	19.189	19.189	0.000	0.000	0.000	0.000
124	A	119	ALA	0	-0.001	-0.006	10.128	1.320	1.320	0.000	0.000	0.000	0.000
125	A	120	GLU	-1	-0.796	-0.883	12.134	-17.194	-17.194	0.000	0.000	0.000	0.000
126	A	121	HIS	0	0.003	0.012	13.126	0.144	0.144	0.000	0.000	0.000	0.000
127	A	122	LEU	0	-0.006	-0.006	14.017	0.872	0.872	0.000	0.000	0.000	0.000
128	A	123	ASP	-1	-0.764	-0.879	11.577	-20.745	-20.745	0.000	0.000	0.000	0.000
129	A	124	PHE	0	-0.069	-0.053	14.384	0.707	0.707	0.000	0.000	0.000	0.000
130	A	125	LYS	1	0.878	0.962	16.531	14.004	14.004	0.000	0.000	0.000	0.000
131	A	126	HIS	0	-0.007	0.014	14.832	0.617	0.617	0.000	0.000	0.000	0.000
132	A	127	VAL	0	0.026	0.024	12.470	-0.932	-0.932	0.000	0.000	0.000	0.000
133	A	128	VAL	0	-0.026	-0.010	7.065	0.088	0.088	0.000	0.000	0.000	0.000
134	A	129	PHE	0	0.016	-0.011	9.267	-0.751	-0.751	0.000	0.000	0.000	0.000
135	A	130	GLY	0	0.053	0.015	6.530	0.164	0.164	0.000	0.000	0.000	0.000
137	A	132	VAL	0	0.007	-0.002	6.429	1.253	1.253	0.000	0.000	0.000	0.000
138	A	133	LYS	1	0.908	0.960	6.865	27.754	27.754	0.000	0.000	0.000	0.000
139	A	134	ASP	-1	-0.843	-0.925	7.871	-23.982	-23.982	0.000	0.000	0.000	0.000
140	A	135	GLY	0	0.050	0.025	11.123	0.931	0.931	0.000	0.000	0.000	0.000
141	A	136	MET	0	-0.011	-0.012	9.930	0.963	0.963	0.000	0.000	0.000	0.000
142	A	137	ASP	-1	-0.886	-0.936	12.893	-17.987	-17.987	0.000	0.000	0.000	0.000
143	A	138	THR	0	-0.044	-0.030	16.371	0.912	0.912	0.000	0.000	0.000	0.000
144	A	139	VAL	0	0.015	0.001	13.062	0.829	0.829	0.000	0.000	0.000	0.000
145	A	140	LYS	1	0.856	0.902	14.625	18.341	18.341	0.000	0.000	0.000	0.000
146	A	141	LYS	1	0.900	0.959	17.991	14.900	14.900	0.000	0.000	0.000	0.000
147	A	142	ILE	0	-0.002	0.011	18.094	0.697	0.697	0.000	0.000	0.000	0.000
148	A	143	GLU	-1	-0.756	-0.883	17.662	-15.609	-15.609	0.000	0.000	0.000	0.000
149	A	144	SER	0	-0.105	-0.053	20.407	0.675	0.675	0.000	0.000	0.000	0.000
150	A	145	PHE	0	0.040	0.001	23.555	0.552	0.552	0.000	0.000	0.000	0.000
151	A	146	GLY	0	0.054	0.028	23.410	0.321	0.321	0.000	0.000	0.000	0.000
152	A	147	SER	0	-0.034	-0.037	24.455	0.408	0.408	0.000	0.000	0.000	0.000
153	A	148	PRO	0	0.014	-0.015	24.220	-0.231	-0.231	0.000	0.000	0.000	0.000
154	A	149	LYS	1	0.904	0.947	25.274	9.937	9.937	0.000	0.000	0.000	0.000
155	A	150	GLY	0	-0.003	0.009	24.094	0.077	0.077	0.000	0.000	0.000	0.000
156	A	151	SER	0	0.012	0.006	25.071	-0.216	-0.216	0.000	0.000	0.000	0.000
157	A	152	VAL	0	0.042	0.042	24.713	-0.112	-0.112	0.000	0.000	0.000	0.000
158	A	153	CYS	0	-0.077	-0.025	27.484	0.282	0.282	0.000	0.000	0.000	0.000
159	A	154	ARG	1	0.856	0.919	27.941	10.575	10.575	0.000	0.000	0.000	0.000
160	A	155	ARG	1	0.913	0.956	28.222	9.759	9.759	0.000	0.000	0.000	0.000
161	A	156	ILE	0	-0.012	-0.004	22.428	-0.045	-0.045	0.000	0.000	0.000	0.000
162	A	157	THR	0	-0.030	-0.022	24.985	0.016	0.016	0.000	0.000	0.000	0.000
163	A	158	ILE	0	0.019	0.016	20.293	-0.238	-0.238	0.000	0.000	0.000	0.000
164	A	159	THR	0	-0.017	-0.023	23.507	0.263	0.263	0.000	0.000	0.000	0.000
165	A	160	GLU	-1	-0.834	-0.904	23.529	-11.258	-11.258	0.000	0.000	0.000	0.000
166	A	161	CYS	0	-0.079	-0.028	20.322	-0.458	-0.458	0.000	0.000	0.000	0.000
167	A	162	GLY	0	0.055	0.038	19.480	0.695	0.695	0.000	0.000	0.000	0.000
168	A	163	GLN	0	-0.017	-0.013	16.474	-0.427	-0.427	0.000	0.000	0.000	0.000
169	A	164	ILE	-1	-0.927	-0.956	14.957	-16.794	-16.794	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-4:MET)