FMO DATABASE

FMODB ID: LQ459

Calculation Name: 1VMD-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VMD

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X0R7

Base Structure: X-ray

Registration Date: 2025-10-03

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	156
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1528472.247308
FMO2-HF: Nuclear repulsion	1466626.377965
FMO2-HF: Total energy	-61845.869344
FMO2-MP2: Total energy	-62029.397823

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:5:PRO)

Summations of interaction energy for fragment #1(A:5: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.
-40.002	-26.027	13.794	-12.616	-15.154	-0.126

Interaction energy analysis for fragmet #1(A:5:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.823 / q_NPA : 0.902

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	7	ARG	1	0.939	0.972	2.226	54.658	56.836	0.729	-1.172	-1.735	-0.001
141	A	145	ILE	0	-0.033	-0.019	3.083	-3.893	-3.406	0.051	-0.132	-0.406	-0.001
142	A	146	ASP	-1	-0.794	-0.878	2.822	-40.080	-39.045	0.168	-0.399	-0.804	-0.002
143	A	147	TYR	0	0.021	-0.020	2.649	-14.983	-12.890	1.880	-1.673	-2.300	-0.019
144	A	148	GLU	-1	-0.872	-0.909	4.969	-25.338	-25.323	-0.001	-0.006	-0.008	0.000
145	A	149	GLU	-1	-0.777	-0.879	2.146	-85.869	-82.788	6.547	-5.403	-4.225	-0.059
146	A	150	GLU	-1	-0.981	-0.997	2.294	-66.026	-62.208	2.324	-2.669	-3.474	-0.035
147	A	151	LEU	0	0.018	0.016	3.923	3.791	3.969	0.007	-0.105	-0.080	-0.001
149	A	153	ARG	1	0.802	0.889	2.378	59.798	60.888	2.089	-1.057	-2.122	-0.008
4	A	8	TYR	0	-0.037	-0.038	6.358	2.883	2.883	0.000	0.000	0.000	0.000
5	A	9	LYS	1	0.844	0.910	9.211	18.765	18.765	0.000	0.000	0.000	0.000
6	A	10	ILE	0	0.021	0.007	10.971	0.199	0.199	0.000	0.000	0.000	0.000
7	A	11	PHE	0	0.013	0.006	14.439	0.236	0.236	0.000	0.000	0.000	0.000
8	A	12	MET	0	0.013	0.032	16.909	-0.552	-0.552	0.000	0.000	0.000	0.000
9	A	13	ASP	-1	-0.800	-0.909	19.568	-11.963	-11.963	0.000	0.000	0.000	0.000
10	A	14	LYS	1	0.896	0.957	23.179	11.303	11.303	0.000	0.000	0.000	0.000
11	A	15	LYS	1	0.882	0.951	26.480	9.718	9.718	0.000	0.000	0.000	0.000
12	A	16	LYS	1	0.820	0.919	23.444	11.960	11.960	0.000	0.000	0.000	0.000
13	A	17	ARG	1	0.811	0.898	23.735	11.924	11.924	0.000	0.000	0.000	0.000
14	A	18	ILE	0	0.038	0.013	24.276	-0.439	-0.439	0.000	0.000	0.000	0.000
15	A	19	ALA	0	0.016	0.012	24.643	0.406	0.406	0.000	0.000	0.000	0.000
16	A	20	LEU	0	-0.015	-0.008	26.581	-0.070	-0.070	0.000	0.000	0.000	0.000
17	A	21	ILE	0	-0.020	-0.024	25.896	0.283	0.283	0.000	0.000	0.000	0.000
18	A	22	ALA	0	0.021	0.011	29.807	-0.052	-0.052	0.000	0.000	0.000	0.000
19	A	23	HIS	0	0.040	0.022	29.023	0.259	0.259	0.000	0.000	0.000	0.000
20	A	24	ASP	-1	-0.808	-0.889	33.163	-8.234	-8.234	0.000	0.000	0.000	0.000
21	A	25	ARG	1	0.867	0.934	36.912	8.128	8.128	0.000	0.000	0.000	0.000
22	A	26	ARG	1	0.807	0.888	32.316	9.163	9.163	0.000	0.000	0.000	0.000
23	A	27	LYS	1	0.794	0.878	34.786	8.759	8.759	0.000	0.000	0.000	0.000
24	A	28	ARG	1	0.965	0.972	37.177	7.091	7.091	0.000	0.000	0.000	0.000
25	A	29	ASP	-1	-0.782	-0.863	35.900	-8.285	-8.285	0.000	0.000	0.000	0.000
26	A	30	LEU	0	-0.016	-0.010	31.902	-0.036	-0.036	0.000	0.000	0.000	0.000
27	A	31	LEU	0	-0.027	-0.010	35.317	-0.018	-0.018	0.000	0.000	0.000	0.000
28	A	32	GLU	-1	-0.818	-0.889	38.532	-7.591	-7.591	0.000	0.000	0.000	0.000
29	A	33	TRP	0	-0.022	-0.033	30.434	0.010	0.010	0.000	0.000	0.000	0.000
30	A	34	VAL	0	0.008	-0.005	33.905	-0.063	-0.063	0.000	0.000	0.000	0.000
31	A	35	SER	0	-0.039	-0.019	36.273	0.067	0.067	0.000	0.000	0.000	0.000
32	A	36	PHE	0	0.006	0.001	38.452	0.110	0.110	0.000	0.000	0.000	0.000
33	A	37	ASN	0	-0.008	0.000	34.325	-0.050	-0.050	0.000	0.000	0.000	0.000
34	A	38	LEU	0	0.011	0.012	35.746	-0.197	-0.197	0.000	0.000	0.000	0.000
35	A	39	GLY	0	0.011	0.020	37.365	-0.063	-0.063	0.000	0.000	0.000	0.000
36	A	40	THR	0	-0.010	-0.009	31.723	0.073	0.073	0.000	0.000	0.000	0.000
37	A	41	LEU	0	0.020	0.004	31.087	-0.206	-0.206	0.000	0.000	0.000	0.000
38	A	42	SER	0	-0.053	-0.036	33.103	-0.136	-0.136	0.000	0.000	0.000	0.000
39	A	43	LYS	1	0.919	0.973	33.007	8.721	8.721	0.000	0.000	0.000	0.000
40	A	44	HIS	0	-0.016	0.000	28.736	-0.341	-0.341	0.000	0.000	0.000	0.000
41	A	45	GLU	-1	-0.850	-0.902	28.797	-9.912	-9.912	0.000	0.000	0.000	0.000
42	A	46	LEU	0	-0.014	0.006	28.917	-0.341	-0.341	0.000	0.000	0.000	0.000
43	A	47	TYR	0	0.031	0.002	27.862	0.294	0.294	0.000	0.000	0.000	0.000
44	A	48	ALA	0	0.013	0.007	29.795	-0.149	-0.149	0.000	0.000	0.000	0.000
45	A	49	THR	0	0.037	0.023	29.627	0.211	0.211	0.000	0.000	0.000	0.000
46	A	50	GLY	0	0.012	0.010	32.085	0.235	0.235	0.000	0.000	0.000	0.000
47	A	51	THR	0	0.022	-0.011	35.516	0.154	0.154	0.000	0.000	0.000	0.000
48	A	52	THR	0	0.019	0.009	33.300	0.270	0.270	0.000	0.000	0.000	0.000
49	A	53	GLY	0	0.044	0.006	35.397	0.107	0.107	0.000	0.000	0.000	0.000
50	A	54	ALA	0	-0.032	-0.005	36.413	0.158	0.158	0.000	0.000	0.000	0.000
51	A	55	LEU	0	0.044	0.018	39.302	0.146	0.146	0.000	0.000	0.000	0.000
52	A	56	LEU	0	0.024	0.010	34.764	0.124	0.124	0.000	0.000	0.000	0.000
53	A	57	GLN	0	-0.016	-0.007	38.265	0.218	0.218	0.000	0.000	0.000	0.000
54	A	58	GLU	-1	-0.880	-0.931	41.325	-6.702	-6.702	0.000	0.000	0.000	0.000
55	A	59	LYS	1	0.819	0.890	42.738	6.889	6.889	0.000	0.000	0.000	0.000
56	A	60	LEU	0	-0.003	0.008	39.292	0.040	0.040	0.000	0.000	0.000	0.000
57	A	61	GLY	0	0.035	0.043	42.973	0.012	0.012	0.000	0.000	0.000	0.000
58	A	62	LEU	0	-0.037	-0.015	35.979	-0.021	-0.021	0.000	0.000	0.000	0.000
59	A	63	LYS	1	0.871	0.922	37.858	7.407	7.407	0.000	0.000	0.000	0.000
60	A	64	VAL	0	-0.002	0.007	34.028	-0.196	-0.196	0.000	0.000	0.000	0.000
61	A	65	HIS	0	0.000	-0.001	31.108	0.402	0.402	0.000	0.000	0.000	0.000
62	A	66	ARG	1	0.790	0.896	32.912	7.858	7.858	0.000	0.000	0.000	0.000
63	A	67	LEU	0	0.027	0.025	27.865	0.021	0.021	0.000	0.000	0.000	0.000
64	A	68	LYS	1	0.998	0.990	31.756	9.386	9.386	0.000	0.000	0.000	0.000
65	A	69	SER	0	0.026	0.002	32.597	-0.156	-0.156	0.000	0.000	0.000	0.000
66	A	70	GLY	0	0.021	0.009	30.527	-0.122	-0.122	0.000	0.000	0.000	0.000
67	A	71	PRO	0	0.034	0.014	30.103	-0.252	-0.252	0.000	0.000	0.000	0.000
68	A	72	LEU	0	-0.044	-0.009	31.782	0.061	0.061	0.000	0.000	0.000	0.000
69	A	73	GLY	0	0.056	0.029	28.654	0.110	0.110	0.000	0.000	0.000	0.000
70	A	74	GLY	0	-0.047	-0.013	28.435	-0.223	-0.223	0.000	0.000	0.000	0.000
71	A	75	ASP	-1	-0.848	-0.935	25.855	-11.480	-11.480	0.000	0.000	0.000	0.000
72	A	76	GLN	0	-0.006	-0.016	23.758	-0.776	-0.776	0.000	0.000	0.000	0.000
73	A	77	GLN	0	0.009	0.008	23.776	-0.168	-0.168	0.000	0.000	0.000	0.000
74	A	78	ILE	0	0.037	0.017	23.090	-0.246	-0.246	0.000	0.000	0.000	0.000
75	A	79	GLY	0	0.000	-0.007	20.522	-0.457	-0.457	0.000	0.000	0.000	0.000
76	A	80	ALA	0	0.009	0.005	19.351	-0.787	-0.787	0.000	0.000	0.000	0.000
77	A	81	MET	0	-0.005	-0.009	20.063	-0.246	-0.246	0.000	0.000	0.000	0.000
78	A	82	ILE	0	-0.030	-0.009	16.570	-0.197	-0.197	0.000	0.000	0.000	0.000
79	A	83	ALA	0	-0.007	-0.005	15.630	-0.662	-0.662	0.000	0.000	0.000	0.000
80	A	84	GLU	-1	-0.895	-0.929	16.156	-13.636	-13.636	0.000	0.000	0.000	0.000
81	A	85	GLY	0	-0.012	0.000	17.989	0.286	0.286	0.000	0.000	0.000	0.000
82	A	86	LYS	1	0.795	0.878	18.739	13.082	13.082	0.000	0.000	0.000	0.000
83	A	87	ILE	0	-0.048	-0.036	21.001	0.694	0.694	0.000	0.000	0.000	0.000
84	A	88	ASP	-1	-0.816	-0.909	19.600	-13.855	-13.855	0.000	0.000	0.000	0.000
85	A	89	VAL	0	0.012	0.006	20.524	-0.222	-0.222	0.000	0.000	0.000	0.000
86	A	90	LEU	0	-0.008	0.005	21.419	0.394	0.394	0.000	0.000	0.000	0.000
87	A	91	ILE	0	-0.005	0.001	23.518	-0.119	-0.119	0.000	0.000	0.000	0.000
88	A	92	PHE	0	-0.012	-0.018	24.549	0.243	0.243	0.000	0.000	0.000	0.000
89	A	93	PHE	0	-0.019	-0.005	27.347	-0.063	-0.063	0.000	0.000	0.000	0.000
90	A	94	TRP	0	0.028	0.014	26.617	0.286	0.286	0.000	0.000	0.000	0.000
91	A	95	ASP	-1	-0.771	-0.894	30.136	-8.542	-8.542	0.000	0.000	0.000	0.000
92	A	96	PRO	0	-0.064	-0.028	30.221	-0.132	-0.132	0.000	0.000	0.000	0.000
93	A	97	LEU	0	-0.042	-0.019	31.577	-0.043	-0.043	0.000	0.000	0.000	0.000
94	A	98	GLU	-1	-0.922	-0.963	34.940	-7.784	-7.784	0.000	0.000	0.000	0.000
95	A	99	PRO	0	-0.066	-0.020	31.939	0.100	0.100	0.000	0.000	0.000	0.000
96	A	100	GLN	0	0.000	-0.011	34.467	0.192	0.192	0.000	0.000	0.000	0.000
97	A	101	ALA	0	0.012	0.000	34.249	-0.247	-0.247	0.000	0.000	0.000	0.000
98	A	102	HIS	0	-0.052	-0.031	33.750	-0.137	-0.137	0.000	0.000	0.000	0.000
99	A	103	ASP	-1	-0.791	-0.909	31.736	-9.197	-9.197	0.000	0.000	0.000	0.000
100	A	104	VAL	0	-0.046	-0.018	26.687	-0.216	-0.216	0.000	0.000	0.000	0.000
101	A	105	ASP	-1	-0.749	-0.880	22.720	-12.970	-12.970	0.000	0.000	0.000	0.000
102	A	106	VAL	0	0.030	0.013	22.718	-0.291	-0.291	0.000	0.000	0.000	0.000
103	A	107	LYS	1	0.922	0.967	19.844	12.046	12.046	0.000	0.000	0.000	0.000
104	A	108	ALA	0	-0.008	-0.009	18.712	-0.929	-0.929	0.000	0.000	0.000	0.000
105	A	109	LEU	0	0.003	0.003	18.358	-0.758	-0.758	0.000	0.000	0.000	0.000
106	A	110	ILE	0	0.037	0.013	18.081	-0.510	-0.510	0.000	0.000	0.000	0.000
107	A	111	ARG	1	0.959	1.003	12.340	18.886	18.886	0.000	0.000	0.000	0.000
108	A	112	ILE	0	-0.020	-0.007	13.883	-1.544	-1.544	0.000	0.000	0.000	0.000
109	A	113	ALA	0	0.051	0.018	14.409	-0.842	-0.842	0.000	0.000	0.000	0.000
110	A	114	THR	0	-0.024	-0.024	11.238	-0.388	-0.388	0.000	0.000	0.000	0.000
111	A	115	VAL	0	-0.069	-0.025	9.382	-1.583	-1.583	0.000	0.000	0.000	0.000
112	A	116	TYR	0	0.035	0.023	9.693	-2.429	-2.429	0.000	0.000	0.000	0.000
113	A	117	ASN	0	-0.057	-0.037	11.192	2.007	2.007	0.000	0.000	0.000	0.000
114	A	118	ILE	0	0.006	0.032	13.051	0.496	0.496	0.000	0.000	0.000	0.000
115	A	119	PRO	0	0.003	0.001	16.845	0.001	0.001	0.000	0.000	0.000	0.000
116	A	120	VAL	0	0.020	0.007	18.736	0.476	0.476	0.000	0.000	0.000	0.000
117	A	121	ALA	0	-0.010	-0.003	21.448	0.040	0.040	0.000	0.000	0.000	0.000
118	A	122	ILE	0	0.029	0.013	22.672	0.283	0.283	0.000	0.000	0.000	0.000
119	A	123	THR	0	0.000	0.005	25.436	0.223	0.223	0.000	0.000	0.000	0.000
120	A	124	ARG	1	0.873	0.913	28.403	8.232	8.232	0.000	0.000	0.000	0.000
121	A	125	SER	0	0.073	0.038	30.172	-0.097	-0.097	0.000	0.000	0.000	0.000
122	A	126	THR	0	-0.013	-0.011	23.810	-0.173	-0.173	0.000	0.000	0.000	0.000
123	A	127	ALA	0	0.023	0.001	26.934	-0.241	-0.241	0.000	0.000	0.000	0.000
124	A	128	ASP	-1	-0.855	-0.921	28.692	-9.262	-9.262	0.000	0.000	0.000	0.000
125	A	129	PHE	0	-0.011	0.006	26.852	0.087	0.087	0.000	0.000	0.000	0.000
126	A	130	LEU	0	-0.041	-0.021	22.988	-0.169	-0.169	0.000	0.000	0.000	0.000
127	A	131	ILE	0	-0.048	-0.028	26.622	-0.045	-0.045	0.000	0.000	0.000	0.000
128	A	132	SER	0	-0.030	-0.032	29.774	0.181	0.181	0.000	0.000	0.000	0.000
129	A	133	SER	0	0.009	0.022	25.093	0.147	0.147	0.000	0.000	0.000	0.000
130	A	134	PRO	0	0.053	0.019	27.870	0.022	0.022	0.000	0.000	0.000	0.000
131	A	135	LEU	0	0.028	0.010	21.744	-0.030	-0.030	0.000	0.000	0.000	0.000
132	A	136	MET	0	-0.019	0.011	24.737	-0.446	-0.446	0.000	0.000	0.000	0.000
133	A	137	ASN	0	-0.052	-0.046	26.860	0.048	0.048	0.000	0.000	0.000	0.000
134	A	138	ASP	-1	-0.873	-0.916	26.644	-10.481	-10.481	0.000	0.000	0.000	0.000
135	A	139	VAL	0	-0.060	-0.045	23.348	-0.248	-0.248	0.000	0.000	0.000	0.000
136	A	140	TYR	0	0.020	0.007	17.949	-0.185	-0.185	0.000	0.000	0.000	0.000
137	A	141	GLU	-1	-0.829	-0.895	16.061	-17.909	-17.909	0.000	0.000	0.000	0.000
138	A	142	LYS	1	0.794	0.884	12.059	20.462	20.462	0.000	0.000	0.000	0.000
139	A	143	ILE	0	0.006	-0.002	8.652	-0.804	-0.804	0.000	0.000	0.000	0.000
140	A	144	GLN	0	0.001	-0.006	7.373	2.619	2.619	0.000	0.000	0.000	0.000
148	A	152	GLU	-1	-0.796	-0.897	7.373	-21.524	-21.524	0.000	0.000	0.000	0.000
150	A	154	ARG	1	0.821	0.896	5.295	40.628	40.628	0.000	0.000	0.000	0.000
151	A	155	ILE	0	0.036	0.023	9.558	1.882	1.882	0.000	0.000	0.000	0.000
152	A	156	ARG	1	0.917	0.939	11.286	24.385	24.385	0.000	0.000	0.000	0.000
153	A	157	LYS	1	0.912	0.959	10.588	25.151	25.151	0.000	0.000	0.000	0.000
154	A	158	VAL	0	-0.034	-0.014	13.361	0.505	0.505	0.000	0.000	0.000	0.000
155	A	159	VAL	0	-0.085	-0.044	15.949	0.894	0.894	0.000	0.000	0.000	0.000
156	A	160	GLU	-2	-1.903	-1.923	17.047	-31.759	-31.759	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:PRO)