FMO DATABASE

FMODB ID: Q5QMY

Calculation Name: 1VMO-A-Xray549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VMO

Chain ID: A

ChEMBL ID:

UniProt ID: P41366

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	159
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1619930.758117
FMO2-HF: Nuclear repulsion	1555969.407629
FMO2-HF: Total energy	-63961.350488
FMO2-MP2: Total energy	-64145.072871

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:ARG)

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

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.
60.619	69.728	4.464	-5.428	-8.145	-0.059

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.787 / q_NPA : 1.893

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	ARG	1	0.862	0.917	2.781	33.643	37.961	0.640	-2.489	-2.470	-0.025
4	A	4	GLU	-1	-0.857	-0.917	2.516	-88.195	-85.844	2.201	-1.704	-2.848	-0.021
5	A	5	TYR	0	0.003	-0.013	2.217	9.605	11.103	1.599	-0.883	-2.214	-0.010
23	A	23	ARG	1	0.819	0.928	4.476	69.894	70.053	-0.001	-0.020	-0.138	0.000
25	A	25	PHE	0	-0.005	-0.035	3.411	-4.812	-4.029	0.025	-0.332	-0.475	-0.003
6	A	6	THR	0	0.022	0.008	5.626	-4.223	-4.223	0.000	0.000	0.000	0.000
7	A	7	SER	0	0.001	0.002	8.433	2.870	2.870	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.034	-0.025	8.043	-3.508	-3.508	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.000	0.003	10.431	2.621	2.621	0.000	0.000	0.000	0.000
10	A	10	THR	0	-0.005	-0.020	13.797	-0.904	-0.904	0.000	0.000	0.000	0.000
11	A	11	VAL	0	0.008	0.004	16.332	0.777	0.777	0.000	0.000	0.000	0.000
12	A	12	PRO	0	-0.022	-0.010	20.118	-0.532	-0.532	0.000	0.000	0.000	0.000
13	A	13	ASN	0	-0.021	-0.009	22.552	0.248	0.248	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.060	0.031	22.030	-0.970	-0.970	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.018	0.025	22.577	0.013	0.013	0.000	0.000	0.000	0.000
16	A	16	HIS	0	-0.067	-0.054	20.591	-2.698	-2.698	0.000	0.000	0.000	0.000
17	A	17	TRP	0	0.029	0.005	20.564	-1.930	-1.930	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.083	0.042	20.590	-0.417	-0.417	0.000	0.000	0.000	0.000
19	A	19	LYS	0	-0.023	0.002	14.429	-1.194	-1.194	0.000	0.000	0.000	0.000
20	A	20	TRP	0	-0.039	-0.049	11.848	-0.724	-0.724	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.056	0.035	12.529	-0.415	-0.415	0.000	0.000	0.000	0.000
22	A	22	ILE	0	0.012	0.006	8.016	-4.267	-4.267	0.000	0.000	0.000	0.000
24	A	24	GLN	0	0.049	0.039	5.723	-4.044	-4.044	0.000	0.000	0.000	0.000
26	A	26	CYS	0	0.005	0.035	8.142	0.840	0.840	0.000	0.000	0.000	0.000
27	A	27	HIS	0	0.015	0.021	9.850	-6.925	-6.925	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.042	-0.039	10.585	-1.855	-1.855	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.015	0.000	12.882	0.590	0.590	0.000	0.000	0.000	0.000
30	A	30	TYR	0	-0.052	-0.065	12.468	-2.627	-2.627	0.000	0.000	0.000	0.000
31	A	31	ALA	0	0.071	0.021	14.339	0.988	0.988	0.000	0.000	0.000	0.000
32	A	32	ASN	0	-0.010	-0.017	15.958	-0.048	-0.048	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.070	0.040	19.194	1.549	1.549	0.000	0.000	0.000	0.000
34	A	34	PHE	0	-0.052	-0.026	19.038	-1.968	-1.968	0.000	0.000	0.000	0.000
35	A	35	ALA	0	0.027	0.033	20.572	1.234	1.234	0.000	0.000	0.000	0.000
36	A	36	LEU	0	0.007	-0.005	21.056	-1.490	-1.490	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.806	0.917	22.550	24.357	24.357	0.000	0.000	0.000	0.000
38	A	38	VAL	0	0.030	0.007	24.192	-0.398	-0.398	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.760	-0.868	27.409	-18.084	-18.084	0.000	0.000	0.000	0.000
40	A	40	PRO	0	-0.025	-0.001	30.823	0.174	0.174	0.000	0.000	0.000	0.000
41	A	41	SER	0	0.069	0.046	33.496	0.124	0.124	0.000	0.000	0.000	0.000
42	A	42	GLN	0	-0.057	-0.039	35.716	0.154	0.154	0.000	0.000	0.000	0.000
43	A	43	PHE	0	0.069	0.022	38.330	-0.260	-0.260	0.000	0.000	0.000	0.000
44	A	44	GLY	0	-0.024	0.002	41.024	-0.014	-0.014	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.811	0.893	34.972	16.519	16.519	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.865	-0.923	36.748	-15.505	-15.505	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.960	-0.980	33.664	-17.455	-17.455	0.000	0.000	0.000	0.000
48	A	48	THR	0	0.016	0.000	30.008	-0.222	-0.222	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.009	0.006	25.811	-0.269	-0.269	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.073	-0.022	22.708	0.003	0.003	0.000	0.000	0.000	0.000
51	A	51	ASN	0	0.035	0.006	23.193	-0.542	-0.542	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.008	-0.010	19.575	-1.096	-1.096	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.008	0.006	17.211	0.924	0.924	0.000	0.000	0.000	0.000
54	A	54	ARG	1	0.833	0.896	16.662	26.621	26.621	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.015	-0.008	13.317	1.261	1.261	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.948	0.978	16.623	24.649	24.649	0.000	0.000	0.000	0.000
57	A	58	LEU	0	0.007	0.001	16.715	1.165	1.165	0.000	0.000	0.000	0.000
58	A	59	ASP	-1	-0.746	-0.827	14.844	-36.221	-36.221	0.000	0.000	0.000	0.000
59	A	60	GLY	0	-0.009	-0.001	18.404	0.223	0.223	0.000	0.000	0.000	0.000
60	A	61	SER	0	-0.076	-0.058	14.520	-0.434	-0.434	0.000	0.000	0.000	0.000
61	A	62	VAL	0	0.002	-0.022	16.020	0.863	0.863	0.000	0.000	0.000	0.000
62	A	63	ILE	0	-0.046	-0.009	10.687	-1.434	-1.434	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.760	-0.865	13.568	-28.579	-28.579	0.000	0.000	0.000	0.000
64	A	65	SER	0	-0.041	-0.057	10.773	-2.457	-2.457	0.000	0.000	0.000	0.000
65	A	66	LEU	0	-0.004	0.021	12.724	0.223	0.223	0.000	0.000	0.000	0.000
66	A	67	VAL	0	-0.043	-0.012	15.461	0.328	0.328	0.000	0.000	0.000	0.000
67	A	68	GLY	0	0.060	0.039	18.922	0.032	0.032	0.000	0.000	0.000	0.000
68	A	69	LYS	1	0.893	0.955	22.452	20.451	20.451	0.000	0.000	0.000	0.000
69	A	70	TRP	0	0.006	0.001	24.914	0.835	0.835	0.000	0.000	0.000	0.000
70	A	71	GLY	0	0.043	0.025	26.107	-0.715	-0.715	0.000	0.000	0.000	0.000
71	A	72	THR	0	-0.010	-0.014	27.576	-0.114	-0.114	0.000	0.000	0.000	0.000
72	A	73	TRP	0	-0.042	-0.031	19.243	-0.378	-0.378	0.000	0.000	0.000	0.000
73	A	74	THR	0	0.022	0.016	25.808	0.439	0.439	0.000	0.000	0.000	0.000
74	A	75	SER	0	0.010	0.004	26.021	-0.603	-0.603	0.000	0.000	0.000	0.000
75	A	76	PHE	0	-0.047	-0.031	19.750	-0.314	-0.314	0.000	0.000	0.000	0.000
76	A	77	LEU	0	0.061	0.053	24.650	0.634	0.634	0.000	0.000	0.000	0.000
77	A	78	VAL	0	-0.046	-0.050	23.299	-1.377	-1.377	0.000	0.000	0.000	0.000
78	A	79	CYS	0	-0.034	-0.001	21.284	-1.068	-1.068	0.000	0.000	0.000	0.000
79	A	80	PRO	0	0.007	0.005	25.010	0.026	0.026	0.000	0.000	0.000	0.000
80	A	81	THR	0	-0.042	-0.014	26.561	0.466	0.466	0.000	0.000	0.000	0.000
81	A	82	GLY	0	-0.038	0.003	23.400	-0.567	-0.567	0.000	0.000	0.000	0.000
82	A	83	TYR	0	0.001	-0.018	17.589	-0.613	-0.613	0.000	0.000	0.000	0.000
83	A	84	LEU	0	0.001	-0.010	17.022	0.776	0.776	0.000	0.000	0.000	0.000
84	A	85	VAL	0	-0.028	-0.027	16.908	-1.657	-1.657	0.000	0.000	0.000	0.000
85	A	86	SER	0	-0.054	-0.028	17.837	-0.349	-0.349	0.000	0.000	0.000	0.000
86	A	87	PHE	0	0.056	0.016	16.462	0.368	0.368	0.000	0.000	0.000	0.000
87	A	88	SER	0	0.019	0.006	20.555	0.227	0.227	0.000	0.000	0.000	0.000
88	A	89	LEU	0	0.053	0.018	20.799	-0.018	-0.018	0.000	0.000	0.000	0.000
89	A	90	ARG	1	0.845	0.934	23.877	19.064	19.064	0.000	0.000	0.000	0.000
90	A	91	SER	0	0.066	0.039	26.097	-0.425	-0.425	0.000	0.000	0.000	0.000
91	A	92	GLU	-1	-0.855	-0.918	28.335	-18.270	-18.270	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.848	0.920	29.932	18.839	18.839	0.000	0.000	0.000	0.000
93	A	94	SER	0	0.059	0.053	29.983	0.190	0.190	0.000	0.000	0.000	0.000
94	A	95	GLN	0	-0.002	-0.001	32.048	0.278	0.278	0.000	0.000	0.000	0.000
95	A	96	GLY	0	-0.026	-0.027	32.259	-0.499	-0.499	0.000	0.000	0.000	0.000
96	A	97	GLY	0	0.009	0.010	31.915	-0.331	-0.331	0.000	0.000	0.000	0.000
97	A	98	GLY	0	0.052	0.036	31.763	-0.307	-0.307	0.000	0.000	0.000	0.000
98	A	99	ASP	-1	-0.826	-0.906	27.722	-20.648	-20.648	0.000	0.000	0.000	0.000
99	A	100	ASP	-1	-0.848	-0.927	28.365	-19.078	-19.078	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.079	-0.064	25.895	0.167	0.167	0.000	0.000	0.000	0.000
101	A	102	ALA	0	0.002	0.011	24.526	-1.112	-1.112	0.000	0.000	0.000	0.000
102	A	103	ALA	0	-0.043	-0.028	22.127	0.390	0.390	0.000	0.000	0.000	0.000
103	A	104	ASN	0	0.017	0.000	24.246	-0.166	-0.166	0.000	0.000	0.000	0.000
104	A	105	ASN	0	-0.021	-0.039	25.834	-0.414	-0.414	0.000	0.000	0.000	0.000
105	A	106	ILE	0	-0.047	-0.015	19.360	-0.664	-0.664	0.000	0.000	0.000	0.000
106	A	107	GLN	0	-0.017	0.003	23.839	1.064	1.064	0.000	0.000	0.000	0.000
107	A	108	PHE	0	0.014	-0.007	17.259	-1.257	-1.257	0.000	0.000	0.000	0.000
108	A	109	ARG	1	0.910	0.969	21.785	23.135	23.135	0.000	0.000	0.000	0.000
109	A	111	SER	0	-0.025	-0.022	20.895	0.681	0.681	0.000	0.000	0.000	0.000
110	A	112	ASP	-1	-0.760	-0.899	22.792	-21.864	-21.864	0.000	0.000	0.000	0.000
111	A	113	GLU	-1	-0.827	-0.906	25.747	-21.128	-21.128	0.000	0.000	0.000	0.000
112	A	114	ALA	0	-0.011	0.025	26.835	0.371	0.371	0.000	0.000	0.000	0.000
113	A	115	VAL	0	-0.020	-0.023	25.892	-1.004	-1.004	0.000	0.000	0.000	0.000
114	A	116	LEU	0	-0.017	-0.004	23.477	0.515	0.515	0.000	0.000	0.000	0.000
115	A	117	VAL	0	0.002	-0.016	25.490	-0.926	-0.926	0.000	0.000	0.000	0.000
116	A	118	GLY	0	0.028	0.020	26.163	0.220	0.220	0.000	0.000	0.000	0.000
117	A	119	ASP	-1	-0.897	-0.936	26.993	-18.648	-18.648	0.000	0.000	0.000	0.000
118	A	120	GLY	0	-0.040	-0.021	27.970	-0.070	-0.070	0.000	0.000	0.000	0.000
119	A	121	LEU	0	0.032	0.028	28.783	0.603	0.603	0.000	0.000	0.000	0.000
120	A	122	SER	0	-0.074	-0.052	30.411	-0.414	-0.414	0.000	0.000	0.000	0.000
121	A	123	TRP	0	0.082	0.045	32.631	0.222	0.222	0.000	0.000	0.000	0.000
122	A	124	GLY	0	0.079	0.043	31.628	-0.602	-0.602	0.000	0.000	0.000	0.000
123	A	125	ARG	1	0.861	0.921	31.465	17.484	17.484	0.000	0.000	0.000	0.000
124	A	126	PHE	0	0.037	0.017	26.246	-0.398	-0.398	0.000	0.000	0.000	0.000
125	A	127	GLY	0	0.001	0.016	26.318	0.553	0.553	0.000	0.000	0.000	0.000
126	A	128	PRO	0	-0.021	-0.005	24.744	0.109	0.109	0.000	0.000	0.000	0.000
127	A	129	TRP	0	-0.012	-0.009	22.746	-0.853	-0.853	0.000	0.000	0.000	0.000
128	A	130	SER	0	-0.016	0.001	18.020	0.025	0.025	0.000	0.000	0.000	0.000
129	A	131	LYS	1	0.945	0.967	17.135	29.817	29.817	0.000	0.000	0.000	0.000
130	A	132	ARG	1	0.878	0.926	18.018	23.677	23.677	0.000	0.000	0.000	0.000
131	A	133	CYS	0	-0.041	-0.003	8.584	2.172	2.172	0.000	0.000	0.000	0.000
132	A	134	LYS	1	0.879	0.937	13.537	35.742	35.742	0.000	0.000	0.000	0.000
133	A	135	ILE	0	0.018	0.020	12.315	-3.536	-3.536	0.000	0.000	0.000	0.000
134	A	136	CYS	0	-0.052	-0.033	8.725	-6.231	-6.231	0.000	0.000	0.000	0.000
135	A	137	GLY	0	0.055	0.024	8.236	-2.692	-2.692	0.000	0.000	0.000	0.000
136	A	138	LEU	0	-0.029	0.004	9.141	2.181	2.181	0.000	0.000	0.000	0.000
137	A	139	GLN	0	0.008	-0.010	8.983	-5.168	-5.168	0.000	0.000	0.000	0.000
138	A	140	THR	0	0.034	0.006	10.738	0.850	0.850	0.000	0.000	0.000	0.000
139	A	141	LYS	1	0.803	0.914	14.071	28.956	28.956	0.000	0.000	0.000	0.000
140	A	142	VAL	0	-0.018	-0.016	16.622	1.183	1.183	0.000	0.000	0.000	0.000
141	A	143	GLU	-1	-0.762	-0.869	19.487	-24.969	-24.969	0.000	0.000	0.000	0.000
142	A	144	SER	0	0.008	-0.006	22.603	0.251	0.251	0.000	0.000	0.000	0.000
143	A	145	PRO	0	-0.034	0.007	19.290	0.751	0.751	0.000	0.000	0.000	0.000
144	A	146	GLN	0	0.017	-0.019	22.235	0.032	0.032	0.000	0.000	0.000	0.000
145	A	147	GLY	0	0.005	0.013	24.385	0.752	0.752	0.000	0.000	0.000	0.000
146	A	148	LEU	0	0.016	-0.012	27.441	0.182	0.182	0.000	0.000	0.000	0.000
147	A	149	ARG	1	0.814	0.878	29.633	17.351	17.351	0.000	0.000	0.000	0.000
148	A	150	ASP	-1	-0.897	-0.943	30.484	-17.597	-17.597	0.000	0.000	0.000	0.000
149	A	151	ASP	-1	-0.852	-0.920	28.231	-20.026	-20.026	0.000	0.000	0.000	0.000
150	A	152	THR	0	-0.136	-0.057	24.272	-0.743	-0.743	0.000	0.000	0.000	0.000
151	A	153	ALA	0	0.058	0.025	24.452	0.282	0.282	0.000	0.000	0.000	0.000
152	A	154	LEU	0	-0.060	-0.023	18.239	-1.311	-1.311	0.000	0.000	0.000	0.000
153	A	155	ASN	0	0.024	0.008	20.461	1.143	1.143	0.000	0.000	0.000	0.000
154	A	156	ASN	0	-0.016	-0.008	17.518	-0.375	-0.375	0.000	0.000	0.000	0.000
155	A	157	VAL	0	0.000	-0.009	14.672	-1.054	-1.054	0.000	0.000	0.000	0.000
156	A	158	ARG	1	0.833	0.942	10.514	45.287	45.287	0.000	0.000	0.000	0.000
157	A	159	PHE	0	0.037	0.017	11.294	-2.107	-2.107	0.000	0.000	0.000	0.000
158	A	160	PHE	0	-0.047	-0.023	6.490	-2.846	-2.846	0.000	0.000	0.000	0.000
159	A	163	LYS	0	0.133	0.111	8.592	21.608	21.608	0.000	0.000	0.000	0.000

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