FMO DATABASE

FMODB ID: XQN8Y

Calculation Name: 1VMG-A-Xray27

Preferred Name:

Target Type:

Ligand Name: lithium ion

ligand 3-letter code: LI

PDB ID: 1VMG

Chain ID: A

ChEMBL ID:

UniProt ID: Q97U11

Base Structure: X-ray

Registration Date: 2018-07-26

Reference:

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water	Apo structure with with a 3 angstrom solvent shell.
Procedure	Auto-FMO protocol ver. 1.20180227

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	153
LigandCharge	UNL=-2,LI+=1
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-686179.713515
FMO2-HF: Nuclear repulsion	646570.656151
FMO2-HF: Total energy	-39609.057364
FMO2-MP2: Total energy	-39721.991662

3D Structure

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:0:ACE)

Summations of interaction energy for fragment #1(A:0:ACE)

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.
0.524	1.735	-0.014	-0.538	-0.659	-0.002

Interaction energy analysis for fragmet #1(A:0:ACE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : -0.011

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

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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	ASP	-1	-0.821	-0.875	3.821	-0.500	0.711	-0.014	-0.538	-0.659	-0.002
4	A	3	LEU	0	-0.028	-0.008	5.621	0.366	0.366	0.000	0.000	0.000	0.000
5	A	4	GLU	-1	-0.864	-0.938	6.692	0.977	0.977	0.000	0.000	0.000	0.000
6	A	5	LEU	0	0.023	0.000	8.803	-0.044	-0.044	0.000	0.000	0.000	0.000
7	A	6	LYS	1	0.935	0.970	9.412	-0.511	-0.511	0.000	0.000	0.000	0.000
8	A	7	GLU	-1	-0.850	-0.909	6.960	0.241	0.241	0.000	0.000	0.000	0.000
9	A	8	LEU	0	-0.020	0.000	10.113	-0.041	-0.041	0.000	0.000	0.000	0.000
10	A	9	GLN	0	0.017	-0.003	12.351	0.004	0.004	0.000	0.000	0.000	0.000
11	A	10	SER	0	-0.004	-0.011	11.949	-0.023	-0.023	0.000	0.000	0.000	0.000
12	A	11	LYS	1	0.976	0.986	7.577	0.231	0.231	0.000	0.000	0.000	0.000
13	A	12	MET	0	-0.005	0.008	13.853	-0.010	-0.010	0.000	0.000	0.000	0.000
14	A	13	LYS	1	0.855	0.925	16.918	-0.046	-0.046	0.000	0.000	0.000	0.000
15	A	14	GLU	-1	-0.963	-0.990	15.020	0.059	0.059	0.000	0.000	0.000	0.000
16	A	15	MET	0	-0.064	-0.018	15.530	-0.009	-0.009	0.000	0.000	0.000	0.000
17	A	16	TYR	0	0.035	0.022	19.082	0.002	0.002	0.000	0.000	0.000	0.000
18	A	17	PHE	0	0.025	0.026	21.808	0.005	0.005	0.000	0.000	0.000	0.000
19	A	18	GLU	-1	-0.920	-0.924	23.607	0.006	0.006	0.000	0.000	0.000	0.000
20	A	19	LYS	1	0.866	0.927	23.742	0.042	0.042	0.000	0.000	0.000	0.000
21	A	20	ASP	-1	-0.679	-0.811	24.335	-0.027	-0.027	0.000	0.000	0.000	0.000
22	A	21	SER	0	-0.024	-0.025	26.883	0.004	0.004	0.000	0.000	0.000	0.000
23	A	22	GLN	0	-0.128	-0.062	29.229	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	23	ARG	1	0.815	0.918	27.570	0.030	0.030	0.000	0.000	0.000	0.000
25	A	24	GLY	0	0.057	0.049	31.624	0.000	0.000	0.000	0.000	0.000	0.000
26	A	25	ILE	0	0.059	0.023	29.648	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	26	TYR	0	-0.003	-0.005	31.925	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	27	ALA	0	0.014	0.014	33.856	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	28	THR	0	0.039	0.009	27.300	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	29	PHE	0	-0.022	-0.006	29.575	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	30	THR	0	-0.048	-0.038	31.145	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	31	TRP	0	0.013	0.024	28.821	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	32	LEU	0	0.016	0.018	26.061	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	33	VAL	0	-0.060	-0.034	28.780	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	34	GLH	0	-0.078	-0.072	30.069	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	35	GLU	-1	-0.560	-0.803	26.724	-0.076	-0.076	0.000	0.000	0.000	0.000
37	A	36	VAL	0	-0.046	-0.017	28.832	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	37	GLY	0	-0.045	-0.021	30.207	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	38	GLU	-1	-0.730	-0.881	29.626	-0.062	-0.062	0.000	0.000	0.000	0.000
40	A	39	LEU	0	0.007	0.003	26.738	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	40	ALA	0	-0.070	-0.040	29.697	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	41	GLU	-1	-0.855	-0.884	33.258	-0.060	-0.060	0.000	0.000	0.000	0.000
43	A	42	ALA	0	0.046	0.021	29.592	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	43	LEU	0	-0.080	-0.056	29.254	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	44	LEU	0	-0.071	-0.026	32.468	0.002	0.002	0.000	0.000	0.000	0.000
46	A	45	SER	0	-0.053	-0.016	33.505	0.000	0.000	0.000	0.000	0.000	0.000
47	A	46	ASN	0	-0.080	-0.042	32.875	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	47	ASN	0	0.046	0.042	30.254	-0.009	-0.009	0.000	0.000	0.000	0.000
49	A	48	LEU	0	0.021	-0.012	25.571	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	49	ASP	-1	-0.844	-0.911	25.693	-0.137	-0.137	0.000	0.000	0.000	0.000
51	A	50	SER	0	0.061	0.026	25.661	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	51	ILE	0	-0.037	-0.009	25.495	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	52	GLN	0	-0.081	-0.045	19.562	0.008	0.008	0.000	0.000	0.000	0.000
54	A	53	GLU	-1	-0.729	-0.840	21.902	-0.126	-0.126	0.000	0.000	0.000	0.000
55	A	54	GLU	-1	-0.542	-0.807	23.098	-0.090	-0.090	0.000	0.000	0.000	0.000
56	A	55	LEU	0	-0.089	-0.036	21.863	0.007	0.007	0.000	0.000	0.000	0.000
57	A	56	ALA	0	-0.031	-0.010	18.993	0.003	0.003	0.000	0.000	0.000	0.000
58	A	57	ASP	-1	-0.610	-0.849	20.281	-0.104	-0.104	0.000	0.000	0.000	0.000
59	A	58	VAL	0	-0.042	-0.017	22.878	0.013	0.013	0.000	0.000	0.000	0.000
60	A	59	ILE	0	-0.041	-0.013	17.550	0.013	0.013	0.000	0.000	0.000	0.000
61	A	60	ALA	0	0.020	0.010	19.358	0.013	0.013	0.000	0.000	0.000	0.000
62	A	61	TRP	0	0.133	0.055	20.304	0.020	0.020	0.000	0.000	0.000	0.000
63	A	62	THR	0	-0.076	-0.046	22.315	0.013	0.013	0.000	0.000	0.000	0.000
64	A	63	VAL	0	-0.053	-0.027	17.424	0.014	0.014	0.000	0.000	0.000	0.000
65	A	64	SER	0	0.013	-0.005	20.588	0.011	0.011	0.000	0.000	0.000	0.000
66	A	65	ILE	0	-0.021	-0.012	22.911	0.010	0.010	0.000	0.000	0.000	0.000
67	A	66	ALA	0	-0.031	-0.007	21.271	0.007	0.007	0.000	0.000	0.000	0.000
68	A	67	ASN	0	-0.009	-0.021	18.332	0.025	0.025	0.000	0.000	0.000	0.000
69	A	68	LEU	0	-0.029	0.004	22.457	0.008	0.008	0.000	0.000	0.000	0.000
70	A	69	GLU	-1	-0.784	-0.871	25.936	0.016	0.016	0.000	0.000	0.000	0.000
71	A	70	GLY	0	-0.047	0.007	24.045	0.004	0.004	0.000	0.000	0.000	0.000
72	A	71	ILE	0	-0.064	-0.028	22.817	0.008	0.008	0.000	0.000	0.000	0.000
73	A	72	ASP	-1	-0.795	-0.884	17.485	0.107	0.107	0.000	0.000	0.000	0.000
74	A	73	ILE	0	0.039	-0.007	16.846	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	74	GLU	-1	-0.763	-0.858	14.200	0.171	0.171	0.000	0.000	0.000	0.000
76	A	75	GLU	-1	-0.792	-0.883	17.517	0.111	0.111	0.000	0.000	0.000	0.000
77	A	76	ALA	0	-0.025	-0.005	20.508	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	77	LEU	0	0.001	-0.004	18.482	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	78	LYS	1	0.792	0.895	15.731	-0.145	-0.145	0.000	0.000	0.000	0.000
80	A	79	LYS	1	0.954	0.998	21.768	-0.042	-0.042	0.000	0.000	0.000	0.000
81	A	80	LYS	1	0.879	0.951	24.959	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	81	TYR	0	-0.038	-0.030	23.207	-0.007	-0.007	0.000	0.000	0.000	0.000
83	A	82	LYS	1	0.930	0.958	23.916	-0.008	-0.008	0.000	0.000	0.000	0.000
84	A	83	LEU	-1	-0.799	-0.859	18.977	0.056	0.056	0.000	0.000	0.000	0.000
85	A	84	LI+	1	0.008	0.717	27.034	0.088	0.088	0.000	0.000	0.000	0.000
86	A	85	UNL	-2	-1.708	-1.838	22.506	-0.119	-0.119	0.000	0.000	0.000	0.000
87	A	86	HOH	0	0.019	0.020	17.853	0.004	0.004	0.000	0.000	0.000	0.000
88	A	87	HOH	0	-0.057	-0.032	33.289	0.002	0.002	0.000	0.000	0.000	0.000
89	A	88	HOH	0	-0.003	-0.019	20.566	0.001	0.001	0.000	0.000	0.000	0.000
90	A	89	HOH	0	0.002	-0.008	11.366	-0.013	-0.013	0.000	0.000	0.000	0.000
91	A	90	HOH	0	-0.036	-0.031	23.391	0.003	0.003	0.000	0.000	0.000	0.000
92	A	91	HOH	0	-0.016	-0.006	20.587	0.004	0.004	0.000	0.000	0.000	0.000
93	A	92	HOH	0	-0.018	-0.016	23.132	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	93	HOH	0	-0.043	-0.033	22.940	0.000	0.000	0.000	0.000	0.000	0.000
95	A	94	HOH	0	-0.047	-0.035	25.510	0.001	0.001	0.000	0.000	0.000	0.000
96	A	95	HOH	0	-0.031	-0.012	28.856	0.001	0.001	0.000	0.000	0.000	0.000
97	A	96	HOH	0	-0.031	-0.015	30.425	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	97	HOH	0	0.004	0.000	22.060	0.003	0.003	0.000	0.000	0.000	0.000
99	A	98	HOH	0	0.012	0.006	15.974	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	99	HOH	0	0.030	0.020	13.620	0.027	0.027	0.000	0.000	0.000	0.000
101	A	101	HOH	0	-0.070	-0.047	28.740	0.001	0.001	0.000	0.000	0.000	0.000
102	A	102	HOH	0	0.040	0.016	5.473	-0.179	-0.179	0.000	0.000	0.000	0.000
103	A	103	HOH	0	-0.019	-0.013	35.054	0.000	0.000	0.000	0.000	0.000	0.000
104	A	104	HOH	0	-0.039	-0.036	27.795	0.000	0.000	0.000	0.000	0.000	0.000
105	A	105	HOH	0	0.045	0.032	23.792	-0.003	-0.003	0.000	0.000	0.000	0.000
106	A	106	HOH	0	-0.058	-0.036	14.155	0.010	0.010	0.000	0.000	0.000	0.000
107	A	107	HOH	0	0.007	0.003	26.888	0.002	0.002	0.000	0.000	0.000	0.000
108	A	108	HOH	0	0.047	-0.046	27.612	0.000	0.000	0.000	0.000	0.000	0.000
109	A	111	HOH	0	-0.028	-0.023	20.582	0.004	0.004	0.000	0.000	0.000	0.000
110	A	114	HOH	0	-0.044	-0.033	13.879	0.022	0.022	0.000	0.000	0.000	0.000
111	A	115	HOH	0	-0.027	-0.023	21.796	0.001	0.001	0.000	0.000	0.000	0.000
112	A	116	HOH	0	0.037	0.028	19.773	-0.007	-0.007	0.000	0.000	0.000	0.000
113	A	117	HOH	0	-0.072	-0.049	22.149	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	118	HOH	0	-0.023	-0.023	31.915	0.002	0.002	0.000	0.000	0.000	0.000
115	A	121	HOH	0	0.066	0.029	29.276	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	122	HOH	0	-0.065	-0.055	28.125	0.000	0.000	0.000	0.000	0.000	0.000
117	A	123	HOH	0	-0.070	-0.073	34.879	0.001	0.001	0.000	0.000	0.000	0.000
118	A	124	HOH	0	-0.041	-0.019	7.724	-0.046	-0.046	0.000	0.000	0.000	0.000
119	A	125	HOH	0	-0.062	-0.031	30.159	0.003	0.003	0.000	0.000	0.000	0.000
120	A	126	HOH	0	-0.002	0.000	21.851	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	127	HOH	0	-0.016	-0.011	29.910	0.000	0.000	0.000	0.000	0.000	0.000
122	A	128	HOH	0	-0.019	-0.016	25.535	0.003	0.003	0.000	0.000	0.000	0.000
123	A	130	HOH	0	0.017	0.014	28.346	0.002	0.002	0.000	0.000	0.000	0.000
124	A	131	HOH	0	-0.050	-0.037	31.573	0.000	0.000	0.000	0.000	0.000	0.000
125	A	134	HOH	0	-0.010	-0.008	14.364	0.004	0.004	0.000	0.000	0.000	0.000
126	A	135	HOH	0	-0.038	-0.027	31.661	0.000	0.000	0.000	0.000	0.000	0.000
127	A	136	HOH	0	0.006	0.013	27.868	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	137	HOH	0	-0.037	-0.022	15.772	0.002	0.002	0.000	0.000	0.000	0.000
129	A	140	HOH	0	-0.045	-0.034	30.542	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	141	HOH	0	-0.044	-0.030	35.576	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	142	HOH	0	-0.027	-0.014	12.354	0.001	0.001	0.000	0.000	0.000	0.000
132	A	144	HOH	0	-0.041	-0.019	24.533	-0.004	-0.004	0.000	0.000	0.000	0.000
133	A	145	HOH	0	-0.011	-0.010	32.438	0.002	0.002	0.000	0.000	0.000	0.000
134	A	148	HOH	0	-0.010	0.028	32.393	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	150	HOH	0	0.035	0.021	32.638	0.001	0.001	0.000	0.000	0.000	0.000
136	A	153	HOH	0	-0.045	-0.031	27.917	0.001	0.001	0.000	0.000	0.000	0.000
137	A	154	HOH	0	-0.052	-0.073	34.250	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	156	HOH	0	-0.010	-0.016	9.984	-0.020	-0.020	0.000	0.000	0.000	0.000
139	A	157	HOH	0	-0.023	-0.033	21.499	0.000	0.000	0.000	0.000	0.000	0.000
140	A	158	HOH	0	-0.011	-0.006	17.944	0.000	0.000	0.000	0.000	0.000	0.000
141	A	159	HOH	0	-0.048	-0.027	24.964	-0.003	-0.003	0.000	0.000	0.000	0.000
142	A	163	HOH	0	-0.021	-0.016	17.273	-0.005	-0.005	0.000	0.000	0.000	0.000
143	A	165	HOH	0	-0.050	-0.022	32.379	-0.002	-0.002	0.000	0.000	0.000	0.000
144	A	169	HOH	0	-0.049	-0.034	27.577	0.000	0.000	0.000	0.000	0.000	0.000
145	A	172	HOH	0	-0.015	-0.002	28.409	-0.001	-0.001	0.000	0.000	0.000	0.000
146	A	174	HOH	0	-0.051	-0.033	6.603	0.117	0.117	0.000	0.000	0.000	0.000
147	A	175	HOH	0	-0.058	-0.041	23.623	0.001	0.001	0.000	0.000	0.000	0.000
148	A	176	HOH	0	-0.033	-0.026	7.164	0.038	0.038	0.000	0.000	0.000	0.000
149	A	179	HOH	0	-0.054	-0.064	6.506	0.118	0.118	0.000	0.000	0.000	0.000
150	A	180	HOH	0	0.055	0.033	26.597	0.004	0.004	0.000	0.000	0.000	0.000
151	A	184	HOH	0	-0.030	-0.018	19.485	0.007	0.007	0.000	0.000	0.000	0.000
152	A	188	HOH	0	-0.004	-0.010	28.131	0.000	0.000	0.000	0.000	0.000	0.000
153	A	189	HOH	0	-0.011	-0.006	17.127	0.008	0.008	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:ACE)