FMO DATABASE

FMODB ID: XYVL2

Calculation Name: 4YPC-A-Xray25

Preferred Name: Vimentin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4YPC

Chain ID: A

ChEMBL ID: CHEMBL3712854

UniProt ID: P08670

Base Structure: X-ray

Registration Date: 2018-07-25

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	132
LigandCharge
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-465349.790345
FMO2-HF: Nuclear repulsion	426751.63467
FMO2-HF: Total energy	-38598.155675
FMO2-MP2: Total energy	-38709.224017

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:161:VAL)

Summations of interaction energy for fragment #1(A:161:VAL)

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.
-0.178	1.372	0.007	-0.605	-0.952	0.005

Interaction energy analysis for fragmet #1(A:161:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : 0.006

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	163	GLN	0	-0.095	-0.074	3.469	-0.959	0.591	0.007	-0.605	-0.952	0.005
4	A	164	LEU	0	0.062	0.043	6.232	0.575	0.575	0.000	0.000	0.000	0.000
5	A	165	THR	0	-0.030	-0.031	9.504	0.333	0.333	0.000	0.000	0.000	0.000
6	A	166	ASN	0	0.001	-0.006	11.240	0.036	0.036	0.000	0.000	0.000	0.000
7	A	167	ASP	-1	-0.887	-0.948	11.216	-0.909	-0.909	0.000	0.000	0.000	0.000
8	A	168	LYS	1	0.942	0.966	13.813	0.781	0.781	0.000	0.000	0.000	0.000
9	A	169	ALA	0	0.022	0.019	15.894	0.063	0.063	0.000	0.000	0.000	0.000
10	A	170	ARG	1	0.947	0.985	17.124	0.438	0.438	0.000	0.000	0.000	0.000
11	A	171	VAL	0	0.002	-0.005	17.296	0.046	0.046	0.000	0.000	0.000	0.000
12	A	172	GLU	-1	-0.962	-0.985	19.320	-0.424	-0.424	0.000	0.000	0.000	0.000
13	A	173	VAL	0	0.040	0.020	21.893	0.031	0.031	0.000	0.000	0.000	0.000
14	A	174	GLU	-1	-0.845	-0.895	22.991	-0.220	-0.220	0.000	0.000	0.000	0.000
15	A	175	ARG	1	0.890	0.951	23.529	0.302	0.302	0.000	0.000	0.000	0.000
16	A	176	ASP	-1	-0.914	-0.933	25.703	-0.191	-0.191	0.000	0.000	0.000	0.000
17	A	177	ASN	0	0.059	0.015	27.267	0.026	0.026	0.000	0.000	0.000	0.000
18	A	178	LEU	0	0.008	0.006	27.254	0.014	0.014	0.000	0.000	0.000	0.000
19	A	179	ALA	0	-0.054	-0.027	29.701	0.013	0.013	0.000	0.000	0.000	0.000
20	A	180	GLU	-1	-0.880	-0.935	31.410	-0.151	-0.151	0.000	0.000	0.000	0.000
21	A	181	ASP	-1	-0.751	-0.783	33.850	-0.127	-0.127	0.000	0.000	0.000	0.000
22	A	182	ILE	0	-0.063	-0.040	31.830	0.010	0.010	0.000	0.000	0.000	0.000
23	A	183	MET	0	-0.034	-0.011	35.439	0.009	0.009	0.000	0.000	0.000	0.000
24	A	184	ARG	1	0.955	0.972	37.163	0.109	0.109	0.000	0.000	0.000	0.000
25	A	185	LEU	0	-0.029	-0.013	38.347	0.007	0.007	0.000	0.000	0.000	0.000
26	A	186	ARG	1	0.956	0.989	35.054	0.132	0.132	0.000	0.000	0.000	0.000
27	A	187	GLU	-1	-0.886	-0.938	41.002	-0.098	-0.098	0.000	0.000	0.000	0.000
28	A	188	LYS	1	0.971	0.983	43.395	0.091	0.091	0.000	0.000	0.000	0.000
29	A	189	LEU	0	-0.010	0.013	42.651	0.004	0.004	0.000	0.000	0.000	0.000
30	A	190	GLN	0	0.031	0.007	42.874	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	191	GLU	-1	-0.804	-0.872	46.698	-0.074	-0.074	0.000	0.000	0.000	0.000
32	A	192	GLU	-1	-0.831	-0.890	48.348	-0.066	-0.066	0.000	0.000	0.000	0.000
33	A	193	MET	0	-0.125	-0.059	47.329	0.002	0.002	0.000	0.000	0.000	0.000
34	A	194	LEU	0	0.036	0.022	50.537	0.003	0.003	0.000	0.000	0.000	0.000
35	A	195	GLN	0	0.028	0.049	52.998	0.002	0.002	0.000	0.000	0.000	0.000
36	A	196	ARG	1	0.836	0.913	52.605	0.061	0.061	0.000	0.000	0.000	0.000
37	A	197	GLU	-1	-0.886	-0.956	52.767	-0.062	-0.062	0.000	0.000	0.000	0.000
38	A	198	GLU	-1	-0.947	-0.965	56.369	-0.049	-0.049	0.000	0.000	0.000	0.000
39	A	199	ALA	0	-0.016	-0.001	58.574	0.002	0.002	0.000	0.000	0.000	0.000
40	A	200	GLU	-1	-0.870	-0.928	58.270	-0.047	-0.047	0.000	0.000	0.000	0.000
41	A	201	ASN	0	-0.009	-0.009	60.631	0.003	0.003	0.000	0.000	0.000	0.000
42	A	202	THR	0	-0.028	-0.021	62.889	0.002	0.002	0.000	0.000	0.000	0.000
43	A	203	LEU	0	0.000	-0.001	62.173	0.002	0.002	0.000	0.000	0.000	0.000
44	A	204	GLN	0	-0.004	0.044	64.995	0.001	0.001	0.000	0.000	0.000	0.000
45	A	205	SER	0	-0.011	-0.026	66.752	0.002	0.002	0.000	0.000	0.000	0.000
46	A	206	PHE	0	0.020	0.023	67.467	0.001	0.001	0.000	0.000	0.000	0.000
47	A	207	ARG	1	0.924	0.965	69.020	0.034	0.034	0.000	0.000	0.000	0.000
48	A	208	GLN	0	0.002	0.023	70.910	0.002	0.002	0.000	0.000	0.000	0.000
49	A	209	ASP	-1	-0.861	-0.924	72.923	-0.032	-0.032	0.000	0.000	0.000	0.000
50	A	210	VAL	0	-0.039	-0.023	73.144	0.001	0.001	0.000	0.000	0.000	0.000
51	A	211	ASP	-1	-0.798	-0.841	75.136	-0.029	-0.029	0.000	0.000	0.000	0.000
52	A	212	ASN	0	0.005	0.009	76.866	0.001	0.001	0.000	0.000	0.000	0.000
53	A	213	ALA	0	-0.029	-0.008	78.731	0.001	0.001	0.000	0.000	0.000	0.000
54	A	214	SER	0	-0.031	-0.060	78.883	0.001	0.001	0.000	0.000	0.000	0.000
55	A	215	LEU	0	-0.032	0.010	80.422	0.001	0.001	0.000	0.000	0.000	0.000
56	A	216	ALA	0	0.025	0.008	83.448	0.001	0.001	0.000	0.000	0.000	0.000
57	A	217	ARG	1	0.849	0.916	80.429	0.026	0.026	0.000	0.000	0.000	0.000
58	A	218	LEU	0	-0.006	0.013	85.395	0.001	0.001	0.000	0.000	0.000	0.000
59	A	219	ASP	-1	-0.885	-0.958	87.487	-0.021	-0.021	0.000	0.000	0.000	0.000
60	A	220	LEU	0	-0.032	-0.019	87.843	0.001	0.001	0.000	0.000	0.000	0.000
61	A	221	GLU	-1	-0.817	-0.861	87.545	-0.022	-0.022	0.000	0.000	0.000	0.000
62	A	222	ARG	1	0.952	0.978	89.356	0.021	0.021	0.000	0.000	0.000	0.000
63	A	223	LYS	1	0.928	0.967	92.849	0.021	0.021	0.000	0.000	0.000	0.000
64	A	224	VAL	0	-0.007	0.000	93.844	0.000	0.000	0.000	0.000	0.000	0.000
65	A	225	GLU	-1	-0.860	-0.928	94.532	-0.019	-0.019	0.000	0.000	0.000	0.000
66	A	226	SER	0	0.015	0.034	97.868	0.000	0.000	0.000	0.000	0.000	0.000
67	A	227	LEU	0	-0.016	-0.012	98.118	0.000	0.000	0.000	0.000	0.000	0.000
68	A	228	GLN	0	-0.038	-0.024	98.073	0.000	0.000	0.000	0.000	0.000	0.000
69	A	229	GLU	-1	-0.913	-0.932	101.039	-0.016	-0.016	0.000	0.000	0.000	0.000
70	A	230	GLU	-1	-0.807	-0.905	103.549	-0.016	-0.016	0.000	0.000	0.000	0.000
71	A	231	ILE	0	-0.028	-0.015	103.595	0.000	0.000	0.000	0.000	0.000	0.000
72	A	232	ALA	0	-0.010	-0.007	106.209	0.000	0.000	0.000	0.000	0.000	0.000
73	A	233	PHE	0	-0.028	-0.026	107.928	0.000	0.000	0.000	0.000	0.000	0.000
74	A	234	LEU	0	0.008	-0.006	108.555	0.000	0.000	0.000	0.000	0.000	0.000
75	A	235	LYS	1	0.939	0.976	108.255	0.015	0.015	0.000	0.000	0.000	0.000
76	A	236	LYS	1	0.924	1.050	111.787	0.014	0.014	0.000	0.000	0.000	0.000
77	A	237	LEU	0	-0.062	-0.021	113.937	0.000	0.000	0.000	0.000	0.000	0.000
78	A	238	HIS	0	0.017	0.051	114.174	0.000	0.000	0.000	0.000	0.000	0.000
79	A	239	GLU	-1	-0.712	-0.746	114.565	-0.013	-0.013	0.000	0.000	0.000	0.000
80	A	240	GLU	-1	-0.819	-0.863	116.942	-0.012	-0.012	0.000	0.000	0.000	0.000
81	A	241	GLU	-1	-0.830	-0.872	119.789	-0.012	-0.012	0.000	0.000	0.000	0.000
82	A	242	ILE	0	-0.102	-0.054	121.938	0.000	0.000	0.000	0.000	0.000	0.000
83	A	243	GLN	-1	-0.929	-0.941	121.933	-0.011	-0.011	0.000	0.000	0.000	0.000
84	A	301	HOH	0	-0.102	-0.077	122.906	0.000	0.000	0.000	0.000	0.000	0.000
85	A	302	HOH	0	-0.096	-0.093	77.270	0.000	0.000	0.000	0.000	0.000	0.000
86	A	303	HOH	0	-0.053	-0.099	34.449	0.000	0.000	0.000	0.000	0.000	0.000
87	A	304	HOH	0	-0.093	-0.071	113.474	0.000	0.000	0.000	0.000	0.000	0.000
88	A	305	HOH	0	0.024	0.009	112.137	0.000	0.000	0.000	0.000	0.000	0.000
89	A	306	HOH	0	-0.089	-0.105	50.610	0.000	0.000	0.000	0.000	0.000	0.000
90	A	307	HOH	0	-0.038	-0.081	118.068	0.000	0.000	0.000	0.000	0.000	0.000
91	A	308	HOH	0	0.023	0.010	41.943	0.002	0.002	0.000	0.000	0.000	0.000
92	A	309	HOH	0	-0.042	-0.049	78.406	0.000	0.000	0.000	0.000	0.000	0.000
93	A	310	HOH	0	0.029	0.028	78.292	0.000	0.000	0.000	0.000	0.000	0.000
94	A	311	HOH	0	-0.050	-0.060	116.314	0.000	0.000	0.000	0.000	0.000	0.000
95	A	312	HOH	0	-0.114	-0.068	34.884	0.001	0.001	0.000	0.000	0.000	0.000
96	A	313	HOH	0	-0.066	-0.061	22.975	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	314	HOH	0	-0.064	-0.055	121.334	0.000	0.000	0.000	0.000	0.000	0.000
98	A	315	HOH	0	-0.040	-0.050	89.514	0.000	0.000	0.000	0.000	0.000	0.000
99	A	316	HOH	0	-0.097	-0.084	46.368	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	317	HOH	0	-0.059	-0.043	100.988	0.000	0.000	0.000	0.000	0.000	0.000
101	A	318	HOH	0	-0.049	-0.041	42.321	0.001	0.001	0.000	0.000	0.000	0.000
102	A	319	HOH	0	-0.001	0.000	79.861	0.000	0.000	0.000	0.000	0.000	0.000
103	A	320	HOH	0	-0.056	-0.043	102.435	0.000	0.000	0.000	0.000	0.000	0.000
104	A	321	HOH	0	-0.058	-0.046	88.141	0.000	0.000	0.000	0.000	0.000	0.000
105	A	322	HOH	0	0.009	0.013	74.471	0.000	0.000	0.000	0.000	0.000	0.000
106	A	324	HOH	0	0.009	0.005	69.529	0.000	0.000	0.000	0.000	0.000	0.000
107	A	325	HOH	0	0.011	0.004	98.199	0.000	0.000	0.000	0.000	0.000	0.000
108	A	326	HOH	0	-0.037	-0.028	101.385	0.000	0.000	0.000	0.000	0.000	0.000
109	A	327	HOH	0	-0.093	-0.081	112.448	0.000	0.000	0.000	0.000	0.000	0.000
110	A	328	HOH	0	-0.016	-0.018	32.695	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	330	HOH	0	-0.045	-0.022	95.835	0.000	0.000	0.000	0.000	0.000	0.000
112	A	331	HOH	0	-0.045	-0.021	34.317	0.003	0.003	0.000	0.000	0.000	0.000
113	A	332	HOH	0	0.008	0.001	18.115	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	333	HOH	0	-0.053	-0.025	102.516	0.000	0.000	0.000	0.000	0.000	0.000
115	A	334	HOH	0	-0.012	-0.009	51.310	0.000	0.000	0.000	0.000	0.000	0.000
116	A	335	HOH	0	0.026	0.014	43.805	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	336	HOH	0	-0.037	-0.016	51.795	0.000	0.000	0.000	0.000	0.000	0.000
118	A	338	HOH	0	0.015	0.007	82.070	0.000	0.000	0.000	0.000	0.000	0.000
119	A	363	HOH	0	-0.008	-0.004	49.170	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	378	HOH	0	0.029	0.028	76.828	0.000	0.000	0.000	0.000	0.000	0.000
121	A	380	HOH	0	-0.027	-0.019	93.926	0.000	0.000	0.000	0.000	0.000	0.000
122	A	382	HOH	0	-0.110	-0.052	44.770	0.002	0.002	0.000	0.000	0.000	0.000
123	A	389	HOH	0	-0.089	-0.079	114.693	0.000	0.000	0.000	0.000	0.000	0.000
124	A	390	HOH	0	-0.045	-0.059	75.610	0.000	0.000	0.000	0.000	0.000	0.000
125	A	391	HOH	0	-0.028	-0.050	68.355	0.000	0.000	0.000	0.000	0.000	0.000
126	A	393	HOH	0	-0.004	0.013	114.716	0.000	0.000	0.000	0.000	0.000	0.000
127	A	394	HOH	0	-0.151	-0.159	115.320	0.000	0.000	0.000	0.000	0.000	0.000
128	A	397	HOH	0	0.027	0.015	121.676	0.000	0.000	0.000	0.000	0.000	0.000
129	A	402	HOH	0	-0.034	-0.020	95.931	0.000	0.000	0.000	0.000	0.000	0.000
130	A	405	HOH	0	-0.063	-0.054	30.356	0.000	0.000	0.000	0.000	0.000	0.000
131	A	407	HOH	0	0.002	0.003	66.851	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	409	HOH	0	0.062	0.043	7.106	0.167	0.167	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:161:VAL)