FMO DATABASE

FMODB ID: P8J5Y

Calculation Name: 2Y72-A-Xray13

Preferred Name: Collagenase

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2Y72

Chain ID: A

ChEMBL ID: CHEMBL2268009

UniProt ID: Q9X721

Base Structure: X-ray

Registration Date: 2018-02-15

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	No
Procedure	Auto-FMO protocol ver. 1.20181228

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	85
LigandCharge
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-504825.171941
FMO2-HF: Nuclear repulsion	473862.762973
FMO2-HF: Total energy	-30962.408968
FMO2-MP2: Total energy	-31054.575825

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:796:GLY)

Summations of interaction energy for fragment #1(A:796:GLY)

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.
-62.387	-60.986	0.007	-0.646	-0.762	-0.001

Interaction energy analysis for fragmet #1(A:796:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.824 / q_NPA : 0.886

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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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	798	THR	0	-0.045	-0.059	3.683	-2.577	-1.590	0.009	-0.407	-0.589	0.000
4	A	799	ILE	0	-0.079	-0.025	4.369	-4.634	-4.525	-0.001	-0.027	-0.081	0.000
5	A	800	ALA	0	0.057	0.029	6.797	3.822	3.822	0.000	0.000	0.000	0.000
6	A	801	LYS	1	0.948	0.961	10.203	24.695	24.695	0.000	0.000	0.000	0.000
7	A	802	VAL	0	0.042	0.019	12.936	0.959	0.959	0.000	0.000	0.000	0.000
8	A	803	THR	0	-0.062	-0.025	16.393	0.171	0.171	0.000	0.000	0.000	0.000
9	A	804	GLY	0	0.064	0.019	19.469	0.301	0.301	0.000	0.000	0.000	0.000
10	A	805	PRO	0	-0.024	0.010	22.826	-0.179	-0.179	0.000	0.000	0.000	0.000
11	A	806	SER	0	0.092	0.026	24.430	-0.067	-0.067	0.000	0.000	0.000	0.000
12	A	807	THR	0	-0.010	0.001	25.571	0.263	0.263	0.000	0.000	0.000	0.000
13	A	808	GLY	0	0.032	0.003	29.007	-0.102	-0.102	0.000	0.000	0.000	0.000
14	A	809	ALA	0	-0.057	-0.024	31.146	0.156	0.156	0.000	0.000	0.000	0.000
15	A	810	VAL	0	0.049	0.025	33.841	-0.189	-0.189	0.000	0.000	0.000	0.000
16	A	811	GLY	0	-0.032	-0.011	34.731	0.227	0.227	0.000	0.000	0.000	0.000
17	A	812	ARG	1	0.892	0.950	33.606	8.706	8.706	0.000	0.000	0.000	0.000
18	A	813	ASN	0	-0.018	-0.016	31.483	-0.382	-0.382	0.000	0.000	0.000	0.000
19	A	814	ILE	0	-0.008	-0.004	26.205	0.117	0.117	0.000	0.000	0.000	0.000
20	A	815	GLU	-1	-0.937	-0.960	26.226	-11.284	-11.284	0.000	0.000	0.000	0.000
21	A	816	PHE	0	-0.001	0.001	20.974	-0.152	-0.152	0.000	0.000	0.000	0.000
22	A	817	SER	0	-0.014	-0.025	20.295	-0.196	-0.196	0.000	0.000	0.000	0.000
23	A	818	GLY	0	0.073	0.029	16.273	-0.543	-0.543	0.000	0.000	0.000	0.000
24	A	819	LYS	1	0.804	0.895	15.425	14.484	14.484	0.000	0.000	0.000	0.000
25	A	820	ASP	-1	-0.862	-0.930	14.512	-18.233	-18.233	0.000	0.000	0.000	0.000
26	A	821	SER	0	-0.064	-0.022	11.342	-1.940	-1.940	0.000	0.000	0.000	0.000
27	A	822	LYS	1	0.920	0.952	5.934	44.200	44.200	0.000	0.000	0.000	0.000
28	A	823	ASP	-1	-0.732	-0.861	7.905	-38.473	-38.473	0.000	0.000	0.000	0.000
29	A	824	GLU	-1	-1.006	-1.014	4.364	-57.554	-57.249	-0.001	-0.212	-0.092	-0.001
30	A	825	ASP	-1	-0.949	-0.966	8.033	-24.920	-24.920	0.000	0.000	0.000	0.000
31	A	826	GLY	0	0.052	0.038	10.282	0.961	0.961	0.000	0.000	0.000	0.000
32	A	827	LYS	1	0.898	0.948	12.755	17.230	17.230	0.000	0.000	0.000	0.000
33	A	828	ILE	0	0.010	0.003	10.547	-0.517	-0.517	0.000	0.000	0.000	0.000
34	A	829	VAL	0	-0.033	-0.015	13.489	1.684	1.684	0.000	0.000	0.000	0.000
35	A	830	SER	0	-0.096	-0.051	15.279	1.476	1.476	0.000	0.000	0.000	0.000
36	A	831	TYR	0	0.059	0.016	14.968	-1.024	-1.024	0.000	0.000	0.000	0.000
37	A	832	ASP	-1	-0.854	-0.932	16.204	-15.767	-15.767	0.000	0.000	0.000	0.000
38	A	833	TRP	0	-0.005	-0.020	17.097	-1.102	-1.102	0.000	0.000	0.000	0.000
39	A	834	ASP	-1	-0.850	-0.921	19.427	-13.462	-13.462	0.000	0.000	0.000	0.000
40	A	835	PHE	0	-0.027	-0.027	20.814	-0.365	-0.365	0.000	0.000	0.000	0.000
41	A	836	GLY	0	0.072	0.044	23.260	0.295	0.295	0.000	0.000	0.000	0.000
42	A	837	ASP	-1	-0.846	-0.914	24.138	-10.947	-10.947	0.000	0.000	0.000	0.000
43	A	838	GLY	0	-0.009	0.003	26.089	0.462	0.462	0.000	0.000	0.000	0.000
44	A	839	ALA	0	-0.056	-0.010	26.983	0.047	0.047	0.000	0.000	0.000	0.000
45	A	840	THR	0	0.030	0.009	22.681	-0.344	-0.344	0.000	0.000	0.000	0.000
46	A	841	SER	0	-0.007	-0.005	22.661	0.691	0.691	0.000	0.000	0.000	0.000
47	A	842	ARG	1	0.916	0.960	19.378	14.417	14.417	0.000	0.000	0.000	0.000
48	A	843	GLY	0	0.021	0.018	20.472	0.617	0.617	0.000	0.000	0.000	0.000
49	A	844	LYS	1	0.915	0.971	18.061	16.539	16.539	0.000	0.000	0.000	0.000
50	A	845	ASN	0	0.031	0.019	19.815	-0.759	-0.759	0.000	0.000	0.000	0.000
51	A	846	SER	0	0.058	0.038	22.540	0.567	0.567	0.000	0.000	0.000	0.000
52	A	847	VAL	0	0.016	0.008	24.182	-0.055	-0.055	0.000	0.000	0.000	0.000
53	A	848	HIS	1	0.796	0.885	26.437	11.365	11.365	0.000	0.000	0.000	0.000
54	A	849	ALA	0	0.066	0.048	28.260	0.010	0.010	0.000	0.000	0.000	0.000
55	A	850	TYR	0	-0.032	-0.029	24.924	0.072	0.072	0.000	0.000	0.000	0.000
56	A	851	LYS	1	0.998	0.982	31.634	9.508	9.508	0.000	0.000	0.000	0.000
57	A	852	LYS	1	0.934	0.972	33.188	9.745	9.745	0.000	0.000	0.000	0.000
58	A	853	ALA	0	0.041	0.042	33.105	-0.311	-0.311	0.000	0.000	0.000	0.000
59	A	854	GLY	0	-0.044	-0.029	31.143	0.110	0.110	0.000	0.000	0.000	0.000
60	A	855	THR	0	0.059	0.040	25.652	0.133	0.133	0.000	0.000	0.000	0.000
61	A	856	TYR	0	-0.075	-0.044	25.248	0.101	0.101	0.000	0.000	0.000	0.000
62	A	857	ASN	0	0.040	0.007	18.037	-0.347	-0.347	0.000	0.000	0.000	0.000
63	A	858	VAL	0	-0.022	0.000	19.184	0.062	0.062	0.000	0.000	0.000	0.000
64	A	859	THR	0	-0.025	-0.019	15.722	-1.003	-1.003	0.000	0.000	0.000	0.000
65	A	860	LEU	0	-0.030	0.000	13.809	0.964	0.964	0.000	0.000	0.000	0.000
66	A	861	LYS	1	0.927	0.970	12.189	18.412	18.412	0.000	0.000	0.000	0.000
67	A	862	VAL	0	-0.030	-0.022	9.707	1.693	1.693	0.000	0.000	0.000	0.000
68	A	863	THR	0	-0.009	-0.004	10.903	-1.862	-1.862	0.000	0.000	0.000	0.000
69	A	864	ASP	-1	-0.760	-0.874	8.550	-32.895	-32.895	0.000	0.000	0.000	0.000
70	A	865	ASP	-1	-0.859	-0.933	11.772	-22.325	-22.325	0.000	0.000	0.000	0.000
71	A	866	LYS	1	0.788	0.882	8.830	31.425	31.425	0.000	0.000	0.000	0.000
72	A	867	GLY	0	-0.045	-0.012	12.614	0.468	0.468	0.000	0.000	0.000	0.000
73	A	868	ALA	0	-0.026	0.005	7.442	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	869	THR	0	-0.047	-0.039	8.749	1.936	1.936	0.000	0.000	0.000	0.000
75	A	870	ALA	0	-0.001	0.005	6.060	-4.334	-4.334	0.000	0.000	0.000	0.000
76	A	871	THR	0	-0.035	-0.028	7.898	4.316	4.316	0.000	0.000	0.000	0.000
77	A	872	GLU	-1	-0.900	-0.918	9.711	-28.984	-28.984	0.000	0.000	0.000	0.000
78	A	873	SER	0	-0.083	-0.054	12.034	1.879	1.879	0.000	0.000	0.000	0.000
79	A	874	PHE	0	-0.004	-0.007	15.567	-0.330	-0.330	0.000	0.000	0.000	0.000
80	A	875	THR	0	-0.015	-0.002	18.571	0.453	0.453	0.000	0.000	0.000	0.000
81	A	876	ILE	0	-0.012	0.005	21.903	0.182	0.182	0.000	0.000	0.000	0.000
82	A	877	GLU	-1	-0.972	-0.976	25.167	-10.993	-10.993	0.000	0.000	0.000	0.000
83	A	878	ILE	0	-0.050	-0.023	28.661	0.198	0.198	0.000	0.000	0.000	0.000
84	A	879	LYS	1	0.964	0.974	31.272	9.043	9.043	0.000	0.000	0.000	0.000
85	A	880	ASN	-1	-0.868	-0.950	34.871	-8.396	-8.396	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:796:GLY)