FMO DATABASE

FMODB ID: 3JV6L

Calculation Name: 2Y72-A-Xray372

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: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	85
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-503904.032598
FMO2-HF: Nuclear repulsion	472941.11863
FMO2-HF: Total energy	-30962.913968
FMO2-MP2: Total energy	-31055.118549

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.
0.039999999999999	1.174	0.006	-0.444	-0.695	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 : 0 / q_Mulliken : 0.016 / q_NPA : -0.007

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	-0.046	-0.052	3.847	-1.348	-0.548	-0.005	-0.328	-0.466	0.001
4	A	799	ILE	0	-0.039	-0.019	3.411	-0.914	-0.715	0.013	-0.080	-0.132	0.000
5	A	800	ALA	0	0.024	0.017	6.706	0.385	0.385	0.000	0.000	0.000	0.000
6	A	801	LYS	1	0.905	0.926	9.943	0.676	0.676	0.000	0.000	0.000	0.000
7	A	802	VAL	0	-0.007	0.010	12.553	0.064	0.064	0.000	0.000	0.000	0.000
8	A	803	THR	0	-0.042	-0.037	16.264	-0.008	-0.008	0.000	0.000	0.000	0.000
9	A	804	GLY	0	0.041	0.008	19.012	0.019	0.019	0.000	0.000	0.000	0.000
10	A	805	PRO	0	-0.014	0.014	22.534	-0.006	-0.006	0.000	0.000	0.000	0.000
11	A	806	SER	0	0.087	0.026	24.004	0.002	0.002	0.000	0.000	0.000	0.000
12	A	807	THR	0	-0.040	-0.014	25.059	0.011	0.011	0.000	0.000	0.000	0.000
13	A	808	GLY	0	0.066	0.019	28.584	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	809	ALA	0	-0.072	-0.040	30.931	0.006	0.006	0.000	0.000	0.000	0.000
15	A	810	VAL	0	0.032	0.019	33.969	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	811	GLY	0	-0.028	-0.004	35.289	0.003	0.003	0.000	0.000	0.000	0.000
17	A	812	ARG	1	0.892	0.949	33.940	0.084	0.084	0.000	0.000	0.000	0.000
18	A	813	ASN	0	0.021	0.001	31.779	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	814	ILE	0	-0.034	-0.008	26.686	0.002	0.002	0.000	0.000	0.000	0.000
20	A	815	GLU	-1	-0.935	-0.964	26.491	-0.140	-0.140	0.000	0.000	0.000	0.000
21	A	816	PHE	0	0.001	-0.004	21.359	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	817	SER	0	-0.014	-0.031	20.474	0.001	0.001	0.000	0.000	0.000	0.000
23	A	818	GLY	0	0.099	0.041	16.392	-0.022	-0.022	0.000	0.000	0.000	0.000
24	A	819	LYS	1	0.797	0.874	15.521	0.256	0.256	0.000	0.000	0.000	0.000
25	A	820	ASP	-1	-0.772	-0.854	14.620	-0.378	-0.378	0.000	0.000	0.000	0.000
26	A	821	SER	0	-0.022	0.003	11.258	-0.110	-0.110	0.000	0.000	0.000	0.000
27	A	822	LYS	1	0.754	0.864	4.366	4.069	4.136	-0.001	-0.023	-0.043	0.000
28	A	823	ASP	-1	-0.735	-0.879	7.877	-0.392	-0.392	0.000	0.000	0.000	0.000
29	A	824	GLU	-1	-0.902	-0.928	4.792	-2.737	-2.669	-0.001	-0.013	-0.054	0.000
30	A	825	ASP	-1	-0.935	-0.960	8.355	0.485	0.485	0.000	0.000	0.000	0.000
31	A	826	GLY	0	0.032	0.035	10.564	0.129	0.129	0.000	0.000	0.000	0.000
32	A	827	LYS	1	0.899	0.955	12.871	-0.022	-0.022	0.000	0.000	0.000	0.000
33	A	828	ILE	0	0.012	0.005	10.563	0.051	0.051	0.000	0.000	0.000	0.000
34	A	829	VAL	0	-0.030	-0.018	13.377	0.021	0.021	0.000	0.000	0.000	0.000
35	A	830	SER	0	-0.084	-0.041	15.240	0.024	0.024	0.000	0.000	0.000	0.000
36	A	831	TYR	0	0.062	0.014	14.520	-0.016	-0.016	0.000	0.000	0.000	0.000
37	A	832	ASP	-1	-0.792	-0.861	16.147	-0.113	-0.113	0.000	0.000	0.000	0.000
38	A	833	TRP	0	-0.020	-0.023	16.945	-0.045	-0.045	0.000	0.000	0.000	0.000
39	A	834	ASP	-1	-0.810	-0.907	19.516	-0.111	-0.111	0.000	0.000	0.000	0.000
40	A	835	PHE	0	-0.015	-0.013	20.884	-0.021	-0.021	0.000	0.000	0.000	0.000
41	A	836	GLY	0	0.037	0.031	23.262	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	837	ASP	-1	-0.860	-0.955	24.068	-0.102	-0.102	0.000	0.000	0.000	0.000
43	A	838	GLY	0	0.013	0.019	25.936	0.010	0.010	0.000	0.000	0.000	0.000
44	A	839	ALA	0	-0.071	-0.017	27.037	0.006	0.006	0.000	0.000	0.000	0.000
45	A	840	THR	0	0.048	0.019	22.633	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	841	SER	0	-0.025	-0.016	22.632	0.008	0.008	0.000	0.000	0.000	0.000
47	A	842	ARG	1	0.886	0.923	18.993	0.093	0.093	0.000	0.000	0.000	0.000
48	A	843	GLY	0	0.026	0.023	20.377	0.015	0.015	0.000	0.000	0.000	0.000
49	A	844	LYS	1	0.864	0.964	16.767	0.309	0.309	0.000	0.000	0.000	0.000
50	A	845	ASN	0	0.024	0.021	19.874	-0.047	-0.047	0.000	0.000	0.000	0.000
51	A	846	SER	0	0.024	0.015	22.685	0.021	0.021	0.000	0.000	0.000	0.000
52	A	847	VAL	0	0.024	0.009	24.309	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	848	HIS	1	0.816	0.925	26.729	0.127	0.127	0.000	0.000	0.000	0.000
54	A	849	ALA	0	0.046	0.029	28.588	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	850	TYR	0	-0.020	-0.020	25.150	0.005	0.005	0.000	0.000	0.000	0.000
56	A	851	LYS	1	0.984	0.971	31.764	0.079	0.079	0.000	0.000	0.000	0.000
57	A	852	LYS	1	0.937	0.970	33.966	0.078	0.078	0.000	0.000	0.000	0.000
58	A	853	ALA	0	0.019	0.025	33.439	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	854	GLY	0	-0.026	-0.012	31.783	0.006	0.006	0.000	0.000	0.000	0.000
60	A	855	THR	0	-0.019	-0.022	26.205	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	856	TYR	0	-0.053	-0.033	25.689	0.007	0.007	0.000	0.000	0.000	0.000
62	A	857	ASN	0	0.032	0.002	18.110	-0.013	-0.013	0.000	0.000	0.000	0.000
63	A	858	VAL	0	-0.010	0.016	19.490	0.005	0.005	0.000	0.000	0.000	0.000
64	A	859	THR	0	-0.033	-0.022	16.036	-0.023	-0.023	0.000	0.000	0.000	0.000
65	A	860	LEU	0	-0.027	-0.003	13.889	0.033	0.033	0.000	0.000	0.000	0.000
66	A	861	LYS	1	0.863	0.920	12.376	0.114	0.114	0.000	0.000	0.000	0.000
67	A	862	VAL	0	-0.022	-0.007	9.690	0.067	0.067	0.000	0.000	0.000	0.000
68	A	863	THR	0	0.010	-0.011	11.192	-0.008	-0.008	0.000	0.000	0.000	0.000
69	A	864	ASP	-1	-0.763	-0.859	8.684	0.085	0.085	0.000	0.000	0.000	0.000
70	A	865	ASP	-1	-0.842	-0.929	11.983	0.099	0.099	0.000	0.000	0.000	0.000
71	A	866	LYS	1	0.738	0.852	8.977	-0.207	-0.207	0.000	0.000	0.000	0.000
72	A	867	GLY	0	-0.045	-0.012	12.952	0.047	0.047	0.000	0.000	0.000	0.000
73	A	868	ALA	0	-0.024	0.006	7.722	0.004	0.004	0.000	0.000	0.000	0.000
74	A	869	THR	0	-0.013	-0.025	8.552	-0.115	-0.115	0.000	0.000	0.000	0.000
75	A	870	ALA	0	-0.022	0.004	5.969	-0.031	-0.031	0.000	0.000	0.000	0.000
76	A	871	THR	0	-0.021	-0.033	7.775	0.157	0.157	0.000	0.000	0.000	0.000
77	A	872	GLU	-1	-0.868	-0.891	9.862	-0.749	-0.749	0.000	0.000	0.000	0.000
78	A	873	SER	0	-0.074	-0.065	12.098	0.105	0.105	0.000	0.000	0.000	0.000
79	A	874	PHE	0	-0.021	-0.018	15.700	-0.021	-0.021	0.000	0.000	0.000	0.000
80	A	875	THR	0	-0.005	-0.001	18.761	0.023	0.023	0.000	0.000	0.000	0.000
81	A	876	ILE	0	-0.037	-0.007	21.882	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	877	GLU	-1	-0.844	-0.895	25.115	-0.114	-0.114	0.000	0.000	0.000	0.000
83	A	878	ILE	0	-0.076	-0.024	28.699	0.003	0.003	0.000	0.000	0.000	0.000
84	A	879	LYS	1	0.975	0.983	31.629	0.107	0.107	0.000	0.000	0.000	0.000
85	A	880	ASN	0	0.044	0.003	35.187	-0.002	-0.002	0.000	0.000	0.000	0.000

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