FMO DATABASE

FMODB ID: P952P

Calculation Name: 1NQJ-A-Xray13

Preferred Name: Collagenase

Target Type: SINGLE PROTEIN

Ligand Name: lithium ion

ligand 3-letter code: LI

PDB ID: 1NQJ

Chain ID: A

ChEMBL ID: CHEMBL2268009

UniProt ID: Q9X721

Base Structure: X-ray

Registration Date: 2017-11-22

Reference:

DOI:

Apendix: None

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. 1.20171117

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	103
LigandResidueName
LigandFragmentNumber	0
LigandCharge	CL-=-1,LI+=1
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-784193.105078
FMO2-HF: Nuclear repulsion	743814.8918
FMO2-HF: Total energy	-40378.213278
FMO2-MP2: Total energy	-40496.716694

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:908:ACE)

Summations of interaction energy for fragment #1(A:908: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.
0.371	1.675	-0.018	-0.572	-0.713	-0.002

Interaction energy analysis for fragmet #1(A:908:ACE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.009

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	910	THR	0	-0.005	0.010	3.804	0.776	1.911	-0.017	-0.529	-0.589	-0.002
4	A	911	VAL	0	-0.023	-0.014	7.098	-0.043	-0.043	0.000	0.000	0.000	0.000
5	A	912	ILE	0	0.015	0.006	9.239	0.108	0.108	0.000	0.000	0.000	0.000
6	A	913	PRO	0	-0.066	-0.026	12.691	0.019	0.019	0.000	0.000	0.000	0.000
7	A	914	ASN	0	-0.022	-0.024	14.893	0.029	0.029	0.000	0.000	0.000	0.000
8	A	915	PHE	0	0.042	0.021	17.398	-0.028	-0.028	0.000	0.000	0.000	0.000
9	A	916	ASN	0	-0.052	-0.027	19.852	0.009	0.009	0.000	0.000	0.000	0.000
10	A	917	THR	0	0.008	0.006	18.993	0.030	0.030	0.000	0.000	0.000	0.000
11	A	918	THR	0	-0.016	-0.008	18.792	-0.026	-0.026	0.000	0.000	0.000	0.000
12	A	919	MET	0	-0.015	0.010	12.087	0.031	0.031	0.000	0.000	0.000	0.000
13	A	920	GLN	0	-0.052	-0.057	15.816	0.013	0.013	0.000	0.000	0.000	0.000
14	A	921	GLY	0	0.028	0.020	14.226	-0.039	-0.039	0.000	0.000	0.000	0.000
15	A	922	SER	0	-0.029	-0.007	14.098	0.048	0.048	0.000	0.000	0.000	0.000
16	A	923	LEU	0	0.125	0.000	12.850	-0.024	-0.024	0.000	0.000	0.000	0.000
17	A	924	LEU	0	0.048	0.041	16.057	0.024	0.024	0.000	0.000	0.000	0.000
18	A	925	GLY	0	-0.013	-0.009	17.462	0.007	0.007	0.000	0.000	0.000	0.000
19	A	926	ASP	-1	-0.874	-0.941	15.965	-0.033	-0.033	0.000	0.000	0.000	0.000
20	A	927	ASP	-1	-0.735	-0.899	11.744	-0.293	-0.293	0.000	0.000	0.000	0.000
21	A	928	SER	0	0.003	-0.008	13.341	-0.026	-0.026	0.000	0.000	0.000	0.000
22	A	929	ARG	1	0.891	0.927	9.013	0.221	0.221	0.000	0.000	0.000	0.000
23	A	930	ASP	-1	-0.559	-0.797	8.675	-0.474	-0.474	0.000	0.000	0.000	0.000
24	A	931	TYR	0	0.005	0.007	4.828	-0.053	0.116	-0.001	-0.043	-0.124	0.000
25	A	932	TYR	0	0.010	-0.005	6.667	-0.195	-0.195	0.000	0.000	0.000	0.000
26	A	933	SER	0	-0.035	-0.023	7.017	-0.044	-0.044	0.000	0.000	0.000	0.000
27	A	934	PHE	0	0.038	0.014	8.850	0.108	0.108	0.000	0.000	0.000	0.000
28	A	935	GLU	-1	-0.917	-0.967	11.893	-0.270	-0.270	0.000	0.000	0.000	0.000
29	A	936	VAL	0	-0.036	-0.002	14.468	0.015	0.015	0.000	0.000	0.000	0.000
30	A	937	LYS	1	0.910	0.932	16.637	0.161	0.161	0.000	0.000	0.000	0.000
31	A	938	GLU	-1	-0.925	-0.965	20.554	-0.079	-0.079	0.000	0.000	0.000	0.000
32	A	939	GLU	-1	-0.953	-0.992	23.076	-0.120	-0.120	0.000	0.000	0.000	0.000
33	A	940	GLY	0	0.000	-0.007	23.590	0.011	0.011	0.000	0.000	0.000	0.000
34	A	941	GLU	-1	-0.985	-0.994	23.334	-0.147	-0.147	0.000	0.000	0.000	0.000
35	A	942	VAL	0	0.046	0.040	18.954	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	943	ASN	0	-0.010	-0.027	22.093	0.000	0.000	0.000	0.000	0.000	0.000
37	A	944	ILE	0	-0.024	-0.004	16.205	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	945	GLU	-1	-0.880	-0.957	19.725	-0.153	-0.153	0.000	0.000	0.000	0.000
39	A	946	LEU	0	-0.029	-0.004	16.727	-0.021	-0.021	0.000	0.000	0.000	0.000
40	A	947	ASP	-1	-0.853	-0.931	20.003	-0.157	-0.157	0.000	0.000	0.000	0.000
41	A	948	LYS	1	0.851	0.921	21.705	0.141	0.141	0.000	0.000	0.000	0.000
42	A	949	LYS	1	0.907	0.962	22.214	0.158	0.158	0.000	0.000	0.000	0.000
43	A	950	ASP	-1	-0.822	-0.906	23.047	-0.112	-0.112	0.000	0.000	0.000	0.000
44	A	951	GLU	-1	-0.955	-0.971	24.470	-0.100	-0.100	0.000	0.000	0.000	0.000
45	A	952	PHE	0	-0.049	-0.029	18.645	0.004	0.004	0.000	0.000	0.000	0.000
46	A	953	GLY	0	-0.025	-0.005	22.791	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	954	VAL	0	0.027	0.017	17.147	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	955	THR	0	0.003	-0.014	17.778	0.012	0.012	0.000	0.000	0.000	0.000
49	A	956	TRP	0	0.007	0.002	14.848	-0.055	-0.055	0.000	0.000	0.000	0.000
50	A	957	THR	0	-0.018	-0.018	13.734	0.073	0.073	0.000	0.000	0.000	0.000
51	A	958	LEU	0	-0.015	0.004	12.910	-0.098	-0.098	0.000	0.000	0.000	0.000
52	A	959	HIS	0	0.004	-0.015	9.605	-0.030	-0.030	0.000	0.000	0.000	0.000
53	A	960	PRO	0	0.032	0.021	12.493	-0.081	-0.081	0.000	0.000	0.000	0.000
54	A	961	GLU	-1	-0.904	-0.967	9.887	-0.211	-0.211	0.000	0.000	0.000	0.000
55	A	962	SER	0	-0.033	-0.012	12.261	0.062	0.062	0.000	0.000	0.000	0.000
56	A	963	ASN	0	0.024	0.004	13.270	0.004	0.004	0.000	0.000	0.000	0.000
57	A	964	ILE	0	-0.032	-0.017	16.399	0.018	0.018	0.000	0.000	0.000	0.000
58	A	965	ASN	0	-0.072	-0.031	17.633	0.011	0.011	0.000	0.000	0.000	0.000
59	A	966	ASP	-1	-0.839	-0.910	17.699	-0.140	-0.140	0.000	0.000	0.000	0.000
60	A	967	ARG	1	0.889	0.940	18.526	0.161	0.161	0.000	0.000	0.000	0.000
61	A	968	ILE	0	-0.017	-0.002	15.720	-0.027	-0.027	0.000	0.000	0.000	0.000
62	A	969	THR	0	-0.084	-0.048	17.483	0.035	0.035	0.000	0.000	0.000	0.000
63	A	970	TYR	0	0.008	0.002	17.584	-0.033	-0.033	0.000	0.000	0.000	0.000
64	A	971	GLY	0	0.042	0.037	19.018	0.015	0.015	0.000	0.000	0.000	0.000
65	A	972	GLN	0	-0.024	-0.029	20.717	0.002	0.002	0.000	0.000	0.000	0.000
66	A	973	VAL	0	-0.024	-0.015	23.119	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	974	ASP	-1	-0.951	-0.971	25.333	-0.100	-0.100	0.000	0.000	0.000	0.000
68	A	975	GLY	0	0.037	0.013	28.416	0.001	0.001	0.000	0.000	0.000	0.000
69	A	976	ASN	0	-0.028	-0.038	26.167	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	977	LYS	1	0.927	0.999	24.520	0.136	0.136	0.000	0.000	0.000	0.000
71	A	978	VAL	0	-0.017	0.000	20.841	0.007	0.007	0.000	0.000	0.000	0.000
72	A	979	SER	0	-0.011	0.005	21.256	-0.021	-0.021	0.000	0.000	0.000	0.000
73	A	980	ASN	0	-0.015	-0.021	21.826	0.024	0.024	0.000	0.000	0.000	0.000
74	A	981	LYS	1	0.949	0.989	22.400	0.120	0.120	0.000	0.000	0.000	0.000
75	A	982	VAL	0	-0.005	0.000	19.964	0.010	0.010	0.000	0.000	0.000	0.000
76	A	983	LYS	1	0.930	0.976	22.764	0.098	0.098	0.000	0.000	0.000	0.000
77	A	984	LEU	0	-0.025	-0.002	17.494	0.002	0.002	0.000	0.000	0.000	0.000
78	A	985	ARG	1	1.014	1.003	21.057	0.120	0.120	0.000	0.000	0.000	0.000
79	A	986	PRO	0	0.016	0.005	19.515	-0.023	-0.023	0.000	0.000	0.000	0.000
80	A	987	GLY	0	-0.004	0.004	16.513	0.016	0.016	0.000	0.000	0.000	0.000
81	A	988	LYS	1	0.967	1.015	6.642	0.508	0.508	0.000	0.000	0.000	0.000
82	A	989	TYR	0	-0.051	-0.036	12.137	0.028	0.028	0.000	0.000	0.000	0.000
83	A	990	TYR	0	-0.006	-0.017	5.543	-0.174	-0.174	0.000	0.000	0.000	0.000
84	A	991	LEU	0	-0.007	0.003	9.254	0.193	0.193	0.000	0.000	0.000	0.000
85	A	992	LEU	0	-0.002	0.004	8.596	-0.228	-0.228	0.000	0.000	0.000	0.000
86	A	993	VAL	0	0.027	0.011	10.491	0.155	0.155	0.000	0.000	0.000	0.000
87	A	994	TYR	0	-0.031	-0.019	12.117	-0.028	-0.028	0.000	0.000	0.000	0.000
88	A	995	LYS	1	0.806	0.898	14.250	0.177	0.177	0.000	0.000	0.000	0.000
89	A	996	TYR	0	-0.042	-0.022	17.545	0.012	0.012	0.000	0.000	0.000	0.000
90	A	997	SER	0	-0.012	-0.011	20.290	0.022	0.022	0.000	0.000	0.000	0.000
91	A	998	GLY	0	0.042	0.028	22.461	-0.009	-0.009	0.000	0.000	0.000	0.000
92	A	999	SER	0	-0.017	-0.027	20.388	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	1000	GLY	0	0.038	0.028	19.751	0.014	0.014	0.000	0.000	0.000	0.000
94	A	1001	ASN	0	0.013	0.005	18.551	-0.032	-0.032	0.000	0.000	0.000	0.000
95	A	1002	TYR	0	-0.042	-0.046	12.705	-0.010	-0.010	0.000	0.000	0.000	0.000
96	A	1003	GLU	-1	-0.839	-0.903	18.203	-0.176	-0.176	0.000	0.000	0.000	0.000
97	A	1004	LEU	0	-0.019	-0.018	13.607	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	1005	ARG	1	0.894	0.965	17.626	0.184	0.184	0.000	0.000	0.000	0.000
99	A	1006	VAL	0	0.008	0.009	15.131	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	1007	ASN	0	0.015	-0.010	18.433	0.015	0.015	0.000	0.000	0.000	0.000
101	A	1008	LYS	0	0.041	0.036	20.676	0.005	0.005	0.000	0.000	0.000	0.000
102	A	1009	CL-	-1	-0.829	-0.891	21.068	-0.173	-0.173	0.000	0.000	0.000	0.000
103	A	1010	LI+	1	0.315	0.814	12.300	0.354	0.354	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:908:ACE)