FMO DATABASE

FMODB ID: G5J61

Calculation Name: 4TSA-A-Xray372

Preferred Name: Lysozyme C

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4TSA

Chain ID: A

ChEMBL ID: CHEMBL1932892

UniProt ID: P00698

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	OptH
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	66
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-388163.222635
FMO2-HF: Nuclear repulsion	360649.111551
FMO2-HF: Total energy	-27514.111084
FMO2-MP2: Total energy	-27590.513516

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:8:LEU)

Summations of interaction energy for fragment #1(A:8:LEU)

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.
-11.522	-6.774	8.885	-4.507	-9.124	0.007

Interaction energy analysis for fragmet #1(A:8:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.056 / q_NPA : 0.015

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	10	ALA	0	0.058	0.007	3.866	-2.551	-0.901	0.000	-0.721	-0.928	0.003
4	A	11	ALA	0	-0.018	0.006	2.052	-1.176	-2.130	5.612	-2.288	-2.369	0.005
5	A	12	MET	0	0.024	0.017	2.369	-3.381	-1.305	2.775	-1.061	-3.790	-0.001
6	A	13	LYS	1	0.978	1.004	3.997	-0.835	-0.657	0.004	-0.033	-0.149	0.000
7	A	14	ARG	1	0.953	0.972	6.189	-2.226	-2.226	0.000	0.000	0.000	0.000
8	A	15	HIS	0	-0.073	-0.037	6.078	-0.194	-0.194	0.000	0.000	0.000	0.000
9	A	16	GLY	0	0.018	0.006	8.467	-0.135	-0.135	0.000	0.000	0.000	0.000
10	A	17	LEU	0	0.000	-0.013	5.796	-0.048	-0.048	0.000	0.000	0.000	0.000
11	A	18	ASP	-1	-0.931	-0.975	9.222	-0.017	-0.017	0.000	0.000	0.000	0.000
12	A	19	ASN	0	0.035	0.024	10.307	0.036	0.036	0.000	0.000	0.000	0.000
13	A	20	TYR	0	-0.033	-0.004	12.329	0.045	0.045	0.000	0.000	0.000	0.000
14	A	21	ARG	1	0.924	0.943	14.000	0.080	0.080	0.000	0.000	0.000	0.000
15	A	22	GLY	0	0.050	0.041	16.854	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	23	TYR	0	0.039	0.022	12.599	-0.012	-0.012	0.000	0.000	0.000	0.000
17	A	24	SER	0	0.074	0.032	12.014	-0.041	-0.041	0.000	0.000	0.000	0.000
18	A	25	LEU	0	0.003	-0.009	5.434	-0.092	-0.092	0.000	0.000	0.000	0.000
19	A	26	GLY	0	0.030	0.019	6.918	-0.292	-0.292	0.000	0.000	0.000	0.000
20	A	27	ASN	0	-0.014	-0.008	8.478	-0.120	-0.120	0.000	0.000	0.000	0.000
21	A	28	TRP	0	0.030	0.005	6.250	-0.093	-0.093	0.000	0.000	0.000	0.000
22	A	29	VAL	0	0.002	-0.009	2.804	-1.578	-0.475	0.216	-0.224	-1.096	0.000
23	A	30	CYS	0	-0.033	0.021	4.314	-0.403	-0.195	-0.001	-0.017	-0.190	0.000
24	A	31	ALA	0	0.006	-0.017	7.118	0.067	0.067	0.000	0.000	0.000	0.000
25	A	32	ALA	0	-0.065	-0.022	2.877	-0.405	-0.013	0.280	-0.158	-0.514	0.000
26	A	33	LYS	1	0.915	0.979	4.740	1.001	1.096	-0.001	-0.005	-0.088	0.000
27	A	34	PHE	0	-0.026	-0.012	6.370	0.233	0.233	0.000	0.000	0.000	0.000
28	A	74	ASN	0	0.010	-0.015	20.777	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	75	LEU	0	0.065	0.041	20.696	0.009	0.009	0.000	0.000	0.000	0.000
30	A	76	CYS	0	-0.052	-0.012	12.023	0.007	0.007	0.000	0.000	0.000	0.000
31	A	77	ASN	0	-0.020	0.003	18.355	0.002	0.002	0.000	0.000	0.000	0.000
32	A	78	ILE	0	0.012	0.011	15.582	0.002	0.002	0.000	0.000	0.000	0.000
33	A	89	THR	0	0.027	0.000	7.494	0.000	0.000	0.000	0.000	0.000	0.000
34	A	90	ALA	0	0.053	0.021	9.442	-0.025	-0.025	0.000	0.000	0.000	0.000
35	A	91	SER	0	0.047	0.013	7.577	0.013	0.013	0.000	0.000	0.000	0.000
36	A	92	VAL	0	-0.017	0.000	5.949	-0.044	-0.044	0.000	0.000	0.000	0.000
37	A	93	ASN	0	0.019	-0.001	8.484	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	95	ALA	0	0.041	0.013	9.710	0.004	0.004	0.000	0.000	0.000	0.000
39	A	96	LYS	1	0.911	0.964	11.276	0.038	0.038	0.000	0.000	0.000	0.000
40	A	97	LYS	1	0.954	0.984	13.426	0.111	0.111	0.000	0.000	0.000	0.000
41	A	98	ILE	0	0.053	0.024	13.391	0.007	0.007	0.000	0.000	0.000	0.000
42	A	99	VAL	0	-0.060	-0.023	13.836	0.008	0.008	0.000	0.000	0.000	0.000
43	A	100	SER	0	-0.114	-0.072	15.926	0.026	0.026	0.000	0.000	0.000	0.000
44	A	101	ASP	-1	-0.884	-0.930	19.021	-0.140	-0.140	0.000	0.000	0.000	0.000
45	A	102	GLY	0	-0.005	-0.017	21.001	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	103	ASN	0	0.008	0.013	19.302	0.012	0.012	0.000	0.000	0.000	0.000
47	A	104	GLY	0	0.032	0.038	17.934	-0.009	-0.009	0.000	0.000	0.000	0.000
48	A	105	MET	0	-0.011	-0.028	9.440	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	106	ASN	0	-0.023	-0.022	14.132	-0.051	-0.051	0.000	0.000	0.000	0.000
50	A	107	ALA	0	0.004	0.023	15.420	0.008	0.008	0.000	0.000	0.000	0.000
51	A	108	TRP	0	0.003	0.023	10.576	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	109	VAL	0	0.062	0.012	13.759	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	110	ALA	0	-0.001	-0.009	11.876	0.021	0.021	0.000	0.000	0.000	0.000
54	A	111	TRP	0	0.041	0.008	10.514	0.024	0.024	0.000	0.000	0.000	0.000
55	A	112	ARG	1	0.924	0.968	12.715	0.267	0.267	0.000	0.000	0.000	0.000
56	A	113	ASN	0	-0.011	-0.021	16.431	0.039	0.039	0.000	0.000	0.000	0.000
57	A	114	ARG	1	0.934	0.977	12.906	0.438	0.438	0.000	0.000	0.000	0.000
58	A	116	LYS	1	0.875	0.957	13.278	0.262	0.262	0.000	0.000	0.000	0.000
59	A	117	GLY	0	0.001	0.011	16.195	0.021	0.021	0.000	0.000	0.000	0.000
60	A	118	THR	0	-0.023	-0.019	14.477	0.001	0.001	0.000	0.000	0.000	0.000
61	A	119	ASP	-1	-0.846	-0.919	15.656	-0.175	-0.175	0.000	0.000	0.000	0.000
62	A	120	VAL	0	-0.037	-0.033	11.394	-0.040	-0.040	0.000	0.000	0.000	0.000
63	A	121	GLN	0	-0.011	-0.028	10.620	-0.067	-0.067	0.000	0.000	0.000	0.000
64	A	122	ALA	0	0.047	0.041	11.738	0.046	0.046	0.000	0.000	0.000	0.000
65	A	123	TRP	0	-0.032	-0.017	6.577	-0.065	-0.065	0.000	0.000	0.000	0.000
66	A	124	ILE	0	-0.053	-0.020	6.242	-0.091	-0.091	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:LEU)