FMO DATABASE

FMODB ID: 89R5Y

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	OptHSide
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	-388371.598907
FMO2-HF: Nuclear repulsion	360857.214437
FMO2-HF: Total energy	-27514.38447
FMO2-MP2: Total energy	-27590.778078

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.
-11.075	-5.725	7.012	-3.867	-8.496	0.003

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 : 0.050 / q_NPA : 0.013

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	0.067	0.011	3.866	-2.112	-0.452	0.001	-0.717	-0.944	0.003
4	A	11	ALA	0	-0.010	0.006	2.083	-1.527	-1.791	4.284	-1.910	-2.110	0.002
5	A	12	MET	0	0.029	0.012	2.410	-3.123	-1.108	1.922	-0.771	-3.166	-0.001
6	A	13	LYS	1	0.905	0.951	4.559	-0.477	-0.343	-0.001	-0.019	-0.115	0.000
7	A	14	ARG	1	0.963	0.982	6.591	-2.326	-2.326	0.000	0.000	0.000	0.000
8	A	15	HIS	0	-0.033	-0.008	6.224	-0.216	-0.216	0.000	0.000	0.000	0.000
9	A	16	GLY	0	0.038	0.025	8.904	-0.137	-0.137	0.000	0.000	0.000	0.000
10	A	17	LEU	0	0.010	-0.007	5.939	-0.044	-0.044	0.000	0.000	0.000	0.000
11	A	18	ASP	-1	-0.875	-0.935	9.272	-0.078	-0.078	0.000	0.000	0.000	0.000
12	A	19	ASN	0	0.021	0.015	10.329	0.042	0.042	0.000	0.000	0.000	0.000
13	A	20	TYR	0	-0.016	0.005	12.402	0.045	0.045	0.000	0.000	0.000	0.000
14	A	21	ARG	1	0.899	0.930	14.025	0.075	0.075	0.000	0.000	0.000	0.000
15	A	22	GLY	0	0.044	0.038	16.892	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	23	TYR	0	0.029	0.020	12.696	-0.023	-0.023	0.000	0.000	0.000	0.000
17	A	24	SER	0	0.065	0.025	12.063	-0.039	-0.039	0.000	0.000	0.000	0.000
18	A	25	LEU	0	0.021	0.003	5.249	-0.073	-0.073	0.000	0.000	0.000	0.000
19	A	26	GLY	0	0.034	0.021	6.990	-0.280	-0.280	0.000	0.000	0.000	0.000
20	A	27	ASN	0	-0.017	-0.011	8.249	-0.104	-0.104	0.000	0.000	0.000	0.000
21	A	28	TRP	0	0.026	0.000	6.344	-0.070	-0.070	0.000	0.000	0.000	0.000
22	A	29	VAL	0	0.008	-0.007	2.448	-1.529	-0.448	0.533	-0.266	-1.349	0.000
23	A	30	CYS	0	-0.050	0.016	4.229	-0.375	-0.146	-0.001	-0.019	-0.209	0.000
24	A	31	ALA	0	0.017	-0.009	7.033	0.065	0.065	0.000	0.000	0.000	0.000
25	A	32	ALA	0	-0.049	-0.014	2.790	-0.376	0.021	0.275	-0.161	-0.511	-0.001
26	A	33	LYS	1	0.906	0.976	4.746	1.013	1.111	-0.001	-0.004	-0.092	0.000
27	A	34	PHE	0	-0.039	-0.025	6.403	0.278	0.278	0.000	0.000	0.000	0.000
28	A	74	ASN	0	0.001	-0.014	20.534	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	75	LEU	0	0.069	0.043	20.757	0.009	0.009	0.000	0.000	0.000	0.000
30	A	76	CYS	0	-0.044	-0.011	12.198	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	77	ASN	0	-0.016	0.006	18.518	0.006	0.006	0.000	0.000	0.000	0.000
32	A	78	ILE	0	0.012	0.008	15.622	0.003	0.003	0.000	0.000	0.000	0.000
33	A	89	THR	0	-0.008	-0.016	7.621	-0.047	-0.047	0.000	0.000	0.000	0.000
34	A	90	ALA	0	0.055	0.018	9.511	-0.034	-0.034	0.000	0.000	0.000	0.000
35	A	91	SER	0	0.041	0.013	7.497	0.017	0.017	0.000	0.000	0.000	0.000
36	A	92	VAL	0	-0.006	0.002	6.133	-0.052	-0.052	0.000	0.000	0.000	0.000
37	A	93	ASN	0	0.012	-0.005	8.699	-0.016	-0.016	0.000	0.000	0.000	0.000
38	A	95	ALA	0	0.040	0.013	9.864	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	96	LYS	1	0.885	0.939	10.880	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	97	LYS	1	0.950	0.985	13.643	0.088	0.088	0.000	0.000	0.000	0.000
41	A	98	ILE	0	0.052	0.018	13.685	0.004	0.004	0.000	0.000	0.000	0.000
42	A	99	VAL	0	-0.062	-0.025	14.013	0.005	0.005	0.000	0.000	0.000	0.000
43	A	100	SER	0	-0.101	-0.067	16.079	0.021	0.021	0.000	0.000	0.000	0.000
44	A	101	ASP	-1	-0.862	-0.909	19.207	-0.120	-0.120	0.000	0.000	0.000	0.000
45	A	102	GLY	0	-0.013	-0.023	21.137	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	103	ASN	0	0.005	0.018	19.502	0.008	0.008	0.000	0.000	0.000	0.000
47	A	104	GLY	0	0.026	0.035	18.042	-0.011	-0.011	0.000	0.000	0.000	0.000
48	A	105	MET	0	-0.003	-0.016	9.507	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	106	ASN	0	-0.024	-0.025	14.187	-0.046	-0.046	0.000	0.000	0.000	0.000
50	A	107	ALA	0	0.007	0.024	15.584	0.007	0.007	0.000	0.000	0.000	0.000
51	A	108	TRP	0	0.007	0.023	10.902	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	109	VAL	0	0.057	0.008	13.836	-0.012	-0.012	0.000	0.000	0.000	0.000
53	A	110	ALA	0	0.010	0.000	11.869	0.018	0.018	0.000	0.000	0.000	0.000
54	A	111	TRP	0	0.045	0.007	10.429	0.020	0.020	0.000	0.000	0.000	0.000
55	A	112	ARG	1	0.910	0.949	12.678	0.262	0.262	0.000	0.000	0.000	0.000
56	A	113	ASN	0	0.012	0.000	16.365	0.031	0.031	0.000	0.000	0.000	0.000
57	A	114	ARG	1	0.935	0.979	12.823	0.439	0.439	0.000	0.000	0.000	0.000
58	A	116	LYS	1	0.869	0.940	13.144	0.255	0.255	0.000	0.000	0.000	0.000
59	A	117	GLY	0	0.003	0.013	16.099	0.021	0.021	0.000	0.000	0.000	0.000
60	A	118	THR	0	-0.031	-0.017	14.191	0.002	0.002	0.000	0.000	0.000	0.000
61	A	119	ASP	-1	-0.822	-0.914	15.170	-0.244	-0.244	0.000	0.000	0.000	0.000
62	A	120	VAL	0	-0.040	-0.035	11.167	-0.049	-0.049	0.000	0.000	0.000	0.000
63	A	121	GLN	0	-0.012	-0.021	10.305	-0.078	-0.078	0.000	0.000	0.000	0.000
64	A	122	ALA	0	0.052	0.042	11.470	0.020	0.020	0.000	0.000	0.000	0.000
65	A	123	TRP	0	-0.033	-0.022	6.258	-0.068	-0.068	0.000	0.000	0.000	0.000
66	A	124	ILE	0	-0.084	-0.028	6.359	-0.099	-0.099	0.000	0.000	0.000	0.000

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