FMO DATABASE

FMODB ID: NNK9Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-390057.836482
FMO2-HF: Nuclear repulsion	362543.188694
FMO2-HF: Total energy	-27514.647787
FMO2-MP2: Total energy	-27591.039618

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.
-10.311	-4.002	4.375	-2.542	-8.143	0.001

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 : 0.058 / q_NPA : 0.025

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	0.072	0.019	3.883	-1.787	-0.107	-0.005	-0.732	-0.943	0.003
4	A	11	ALA	0	-0.017	0.000	2.629	-1.704	-0.752	0.418	-0.368	-1.003	0.001
5	A	12	MET	0	0.011	0.003	2.340	-2.783	-1.044	2.528	-0.852	-3.415	-0.002
6	A	13	LYS	1	0.908	0.945	4.834	-0.320	-0.201	-0.001	-0.011	-0.107	0.000
7	A	14	ARG	1	0.972	0.987	6.666	-2.113	-2.113	0.000	0.000	0.000	0.000
8	A	15	HIS	0	-0.012	0.016	6.188	-0.171	-0.171	0.000	0.000	0.000	0.000
9	A	16	GLY	0	0.020	0.018	8.996	-0.097	-0.097	0.000	0.000	0.000	0.000
10	A	17	LEU	0	0.014	-0.011	5.965	-0.041	-0.041	0.000	0.000	0.000	0.000
11	A	18	ASP	-1	-0.875	-0.926	9.520	-0.069	-0.069	0.000	0.000	0.000	0.000
12	A	19	ASN	0	0.042	0.019	10.528	0.035	0.035	0.000	0.000	0.000	0.000
13	A	20	TYR	0	-0.004	0.013	12.558	0.027	0.027	0.000	0.000	0.000	0.000
14	A	21	ARG	1	0.855	0.913	14.234	0.083	0.083	0.000	0.000	0.000	0.000
15	A	22	GLY	0	0.036	0.039	16.445	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	23	TYR	0	0.006	0.006	12.306	-0.016	-0.016	0.000	0.000	0.000	0.000
17	A	24	SER	0	0.051	0.025	11.756	-0.039	-0.039	0.000	0.000	0.000	0.000
18	A	25	LEU	0	0.002	-0.016	5.347	-0.081	-0.081	0.000	0.000	0.000	0.000
19	A	26	GLY	0	0.036	0.026	6.688	-0.247	-0.247	0.000	0.000	0.000	0.000
20	A	27	ASN	0	0.000	0.000	7.800	-0.105	-0.105	0.000	0.000	0.000	0.000
21	A	28	TRP	0	0.036	0.008	5.999	-0.083	-0.083	0.000	0.000	0.000	0.000
22	A	29	VAL	0	0.001	-0.001	2.370	-1.723	-0.538	0.819	-0.348	-1.657	0.000
23	A	30	CYS	0	-0.043	0.021	3.985	-0.309	-0.108	-0.002	0.019	-0.218	0.000
24	A	31	ALA	0	0.022	-0.005	6.898	0.054	0.054	0.000	0.000	0.000	0.000
25	A	32	ALA	0	-0.057	-0.023	2.541	-0.367	-0.061	0.619	-0.244	-0.681	-0.001
26	A	33	LYS	1	0.905	0.979	4.540	0.797	0.924	-0.001	-0.006	-0.119	0.000
27	A	34	PHE	0	-0.055	-0.041	6.201	0.269	0.269	0.000	0.000	0.000	0.000
28	A	74	ASN	0	0.017	-0.017	20.473	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	75	LEU	0	0.095	0.045	20.726	0.008	0.008	0.000	0.000	0.000	0.000
30	A	76	CYS	0	-0.055	-0.011	12.394	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	77	ASN	0	-0.008	0.005	18.311	0.003	0.003	0.000	0.000	0.000	0.000
32	A	78	ILE	0	0.019	0.034	15.497	0.006	0.006	0.000	0.000	0.000	0.000
33	A	89	THR	0	0.011	-0.020	7.791	-0.044	-0.044	0.000	0.000	0.000	0.000
34	A	90	ALA	0	0.039	0.016	9.563	-0.030	-0.030	0.000	0.000	0.000	0.000
35	A	91	SER	0	0.047	0.011	7.934	0.022	0.022	0.000	0.000	0.000	0.000
36	A	92	VAL	0	0.000	0.014	6.103	-0.050	-0.050	0.000	0.000	0.000	0.000
37	A	93	ASN	0	0.052	0.011	8.773	-0.008	-0.008	0.000	0.000	0.000	0.000
38	A	95	ALA	0	0.015	0.002	9.781	0.001	0.001	0.000	0.000	0.000	0.000
39	A	96	LYS	1	0.865	0.927	10.983	0.040	0.040	0.000	0.000	0.000	0.000
40	A	97	LYS	1	0.905	0.964	13.677	0.110	0.110	0.000	0.000	0.000	0.000
41	A	98	ILE	0	0.074	0.030	13.905	0.006	0.006	0.000	0.000	0.000	0.000
42	A	99	VAL	0	-0.083	-0.031	13.768	0.006	0.006	0.000	0.000	0.000	0.000
43	A	100	SER	0	-0.049	-0.056	15.986	0.022	0.022	0.000	0.000	0.000	0.000
44	A	101	ASP	-1	-0.863	-0.917	19.017	-0.119	-0.119	0.000	0.000	0.000	0.000
45	A	102	GLY	0	-0.010	-0.020	20.749	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	103	ASN	0	0.011	0.017	19.101	0.004	0.004	0.000	0.000	0.000	0.000
47	A	104	GLY	0	0.016	0.027	17.646	-0.011	-0.011	0.000	0.000	0.000	0.000
48	A	105	MET	0	-0.015	-0.022	9.235	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	106	ASN	0	-0.025	-0.017	14.270	-0.036	-0.036	0.000	0.000	0.000	0.000
50	A	107	ALA	0	0.021	0.029	15.595	0.003	0.003	0.000	0.000	0.000	0.000
51	A	108	TRP	0	-0.012	0.010	10.420	-0.009	-0.009	0.000	0.000	0.000	0.000
52	A	109	VAL	0	0.052	0.014	13.500	-0.013	-0.013	0.000	0.000	0.000	0.000
53	A	110	ALA	0	0.023	0.015	11.462	0.013	0.013	0.000	0.000	0.000	0.000
54	A	111	TRP	0	0.049	-0.013	10.281	0.020	0.020	0.000	0.000	0.000	0.000
55	A	112	ARG	1	0.892	0.935	12.290	0.255	0.255	0.000	0.000	0.000	0.000
56	A	113	ASN	0	0.011	0.014	15.507	0.046	0.046	0.000	0.000	0.000	0.000
57	A	114	ARG	1	0.905	0.966	12.413	0.407	0.407	0.000	0.000	0.000	0.000
58	A	116	LYS	1	0.899	0.949	12.966	0.240	0.240	0.000	0.000	0.000	0.000
59	A	117	GLY	0	0.032	0.021	15.916	0.021	0.021	0.000	0.000	0.000	0.000
60	A	118	THR	0	-0.072	-0.032	13.717	0.004	0.004	0.000	0.000	0.000	0.000
61	A	119	ASP	-1	-0.777	-0.899	14.707	-0.208	-0.208	0.000	0.000	0.000	0.000
62	A	120	VAL	0	-0.052	-0.039	11.246	-0.047	-0.047	0.000	0.000	0.000	0.000
63	A	121	GLN	0	-0.015	-0.019	10.364	-0.049	-0.049	0.000	0.000	0.000	0.000
64	A	122	ALA	0	0.050	0.042	11.384	0.011	0.011	0.000	0.000	0.000	0.000
65	A	123	TRP	0	-0.037	-0.022	6.289	-0.043	-0.043	0.000	0.000	0.000	0.000
66	A	124	ILE	0	-0.091	-0.039	6.501	-0.075	-0.075	0.000	0.000	0.000	0.000

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