FMO DATABASE

FMODB ID: R8VR8

Calculation Name: 3ZVQ-B-Xray372

Preferred Name: Lysozyme C

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZVQ

Chain ID: B

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	57
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-253994.794793
FMO2-HF: Nuclear repulsion	230570.718043
FMO2-HF: Total energy	-23424.07675
FMO2-MP2: Total energy	-23487.801218

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(B:72:SER)

Summations of interaction energy for fragment #1(B:72:SER)

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.
-0.25	1.5	-0.019	-0.772	-0.96	0.005

Interaction energy analysis for fragmet #1(B:72:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.008

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	B	74	ASN	0	0.063	0.035	3.780	1.080	2.830	-0.019	-0.772	-0.960	0.005
4	B	75	LEU	0	0.040	0.009	5.808	-0.598	-0.598	0.000	0.000	0.000	0.000
5	B	76	CYS	0	-0.109	-0.043	8.913	-0.135	-0.135	0.000	0.000	0.000	0.000
6	B	77	ASN	0	-0.024	-0.006	9.322	-0.233	-0.233	0.000	0.000	0.000	0.000
7	B	78	ILE	0	0.014	-0.002	9.078	-0.131	-0.131	0.000	0.000	0.000	0.000
8	B	79	PRO	0	0.017	0.031	8.474	0.057	0.057	0.000	0.000	0.000	0.000
9	B	80	CYS	0	0.064	-0.001	6.932	0.139	0.139	0.000	0.000	0.000	0.000
10	B	81	SER	0	0.028	0.023	9.454	0.068	0.068	0.000	0.000	0.000	0.000
11	B	82	ALA	0	0.012	0.003	12.351	0.033	0.033	0.000	0.000	0.000	0.000
12	B	83	LEU	0	-0.063	-0.036	10.872	0.052	0.052	0.000	0.000	0.000	0.000
13	B	84	LEU	0	-0.038	-0.019	13.954	0.021	0.021	0.000	0.000	0.000	0.000
14	B	85	SER	0	0.007	0.021	16.725	-0.021	-0.021	0.000	0.000	0.000	0.000
15	B	86	SER	0	0.005	0.005	19.427	0.022	0.022	0.000	0.000	0.000	0.000
16	B	87	ASP	-1	-0.831	-0.858	21.910	0.079	0.079	0.000	0.000	0.000	0.000
17	B	88	ILE	0	0.019	-0.010	20.149	0.009	0.009	0.000	0.000	0.000	0.000
18	B	89	THR	0	-0.028	-0.058	20.146	0.040	0.040	0.000	0.000	0.000	0.000
19	B	90	ALA	0	-0.001	0.000	15.379	0.031	0.031	0.000	0.000	0.000	0.000
20	B	91	SER	0	0.044	0.002	15.653	0.065	0.065	0.000	0.000	0.000	0.000
21	B	92	VAL	0	-0.004	0.009	16.710	0.065	0.065	0.000	0.000	0.000	0.000
22	B	93	ASN	0	0.009	-0.008	17.632	0.037	0.037	0.000	0.000	0.000	0.000
23	B	95	ALA	0	0.048	0.013	14.828	0.090	0.090	0.000	0.000	0.000	0.000
24	B	96	LYS	1	0.972	0.980	16.782	-0.212	-0.212	0.000	0.000	0.000	0.000
25	B	97	LYS	1	0.925	0.980	12.990	-0.546	-0.546	0.000	0.000	0.000	0.000
26	B	98	ILE	0	0.009	0.000	12.557	0.028	0.028	0.000	0.000	0.000	0.000
27	B	99	VAL	0	-0.054	-0.023	14.927	0.008	0.008	0.000	0.000	0.000	0.000
28	B	100	SER	0	-0.029	-0.036	17.966	-0.052	-0.052	0.000	0.000	0.000	0.000
29	B	101	ASP	-1	-0.995	-0.978	13.596	0.965	0.965	0.000	0.000	0.000	0.000
30	B	102	GLY	0	0.068	0.031	16.266	-0.002	-0.002	0.000	0.000	0.000	0.000
31	B	103	ASN	0	-0.047	-0.012	15.955	-0.108	-0.108	0.000	0.000	0.000	0.000
32	B	104	GLY	0	0.062	0.030	19.058	-0.038	-0.038	0.000	0.000	0.000	0.000
33	B	105	MET	0	0.034	-0.007	18.579	0.041	0.041	0.000	0.000	0.000	0.000
34	B	106	ASN	0	-0.021	-0.005	19.959	-0.034	-0.034	0.000	0.000	0.000	0.000
35	B	107	ALA	0	0.005	0.016	14.597	0.008	0.008	0.000	0.000	0.000	0.000
36	B	108	TRP	0	-0.007	0.014	15.404	0.053	0.053	0.000	0.000	0.000	0.000
37	B	109	VAL	0	0.014	-0.009	16.468	-0.056	-0.056	0.000	0.000	0.000	0.000
38	B	110	ALA	0	0.031	0.005	19.161	-0.036	-0.036	0.000	0.000	0.000	0.000
39	B	111	TRP	0	0.075	0.026	21.288	-0.021	-0.021	0.000	0.000	0.000	0.000
40	B	112	ARG	1	0.917	0.957	19.412	-0.417	-0.417	0.000	0.000	0.000	0.000
41	B	113	ASN	0	0.000	0.001	22.528	-0.014	-0.014	0.000	0.000	0.000	0.000
42	B	114	ARG	1	0.935	0.963	25.241	-0.191	-0.191	0.000	0.000	0.000	0.000
43	B	115	CYS	0	-0.018	0.027	25.966	-0.013	-0.013	0.000	0.000	0.000	0.000
44	B	116	LYS	1	0.917	0.964	24.713	-0.312	-0.312	0.000	0.000	0.000	0.000
45	B	117	GLY	0	0.003	0.001	27.816	-0.005	-0.005	0.000	0.000	0.000	0.000
46	B	118	THR	0	-0.048	-0.022	30.700	-0.015	-0.015	0.000	0.000	0.000	0.000
47	B	119	ASP	-1	-0.855	-0.938	32.968	0.126	0.126	0.000	0.000	0.000	0.000
48	B	120	VAL	0	-0.013	-0.026	29.277	-0.004	-0.004	0.000	0.000	0.000	0.000
49	B	121	GLN	0	0.023	0.007	32.369	-0.003	-0.003	0.000	0.000	0.000	0.000
50	B	122	ALA	0	0.002	0.000	35.069	-0.007	-0.007	0.000	0.000	0.000	0.000
51	B	123	TRP	0	-0.045	-0.022	30.989	-0.007	-0.007	0.000	0.000	0.000	0.000
52	B	124	ILE	0	0.008	0.013	32.052	-0.001	-0.001	0.000	0.000	0.000	0.000
53	B	125	ARG	1	0.986	0.993	34.488	-0.095	-0.095	0.000	0.000	0.000	0.000
54	B	126	GLY	0	-0.038	-0.016	37.923	-0.002	-0.002	0.000	0.000	0.000	0.000
55	B	127	CYS	0	-0.042	0.001	35.430	-0.005	-0.005	0.000	0.000	0.000	0.000
56	B	128	ARG	1	0.942	0.968	37.889	-0.052	-0.052	0.000	0.000	0.000	0.000
57	B	129	LEU	0	0.023	0.016	33.012	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:72:SER)