FMO DATABASE

FMODB ID: QVJQY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-254276.789606
FMO2-HF: Nuclear repulsion	230852.495065
FMO2-HF: Total energy	-23424.294541
FMO2-MP2: Total energy	-23487.984228

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.
0.098	1.829	-0.023	-0.796	-0.913	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 : 0.001 / q_NPA : -0.006

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	0.037	0.014	3.780	1.192	2.923	-0.023	-0.796	-0.913	0.005
4	B	75	LEU	0	0.048	0.015	6.072	-0.458	-0.458	0.000	0.000	0.000	0.000
5	B	76	CYS	0	-0.101	-0.042	9.034	-0.100	-0.100	0.000	0.000	0.000	0.000
6	B	77	ASN	0	-0.028	-0.002	9.534	-0.230	-0.230	0.000	0.000	0.000	0.000
7	B	78	ILE	0	0.042	0.014	9.287	-0.093	-0.093	0.000	0.000	0.000	0.000
8	B	79	PRO	0	0.018	0.031	8.635	0.010	0.010	0.000	0.000	0.000	0.000
9	B	80	CYS	0	0.059	0.001	6.445	0.132	0.132	0.000	0.000	0.000	0.000
10	B	81	SER	0	0.042	0.029	9.378	0.082	0.082	0.000	0.000	0.000	0.000
11	B	82	ALA	0	0.000	-0.002	12.373	0.046	0.046	0.000	0.000	0.000	0.000
12	B	83	LEU	0	-0.060	-0.038	10.774	0.061	0.061	0.000	0.000	0.000	0.000
13	B	84	LEU	0	-0.038	-0.021	13.708	0.031	0.031	0.000	0.000	0.000	0.000
14	B	85	SER	0	0.009	0.023	16.560	-0.016	-0.016	0.000	0.000	0.000	0.000
15	B	86	SER	0	0.034	0.016	19.341	0.020	0.020	0.000	0.000	0.000	0.000
16	B	87	ASP	-1	-0.866	-0.893	21.808	0.057	0.057	0.000	0.000	0.000	0.000
17	B	88	ILE	0	0.018	-0.008	20.014	0.006	0.006	0.000	0.000	0.000	0.000
18	B	89	THR	0	-0.025	-0.038	20.039	0.042	0.042	0.000	0.000	0.000	0.000
19	B	90	ALA	0	-0.008	-0.003	15.428	0.030	0.030	0.000	0.000	0.000	0.000
20	B	91	SER	0	0.047	0.007	15.501	0.056	0.056	0.000	0.000	0.000	0.000
21	B	92	VAL	0	0.006	0.010	16.568	0.068	0.068	0.000	0.000	0.000	0.000
22	B	93	ASN	0	0.026	0.001	17.872	0.044	0.044	0.000	0.000	0.000	0.000
23	B	95	ALA	0	0.045	0.012	14.788	0.096	0.096	0.000	0.000	0.000	0.000
24	B	96	LYS	1	0.927	0.961	16.676	-0.188	-0.188	0.000	0.000	0.000	0.000
25	B	97	LYS	1	0.921	0.972	12.974	-0.497	-0.497	0.000	0.000	0.000	0.000
26	B	98	ILE	0	0.012	0.003	11.930	0.037	0.037	0.000	0.000	0.000	0.000
27	B	99	VAL	0	-0.048	-0.022	14.944	0.013	0.013	0.000	0.000	0.000	0.000
28	B	100	SER	0	-0.022	-0.028	17.986	-0.050	-0.050	0.000	0.000	0.000	0.000
29	B	101	ASP	-1	-1.006	-0.984	13.289	0.987	0.987	0.000	0.000	0.000	0.000
30	B	102	GLY	0	0.077	0.034	16.268	-0.002	-0.002	0.000	0.000	0.000	0.000
31	B	103	ASN	0	-0.044	-0.010	15.941	-0.107	-0.107	0.000	0.000	0.000	0.000
32	B	104	GLY	0	0.063	0.040	19.056	-0.040	-0.040	0.000	0.000	0.000	0.000
33	B	105	MET	0	0.026	-0.007	18.588	0.044	0.044	0.000	0.000	0.000	0.000
34	B	106	ASN	0	-0.035	-0.016	19.930	-0.036	-0.036	0.000	0.000	0.000	0.000
35	B	107	ALA	0	0.017	0.020	14.645	0.012	0.012	0.000	0.000	0.000	0.000
36	B	108	TRP	0	-0.011	0.011	15.418	0.052	0.052	0.000	0.000	0.000	0.000
37	B	109	VAL	0	0.013	-0.009	16.500	-0.059	-0.059	0.000	0.000	0.000	0.000
38	B	110	ALA	0	0.031	0.008	19.175	-0.039	-0.039	0.000	0.000	0.000	0.000
39	B	111	TRP	0	0.091	0.035	21.309	-0.022	-0.022	0.000	0.000	0.000	0.000
40	B	112	ARG	1	0.904	0.953	19.085	-0.459	-0.459	0.000	0.000	0.000	0.000
41	B	113	ASN	0	0.006	0.003	22.815	-0.005	-0.005	0.000	0.000	0.000	0.000
42	B	114	ARG	1	0.937	0.966	25.253	-0.200	-0.200	0.000	0.000	0.000	0.000
43	B	115	CYS	0	-0.027	0.015	25.991	-0.012	-0.012	0.000	0.000	0.000	0.000
44	B	116	LYS	1	0.912	0.954	24.598	-0.330	-0.330	0.000	0.000	0.000	0.000
45	B	117	GLY	0	0.008	0.004	27.828	-0.005	-0.005	0.000	0.000	0.000	0.000
46	B	118	THR	0	-0.040	-0.016	30.748	-0.015	-0.015	0.000	0.000	0.000	0.000
47	B	119	ASP	-1	-0.799	-0.906	32.983	0.129	0.129	0.000	0.000	0.000	0.000
48	B	120	VAL	0	-0.017	-0.027	29.263	-0.004	-0.004	0.000	0.000	0.000	0.000
49	B	121	GLN	0	0.027	0.018	32.283	-0.009	-0.009	0.000	0.000	0.000	0.000
50	B	122	ALA	0	-0.003	-0.004	34.866	-0.007	-0.007	0.000	0.000	0.000	0.000
51	B	123	TRP	0	-0.054	-0.025	30.626	-0.008	-0.008	0.000	0.000	0.000	0.000
52	B	124	ILE	0	0.005	0.009	31.787	-0.002	-0.002	0.000	0.000	0.000	0.000
53	B	125	ARG	1	0.926	0.957	34.270	-0.100	-0.100	0.000	0.000	0.000	0.000
54	B	126	GLY	0	-0.019	-0.007	37.645	-0.002	-0.002	0.000	0.000	0.000	0.000
55	B	127	CYS	0	-0.052	-0.008	35.442	-0.005	-0.005	0.000	0.000	0.000	0.000
56	B	128	ARG	1	0.948	0.968	37.623	-0.048	-0.048	0.000	0.000	0.000	0.000
57	B	129	LEU	0	0.019	0.017	32.776	-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)