FMO DATABASE

FMODB ID: Q898Y

Calculation Name: 3F6Z-B-Xray312

Preferred Name: Lysozyme C

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3F6Z

Chain ID: B

ChEMBL ID: CHEMBL1932892

UniProt ID: P00698

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	94
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-608299.23303
FMO2-HF: Nuclear repulsion	572516.808118
FMO2-HF: Total energy	-35782.424912
FMO2-MP2: Total energy	-35887.257775

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:27:LYS )

Summations of interaction energy for fragment #1(B:27:LYS )

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.
-113.626	-108.014	0.935	-3.425	-3.121	-0.036

Interaction energy analysis for fragmet #1(B:27:LYS )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.788 / q_NPA : 1.885

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	B	29	ALA	0	0.012	-0.015	2.581	-25.967	-20.413	0.935	-3.419	-3.069	-0.036
4	B	30	GLN	0	0.005	0.019	5.317	4.126	4.184	0.000	-0.006	-0.052	0.000
5	B	31	VAL	0	-0.005	-0.002	8.858	-0.679	-0.679	0.000	0.000	0.000	0.000
6	B	32	ASP	-1	-0.905	-0.930	11.829	-38.363	-38.363	0.000	0.000	0.000	0.000
7	B	33	TYR	0	-0.025	-0.028	13.666	0.625	0.625	0.000	0.000	0.000	0.000
8	B	34	LEU	0	0.010	0.012	18.291	0.866	0.866	0.000	0.000	0.000	0.000
9	B	35	ALA	0	-0.021	-0.011	21.742	0.010	0.010	0.000	0.000	0.000	0.000
10	B	36	LEU	0	-0.001	-0.007	24.560	0.688	0.688	0.000	0.000	0.000	0.000
11	B	37	PRO	0	0.028	0.014	27.087	0.221	0.221	0.000	0.000	0.000	0.000
12	B	38	GLY	0	0.039	0.019	30.768	0.189	0.189	0.000	0.000	0.000	0.000
13	B	39	ASP	-1	-0.865	-0.935	31.718	-19.096	-19.096	0.000	0.000	0.000	0.000
14	B	40	ALA	0	-0.054	-0.016	33.422	0.100	0.100	0.000	0.000	0.000	0.000
15	B	41	LYS	1	0.960	0.975	30.665	19.300	19.300	0.000	0.000	0.000	0.000
16	B	42	LEU	0	-0.018	-0.004	24.312	0.222	0.222	0.000	0.000	0.000	0.000
17	B	43	ASP	-1	-0.939	-0.963	28.419	-21.346	-21.346	0.000	0.000	0.000	0.000
18	B	44	THR	0	-0.023	-0.025	21.914	-0.604	-0.604	0.000	0.000	0.000	0.000
19	B	45	ARG	1	0.960	0.985	24.710	21.498	21.498	0.000	0.000	0.000	0.000
20	B	46	SER	0	-0.012	-0.004	19.524	-0.152	-0.152	0.000	0.000	0.000	0.000
21	B	47	VAL	0	-0.030	-0.006	22.473	0.652	0.652	0.000	0.000	0.000	0.000
22	B	48	ASP	-1	-0.820	-0.870	21.158	-28.543	-28.543	0.000	0.000	0.000	0.000
23	B	49	TYR	0	0.032	0.049	23.439	1.148	1.148	0.000	0.000	0.000	0.000
24	B	50	LYS	1	0.927	0.949	24.286	20.701	20.701	0.000	0.000	0.000	0.000
25	B	124	CYS	0	-0.140	-0.075	26.647	0.136	0.136	0.000	0.000	0.000	0.000
26	B	52	GLU	-1	-0.971	-0.992	28.598	-17.558	-17.558	0.000	0.000	0.000	0.000
27	B	53	ASN	0	0.034	0.010	26.416	0.198	0.198	0.000	0.000	0.000	0.000
28	B	54	GLY	0	-0.038	-0.013	27.072	-0.412	-0.412	0.000	0.000	0.000	0.000
29	B	55	ARG	1	0.840	0.905	20.242	26.181	26.181	0.000	0.000	0.000	0.000
30	B	56	LYN	0	0.103	0.063	21.580	1.445	1.445	0.000	0.000	0.000	0.000
31	B	57	PHE	0	-0.064	-0.018	19.421	-1.407	-1.407	0.000	0.000	0.000	0.000
32	B	58	THR	0	0.026	-0.009	18.269	0.615	0.615	0.000	0.000	0.000	0.000
33	B	59	VAL	0	-0.067	-0.017	19.580	-1.032	-1.032	0.000	0.000	0.000	0.000
34	B	60	GLN	0	0.004	0.006	18.758	-0.012	-0.012	0.000	0.000	0.000	0.000
35	B	61	TYR	0	0.002	-0.018	21.859	0.336	0.336	0.000	0.000	0.000	0.000
36	B	62	LEU	0	-0.019	-0.012	21.832	-0.313	-0.313	0.000	0.000	0.000	0.000
37	B	63	ASN	0	0.027	0.033	26.091	0.662	0.662	0.000	0.000	0.000	0.000
38	B	64	LYS	1	0.845	0.904	28.298	20.860	20.860	0.000	0.000	0.000	0.000
39	B	65	GLY	0	0.007	0.002	30.973	0.090	0.090	0.000	0.000	0.000	0.000
40	B	66	ASP	-1	-0.896	-0.939	34.554	-16.795	-16.795	0.000	0.000	0.000	0.000
41	B	67	ASN	0	-0.087	-0.034	29.517	-0.036	-0.036	0.000	0.000	0.000	0.000
42	B	68	SER	0	0.025	-0.007	29.666	-0.097	-0.097	0.000	0.000	0.000	0.000
43	B	69	LEU	0	-0.036	-0.032	24.428	0.164	0.164	0.000	0.000	0.000	0.000
44	B	70	ALA	0	0.035	0.021	24.626	0.034	0.034	0.000	0.000	0.000	0.000
45	B	71	VAL	0	-0.019	0.004	17.957	0.039	0.039	0.000	0.000	0.000	0.000
46	B	72	VAL	0	0.055	0.011	20.889	-0.402	-0.402	0.000	0.000	0.000	0.000
47	B	73	PRO	0	0.055	0.044	17.262	-0.031	-0.031	0.000	0.000	0.000	0.000
48	B	74	VAL	0	0.004	0.012	19.114	0.899	0.899	0.000	0.000	0.000	0.000
49	B	75	SER	0	-0.047	-0.037	19.436	0.892	0.892	0.000	0.000	0.000	0.000
50	B	76	ASP	-1	-0.944	-0.970	14.780	-37.555	-37.555	0.000	0.000	0.000	0.000
51	B	77	ASN	0	0.022	0.011	14.211	-0.982	-0.982	0.000	0.000	0.000	0.000
52	B	78	SER	0	-0.039	-0.010	15.236	-0.611	-0.611	0.000	0.000	0.000	0.000
53	B	79	THR	0	0.014	0.003	15.680	0.888	0.888	0.000	0.000	0.000	0.000
54	B	80	LEU	0	-0.051	-0.014	17.636	-0.397	-0.397	0.000	0.000	0.000	0.000
55	B	81	VAL	0	0.031	0.015	19.680	0.005	0.005	0.000	0.000	0.000	0.000
56	B	82	PHE	0	-0.027	-0.019	22.011	0.913	0.913	0.000	0.000	0.000	0.000
57	B	83	SER	0	0.024	-0.001	25.606	-0.248	-0.248	0.000	0.000	0.000	0.000
58	B	84	ASN	0	-0.016	-0.006	28.515	0.445	0.445	0.000	0.000	0.000	0.000
59	B	85	VAL	0	-0.055	-0.029	31.575	0.311	0.311	0.000	0.000	0.000	0.000
60	B	86	ILE	0	0.013	0.005	34.634	0.105	0.105	0.000	0.000	0.000	0.000
61	B	87	SER	0	-0.047	-0.027	37.849	0.013	0.013	0.000	0.000	0.000	0.000
62	B	88	ALA	0	0.011	0.016	39.787	0.150	0.150	0.000	0.000	0.000	0.000
63	B	89	SER	0	-0.014	-0.016	41.082	0.034	0.034	0.000	0.000	0.000	0.000
64	B	90	GLY	0	0.026	0.010	37.380	-0.186	-0.186	0.000	0.000	0.000	0.000
65	B	91	ALA	0	0.016	0.020	32.707	0.185	0.185	0.000	0.000	0.000	0.000
66	B	92	LYS	1	0.959	0.998	32.947	16.365	16.365	0.000	0.000	0.000	0.000
67	B	93	TYR	0	0.037	0.014	28.513	-0.016	-0.016	0.000	0.000	0.000	0.000
68	B	94	ALA	0	-0.022	-0.016	29.731	0.107	0.107	0.000	0.000	0.000	0.000
69	B	95	ALA	0	0.065	0.022	24.765	-0.497	-0.497	0.000	0.000	0.000	0.000
70	B	96	GLY	0	-0.008	0.017	25.916	-0.076	-0.076	0.000	0.000	0.000	0.000
71	B	97	GLN	0	-0.016	-0.018	26.119	1.000	1.000	0.000	0.000	0.000	0.000
72	B	98	TYR	0	0.009	0.004	24.241	0.062	0.062	0.000	0.000	0.000	0.000
73	B	99	ILE	0	-0.047	-0.022	28.626	0.311	0.311	0.000	0.000	0.000	0.000
74	B	100	TRP	0	0.011	0.001	27.100	-0.031	-0.031	0.000	0.000	0.000	0.000
75	B	101	TRP	0	-0.039	-0.043	29.433	0.282	0.282	0.000	0.000	0.000	0.000
76	B	102	THR	0	0.000	0.010	29.831	0.195	0.195	0.000	0.000	0.000	0.000
77	B	103	LYS	1	0.974	0.970	32.937	15.954	15.954	0.000	0.000	0.000	0.000
78	B	104	GLY	0	-0.017	0.001	35.725	0.145	0.145	0.000	0.000	0.000	0.000
79	B	105	GLU	-1	-0.905	-0.957	32.386	-18.617	-18.617	0.000	0.000	0.000	0.000
80	B	106	GLU	-1	-0.983	-0.981	31.864	-17.033	-17.033	0.000	0.000	0.000	0.000
81	B	107	ALA	0	0.003	-0.012	29.948	-0.154	-0.154	0.000	0.000	0.000	0.000
82	B	108	THR	0	-0.023	0.002	31.992	0.325	0.325	0.000	0.000	0.000	0.000
83	B	109	LEU	0	-0.013	-0.005	25.876	-0.242	-0.242	0.000	0.000	0.000	0.000
84	B	110	TYR	0	-0.022	-0.025	29.800	0.307	0.307	0.000	0.000	0.000	0.000
85	B	111	GLY	0	0.047	0.020	29.833	-0.402	-0.402	0.000	0.000	0.000	0.000
86	B	112	ASP	-1	-0.936	-0.961	28.780	-19.386	-19.386	0.000	0.000	0.000	0.000
87	B	113	NME	0	-0.042	-0.015	25.277	-0.069	-0.069	0.000	0.000	0.000	0.000
88	B	120	ACE	0	0.011	-0.007	37.120	0.125	0.125	0.000	0.000	0.000	0.000
89	B	121	GLY	0	-0.006	-0.010	33.263	-0.282	-0.282	0.000	0.000	0.000	0.000
90	B	122	VAL	0	-0.009	0.009	28.930	0.330	0.330	0.000	0.000	0.000	0.000
91	B	123	ALA	0	0.065	0.040	31.631	-0.222	-0.222	0.000	0.000	0.000	0.000
92	B	125	LYS	1	0.969	0.973	29.732	18.831	18.831	0.000	0.000	0.000	0.000
93	B	126	GLU	-1	-0.867	-0.934	28.169	-21.018	-21.018	0.000	0.000	0.000	0.000
94	B	127	ARG	0	-0.020	-0.034	25.033	-3.042	-3.042	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:27:LYS )