FMO DATABASE

FMODB ID: Q1ZKY

Calculation Name: 3F6Z-B-Xray372

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: 2023-06-19

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	92
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-603117.796227
FMO2-HF: Nuclear repulsion	567505.422932
FMO2-HF: Total energy	-35612.373295
FMO2-MP2: Total energy	-35716.641278

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.
-83.127	-82.102	9.817	-6.16	-4.682	-0.058

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 : 1 / q_Mulliken : 0.950 / q_NPA : 0.971

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

Sort

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	-0.031	-0.021	1.794	-46.411	-45.570	9.818	-6.095	-4.564	-0.058
4	B	30	GLN	0	-0.035	-0.021	4.229	5.439	5.623	-0.001	-0.065	-0.118	0.000
5	B	31	VAL	0	-0.011	-0.005	7.911	-1.841	-1.841	0.000	0.000	0.000	0.000
6	B	32	ASP	-1	-0.856	-0.899	10.646	-23.321	-23.321	0.000	0.000	0.000	0.000
7	B	33	TYR	0	-0.018	-0.024	12.733	0.468	0.468	0.000	0.000	0.000	0.000
8	B	34	LEU	0	0.007	0.004	17.257	0.547	0.547	0.000	0.000	0.000	0.000
9	B	35	ALA	0	-0.009	-0.007	20.883	0.029	0.029	0.000	0.000	0.000	0.000
10	B	36	LEU	0	0.015	0.006	23.135	0.464	0.464	0.000	0.000	0.000	0.000
11	B	37	PRO	0	0.025	0.020	25.844	0.123	0.123	0.000	0.000	0.000	0.000
12	B	38	GLY	0	0.046	0.021	29.559	0.133	0.133	0.000	0.000	0.000	0.000
13	B	39	ASP	-1	-0.889	-0.950	30.818	-10.002	-10.002	0.000	0.000	0.000	0.000
14	B	40	ALA	0	-0.029	0.000	32.283	0.020	0.020	0.000	0.000	0.000	0.000
15	B	41	LYS	1	0.947	0.968	29.877	10.185	10.185	0.000	0.000	0.000	0.000
16	B	42	LEU	0	-0.006	0.007	23.183	0.127	0.127	0.000	0.000	0.000	0.000
17	B	43	ASP	-1	-0.856	-0.922	27.325	-11.448	-11.448	0.000	0.000	0.000	0.000
18	B	44	THR	0	-0.070	-0.054	20.817	-0.603	-0.603	0.000	0.000	0.000	0.000
19	B	45	ARG	1	0.827	0.896	23.766	11.560	11.560	0.000	0.000	0.000	0.000
20	B	46	SER	0	0.021	0.006	18.550	-0.048	-0.048	0.000	0.000	0.000	0.000
21	B	47	VAL	0	-0.054	-0.024	21.171	0.584	0.584	0.000	0.000	0.000	0.000
22	B	48	ASP	-1	-0.830	-0.880	19.888	-15.969	-15.969	0.000	0.000	0.000	0.000
23	B	49	TYR	0	-0.033	-0.019	22.478	0.793	0.793	0.000	0.000	0.000	0.000
24	B	50	LYS	1	0.885	0.925	23.696	10.713	10.713	0.000	0.000	0.000	0.000
25	B	51	CYS	0	-0.090	-0.052	26.251	0.000	0.000	0.000	0.000	0.000	0.000
26	B	52	GLU	-1	-0.905	-0.959	27.907	-9.289	-9.289	0.000	0.000	0.000	0.000
27	B	53	ASN	0	-0.010	-0.011	26.285	0.014	0.014	0.000	0.000	0.000	0.000
28	B	54	GLY	0	-0.004	0.001	27.377	-0.213	-0.213	0.000	0.000	0.000	0.000
29	B	55	ARG	1	0.839	0.921	19.019	14.874	14.874	0.000	0.000	0.000	0.000
30	B	56	LYN	0	0.063	0.033	21.627	0.834	0.834	0.000	0.000	0.000	0.000
31	B	57	PHE	0	-0.017	-0.007	18.699	-0.708	-0.708	0.000	0.000	0.000	0.000
32	B	58	THR	0	0.004	-0.010	17.093	0.425	0.425	0.000	0.000	0.000	0.000
33	B	59	VAL	0	-0.051	-0.015	18.559	-0.512	-0.512	0.000	0.000	0.000	0.000
34	B	60	GLN	0	0.019	0.001	17.664	-0.436	-0.436	0.000	0.000	0.000	0.000
35	B	61	TYR	0	0.011	0.008	20.431	0.041	0.041	0.000	0.000	0.000	0.000
36	B	62	LEU	0	-0.019	-0.008	20.325	-0.290	-0.290	0.000	0.000	0.000	0.000
37	B	63	ASN	0	-0.024	-0.004	24.569	0.371	0.371	0.000	0.000	0.000	0.000
38	B	64	LYS	1	0.831	0.895	27.188	11.195	11.195	0.000	0.000	0.000	0.000
39	B	65	GLY	0	0.034	0.022	29.835	0.051	0.051	0.000	0.000	0.000	0.000
40	B	66	ASP	-1	-0.911	-0.947	33.286	-9.062	-9.062	0.000	0.000	0.000	0.000
41	B	67	ASN	0	-0.094	-0.044	28.515	-0.349	-0.349	0.000	0.000	0.000	0.000
42	B	68	SER	0	0.018	-0.007	28.264	-0.070	-0.070	0.000	0.000	0.000	0.000
43	B	69	LEU	0	-0.016	-0.009	23.072	0.117	0.117	0.000	0.000	0.000	0.000
44	B	70	ALA	0	0.019	0.001	23.342	0.109	0.109	0.000	0.000	0.000	0.000
45	B	71	VAL	0	-0.008	0.007	16.605	0.014	0.014	0.000	0.000	0.000	0.000
46	B	72	VAL	0	0.054	0.016	19.801	-0.086	-0.086	0.000	0.000	0.000	0.000
47	B	73	PRO	0	0.025	0.029	16.280	-0.060	-0.060	0.000	0.000	0.000	0.000
48	B	74	VAL	0	0.022	0.012	18.223	0.592	0.592	0.000	0.000	0.000	0.000
49	B	75	SER	0	-0.044	-0.035	18.715	0.630	0.630	0.000	0.000	0.000	0.000
50	B	76	ASP	-1	-0.940	-0.977	15.179	-20.355	-20.355	0.000	0.000	0.000	0.000
51	B	77	ASN	0	-0.003	0.006	14.092	-0.806	-0.806	0.000	0.000	0.000	0.000
52	B	78	SER	0	-0.006	0.008	15.096	-0.483	-0.483	0.000	0.000	0.000	0.000
53	B	79	THR	0	0.000	-0.008	14.930	0.362	0.362	0.000	0.000	0.000	0.000
54	B	80	LEU	0	-0.029	0.003	16.964	-0.302	-0.302	0.000	0.000	0.000	0.000
55	B	81	VAL	0	0.024	0.006	18.525	0.001	0.001	0.000	0.000	0.000	0.000
56	B	82	PHE	0	-0.017	0.002	20.948	0.567	0.567	0.000	0.000	0.000	0.000
57	B	83	SER	0	0.035	0.012	24.517	-0.195	-0.195	0.000	0.000	0.000	0.000
58	B	84	ASN	0	-0.023	-0.012	27.419	0.205	0.205	0.000	0.000	0.000	0.000
59	B	85	VAL	0	-0.014	-0.014	30.545	0.148	0.148	0.000	0.000	0.000	0.000
60	B	86	ILE	0	0.034	0.019	33.736	0.052	0.052	0.000	0.000	0.000	0.000
61	B	87	SER	0	-0.041	-0.028	36.517	0.073	0.073	0.000	0.000	0.000	0.000
62	B	88	ALA	0	0.049	0.024	38.616	0.108	0.108	0.000	0.000	0.000	0.000
63	B	89	SER	0	0.007	-0.002	39.268	0.203	0.203	0.000	0.000	0.000	0.000
64	B	90	GLY	0	0.019	0.032	36.069	-0.099	-0.099	0.000	0.000	0.000	0.000
65	B	91	ALA	0	0.014	0.033	31.366	0.121	0.121	0.000	0.000	0.000	0.000
66	B	92	LYS	1	0.896	0.952	32.112	8.841	8.841	0.000	0.000	0.000	0.000
67	B	93	TYR	0	0.014	-0.005	27.090	0.050	0.050	0.000	0.000	0.000	0.000
68	B	94	ALA	0	-0.003	-0.007	28.651	0.103	0.103	0.000	0.000	0.000	0.000
69	B	95	ALA	0	0.058	0.015	23.737	-0.290	-0.290	0.000	0.000	0.000	0.000
70	B	96	GLY	0	-0.007	0.004	25.452	-0.103	-0.103	0.000	0.000	0.000	0.000
71	B	97	GLN	0	-0.011	-0.007	25.890	0.649	0.649	0.000	0.000	0.000	0.000
72	B	98	TYR	0	0.001	0.013	23.586	0.063	0.063	0.000	0.000	0.000	0.000
73	B	99	ILE	0	-0.051	-0.032	27.892	0.091	0.091	0.000	0.000	0.000	0.000
74	B	100	TRP	0	0.013	-0.004	25.983	-0.031	-0.031	0.000	0.000	0.000	0.000
75	B	101	TRP	0	-0.016	-0.025	28.503	0.119	0.119	0.000	0.000	0.000	0.000
76	B	102	THR	0	0.019	0.004	28.770	0.108	0.108	0.000	0.000	0.000	0.000
77	B	103	LYS	1	0.888	0.922	31.980	8.403	8.403	0.000	0.000	0.000	0.000
78	B	104	GLY	0	0.000	0.007	33.556	0.290	0.290	0.000	0.000	0.000	0.000
79	B	105	GLU	-1	-0.794	-0.878	31.300	-9.898	-9.898	0.000	0.000	0.000	0.000
80	B	106	GLU	-1	-0.872	-0.914	31.159	-9.290	-9.290	0.000	0.000	0.000	0.000
81	B	107	ALA	0	0.014	-0.001	29.019	0.025	0.025	0.000	0.000	0.000	0.000
82	B	108	THR	0	-0.067	-0.028	30.889	0.282	0.282	0.000	0.000	0.000	0.000
83	B	109	LEU	0	0.013	0.021	24.909	-0.129	-0.129	0.000	0.000	0.000	0.000
84	B	110	TYR	0	0.003	-0.011	28.908	0.252	0.252	0.000	0.000	0.000	0.000
85	B	111	GLY	0	0.061	0.030	29.084	-0.258	-0.258	0.000	0.000	0.000	0.000
86	B	112	ASP	-1	-0.982	-0.982	25.971	-10.614	-10.614	0.000	0.000	0.000	0.000
87	B	121	GLY	0	0.041	0.012	32.642	0.033	0.033	0.000	0.000	0.000	0.000
88	B	122	VAL	0	-0.067	-0.035	28.437	0.211	0.211	0.000	0.000	0.000	0.000
89	B	123	ALA	0	0.057	0.036	30.406	-0.237	-0.237	0.000	0.000	0.000	0.000
90	B	125	LYS	1	0.904	0.936	29.061	9.791	9.791	0.000	0.000	0.000	0.000
91	B	126	GLU	-1	-0.735	-0.812	27.152	-11.589	-11.589	0.000	0.000	0.000	0.000
92	B	127	ARG	1	0.758	0.855	24.518	10.667	10.667	0.000	0.000	0.000	0.000

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