FMO DATABASE

FMODB ID: ZYK7N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-602961.346854
FMO2-HF: Nuclear repulsion	567349.652953
FMO2-HF: Total energy	-35611.693901
FMO2-MP2: Total energy	-35715.98391

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.
-56.504	-50.363	1.013	-3.818	-3.335	-0.023

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 : 0.964 / q_NPA : 0.987

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	-0.009	-0.030	2.581	-23.055	-16.977	1.014	-3.814	-3.278	-0.023
4	B	30	GLN	0	-0.006	0.013	5.311	3.902	3.965	-0.001	-0.004	-0.057	0.000
5	B	31	VAL	0	-0.011	-0.006	8.873	-0.756	-0.756	0.000	0.000	0.000	0.000
6	B	32	ASP	-1	-0.908	-0.932	11.838	-20.674	-20.674	0.000	0.000	0.000	0.000
7	B	33	TYR	0	-0.026	-0.029	13.646	0.336	0.336	0.000	0.000	0.000	0.000
8	B	34	LEU	0	0.006	0.010	18.300	0.457	0.457	0.000	0.000	0.000	0.000
9	B	35	ALA	0	-0.020	-0.010	21.751	0.028	0.028	0.000	0.000	0.000	0.000
10	B	36	LEU	0	-0.004	-0.009	24.569	0.326	0.326	0.000	0.000	0.000	0.000
11	B	37	PRO	0	0.030	0.014	27.096	0.130	0.130	0.000	0.000	0.000	0.000
12	B	38	GLY	0	0.037	0.018	30.777	0.090	0.090	0.000	0.000	0.000	0.000
13	B	39	ASP	-1	-0.864	-0.934	31.701	-9.724	-9.724	0.000	0.000	0.000	0.000
14	B	40	ALA	0	-0.053	-0.016	33.404	0.067	0.067	0.000	0.000	0.000	0.000
15	B	41	LYS	1	0.959	0.975	30.641	9.744	9.744	0.000	0.000	0.000	0.000
16	B	42	LEU	0	-0.017	-0.004	24.291	0.110	0.110	0.000	0.000	0.000	0.000
17	B	43	ASP	-1	-0.938	-0.962	28.394	-10.862	-10.862	0.000	0.000	0.000	0.000
18	B	44	THR	0	-0.020	-0.024	21.892	-0.346	-0.346	0.000	0.000	0.000	0.000
19	B	45	ARG	1	0.963	0.987	24.713	11.075	11.075	0.000	0.000	0.000	0.000
20	B	46	SER	0	-0.007	0.000	19.532	-0.127	-0.127	0.000	0.000	0.000	0.000
21	B	47	VAL	0	-0.023	-0.002	22.475	0.391	0.391	0.000	0.000	0.000	0.000
22	B	48	ASP	-1	-0.816	-0.872	21.158	-14.707	-14.707	0.000	0.000	0.000	0.000
23	B	49	TYR	0	0.031	0.034	23.440	0.611	0.611	0.000	0.000	0.000	0.000
24	B	50	LYS	1	0.861	0.909	24.286	10.637	10.637	0.000	0.000	0.000	0.000
25	B	51	CYS	0	-0.123	-0.061	26.647	0.031	0.031	0.000	0.000	0.000	0.000
26	B	52	GLU	-1	-0.961	-0.988	28.599	-9.155	-9.155	0.000	0.000	0.000	0.000
27	B	53	ASN	0	0.045	0.018	26.418	0.123	0.123	0.000	0.000	0.000	0.000
28	B	54	GLY	0	-0.033	-0.010	27.071	-0.220	-0.220	0.000	0.000	0.000	0.000
29	B	55	ARG	1	0.850	0.910	20.242	14.034	14.034	0.000	0.000	0.000	0.000
30	B	56	LYN	0	0.085	0.051	21.579	0.842	0.842	0.000	0.000	0.000	0.000
31	B	57	PHE	0	-0.042	-0.006	19.419	-0.750	-0.750	0.000	0.000	0.000	0.000
32	B	58	THR	0	0.020	-0.013	18.270	0.431	0.431	0.000	0.000	0.000	0.000
33	B	59	VAL	0	-0.056	-0.011	19.583	-0.618	-0.618	0.000	0.000	0.000	0.000
34	B	60	GLN	0	0.007	0.009	18.737	0.023	0.023	0.000	0.000	0.000	0.000
35	B	61	TYR	0	0.000	-0.020	21.863	0.103	0.103	0.000	0.000	0.000	0.000
36	B	62	LEU	0	-0.014	-0.009	21.838	-0.125	-0.125	0.000	0.000	0.000	0.000
37	B	63	ASN	0	0.027	0.033	26.097	0.275	0.275	0.000	0.000	0.000	0.000
38	B	64	LYS	1	0.842	0.904	28.280	10.720	10.720	0.000	0.000	0.000	0.000
39	B	65	GLY	0	0.012	0.005	30.955	0.020	0.020	0.000	0.000	0.000	0.000
40	B	66	ASP	-1	-0.893	-0.938	34.547	-8.661	-8.661	0.000	0.000	0.000	0.000
41	B	67	ASN	0	-0.084	-0.033	29.525	-0.017	-0.017	0.000	0.000	0.000	0.000
42	B	68	SER	0	0.023	-0.008	29.673	-0.031	-0.031	0.000	0.000	0.000	0.000
43	B	69	LEU	0	-0.034	-0.030	24.434	0.073	0.073	0.000	0.000	0.000	0.000
44	B	70	ALA	0	0.031	0.018	24.631	0.065	0.065	0.000	0.000	0.000	0.000
45	B	71	VAL	0	-0.012	0.008	17.962	0.005	0.005	0.000	0.000	0.000	0.000
46	B	72	VAL	0	0.053	0.009	20.893	-0.176	-0.176	0.000	0.000	0.000	0.000
47	B	73	PRO	0	0.047	0.042	17.265	-0.038	-0.038	0.000	0.000	0.000	0.000
48	B	74	VAL	0	0.009	0.011	19.117	0.523	0.523	0.000	0.000	0.000	0.000
49	B	75	SER	0	-0.049	-0.038	19.485	0.505	0.505	0.000	0.000	0.000	0.000
50	B	76	ASP	-1	-0.948	-0.972	14.778	-20.563	-20.563	0.000	0.000	0.000	0.000
51	B	77	ASN	0	0.030	0.016	14.212	-0.522	-0.522	0.000	0.000	0.000	0.000
52	B	78	SER	0	-0.039	-0.008	15.237	-0.423	-0.423	0.000	0.000	0.000	0.000
53	B	79	THR	0	0.014	0.003	15.683	0.609	0.609	0.000	0.000	0.000	0.000
54	B	80	LEU	0	-0.050	-0.013	17.640	-0.262	-0.262	0.000	0.000	0.000	0.000
55	B	81	VAL	0	0.033	0.016	19.687	0.040	0.040	0.000	0.000	0.000	0.000
56	B	82	PHE	0	-0.026	-0.019	22.017	0.476	0.476	0.000	0.000	0.000	0.000
57	B	83	SER	0	0.025	-0.001	25.612	-0.117	-0.117	0.000	0.000	0.000	0.000
58	B	84	ASN	0	-0.022	-0.009	28.522	0.215	0.215	0.000	0.000	0.000	0.000
59	B	85	VAL	0	-0.051	-0.027	31.581	0.152	0.152	0.000	0.000	0.000	0.000
60	B	86	ILE	0	0.022	0.008	34.640	0.052	0.052	0.000	0.000	0.000	0.000
61	B	87	SER	0	-0.052	-0.029	37.854	-0.008	-0.008	0.000	0.000	0.000	0.000
62	B	88	ALA	0	0.013	0.017	39.792	0.079	0.079	0.000	0.000	0.000	0.000
63	B	89	SER	0	-0.014	-0.015	41.086	0.029	0.029	0.000	0.000	0.000	0.000
64	B	90	GLY	0	0.026	0.009	37.384	-0.100	-0.100	0.000	0.000	0.000	0.000
65	B	91	ALA	0	0.015	0.020	32.715	0.105	0.105	0.000	0.000	0.000	0.000
66	B	92	LYS	1	0.961	0.997	32.951	8.545	8.545	0.000	0.000	0.000	0.000
67	B	93	TYR	0	0.037	0.015	28.518	0.005	0.005	0.000	0.000	0.000	0.000
68	B	94	ALA	0	-0.022	-0.016	29.736	0.051	0.051	0.000	0.000	0.000	0.000
69	B	95	ALA	0	0.067	0.024	24.771	-0.251	-0.251	0.000	0.000	0.000	0.000
70	B	96	GLY	0	-0.004	0.019	25.921	-0.051	-0.051	0.000	0.000	0.000	0.000
71	B	97	GLN	0	-0.019	-0.016	26.001	0.594	0.594	0.000	0.000	0.000	0.000
72	B	98	TYR	0	0.007	0.004	24.238	0.020	0.020	0.000	0.000	0.000	0.000
73	B	99	ILE	0	-0.046	-0.021	28.629	0.172	0.172	0.000	0.000	0.000	0.000
74	B	100	TRP	0	0.007	-0.001	27.103	-0.030	-0.030	0.000	0.000	0.000	0.000
75	B	101	TRP	0	-0.030	-0.039	29.437	0.136	0.136	0.000	0.000	0.000	0.000
76	B	102	THR	0	0.014	0.013	29.834	0.108	0.108	0.000	0.000	0.000	0.000
77	B	103	LYS	1	0.961	0.969	32.940	8.210	8.210	0.000	0.000	0.000	0.000
78	B	104	GLY	0	-0.013	0.003	35.727	0.081	0.081	0.000	0.000	0.000	0.000
79	B	105	GLU	-1	-0.909	-0.959	32.388	-9.533	-9.533	0.000	0.000	0.000	0.000
80	B	106	GLU	-1	-0.986	-0.985	31.865	-8.808	-8.808	0.000	0.000	0.000	0.000
81	B	107	ALA	0	0.007	-0.011	29.952	-0.082	-0.082	0.000	0.000	0.000	0.000
82	B	108	THR	0	-0.023	0.002	31.994	0.170	0.170	0.000	0.000	0.000	0.000
83	B	109	LEU	0	-0.010	-0.002	25.880	-0.123	-0.123	0.000	0.000	0.000	0.000
84	B	110	TYR	0	-0.013	-0.023	29.802	0.169	0.169	0.000	0.000	0.000	0.000
85	B	111	GLY	0	0.055	0.024	29.836	-0.208	-0.208	0.000	0.000	0.000	0.000
86	B	112	ASP	-1	-0.973	-0.977	26.554	-10.328	-10.328	0.000	0.000	0.000	0.000
87	B	121	GLY	0	0.024	0.011	33.260	0.041	0.041	0.000	0.000	0.000	0.000
88	B	122	VAL	0	-0.046	-0.023	28.929	0.175	0.175	0.000	0.000	0.000	0.000
89	B	123	ALA	0	0.068	0.040	31.632	-0.121	-0.121	0.000	0.000	0.000	0.000
90	B	125	LYS	1	0.981	0.982	29.740	9.721	9.721	0.000	0.000	0.000	0.000
91	B	126	GLU	-1	-0.844	-0.919	28.173	-10.846	-10.846	0.000	0.000	0.000	0.000
92	B	127	ARG	1	0.882	0.930	25.032	10.282	10.282	0.000	0.000	0.000	0.000

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