FMO DATABASE

FMODB ID: R56Q8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-603488.851237
FMO2-HF: Nuclear repulsion	567876.715545
FMO2-HF: Total energy	-35612.135692
FMO2-MP2: Total energy	-35716.400432

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.
-79.446	-76.01	8.139	-6.481	-5.094	-0.059

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 : 0.941 / q_NPA : 0.969

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	-0.003	-0.019	1.857	-43.691	-40.410	8.140	-6.425	-4.996	-0.059
4	B	30	GLN	0	-0.012	0.012	4.418	5.334	5.489	-0.001	-0.056	-0.098	0.000
5	B	31	VAL	0	-0.023	-0.013	7.959	-1.075	-1.075	0.000	0.000	0.000	0.000
6	B	32	ASP	-1	-0.886	-0.927	10.785	-22.392	-22.392	0.000	0.000	0.000	0.000
7	B	33	TYR	0	-0.022	-0.025	12.709	0.353	0.353	0.000	0.000	0.000	0.000
8	B	34	LEU	0	0.001	0.008	17.284	0.558	0.558	0.000	0.000	0.000	0.000
9	B	35	ALA	0	-0.014	-0.007	20.786	0.013	0.013	0.000	0.000	0.000	0.000
10	B	36	LEU	0	0.012	-0.001	23.538	0.352	0.352	0.000	0.000	0.000	0.000
11	B	37	PRO	0	0.037	0.019	26.124	0.160	0.160	0.000	0.000	0.000	0.000
12	B	38	GLY	0	0.042	0.021	29.804	0.090	0.090	0.000	0.000	0.000	0.000
13	B	39	ASP	-1	-0.873	-0.930	30.923	-10.065	-10.065	0.000	0.000	0.000	0.000
14	B	40	ALA	0	-0.047	-0.013	32.542	0.073	0.073	0.000	0.000	0.000	0.000
15	B	41	LYS	1	0.969	0.975	30.234	10.077	10.077	0.000	0.000	0.000	0.000
16	B	42	LEU	0	-0.008	-0.001	23.458	0.117	0.117	0.000	0.000	0.000	0.000
17	B	43	ASP	-1	-0.906	-0.942	27.607	-11.341	-11.341	0.000	0.000	0.000	0.000
18	B	44	THR	0	-0.034	-0.028	20.939	-0.398	-0.398	0.000	0.000	0.000	0.000
19	B	45	ARG	1	0.872	0.924	23.686	11.600	11.600	0.000	0.000	0.000	0.000
20	B	46	SER	0	-0.004	-0.003	18.865	-0.130	-0.130	0.000	0.000	0.000	0.000
21	B	47	VAL	0	-0.043	-0.011	21.682	0.432	0.432	0.000	0.000	0.000	0.000
22	B	48	ASP	-1	-0.820	-0.870	20.476	-15.598	-15.598	0.000	0.000	0.000	0.000
23	B	49	TYR	0	0.022	0.021	22.922	0.696	0.696	0.000	0.000	0.000	0.000
24	B	50	LYS	1	0.884	0.924	23.866	10.787	10.787	0.000	0.000	0.000	0.000
25	B	51	CYS	0	-0.101	-0.053	26.229	0.048	0.048	0.000	0.000	0.000	0.000
26	B	52	GLU	-1	-0.929	-0.974	28.026	-9.300	-9.300	0.000	0.000	0.000	0.000
27	B	53	ASN	0	0.017	0.002	26.212	0.022	0.022	0.000	0.000	0.000	0.000
28	B	54	GLY	0	-0.031	-0.007	26.849	-0.206	-0.206	0.000	0.000	0.000	0.000
29	B	55	ARG	1	0.853	0.924	19.060	14.700	14.700	0.000	0.000	0.000	0.000
30	B	56	LYN	0	0.079	0.044	21.389	0.851	0.851	0.000	0.000	0.000	0.000
31	B	57	PHE	0	-0.048	-0.010	18.845	-0.781	-0.781	0.000	0.000	0.000	0.000
32	B	58	THR	0	0.020	-0.015	17.597	0.415	0.415	0.000	0.000	0.000	0.000
33	B	59	VAL	0	-0.060	-0.015	18.610	-0.666	-0.666	0.000	0.000	0.000	0.000
34	B	60	GLN	0	0.016	0.012	17.706	-0.071	-0.071	0.000	0.000	0.000	0.000
35	B	61	TYR	0	0.003	-0.011	20.669	0.116	0.116	0.000	0.000	0.000	0.000
36	B	62	LEU	0	-0.013	-0.010	20.610	-0.174	-0.174	0.000	0.000	0.000	0.000
37	B	63	ASN	0	-0.008	0.012	24.878	0.328	0.328	0.000	0.000	0.000	0.000
38	B	64	LYS	1	0.814	0.885	27.527	11.133	11.133	0.000	0.000	0.000	0.000
39	B	65	GLY	0	0.019	0.008	29.865	0.026	0.026	0.000	0.000	0.000	0.000
40	B	66	ASP	-1	-0.913	-0.950	33.424	-8.998	-8.998	0.000	0.000	0.000	0.000
41	B	67	ASN	0	-0.082	-0.032	28.520	-0.224	-0.224	0.000	0.000	0.000	0.000
42	B	68	SER	0	0.039	-0.001	28.496	-0.055	-0.055	0.000	0.000	0.000	0.000
43	B	69	LEU	0	-0.037	-0.026	23.338	0.095	0.095	0.000	0.000	0.000	0.000
44	B	70	ALA	0	0.030	0.015	23.500	0.063	0.063	0.000	0.000	0.000	0.000
45	B	71	VAL	0	-0.012	0.008	16.897	0.027	0.027	0.000	0.000	0.000	0.000
46	B	72	VAL	0	0.043	0.005	19.810	-0.187	-0.187	0.000	0.000	0.000	0.000
47	B	73	PRO	0	0.049	0.047	16.346	-0.053	-0.053	0.000	0.000	0.000	0.000
48	B	74	VAL	0	0.009	0.000	18.280	0.580	0.580	0.000	0.000	0.000	0.000
49	B	75	SER	0	-0.039	-0.034	18.853	0.499	0.499	0.000	0.000	0.000	0.000
50	B	76	ASP	-1	-0.938	-0.969	14.831	-20.866	-20.866	0.000	0.000	0.000	0.000
51	B	77	ASN	0	-0.005	-0.002	13.858	-0.750	-0.750	0.000	0.000	0.000	0.000
52	B	78	SER	0	-0.017	0.004	14.914	-0.492	-0.492	0.000	0.000	0.000	0.000
53	B	79	THR	0	0.003	-0.002	14.935	0.591	0.591	0.000	0.000	0.000	0.000
54	B	80	LEU	0	-0.042	-0.013	16.917	-0.271	-0.271	0.000	0.000	0.000	0.000
55	B	81	VAL	0	0.031	0.015	18.841	0.038	0.038	0.000	0.000	0.000	0.000
56	B	82	PHE	0	-0.029	-0.017	21.171	0.536	0.536	0.000	0.000	0.000	0.000
57	B	83	SER	0	0.033	0.009	24.741	-0.141	-0.141	0.000	0.000	0.000	0.000
58	B	84	ASN	0	-0.024	-0.008	27.623	0.211	0.211	0.000	0.000	0.000	0.000
59	B	85	VAL	0	-0.055	-0.034	30.604	0.183	0.183	0.000	0.000	0.000	0.000
60	B	86	ILE	0	0.017	0.007	33.736	0.054	0.054	0.000	0.000	0.000	0.000
61	B	87	SER	0	-0.040	-0.023	36.921	-0.005	-0.005	0.000	0.000	0.000	0.000
62	B	88	ALA	0	0.015	0.017	38.829	0.079	0.079	0.000	0.000	0.000	0.000
63	B	89	SER	0	0.028	0.006	39.826	0.076	0.076	0.000	0.000	0.000	0.000
64	B	90	GLY	0	0.015	0.007	36.300	-0.102	-0.102	0.000	0.000	0.000	0.000
65	B	91	ALA	0	0.019	0.021	31.844	0.128	0.128	0.000	0.000	0.000	0.000
66	B	92	LYS	1	0.941	0.993	31.900	8.718	8.718	0.000	0.000	0.000	0.000
67	B	93	TYR	0	0.029	0.008	27.561	-0.022	-0.022	0.000	0.000	0.000	0.000
68	B	94	ALA	0	-0.023	-0.015	28.962	0.066	0.066	0.000	0.000	0.000	0.000
69	B	95	ALA	0	0.082	0.030	24.111	-0.278	-0.278	0.000	0.000	0.000	0.000
70	B	96	GLY	0	-0.006	0.016	25.370	-0.043	-0.043	0.000	0.000	0.000	0.000
71	B	97	GLN	0	-0.036	-0.025	25.551	0.573	0.573	0.000	0.000	0.000	0.000
72	B	98	TYR	0	0.019	0.010	23.670	0.016	0.016	0.000	0.000	0.000	0.000
73	B	99	ILE	0	-0.045	-0.024	28.004	0.164	0.164	0.000	0.000	0.000	0.000
74	B	100	TRP	0	0.013	0.005	25.952	-0.008	-0.008	0.000	0.000	0.000	0.000
75	B	101	TRP	0	-0.033	-0.044	28.535	0.173	0.173	0.000	0.000	0.000	0.000
76	B	102	THR	0	0.017	0.017	28.662	0.187	0.187	0.000	0.000	0.000	0.000
77	B	103	LYS	1	0.932	0.952	31.853	8.415	8.415	0.000	0.000	0.000	0.000
78	B	104	GLY	0	-0.004	0.007	34.838	0.082	0.082	0.000	0.000	0.000	0.000
79	B	105	GLU	-1	-0.795	-0.889	31.635	-9.936	-9.936	0.000	0.000	0.000	0.000
80	B	106	GLU	-1	-0.883	-0.928	31.158	-9.236	-9.236	0.000	0.000	0.000	0.000
81	B	107	ALA	0	0.016	-0.002	28.993	-0.076	-0.076	0.000	0.000	0.000	0.000
82	B	108	THR	0	-0.023	0.001	30.997	0.192	0.192	0.000	0.000	0.000	0.000
83	B	109	LEU	0	-0.009	0.001	24.915	-0.140	-0.140	0.000	0.000	0.000	0.000
84	B	110	TYR	0	-0.012	-0.021	28.996	0.192	0.192	0.000	0.000	0.000	0.000
85	B	111	GLY	0	0.058	0.026	29.289	-0.231	-0.231	0.000	0.000	0.000	0.000
86	B	112	ASP	-1	-0.971	-0.975	26.115	-10.550	-10.550	0.000	0.000	0.000	0.000
87	B	121	GLY	0	0.025	0.011	32.580	0.039	0.039	0.000	0.000	0.000	0.000
88	B	122	VAL	0	-0.057	-0.031	28.281	0.186	0.186	0.000	0.000	0.000	0.000
89	B	123	ALA	0	0.058	0.040	30.790	-0.141	-0.141	0.000	0.000	0.000	0.000
90	B	125	LYS	1	0.906	0.938	29.187	9.671	9.671	0.000	0.000	0.000	0.000
91	B	126	GLU	-1	-0.786	-0.871	27.612	-11.453	-11.453	0.000	0.000	0.000	0.000
92	B	127	ARG	1	0.759	0.851	24.846	10.585	10.585	0.000	0.000	0.000	0.000

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