FMO DATABASE

FMODB ID: JQ629

Calculation Name: 209L-A-Xray372

Preferred Name: Lysozyme

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 209L

Chain ID: A

ChEMBL ID: CHEMBL5206

UniProt ID: P00720

Base Structure: X-ray

Registration Date: 2023-09-20

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	165
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1666752.499695
FMO2-HF: Nuclear repulsion	1601748.271267
FMO2-HF: Total energy	-65004.228427
FMO2-MP2: Total energy	-65195.175065

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(A:1:MET)

Summations of interaction energy for fragment #1(A:1:MET)

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.
-21.957	-7.497	13.508	-9.438	-18.53	-0.04

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : 0.025

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	A	3	ILE	0	0.088	0.026	3.466	-1.481	4.095	0.082	-2.793	-2.865	0.009
4	A	4	PHE	0	0.071	0.051	6.003	0.489	0.489	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.803	-0.901	2.322	-8.853	-5.064	4.738	-3.984	-4.543	-0.036
6	A	6	MET	0	-0.079	0.015	3.692	-1.520	-0.184	0.341	-0.352	-1.325	-0.001
7	A	7	LEU	0	0.006	0.000	4.334	-1.154	-1.197	0.026	0.124	-0.106	0.000
8	A	8	ARG	1	0.895	0.975	7.008	-0.689	-0.689	0.000	0.000	0.000	0.000
9	A	9	ILE	0	-0.070	-0.045	3.589	-0.724	-0.389	0.005	-0.048	-0.293	0.000
10	A	10	ASP	-1	-0.766	-0.860	6.505	1.172	1.172	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.874	-0.914	9.414	0.276	0.276	0.000	0.000	0.000	0.000
12	A	12	GLY	0	-0.043	-0.005	10.659	-0.107	-0.107	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.012	-0.035	12.174	-0.010	-0.010	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.890	0.945	14.295	-0.210	-0.210	0.000	0.000	0.000	0.000
15	A	15	LEU	0	0.023	0.014	18.031	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.940	0.965	20.921	-0.077	-0.077	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.037	0.004	22.889	0.012	0.012	0.000	0.000	0.000	0.000
18	A	18	TYR	0	-0.056	-0.027	17.888	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.936	0.971	24.145	-0.086	-0.086	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.778	-0.874	20.591	0.165	0.165	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.033	-0.052	19.636	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.836	-0.883	22.373	0.170	0.170	0.000	0.000	0.000	0.000
23	A	23	GLY	0	-0.044	-0.019	24.623	-0.014	-0.014	0.000	0.000	0.000	0.000
24	A	24	TYR	0	-0.079	-0.046	24.093	-0.016	-0.016	0.000	0.000	0.000	0.000
25	A	25	TYR	0	-0.047	-0.021	24.891	0.005	0.005	0.000	0.000	0.000	0.000
26	A	26	THR	0	0.032	0.010	20.093	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.068	-0.051	20.600	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.063	0.035	17.672	0.007	0.007	0.000	0.000	0.000	0.000
29	A	29	ILE	0	-0.044	-0.008	11.256	0.006	0.006	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.044	0.006	14.100	0.043	0.043	0.000	0.000	0.000	0.000
31	A	31	HIS	0	-0.062	-0.047	16.238	-0.029	-0.029	0.000	0.000	0.000	0.000
32	A	32	LEU	0	0.019	0.016	19.298	-0.011	-0.011	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.047	-0.022	21.815	-0.013	-0.013	0.000	0.000	0.000	0.000
34	A	34	THR	0	0.008	-0.018	25.042	-0.009	-0.009	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.995	0.998	25.748	-0.092	-0.092	0.000	0.000	0.000	0.000
36	A	36	SER	0	-0.011	0.009	28.806	0.000	0.000	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.031	-0.006	31.058	0.004	0.004	0.000	0.000	0.000	0.000
38	A	38	SER	0	0.012	0.012	33.355	0.002	0.002	0.000	0.000	0.000	0.000
39	A	39	LEU	0	0.037	0.034	29.732	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	40	ASN	0	0.059	0.032	31.611	0.003	0.003	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.051	0.030	33.018	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	42	ALA	0	0.040	0.007	28.057	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.822	0.895	28.846	-0.032	-0.032	0.000	0.000	0.000	0.000
44	A	44	SER	0	0.039	0.015	30.605	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.895	-0.928	28.210	0.026	0.026	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.020	-0.015	24.644	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.828	-0.899	27.670	0.006	0.006	0.000	0.000	0.000	0.000
48	A	48	LYN	0	-0.029	-0.002	30.514	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.045	-0.004	25.113	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.099	-0.059	23.748	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.056	0.031	27.394	-0.007	-0.007	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.729	0.807	26.430	0.003	0.003	0.000	0.000	0.000	0.000
53	A	53	ASN	0	-0.080	-0.032	32.301	0.001	0.001	0.000	0.000	0.000	0.000
54	A	54	THR	0	-0.008	-0.016	27.327	0.001	0.001	0.000	0.000	0.000	0.000
55	A	55	ASN	0	0.017	0.007	29.891	0.005	0.005	0.000	0.000	0.000	0.000
56	A	56	GLY	0	-0.039	-0.026	27.557	0.003	0.003	0.000	0.000	0.000	0.000
57	A	57	VAL	0	-0.016	-0.002	25.487	0.008	0.008	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.022	0.016	20.244	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	59	THR	0	0.022	-0.001	21.984	0.003	0.003	0.000	0.000	0.000	0.000
60	A	60	LYS	1	0.919	0.950	13.286	0.136	0.136	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.806	-0.894	18.025	-0.073	-0.073	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.709	-0.821	19.697	-0.011	-0.011	0.000	0.000	0.000	0.000
63	A	63	ALA	0	-0.021	-0.025	17.254	0.007	0.007	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.903	-0.939	14.322	-0.144	-0.144	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.890	0.951	16.523	0.018	0.018	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.033	-0.027	18.937	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	67	PHE	0	-0.001	0.001	9.447	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	68	ASN	0	-0.005	-0.012	13.951	-0.026	-0.026	0.000	0.000	0.000	0.000
69	A	69	GLN	0	0.053	0.036	15.537	-0.020	-0.020	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.807	-0.890	15.872	0.093	0.093	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.033	-0.026	11.227	0.024	0.024	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.979	-0.983	14.273	-0.186	-0.186	0.000	0.000	0.000	0.000
73	A	73	ALA	0	0.031	0.019	16.347	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	73	ALA	0	-0.016	-0.001	14.371	0.003	0.003	0.000	0.000	0.000	0.000
75	A	73	ALA	0	-0.006	-0.019	13.753	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	73	ALA	0	-0.061	-0.019	15.188	-0.021	-0.021	0.000	0.000	0.000	0.000
77	A	74	ALA	0	0.010	0.000	18.573	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	75	VAL	0	0.001	0.006	14.627	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	76	ARG	1	0.946	0.986	18.052	0.098	0.098	0.000	0.000	0.000	0.000
80	A	77	GLY	0	0.018	-0.004	20.075	0.001	0.001	0.000	0.000	0.000	0.000
81	A	78	ILE	0	-0.025	-0.011	19.877	0.004	0.004	0.000	0.000	0.000	0.000
82	A	79	LEU	0	-0.016	-0.007	18.482	0.002	0.002	0.000	0.000	0.000	0.000
83	A	80	ARG	1	0.920	0.989	22.953	0.040	0.040	0.000	0.000	0.000	0.000
84	A	81	ASN	0	-0.058	-0.043	25.066	0.006	0.006	0.000	0.000	0.000	0.000
85	A	82	ALA	0	0.019	-0.013	25.606	0.001	0.001	0.000	0.000	0.000	0.000
86	A	83	LYN	0	-0.035	-0.012	27.504	0.003	0.003	0.000	0.000	0.000	0.000
87	A	84	LEU	0	0.087	0.037	22.964	0.000	0.000	0.000	0.000	0.000	0.000
88	A	85	LYS	1	0.905	0.949	23.510	0.072	0.072	0.000	0.000	0.000	0.000
89	A	86	PRO	0	0.003	-0.007	22.736	-0.009	-0.009	0.000	0.000	0.000	0.000
90	A	87	VAL	0	0.032	0.025	20.066	-0.009	-0.009	0.000	0.000	0.000	0.000
91	A	88	TYR	0	0.032	0.024	16.654	-0.019	-0.019	0.000	0.000	0.000	0.000
92	A	89	ASP	-1	-0.844	-0.923	18.115	-0.110	-0.110	0.000	0.000	0.000	0.000
93	A	90	SER	0	-0.059	-0.022	19.006	-0.017	-0.017	0.000	0.000	0.000	0.000
94	A	91	LEU	0	-0.054	-0.015	14.543	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	92	ASP	-1	-0.756	-0.858	11.186	-0.159	-0.159	0.000	0.000	0.000	0.000
96	A	93	ALA	0	0.016	-0.019	8.565	0.048	0.048	0.000	0.000	0.000	0.000
97	A	94	VAL	0	0.072	0.042	5.834	0.038	0.038	0.000	0.000	0.000	0.000
98	A	95	ARG	1	0.810	0.907	7.899	0.110	0.110	0.000	0.000	0.000	0.000
99	A	96	ARG	1	0.896	0.940	11.010	0.304	0.304	0.000	0.000	0.000	0.000
100	A	97	ALA	0	-0.018	0.003	6.598	0.034	0.034	0.000	0.000	0.000	0.000
101	A	98	ALA	0	0.033	0.020	8.580	0.195	0.195	0.000	0.000	0.000	0.000
102	A	99	LEU	0	-0.015	0.006	9.674	0.024	0.024	0.000	0.000	0.000	0.000
103	A	100	ILE	0	0.008	-0.005	10.658	0.013	0.013	0.000	0.000	0.000	0.000
104	A	101	ASN	0	-0.008	-0.042	8.178	-0.189	-0.189	0.000	0.000	0.000	0.000
105	A	102	MET	0	-0.069	-0.030	11.232	-0.029	-0.029	0.000	0.000	0.000	0.000
106	A	103	VAL	0	0.010	0.006	14.189	-0.019	-0.019	0.000	0.000	0.000	0.000
107	A	104	PHE	0	0.041	0.057	13.603	-0.043	-0.043	0.000	0.000	0.000	0.000
108	A	105	GLN	0	0.023	0.023	15.416	0.064	0.064	0.000	0.000	0.000	0.000
109	A	106	MET	0	-0.070	-0.038	18.027	-0.013	-0.013	0.000	0.000	0.000	0.000
110	A	107	GLY	0	0.064	0.017	20.553	-0.014	-0.014	0.000	0.000	0.000	0.000
111	A	108	GLU	-1	-0.922	-0.973	24.018	0.053	0.053	0.000	0.000	0.000	0.000
112	A	109	THR	0	0.029	0.011	26.872	0.000	0.000	0.000	0.000	0.000	0.000
113	A	110	GLY	0	0.014	0.013	24.477	0.000	0.000	0.000	0.000	0.000	0.000
114	A	111	VAL	0	-0.014	-0.022	22.065	0.006	0.006	0.000	0.000	0.000	0.000
115	A	112	ALA	0	0.061	0.034	24.254	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	113	GLY	0	0.015	0.015	27.510	-0.004	-0.004	0.000	0.000	0.000	0.000
117	A	114	PHE	0	0.035	0.021	19.162	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	115	THR	0	0.065	0.041	24.426	-0.005	-0.005	0.000	0.000	0.000	0.000
119	A	116	ASN	0	-0.046	-0.028	25.801	-0.009	-0.009	0.000	0.000	0.000	0.000
120	A	117	SER	0	-0.039	-0.038	25.405	0.001	0.001	0.000	0.000	0.000	0.000
121	A	118	LEU	0	-0.004	0.001	22.016	0.000	0.000	0.000	0.000	0.000	0.000
122	A	119	ARG	1	0.942	0.973	25.576	-0.028	-0.028	0.000	0.000	0.000	0.000
123	A	120	MET	0	-0.115	-0.042	28.609	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	121	LEU	0	0.007	0.018	24.829	0.000	0.000	0.000	0.000	0.000	0.000
125	A	122	GLN	0	0.015	-0.002	27.355	-0.008	-0.008	0.000	0.000	0.000	0.000
126	A	123	GLN	0	0.030	0.001	25.748	0.003	0.003	0.000	0.000	0.000	0.000
127	A	124	LYS	1	0.818	0.904	22.262	-0.066	-0.066	0.000	0.000	0.000	0.000
128	A	125	ARG	1	0.940	0.936	24.504	-0.070	-0.070	0.000	0.000	0.000	0.000
129	A	126	TRP	0	-0.016	-0.005	16.555	0.017	0.017	0.000	0.000	0.000	0.000
130	A	127	ASP	-1	-0.813	-0.881	19.446	0.094	0.094	0.000	0.000	0.000	0.000
131	A	128	GLU	-1	-0.848	-0.914	19.729	0.112	0.112	0.000	0.000	0.000	0.000
132	A	129	ALA	0	0.083	0.038	21.644	0.015	0.015	0.000	0.000	0.000	0.000
133	A	130	ALA	0	0.019	0.017	16.981	0.013	0.013	0.000	0.000	0.000	0.000
134	A	131	VAL	0	-0.009	-0.022	17.011	0.025	0.025	0.000	0.000	0.000	0.000
135	A	132	ASN	0	-0.100	-0.060	18.364	0.023	0.023	0.000	0.000	0.000	0.000
136	A	133	LEU	0	0.049	0.041	17.935	0.001	0.001	0.000	0.000	0.000	0.000
137	A	134	ALA	0	0.023	0.003	15.663	0.012	0.012	0.000	0.000	0.000	0.000
138	A	135	LYS	1	0.861	0.944	17.562	-0.161	-0.161	0.000	0.000	0.000	0.000
139	A	136	SER	0	-0.052	-0.031	19.991	-0.016	-0.016	0.000	0.000	0.000	0.000
140	A	137	ARG	1	0.892	0.940	16.417	-0.290	-0.290	0.000	0.000	0.000	0.000
141	A	138	TRP	0	0.004	-0.018	14.036	0.020	0.020	0.000	0.000	0.000	0.000
142	A	139	TYR	0	-0.019	-0.006	18.445	0.013	0.013	0.000	0.000	0.000	0.000
143	A	140	ASN	0	0.030	-0.004	20.310	0.019	0.019	0.000	0.000	0.000	0.000
144	A	141	GLN	0	0.028	0.015	20.619	-0.001	-0.001	0.000	0.000	0.000	0.000
145	A	142	THR	0	-0.031	0.000	15.470	0.015	0.015	0.000	0.000	0.000	0.000
146	A	143	PRO	0	0.078	0.037	16.387	0.051	0.051	0.000	0.000	0.000	0.000
147	A	144	ASN	0	-0.022	-0.024	12.872	0.009	0.009	0.000	0.000	0.000	0.000
148	A	145	ARG	1	0.848	0.927	11.127	-0.578	-0.578	0.000	0.000	0.000	0.000
149	A	146	ALA	0	0.023	0.005	12.145	0.078	0.078	0.000	0.000	0.000	0.000
150	A	147	LYS	1	0.851	0.925	13.838	-0.298	-0.298	0.000	0.000	0.000	0.000
151	A	148	ARG	1	0.875	0.935	7.072	-1.019	-1.019	0.000	0.000	0.000	0.000
152	A	149	VAL	0	0.050	0.035	8.963	0.068	0.068	0.000	0.000	0.000	0.000
153	A	150	ILE	0	-0.029	0.003	10.434	-0.067	-0.067	0.000	0.000	0.000	0.000
154	A	151	THR	0	0.005	-0.030	9.753	-0.044	-0.044	0.000	0.000	0.000	0.000
155	A	152	THR	0	0.054	0.047	5.976	-0.018	-0.018	0.000	0.000	0.000	0.000
156	A	153	PHE	0	-0.029	-0.022	8.731	-0.135	-0.135	0.000	0.000	0.000	0.000
157	A	154	ARG	1	0.914	0.964	11.359	-0.289	-0.289	0.000	0.000	0.000	0.000
158	A	155	THR	0	-0.036	-0.036	9.872	-0.028	-0.028	0.000	0.000	0.000	0.000
159	A	156	GLY	0	-0.014	-0.009	9.555	-0.037	-0.037	0.000	0.000	0.000	0.000
160	A	157	THR	0	0.006	0.021	7.414	-0.103	-0.103	0.000	0.000	0.000	0.000
161	A	158	TRP	0	0.079	0.009	2.168	-3.484	-2.375	7.854	-1.840	-7.123	-0.010
162	A	159	ASP	-1	-0.843	-0.911	4.059	0.819	1.019	-0.001	-0.012	-0.186	0.000
163	A	160	ALA	0	0.030	0.009	6.479	-0.029	-0.029	0.000	0.000	0.000	0.000
164	A	161	TYR	0	-0.091	-0.083	2.717	-0.866	0.277	0.406	-0.267	-1.282	0.000
165	A	162	LYS	1	0.819	0.924	3.484	-3.174	-2.159	0.057	-0.266	-0.807	-0.002

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)