FMO DATABASE

FMODB ID: 3J37L

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1663766.407256
FMO2-HF: Nuclear repulsion	1598759.919613
FMO2-HF: Total energy	-65006.487643
FMO2-MP2: Total energy	-65196.923333

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.
-21.541	-9.35	16.042	-8.472	-19.762	-0.05

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 : 0.011 / q_NPA : 0.019

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	0.036	0.004	3.693	0.958	4.709	0.201	-1.910	-2.041	0.002
4	A	4	PHE	0	0.062	0.037	6.098	0.728	0.728	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.844	-0.925	2.362	-9.621	-6.677	5.602	-3.875	-4.672	-0.036
6	A	6	MET	0	-0.030	0.006	3.371	-2.243	-0.716	1.716	-0.792	-2.451	-0.003
7	A	7	LEU	0	0.003	0.004	3.913	-0.902	-1.687	0.079	0.921	-0.216	0.001
8	A	8	ARG	1	0.908	0.971	6.415	-0.772	-0.772	0.000	0.000	0.000	0.000
9	A	9	ILE	0	-0.046	-0.022	3.521	-0.842	-0.482	0.007	-0.051	-0.316	0.000
10	A	10	ASP	-1	-0.770	-0.846	6.201	1.502	1.502	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.831	-0.890	9.166	0.354	0.354	0.000	0.000	0.000	0.000
12	A	12	GLY	0	-0.050	-0.016	10.142	-0.140	-0.140	0.000	0.000	0.000	0.000
13	A	13	LEU	0	0.021	-0.011	11.313	0.009	0.009	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.839	0.926	13.719	-0.296	-0.296	0.000	0.000	0.000	0.000
15	A	15	LEU	0	0.029	0.025	17.573	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.904	0.953	20.300	-0.120	-0.120	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.002	0.016	22.220	0.016	0.016	0.000	0.000	0.000	0.000
18	A	18	TYR	0	-0.061	-0.029	17.075	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.901	0.956	23.206	-0.119	-0.119	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.795	-0.879	20.097	0.205	0.205	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.041	-0.066	19.187	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.844	-0.875	21.702	0.218	0.218	0.000	0.000	0.000	0.000
23	A	23	GLY	0	-0.003	0.017	24.343	-0.018	-0.018	0.000	0.000	0.000	0.000
24	A	24	TYR	0	-0.022	-0.011	23.585	-0.021	-0.021	0.000	0.000	0.000	0.000
25	A	25	TYR	0	-0.044	-0.046	24.885	0.005	0.005	0.000	0.000	0.000	0.000
26	A	26	THR	0	0.036	-0.009	19.580	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.033	-0.019	19.979	-0.011	-0.011	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.040	0.018	17.085	0.015	0.015	0.000	0.000	0.000	0.000
29	A	29	ILE	0	-0.044	-0.027	10.873	0.014	0.014	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.067	0.025	13.914	0.045	0.045	0.000	0.000	0.000	0.000
31	A	31	HIS	0	-0.072	-0.037	15.976	-0.030	-0.030	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.005	-0.019	18.593	-0.014	-0.014	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.021	0.011	21.460	-0.017	-0.017	0.000	0.000	0.000	0.000
34	A	34	THR	0	0.035	0.003	24.727	-0.011	-0.011	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.917	0.961	25.334	-0.118	-0.118	0.000	0.000	0.000	0.000
36	A	36	SER	0	0.001	0.012	28.440	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.072	0.025	30.814	0.006	0.006	0.000	0.000	0.000	0.000
38	A	38	SER	0	0.002	0.005	32.747	0.002	0.002	0.000	0.000	0.000	0.000
39	A	39	LEU	0	0.010	0.008	28.858	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	40	ASN	0	0.022	0.004	31.271	0.003	0.003	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.059	0.038	32.479	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	42	ALA	0	0.000	0.002	27.304	0.000	0.000	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.860	0.918	28.195	-0.052	-0.052	0.000	0.000	0.000	0.000
44	A	44	SER	0	0.037	0.028	30.205	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.844	-0.914	27.609	0.039	0.039	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.028	-0.013	23.989	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.817	-0.900	27.123	0.025	0.025	0.000	0.000	0.000	0.000
48	A	48	LYN	0	-0.056	-0.032	30.031	-0.009	-0.009	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.028	-0.002	24.521	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.087	-0.052	23.133	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.031	0.027	27.045	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.749	0.830	25.798	-0.016	-0.016	0.000	0.000	0.000	0.000
53	A	53	ASN	0	-0.044	-0.014	31.852	0.002	0.002	0.000	0.000	0.000	0.000
54	A	54	THR	0	0.000	-0.029	26.670	0.003	0.003	0.000	0.000	0.000	0.000
55	A	55	ASN	0	0.017	0.013	29.228	0.007	0.007	0.000	0.000	0.000	0.000
56	A	56	GLY	0	-0.012	-0.012	27.290	0.005	0.005	0.000	0.000	0.000	0.000
57	A	57	VAL	0	-0.026	-0.016	24.997	0.013	0.013	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.006	0.006	19.942	-0.008	-0.008	0.000	0.000	0.000	0.000
59	A	59	THR	0	0.014	-0.023	21.694	0.010	0.010	0.000	0.000	0.000	0.000
60	A	60	LYS	1	0.843	0.896	13.919	0.131	0.131	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.796	-0.887	17.204	-0.043	-0.043	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.724	-0.818	19.371	0.005	0.005	0.000	0.000	0.000	0.000
63	A	63	ALA	0	-0.001	-0.002	16.568	0.010	0.010	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.854	-0.906	13.414	-0.094	-0.094	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.876	0.947	16.086	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.039	-0.025	18.681	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	67	PHE	0	0.023	0.010	8.966	-0.010	-0.010	0.000	0.000	0.000	0.000
68	A	68	ASN	0	-0.039	-0.040	14.009	-0.037	-0.037	0.000	0.000	0.000	0.000
69	A	69	GLN	0	0.037	0.032	15.595	-0.034	-0.034	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.834	-0.891	15.332	0.124	0.124	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.034	-0.016	10.917	0.032	0.032	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.920	-0.947	13.812	-0.202	-0.202	0.000	0.000	0.000	0.000
73	A	73	ALA	0	0.027	0.012	16.210	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	73	ALA	0	0.000	0.000	14.337	0.001	0.001	0.000	0.000	0.000	0.000
75	A	73	ALA	0	-0.002	-0.012	13.880	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	73	ALA	0	-0.063	-0.030	15.388	-0.018	-0.018	0.000	0.000	0.000	0.000
77	A	74	ALA	0	0.020	0.010	18.381	0.000	0.000	0.000	0.000	0.000	0.000
78	A	75	VAL	0	-0.017	-0.007	14.555	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	76	ARG	1	0.934	0.975	17.903	0.126	0.126	0.000	0.000	0.000	0.000
80	A	77	GLY	0	-0.012	-0.011	19.988	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	78	ILE	0	-0.012	-0.013	19.950	0.000	0.000	0.000	0.000	0.000	0.000
82	A	79	LEU	0	0.020	0.018	18.245	0.004	0.004	0.000	0.000	0.000	0.000
83	A	80	ARG	1	0.914	0.977	22.643	0.058	0.058	0.000	0.000	0.000	0.000
84	A	81	ASN	0	-0.034	-0.029	25.360	0.006	0.006	0.000	0.000	0.000	0.000
85	A	82	ALA	0	0.037	0.002	25.462	0.000	0.000	0.000	0.000	0.000	0.000
86	A	83	LYN	0	-0.018	-0.003	27.610	0.003	0.003	0.000	0.000	0.000	0.000
87	A	84	LEU	0	0.052	0.016	22.998	0.002	0.002	0.000	0.000	0.000	0.000
88	A	85	LYS	1	0.858	0.927	23.557	0.098	0.098	0.000	0.000	0.000	0.000
89	A	86	PRO	0	0.020	-0.003	22.661	-0.012	-0.012	0.000	0.000	0.000	0.000
90	A	87	VAL	0	0.021	0.018	19.959	-0.015	-0.015	0.000	0.000	0.000	0.000
91	A	88	TYR	0	0.034	0.023	16.426	-0.027	-0.027	0.000	0.000	0.000	0.000
92	A	89	ASP	-1	-0.825	-0.902	17.995	-0.151	-0.151	0.000	0.000	0.000	0.000
93	A	90	SER	0	-0.061	-0.033	18.998	-0.026	-0.026	0.000	0.000	0.000	0.000
94	A	91	LEU	0	-0.022	0.009	14.208	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	92	ASP	-1	-0.722	-0.837	10.951	-0.336	-0.336	0.000	0.000	0.000	0.000
96	A	93	ALA	0	0.010	-0.016	9.024	0.047	0.047	0.000	0.000	0.000	0.000
97	A	94	VAL	0	0.003	0.021	5.803	-0.018	-0.018	0.000	0.000	0.000	0.000
98	A	95	ARG	1	0.827	0.886	7.806	0.282	0.282	0.000	0.000	0.000	0.000
99	A	96	ARG	1	0.823	0.911	11.011	0.389	0.389	0.000	0.000	0.000	0.000
100	A	97	ALA	0	0.018	0.012	6.616	0.079	0.079	0.000	0.000	0.000	0.000
101	A	98	ALA	0	0.024	0.007	8.275	0.268	0.268	0.000	0.000	0.000	0.000
102	A	99	LEU	0	0.002	-0.012	9.081	0.080	0.080	0.000	0.000	0.000	0.000
103	A	100	ILE	0	-0.003	-0.005	10.627	0.009	0.009	0.000	0.000	0.000	0.000
104	A	101	ASN	0	0.005	-0.029	7.844	-0.217	-0.217	0.000	0.000	0.000	0.000
105	A	102	MET	0	-0.060	-0.013	11.029	-0.032	-0.032	0.000	0.000	0.000	0.000
106	A	103	VAL	0	-0.004	0.013	13.995	-0.025	-0.025	0.000	0.000	0.000	0.000
107	A	104	PHE	0	0.055	0.045	13.017	-0.036	-0.036	0.000	0.000	0.000	0.000
108	A	105	GLN	0	-0.010	-0.003	15.102	0.064	0.064	0.000	0.000	0.000	0.000
109	A	106	MET	0	-0.057	-0.022	17.823	-0.009	-0.009	0.000	0.000	0.000	0.000
110	A	107	GLY	0	0.052	0.028	20.498	-0.020	-0.020	0.000	0.000	0.000	0.000
111	A	108	GLU	-1	-0.810	-0.921	23.875	0.061	0.061	0.000	0.000	0.000	0.000
112	A	109	THR	0	-0.037	-0.017	26.720	0.003	0.003	0.000	0.000	0.000	0.000
113	A	110	GLY	0	0.019	0.008	24.398	0.000	0.000	0.000	0.000	0.000	0.000
114	A	111	VAL	0	0.008	0.003	21.937	0.004	0.004	0.000	0.000	0.000	0.000
115	A	112	ALA	0	0.045	0.036	24.125	-0.005	-0.005	0.000	0.000	0.000	0.000
116	A	113	GLY	0	0.010	0.013	27.246	-0.005	-0.005	0.000	0.000	0.000	0.000
117	A	114	PHE	0	0.005	0.003	18.989	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	115	THR	0	0.035	0.006	24.186	-0.008	-0.008	0.000	0.000	0.000	0.000
119	A	116	ASN	0	-0.056	-0.044	25.619	-0.013	-0.013	0.000	0.000	0.000	0.000
120	A	117	SER	0	-0.042	-0.041	25.043	0.000	0.000	0.000	0.000	0.000	0.000
121	A	118	LEU	0	-0.007	0.001	21.564	-0.002	-0.002	0.000	0.000	0.000	0.000
122	A	119	ARG	1	0.946	0.982	25.330	-0.023	-0.023	0.000	0.000	0.000	0.000
123	A	120	MET	0	-0.065	-0.013	28.564	-0.004	-0.004	0.000	0.000	0.000	0.000
124	A	121	LEU	0	0.019	0.018	25.082	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	122	GLN	0	-0.032	-0.014	27.779	-0.008	-0.008	0.000	0.000	0.000	0.000
126	A	123	GLN	0	0.063	-0.005	26.115	0.001	0.001	0.000	0.000	0.000	0.000
127	A	124	LYS	1	0.827	0.901	21.804	-0.050	-0.050	0.000	0.000	0.000	0.000
128	A	125	ARG	1	0.855	0.903	24.928	-0.062	-0.062	0.000	0.000	0.000	0.000
129	A	126	TRP	0	0.050	0.021	16.391	0.019	0.019	0.000	0.000	0.000	0.000
130	A	127	ASP	-1	-0.812	-0.887	18.767	0.081	0.081	0.000	0.000	0.000	0.000
131	A	128	GLU	-1	-0.819	-0.881	19.352	0.113	0.113	0.000	0.000	0.000	0.000
132	A	129	ALA	0	0.056	0.020	21.838	0.016	0.016	0.000	0.000	0.000	0.000
133	A	130	ALA	0	-0.014	0.003	16.972	0.017	0.017	0.000	0.000	0.000	0.000
134	A	131	VAL	0	-0.022	-0.027	16.500	0.038	0.038	0.000	0.000	0.000	0.000
135	A	132	ASN	0	-0.060	-0.032	18.190	0.030	0.030	0.000	0.000	0.000	0.000
136	A	133	LEU	0	0.027	0.037	17.691	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	134	ALA	0	0.020	0.008	15.205	0.023	0.023	0.000	0.000	0.000	0.000
138	A	135	LYS	1	0.868	0.921	17.134	-0.159	-0.159	0.000	0.000	0.000	0.000
139	A	136	SER	0	-0.036	-0.012	19.816	-0.015	-0.015	0.000	0.000	0.000	0.000
140	A	137	ARG	1	0.883	0.925	15.763	-0.351	-0.351	0.000	0.000	0.000	0.000
141	A	138	TRP	0	0.022	0.011	13.345	0.032	0.032	0.000	0.000	0.000	0.000
142	A	139	TYR	0	-0.029	-0.017	18.213	0.021	0.021	0.000	0.000	0.000	0.000
143	A	140	ASN	0	0.010	-0.003	19.834	0.007	0.007	0.000	0.000	0.000	0.000
144	A	141	GLN	0	0.004	-0.010	20.174	0.000	0.000	0.000	0.000	0.000	0.000
145	A	142	THR	0	-0.006	-0.003	14.789	0.017	0.017	0.000	0.000	0.000	0.000
146	A	143	PRO	0	0.055	0.027	15.816	0.065	0.065	0.000	0.000	0.000	0.000
147	A	144	ASN	0	-0.030	-0.025	12.704	-0.013	-0.013	0.000	0.000	0.000	0.000
148	A	145	ARG	1	0.845	0.923	10.839	-0.719	-0.719	0.000	0.000	0.000	0.000
149	A	146	ALA	0	0.046	0.023	11.806	0.079	0.079	0.000	0.000	0.000	0.000
150	A	147	LYS	1	0.893	0.954	13.462	-0.337	-0.337	0.000	0.000	0.000	0.000
151	A	148	ARG	1	0.871	0.948	6.497	-1.345	-1.345	0.000	0.000	0.000	0.000
152	A	149	VAL	0	0.093	0.057	8.609	0.068	0.068	0.000	0.000	0.000	0.000
153	A	150	ILE	0	-0.082	-0.039	10.189	-0.111	-0.111	0.000	0.000	0.000	0.000
154	A	151	THR	0	-0.025	-0.029	9.914	-0.110	-0.110	0.000	0.000	0.000	0.000
155	A	152	THR	0	0.005	0.001	5.625	-0.042	-0.042	0.000	0.000	0.000	0.000
156	A	153	PHE	0	-0.003	-0.008	8.241	-0.175	-0.175	0.000	0.000	0.000	0.000
157	A	154	ARG	1	0.913	0.964	11.203	-0.316	-0.316	0.000	0.000	0.000	0.000
158	A	155	THR	0	0.013	0.014	9.866	-0.065	-0.065	0.000	0.000	0.000	0.000
159	A	156	GLY	0	0.015	0.012	9.919	-0.045	-0.045	0.000	0.000	0.000	0.000
160	A	157	THR	0	-0.038	-0.023	7.308	-0.112	-0.112	0.000	0.000	0.000	0.000
161	A	158	TRP	0	0.111	0.017	2.257	-3.554	-2.004	6.792	-1.723	-6.620	-0.010
162	A	159	ASP	-1	-0.789	-0.871	3.968	0.686	0.985	0.001	-0.078	-0.221	0.000
163	A	160	ALA	0	-0.048	-0.027	5.549	-0.119	-0.119	0.000	0.000	0.000	0.000
164	A	161	TYR	0	-0.086	-0.087	2.405	-0.998	0.250	1.493	-0.566	-2.176	0.000
165	A	162	LYS	1	0.814	0.913	3.208	-3.328	-2.031	0.151	-0.398	-1.049	-0.004

Top

Graph

Manual

About

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