FMO DATABASE

FMODB ID: NNV2Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1668949.447502
FMO2-HF: Nuclear repulsion	1603949.296971
FMO2-HF: Total energy	-65000.150531
FMO2-MP2: Total energy	-65191.728811

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.
-26.638	-13.112	18.246	-10.746	-21.024	-0.055

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 : 0.006 / q_NPA : 0.013

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	0.123	0.040	3.072	-1.074	3.342	-0.056	-1.719	-2.641	0.007
4	A	4	PHE	0	0.057	0.054	5.597	0.616	0.616	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.839	-0.936	2.257	-9.970	-6.862	8.471	-5.791	-5.788	-0.048
6	A	6	MET	0	-0.075	-0.001	3.482	-0.969	0.331	0.216	-0.380	-1.136	-0.001
7	A	7	LEU	0	0.010	0.007	4.511	-0.818	-0.790	0.016	0.044	-0.087	0.000
8	A	8	ARG	1	0.896	0.984	7.263	-0.501	-0.501	0.000	0.000	0.000	0.000
9	A	9	ILE	0	-0.084	-0.061	3.803	-0.628	-0.356	0.001	-0.037	-0.235	0.000
10	A	10	ASP	-1	-0.755	-0.830	7.082	0.826	0.826	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.899	-0.953	9.734	0.115	0.115	0.000	0.000	0.000	0.000
12	A	12	GLY	0	-0.064	-0.016	11.281	-0.080	-0.080	0.000	0.000	0.000	0.000
13	A	13	LEU	0	0.005	-0.035	12.847	-0.023	-0.023	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.887	0.940	15.108	-0.134	-0.134	0.000	0.000	0.000	0.000
15	A	15	LEU	0	0.015	0.043	18.826	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.987	0.995	21.728	-0.034	-0.034	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.033	-0.002	23.642	0.010	0.010	0.000	0.000	0.000	0.000
18	A	18	TYR	0	-0.104	-0.042	18.179	0.004	0.004	0.000	0.000	0.000	0.000
19	A	19	LYS	1	1.008	0.994	24.635	-0.046	-0.046	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.762	-0.858	20.738	0.095	0.095	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.003	-0.043	19.727	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.971	-0.969	22.749	0.095	0.095	0.000	0.000	0.000	0.000
23	A	23	GLY	0	-0.081	-0.024	24.842	-0.009	-0.009	0.000	0.000	0.000	0.000
24	A	24	TYR	0	-0.067	-0.042	24.378	-0.011	-0.011	0.000	0.000	0.000	0.000
25	A	25	TYR	0	-0.037	-0.014	25.121	0.005	0.005	0.000	0.000	0.000	0.000
26	A	26	THR	0	0.059	0.057	20.148	-0.009	-0.009	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.087	-0.047	20.824	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.048	0.028	18.010	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	29	ILE	0	-0.054	-0.024	11.492	0.020	0.020	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.051	0.011	14.245	0.014	0.014	0.000	0.000	0.000	0.000
31	A	31	HIS	0	-0.045	-0.034	16.386	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	32	LEU	0	0.057	-0.007	19.450	0.003	0.003	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.079	-0.041	21.977	-0.011	-0.011	0.000	0.000	0.000	0.000
34	A	34	THR	0	0.007	-0.001	25.196	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	35	LYS	1	1.001	1.005	25.840	-0.024	-0.024	0.000	0.000	0.000	0.000
36	A	36	SER	0	-0.076	-0.019	28.970	0.003	0.003	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.045	0.008	31.206	0.003	0.003	0.000	0.000	0.000	0.000
38	A	38	SER	0	0.001	-0.034	33.586	0.002	0.002	0.000	0.000	0.000	0.000
39	A	39	LEU	0	0.015	0.033	30.292	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	40	ASN	0	0.083	0.064	31.822	0.000	0.000	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.042	0.025	32.994	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	42	ALA	0	0.064	-0.001	28.198	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.879	0.946	28.981	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	44	SER	0	0.003	-0.006	30.730	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.875	-0.980	28.349	-0.024	-0.024	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.015	-0.004	25.121	-0.005	-0.005	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.845	-0.937	27.801	-0.031	-0.031	0.000	0.000	0.000	0.000
48	A	48	LYN	0	-0.037	0.053	30.102	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.062	-0.006	25.265	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.093	-0.057	24.154	-0.010	-0.010	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.043	0.027	27.511	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.776	0.866	27.340	0.041	0.041	0.000	0.000	0.000	0.000
53	A	53	ASN	0	-0.057	-0.024	32.413	0.004	0.004	0.000	0.000	0.000	0.000
54	A	54	THR	0	-0.008	-0.002	28.086	0.003	0.003	0.000	0.000	0.000	0.000
55	A	55	ASN	0	-0.018	-0.016	30.292	0.004	0.004	0.000	0.000	0.000	0.000
56	A	56	GLY	0	-0.065	-0.042	28.027	0.004	0.004	0.000	0.000	0.000	0.000
57	A	57	VAL	0	-0.014	-0.009	25.956	0.007	0.007	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.019	0.008	20.493	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	59	THR	0	0.040	0.002	22.647	0.003	0.003	0.000	0.000	0.000	0.000
60	A	60	LYS	1	1.036	0.991	13.769	0.097	0.097	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.837	-0.901	18.328	-0.149	-0.149	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.736	-0.858	19.719	-0.062	-0.062	0.000	0.000	0.000	0.000
63	A	63	ALA	0	-0.019	-0.038	17.524	0.000	0.000	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.985	-0.979	14.879	-0.256	-0.256	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.918	0.956	16.545	0.078	0.078	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.037	-0.024	19.008	-0.009	-0.009	0.000	0.000	0.000	0.000
67	A	67	PHE	0	-0.009	-0.008	9.884	-0.014	-0.014	0.000	0.000	0.000	0.000
68	A	68	ASN	0	0.024	0.002	13.446	-0.065	-0.065	0.000	0.000	0.000	0.000
69	A	69	GLN	0	0.020	0.026	15.504	-0.023	-0.023	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.808	-0.894	16.045	-0.029	-0.029	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.027	-0.031	10.830	0.012	0.012	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.944	-0.962	13.856	-0.342	-0.342	0.000	0.000	0.000	0.000
73	A	73	ALA	0	0.005	0.001	15.935	0.008	0.008	0.000	0.000	0.000	0.000
74	A	73	ALA	0	-0.020	0.007	13.907	0.016	0.016	0.000	0.000	0.000	0.000
75	A	73	ALA	0	-0.015	-0.030	13.507	0.009	0.009	0.000	0.000	0.000	0.000
76	A	73	ALA	0	-0.056	-0.019	14.842	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	74	ALA	0	-0.006	-0.001	18.013	0.014	0.014	0.000	0.000	0.000	0.000
78	A	75	VAL	0	0.007	-0.001	14.598	0.009	0.009	0.000	0.000	0.000	0.000
79	A	76	ARG	1	0.957	0.976	17.790	0.183	0.183	0.000	0.000	0.000	0.000
80	A	77	GLY	0	-0.001	-0.020	19.818	0.011	0.011	0.000	0.000	0.000	0.000
81	A	78	ILE	0	0.004	0.006	20.019	0.010	0.010	0.000	0.000	0.000	0.000
82	A	79	LEU	0	0.006	-0.016	18.735	0.007	0.007	0.000	0.000	0.000	0.000
83	A	80	ARG	1	0.901	0.990	22.770	0.090	0.090	0.000	0.000	0.000	0.000
84	A	81	ASN	0	-0.032	-0.036	24.847	0.007	0.007	0.000	0.000	0.000	0.000
85	A	82	ALA	0	0.021	-0.015	25.399	0.001	0.001	0.000	0.000	0.000	0.000
86	A	83	LYN	0	-0.055	0.011	27.372	0.001	0.001	0.000	0.000	0.000	0.000
87	A	84	LEU	0	0.045	0.024	22.973	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	85	LYS	1	1.044	1.005	23.390	0.094	0.094	0.000	0.000	0.000	0.000
89	A	86	PRO	0	-0.033	-0.010	22.601	-0.012	-0.012	0.000	0.000	0.000	0.000
90	A	87	VAL	0	0.012	0.019	19.417	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	88	TYR	0	0.008	0.012	16.558	-0.017	-0.017	0.000	0.000	0.000	0.000
92	A	89	ASP	-1	-0.902	-0.968	17.985	-0.160	-0.160	0.000	0.000	0.000	0.000
93	A	90	SER	0	-0.077	-0.027	18.921	-0.011	-0.011	0.000	0.000	0.000	0.000
94	A	91	LEU	0	-0.076	-0.025	14.380	0.005	0.005	0.000	0.000	0.000	0.000
95	A	92	ASP	-1	-0.769	-0.885	11.315	-0.142	-0.142	0.000	0.000	0.000	0.000
96	A	93	ALA	0	0.007	-0.024	8.241	0.013	0.013	0.000	0.000	0.000	0.000
97	A	94	VAL	0	0.068	0.038	6.106	-0.054	-0.054	0.000	0.000	0.000	0.000
98	A	95	ARG	1	0.778	0.897	7.914	0.020	0.020	0.000	0.000	0.000	0.000
99	A	96	ARG	1	0.954	0.970	10.936	0.361	0.361	0.000	0.000	0.000	0.000
100	A	97	ALA	0	-0.031	-0.007	6.382	-0.009	-0.009	0.000	0.000	0.000	0.000
101	A	98	ALA	0	0.043	0.024	8.379	0.146	0.146	0.000	0.000	0.000	0.000
102	A	99	LEU	0	0.006	0.014	9.554	0.044	0.044	0.000	0.000	0.000	0.000
103	A	100	ILE	0	0.004	-0.005	10.291	0.029	0.029	0.000	0.000	0.000	0.000
104	A	101	ASN	0	-0.012	-0.018	8.297	-0.085	-0.085	0.000	0.000	0.000	0.000
105	A	102	MET	0	-0.087	-0.038	10.979	0.005	0.005	0.000	0.000	0.000	0.000
106	A	103	VAL	0	0.020	0.008	14.007	0.003	0.003	0.000	0.000	0.000	0.000
107	A	104	PHE	0	0.049	0.065	13.299	-0.031	-0.031	0.000	0.000	0.000	0.000
108	A	105	GLN	0	0.007	0.044	15.328	0.062	0.062	0.000	0.000	0.000	0.000
109	A	106	MET	0	-0.047	-0.025	17.895	0.003	0.003	0.000	0.000	0.000	0.000
110	A	107	GLY	0	0.060	0.010	20.265	-0.014	-0.014	0.000	0.000	0.000	0.000
111	A	108	GLU	-1	-1.016	-1.002	23.709	-0.014	-0.014	0.000	0.000	0.000	0.000
112	A	109	THR	0	0.027	0.008	26.573	0.003	0.003	0.000	0.000	0.000	0.000
113	A	110	GLY	0	0.034	0.018	24.239	0.002	0.002	0.000	0.000	0.000	0.000
114	A	111	VAL	0	0.018	-0.012	21.999	0.004	0.004	0.000	0.000	0.000	0.000
115	A	112	ALA	0	0.055	0.022	24.001	0.000	0.000	0.000	0.000	0.000	0.000
116	A	113	GLY	0	0.007	0.006	27.320	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	114	PHE	0	0.066	0.032	18.881	0.000	0.000	0.000	0.000	0.000	0.000
118	A	115	THR	0	0.083	0.045	24.258	-0.003	-0.003	0.000	0.000	0.000	0.000
119	A	116	ASN	0	-0.020	-0.002	25.617	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	117	SER	0	-0.055	-0.046	25.364	0.002	0.002	0.000	0.000	0.000	0.000
121	A	118	LEU	0	0.022	0.001	21.421	0.003	0.003	0.000	0.000	0.000	0.000
122	A	119	ARG	1	0.909	0.966	25.466	0.009	0.009	0.000	0.000	0.000	0.000
123	A	120	MET	0	-0.122	-0.050	28.494	0.002	0.002	0.000	0.000	0.000	0.000
124	A	121	LEU	0	-0.008	0.036	24.880	0.003	0.003	0.000	0.000	0.000	0.000
125	A	122	GLN	0	0.068	0.016	27.352	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	123	GLN	0	0.008	-0.009	25.695	0.000	0.000	0.000	0.000	0.000	0.000
127	A	124	LYS	1	0.846	0.929	21.213	-0.036	-0.036	0.000	0.000	0.000	0.000
128	A	125	ARG	1	1.053	1.018	24.585	-0.038	-0.038	0.000	0.000	0.000	0.000
129	A	126	TRP	0	-0.014	-0.012	16.686	0.013	0.013	0.000	0.000	0.000	0.000
130	A	127	ASP	-1	-0.894	-0.940	19.204	0.064	0.064	0.000	0.000	0.000	0.000
131	A	128	GLU	-1	-0.878	-0.975	19.739	0.073	0.073	0.000	0.000	0.000	0.000
132	A	129	ALA	0	0.067	0.041	21.615	0.011	0.011	0.000	0.000	0.000	0.000
133	A	130	ALA	0	0.036	0.011	16.809	0.005	0.005	0.000	0.000	0.000	0.000
134	A	131	VAL	0	-0.019	-0.005	17.251	0.019	0.019	0.000	0.000	0.000	0.000
135	A	132	ASN	0	-0.073	-0.055	18.264	0.024	0.024	0.000	0.000	0.000	0.000
136	A	133	LEU	0	-0.005	0.017	17.368	0.004	0.004	0.000	0.000	0.000	0.000
137	A	134	ALA	0	0.026	0.009	15.636	0.008	0.008	0.000	0.000	0.000	0.000
138	A	135	LYS	1	0.875	0.958	17.492	-0.111	-0.111	0.000	0.000	0.000	0.000
139	A	136	SER	0	-0.066	-0.040	19.835	-0.014	-0.014	0.000	0.000	0.000	0.000
140	A	137	ARG	1	0.885	0.921	16.140	-0.136	-0.136	0.000	0.000	0.000	0.000
141	A	138	TRP	0	0.027	-0.003	14.252	0.023	0.023	0.000	0.000	0.000	0.000
142	A	139	TYR	0	-0.039	-0.009	18.186	0.006	0.006	0.000	0.000	0.000	0.000
143	A	140	ASN	0	0.057	-0.005	20.187	0.020	0.020	0.000	0.000	0.000	0.000
144	A	141	GLN	0	0.061	0.040	20.751	0.008	0.008	0.000	0.000	0.000	0.000
145	A	142	THR	0	-0.089	-0.047	15.919	0.019	0.019	0.000	0.000	0.000	0.000
146	A	143	PRO	0	0.118	0.075	16.307	0.039	0.039	0.000	0.000	0.000	0.000
147	A	144	ASN	0	-0.060	-0.037	12.893	0.007	0.007	0.000	0.000	0.000	0.000
148	A	145	ARG	1	0.934	0.992	11.333	-0.344	-0.344	0.000	0.000	0.000	0.000
149	A	146	ALA	0	0.027	0.007	12.058	0.050	0.050	0.000	0.000	0.000	0.000
150	A	147	LYS	1	0.851	0.929	13.402	-0.258	-0.258	0.000	0.000	0.000	0.000
151	A	148	ARG	1	0.881	0.942	7.287	-0.769	-0.769	0.000	0.000	0.000	0.000
152	A	149	VAL	0	0.064	0.035	8.919	0.041	0.041	0.000	0.000	0.000	0.000
153	A	150	ILE	0	0.022	0.025	10.278	-0.047	-0.047	0.000	0.000	0.000	0.000
154	A	151	THR	0	-0.027	-0.078	9.375	-0.011	-0.011	0.000	0.000	0.000	0.000
155	A	152	THR	0	0.071	0.053	6.323	-0.006	-0.006	0.000	0.000	0.000	0.000
156	A	153	PHE	0	-0.008	-0.012	8.607	-0.086	-0.086	0.000	0.000	0.000	0.000
157	A	154	ARG	1	0.895	1.006	11.286	-0.222	-0.222	0.000	0.000	0.000	0.000
158	A	155	THR	0	-0.089	-0.083	10.050	-0.019	-0.019	0.000	0.000	0.000	0.000
159	A	156	GLY	0	0.018	0.009	9.543	-0.013	-0.013	0.000	0.000	0.000	0.000
160	A	157	THR	0	0.047	0.078	7.380	-0.048	-0.048	0.000	0.000	0.000	0.000
161	A	158	TRP	0	0.044	-0.014	2.263	-3.984	-2.799	8.521	-1.980	-7.726	-0.012
162	A	159	ASP	-1	-0.916	-0.956	4.133	0.739	0.995	-0.001	-0.032	-0.223	0.000
163	A	160	ALA	0	-0.009	-0.002	5.981	-0.083	-0.083	0.000	0.000	0.000	0.000
164	A	161	TYR	0	-0.116	-0.124	2.745	-0.980	0.032	0.666	-0.309	-1.369	-0.001
165	A	162	LYS	1	0.943	0.988	2.703	-7.843	-5.894	0.412	-0.542	-1.819	0.000

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