FMO DATABASE

FMODB ID: 724JK

Calculation Name: 1JTO-A-Xray372

Preferred Name: Lysozyme C

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1JTO

Chain ID: A

ChEMBL ID: CHEMBL1932892

UniProt ID: P00698

Base Structure: X-ray

Registration Date: 2023-06-26

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	130
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1058627.279942
FMO2-HF: Nuclear repulsion	1008647.619103
FMO2-HF: Total energy	-49979.66084
FMO2-MP2: Total energy	-50121.493634

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:2:VAL)

Summations of interaction energy for fragment #1(A:2:VAL)

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.
-12.795	-3.244	5.57	-5.061	-10.063	-0.04

Interaction energy analysis for fragmet #1(A:2:VAL)

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 : 0.000

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	A	4	LEU	0	0.017	0.011	3.713	-1.137	1.124	-0.029	-1.037	-1.195	0.002
4	A	5	GLN	0	-0.020	-0.003	5.625	0.235	0.235	0.000	0.000	0.000	0.000
5	A	6	ALA	0	0.022	0.016	9.241	0.035	0.035	0.000	0.000	0.000	0.000
6	A	7	SER	0	-0.036	-0.021	12.003	0.075	0.075	0.000	0.000	0.000	0.000
7	A	8	GLY	0	0.029	0.013	15.703	-0.017	-0.017	0.000	0.000	0.000	0.000
8	A	9	GLY	0	0.008	-0.008	19.123	-0.004	-0.004	0.000	0.000	0.000	0.000
9	A	10	GLY	0	0.039	0.022	20.900	0.015	0.015	0.000	0.000	0.000	0.000
10	A	11	SER	0	-0.048	-0.021	23.830	-0.008	-0.008	0.000	0.000	0.000	0.000
11	A	12	VAL	0	-0.002	0.002	27.320	0.005	0.005	0.000	0.000	0.000	0.000
12	A	13	GLN	0	-0.028	0.000	29.486	0.000	0.000	0.000	0.000	0.000	0.000
13	A	14	ALA	0	0.046	0.006	31.987	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	15	GLY	0	-0.004	-0.011	32.220	0.007	0.007	0.000	0.000	0.000	0.000
15	A	16	GLY	0	-0.063	-0.024	31.008	0.002	0.002	0.000	0.000	0.000	0.000
16	A	17	SER	0	-0.010	-0.069	27.227	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	18	LEU	0	-0.036	-0.009	22.980	0.004	0.004	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.948	0.970	20.024	0.168	0.168	0.000	0.000	0.000	0.000
19	A	20	LEU	0	-0.019	0.022	16.443	0.012	0.012	0.000	0.000	0.000	0.000
20	A	21	SER	0	-0.019	-0.011	15.351	0.004	0.004	0.000	0.000	0.000	0.000
21	A	22	CYS	0	-0.012	0.001	9.360	-0.065	-0.065	0.000	0.000	0.000	0.000
22	A	23	ALA	0	0.033	0.011	9.383	0.017	0.017	0.000	0.000	0.000	0.000
23	A	24	ALA	0	0.026	0.022	4.667	-0.160	-0.117	-0.001	-0.004	-0.038	0.000
24	A	25	SER	0	-0.062	-0.037	4.139	0.234	0.399	-0.001	-0.023	-0.141	0.000
25	A	26	GLY	0	0.030	0.011	2.824	-2.163	-0.221	0.860	-1.268	-1.535	-0.012
26	A	27	TYR	0	0.024	-0.003	2.382	-5.384	-1.578	4.479	-2.242	-6.043	-0.028
27	A	28	THR	0	-0.046	-0.012	4.203	0.122	0.196	0.001	-0.017	-0.059	0.000
28	A	29	ILE	0	0.039	-0.009	6.413	0.003	0.003	0.000	0.000	0.000	0.000
29	A	30	GLY	0	-0.031	0.036	6.193	-0.222	-0.222	0.000	0.000	0.000	0.000
30	A	31	PRO	0	0.020	-0.008	5.624	0.070	0.070	0.000	0.000	0.000	0.000
31	A	32	TYR	0	0.035	0.015	7.122	0.259	0.259	0.000	0.000	0.000	0.000
32	A	33	CYS	0	-0.031	0.004	9.513	0.148	0.148	0.000	0.000	0.000	0.000
33	A	34	MET	0	0.027	0.012	7.973	-0.197	-0.197	0.000	0.000	0.000	0.000
34	A	35	GLY	0	0.020	0.004	10.702	0.129	0.129	0.000	0.000	0.000	0.000
35	A	36	TRP	0	-0.024	-0.013	12.116	-0.083	-0.083	0.000	0.000	0.000	0.000
36	A	37	PHE	0	0.006	0.014	12.643	0.046	0.046	0.000	0.000	0.000	0.000
37	A	38	ARG	1	0.804	0.909	15.872	0.232	0.232	0.000	0.000	0.000	0.000
38	A	39	GLN	0	-0.029	-0.012	18.509	-0.014	-0.014	0.000	0.000	0.000	0.000
39	A	40	ALA	0	0.055	0.028	20.365	0.009	0.009	0.000	0.000	0.000	0.000
40	A	41	PRO	0	-0.023	-0.011	23.959	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	42	GLY	0	0.006	-0.008	26.360	0.008	0.008	0.000	0.000	0.000	0.000
42	A	43	LYS	1	0.935	0.978	25.464	0.173	0.173	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.882	-0.944	23.937	-0.205	-0.205	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.881	0.956	14.205	0.479	0.479	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.805	-0.893	20.378	-0.237	-0.237	0.000	0.000	0.000	0.000
46	A	47	GLY	0	0.024	0.010	17.661	-0.032	-0.032	0.000	0.000	0.000	0.000
47	A	48	VAL	0	-0.040	-0.025	17.950	0.032	0.032	0.000	0.000	0.000	0.000
48	A	49	ALA	0	0.017	-0.010	17.637	0.033	0.033	0.000	0.000	0.000	0.000
49	A	50	ALA	0	0.013	0.013	15.042	-0.057	-0.057	0.000	0.000	0.000	0.000
50	A	51	ILE	0	-0.046	-0.024	14.368	0.061	0.061	0.000	0.000	0.000	0.000
51	A	52	ASN	0	0.054	0.007	13.993	-0.082	-0.082	0.000	0.000	0.000	0.000
52	A	53	MET	0	-0.033	-0.013	10.393	0.064	0.064	0.000	0.000	0.000	0.000
53	A	54	GLY	0	-0.023	-0.022	13.704	0.030	0.030	0.000	0.000	0.000	0.000
54	A	55	GLY	0	-0.026	-0.023	16.088	0.030	0.030	0.000	0.000	0.000	0.000
55	A	56	GLY	0	0.002	0.005	17.731	0.027	0.027	0.000	0.000	0.000	0.000
56	A	57	ILE	0	0.017	0.014	19.413	0.009	0.009	0.000	0.000	0.000	0.000
57	A	58	THR	0	-0.040	-0.015	18.770	-0.031	-0.031	0.000	0.000	0.000	0.000
58	A	59	TYR	0	-0.009	-0.008	18.135	0.008	0.008	0.000	0.000	0.000	0.000
59	A	60	TYR	0	-0.005	-0.004	20.233	-0.024	-0.024	0.000	0.000	0.000	0.000
60	A	61	ALA	0	0.043	0.031	22.306	0.012	0.012	0.000	0.000	0.000	0.000
61	A	62	ASP	-1	-0.916	-0.979	23.765	-0.174	-0.174	0.000	0.000	0.000	0.000
62	A	63	SER	0	-0.070	-0.038	25.370	0.010	0.010	0.000	0.000	0.000	0.000
63	A	64	VAL	0	0.019	0.008	22.695	0.008	0.008	0.000	0.000	0.000	0.000
64	A	65	LYS	1	0.937	0.982	26.109	0.193	0.193	0.000	0.000	0.000	0.000
65	A	66	GLY	0	-0.014	-0.001	27.408	0.011	0.011	0.000	0.000	0.000	0.000
66	A	67	ARG	1	0.764	0.859	27.175	0.174	0.174	0.000	0.000	0.000	0.000
67	A	68	PHE	0	0.012	-0.009	21.507	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	69	THR	0	-0.028	-0.021	22.907	0.012	0.012	0.000	0.000	0.000	0.000
69	A	70	ILE	0	-0.011	0.003	15.153	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	71	SER	0	-0.031	-0.011	18.252	0.024	0.024	0.000	0.000	0.000	0.000
71	A	72	GLN	0	0.102	0.074	13.829	-0.029	-0.029	0.000	0.000	0.000	0.000
72	A	73	ASP	-1	-0.879	-0.959	15.298	-0.131	-0.131	0.000	0.000	0.000	0.000
73	A	74	ASN	0	0.040	0.029	15.975	0.005	0.005	0.000	0.000	0.000	0.000
74	A	75	ALA	0	-0.012	-0.042	14.578	0.011	0.011	0.000	0.000	0.000	0.000
75	A	76	LYS	1	0.883	0.964	13.123	0.108	0.108	0.000	0.000	0.000	0.000
76	A	77	ASN	0	-0.043	-0.032	6.818	0.040	0.040	0.000	0.000	0.000	0.000
77	A	78	THR	0	-0.018	-0.003	9.312	-0.083	-0.083	0.000	0.000	0.000	0.000
78	A	79	VAL	0	0.007	0.004	11.909	0.049	0.049	0.000	0.000	0.000	0.000
79	A	80	TYR	0	-0.058	-0.039	14.146	-0.012	-0.012	0.000	0.000	0.000	0.000
80	A	81	LEU	0	-0.006	-0.002	17.143	-0.004	-0.004	0.000	0.000	0.000	0.000
81	A	82	LEU	0	-0.042	-0.017	18.879	0.016	0.016	0.000	0.000	0.000	0.000
82	A	83	MET	0	-0.020	-0.012	21.587	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	84	ASN	0	0.088	0.075	24.430	0.016	0.016	0.000	0.000	0.000	0.000
84	A	85	SER	0	-0.006	-0.008	28.216	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	86	LEU	0	-0.014	0.011	24.906	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	87	GLU	-1	-0.826	-0.918	28.946	-0.104	-0.104	0.000	0.000	0.000	0.000
87	A	88	PRO	0	0.003	-0.003	29.170	-0.010	-0.010	0.000	0.000	0.000	0.000
88	A	89	GLU	-1	-0.903	-0.957	29.297	-0.136	-0.136	0.000	0.000	0.000	0.000
89	A	90	ASP	-1	-0.798	-0.857	25.432	-0.192	-0.192	0.000	0.000	0.000	0.000
90	A	91	THR	0	-0.034	-0.003	24.486	-0.016	-0.016	0.000	0.000	0.000	0.000
91	A	92	ALA	0	-0.038	-0.031	21.699	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	93	ILE	0	-0.014	0.013	16.884	0.000	0.000	0.000	0.000	0.000	0.000
93	A	94	TYR	0	0.001	-0.013	16.617	-0.020	-0.020	0.000	0.000	0.000	0.000
94	A	95	TYR	0	0.003	-0.012	12.041	0.000	0.000	0.000	0.000	0.000	0.000
95	A	97	ALA	0	0.006	-0.003	7.891	-0.099	-0.099	0.000	0.000	0.000	0.000
96	A	98	ALA	0	0.017	-0.009	5.125	0.167	0.167	0.000	0.000	0.000	0.000
97	A	99	ASP	-1	-0.803	-0.838	6.775	-0.964	-0.964	0.000	0.000	0.000	0.000
98	A	100	SER	0	-0.032	-0.063	4.001	-0.628	-0.428	0.000	-0.060	-0.141	0.000
99	A	101	THR	0	-0.022	0.009	6.245	0.224	0.224	0.000	0.000	0.000	0.000
100	A	102	ILE	0	-0.056	-0.026	8.338	0.016	0.016	0.000	0.000	0.000	0.000
101	A	103	TYR	0	-0.078	-0.095	11.640	0.116	0.116	0.000	0.000	0.000	0.000
102	A	104	ALA	0	-0.011	0.007	15.114	0.021	0.021	0.000	0.000	0.000	0.000
103	A	105	SER	0	-0.004	-0.003	18.156	0.023	0.023	0.000	0.000	0.000	0.000
104	A	106	TYR	0	-0.049	-0.035	18.942	-0.030	-0.030	0.000	0.000	0.000	0.000
105	A	107	TYR	0	0.061	0.029	14.021	0.032	0.032	0.000	0.000	0.000	0.000
106	A	108	GLU	-1	-0.839	-0.910	17.676	-0.262	-0.262	0.000	0.000	0.000	0.000
107	A	110	GLY	0	0.018	0.009	15.909	-0.030	-0.030	0.000	0.000	0.000	0.000
108	A	111	HIS	0	-0.023	-0.005	18.462	0.025	0.025	0.000	0.000	0.000	0.000
109	A	112	GLY	0	0.072	0.042	15.585	0.017	0.017	0.000	0.000	0.000	0.000
110	A	113	LEU	0	-0.072	-0.025	15.946	-0.007	-0.007	0.000	0.000	0.000	0.000
111	A	114	SER	0	-0.060	-0.029	16.796	0.014	0.014	0.000	0.000	0.000	0.000
112	A	115	THR	0	-0.025	-0.024	18.837	0.024	0.024	0.000	0.000	0.000	0.000
113	A	116	GLY	0	0.035	0.016	18.446	-0.005	-0.005	0.000	0.000	0.000	0.000
114	A	117	GLY	0	-0.026	-0.018	14.572	-0.025	-0.025	0.000	0.000	0.000	0.000
115	A	118	TYR	0	-0.014	0.001	13.111	-0.081	-0.081	0.000	0.000	0.000	0.000
116	A	119	GLY	0	0.040	0.013	11.871	0.021	0.021	0.000	0.000	0.000	0.000
117	A	120	TYR	0	-0.047	-0.036	8.933	-0.130	-0.130	0.000	0.000	0.000	0.000
118	A	121	ASP	-1	-0.768	-0.852	4.977	-2.174	-2.105	-0.001	0.000	-0.068	0.000
119	A	122	SER	0	-0.037	-0.019	2.888	-1.613	-0.696	0.263	-0.408	-0.772	-0.002
120	A	123	TRP	0	-0.032	-0.038	4.982	0.260	0.334	-0.001	-0.002	-0.071	0.000
121	A	124	GLY	0	0.018	0.020	6.395	-0.197	-0.197	0.000	0.000	0.000	0.000
122	A	125	GLN	0	-0.041	-0.024	8.140	0.022	0.022	0.000	0.000	0.000	0.000
123	A	126	GLY	0	0.012	0.005	11.458	0.003	0.003	0.000	0.000	0.000	0.000
124	A	127	THR	0	-0.054	-0.024	14.279	0.048	0.048	0.000	0.000	0.000	0.000
125	A	128	GLN	0	-0.014	-0.019	16.858	-0.010	-0.010	0.000	0.000	0.000	0.000
126	A	129	VAL	0	0.012	0.021	20.164	0.010	0.010	0.000	0.000	0.000	0.000
127	A	130	THR	0	-0.038	-0.041	22.667	-0.005	-0.005	0.000	0.000	0.000	0.000
128	A	131	VAL	0	0.013	0.031	26.360	0.007	0.007	0.000	0.000	0.000	0.000
129	A	132	SER	0	0.009	0.007	29.118	0.003	0.003	0.000	0.000	0.000	0.000
130	A	133	SER	0	0.033	0.012	32.572	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:VAL)