FMO DATABASE

FMODB ID: 2JGKR

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1059235.030241
FMO2-HF: Nuclear repulsion	1009255.012171
FMO2-HF: Total energy	-49980.01807
FMO2-MP2: Total energy	-50121.822641

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.
-13.311	-3.487	5.869	-5.26	-10.431	-0.043

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 : -0.035 / q_NPA : -0.010

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	0.012	0.010	3.785	-1.261	0.962	-0.029	-1.009	-1.185	0.002
4	A	5	GLN	0	-0.033	-0.009	5.689	0.275	0.275	0.000	0.000	0.000	0.000
5	A	6	ALA	0	0.020	0.017	9.314	0.006	0.006	0.000	0.000	0.000	0.000
6	A	7	SER	0	-0.036	-0.021	12.064	0.075	0.075	0.000	0.000	0.000	0.000
7	A	8	GLY	0	0.036	0.017	15.766	-0.022	-0.022	0.000	0.000	0.000	0.000
8	A	9	GLY	0	0.007	-0.008	19.179	0.000	0.000	0.000	0.000	0.000	0.000
9	A	10	GLY	0	0.043	0.025	20.958	0.015	0.015	0.000	0.000	0.000	0.000
10	A	11	SER	0	-0.039	-0.013	23.898	-0.006	-0.006	0.000	0.000	0.000	0.000
11	A	12	VAL	0	-0.030	-0.017	27.384	0.004	0.004	0.000	0.000	0.000	0.000
12	A	13	GLN	0	-0.016	0.002	29.537	0.001	0.001	0.000	0.000	0.000	0.000
13	A	14	ALA	0	0.045	0.012	32.008	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	15	GLY	0	-0.010	-0.012	32.220	0.006	0.006	0.000	0.000	0.000	0.000
15	A	16	GLY	0	-0.062	-0.022	31.040	0.001	0.001	0.000	0.000	0.000	0.000
16	A	17	SER	0	-0.010	-0.044	27.251	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	18	LEU	0	-0.037	-0.011	23.088	0.006	0.006	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.947	0.969	20.061	0.139	0.139	0.000	0.000	0.000	0.000
19	A	20	LEU	0	-0.009	0.023	16.545	0.014	0.014	0.000	0.000	0.000	0.000
20	A	21	SER	0	-0.020	-0.008	15.372	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	22	CYS	0	-0.023	-0.002	9.368	-0.060	-0.060	0.000	0.000	0.000	0.000
22	A	23	ALA	0	0.028	0.008	9.481	0.003	0.003	0.000	0.000	0.000	0.000
23	A	24	ALA	0	0.021	0.024	4.806	-0.077	-0.077	0.000	0.000	0.000	0.000
24	A	25	SER	0	-0.046	-0.031	4.234	0.183	0.339	-0.001	-0.019	-0.136	0.000
25	A	26	GLY	0	0.029	0.010	2.844	-2.010	-0.079	0.801	-1.257	-1.475	-0.012
26	A	27	TYR	0	0.016	-0.006	2.423	-5.582	-1.725	4.622	-2.258	-6.220	-0.027
27	A	28	THR	0	-0.048	-0.011	4.378	0.189	0.257	0.000	-0.014	-0.054	0.000
28	A	29	ILE	0	0.027	-0.013	6.456	0.061	0.061	0.000	0.000	0.000	0.000
29	A	30	GLY	0	-0.005	0.044	6.205	-0.257	-0.257	0.000	0.000	0.000	0.000
30	A	31	PRO	0	0.026	0.003	5.554	0.075	0.075	0.000	0.000	0.000	0.000
31	A	32	TYR	0	0.025	0.010	7.143	0.259	0.259	0.000	0.000	0.000	0.000
32	A	33	CYS	0	-0.015	0.013	9.403	0.151	0.151	0.000	0.000	0.000	0.000
33	A	34	MET	0	0.029	0.010	7.860	-0.192	-0.192	0.000	0.000	0.000	0.000
34	A	35	GLY	0	0.018	0.003	10.642	0.118	0.118	0.000	0.000	0.000	0.000
35	A	36	TRP	0	-0.023	-0.017	12.098	-0.067	-0.067	0.000	0.000	0.000	0.000
36	A	37	PHE	0	0.008	0.016	12.507	0.040	0.040	0.000	0.000	0.000	0.000
37	A	38	ARG	1	0.773	0.863	15.875	0.203	0.203	0.000	0.000	0.000	0.000
38	A	39	GLN	0	-0.046	-0.029	18.532	-0.013	-0.013	0.000	0.000	0.000	0.000
39	A	40	ALA	0	0.046	0.028	20.401	0.012	0.012	0.000	0.000	0.000	0.000
40	A	41	PRO	0	0.007	-0.008	23.999	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	42	GLY	0	-0.003	-0.006	26.409	0.005	0.005	0.000	0.000	0.000	0.000
42	A	43	LYS	1	0.934	0.980	25.407	0.144	0.144	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.871	-0.930	23.844	-0.177	-0.177	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.890	0.957	13.987	0.425	0.425	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.792	-0.847	20.390	-0.210	-0.210	0.000	0.000	0.000	0.000
46	A	47	GLY	0	0.031	0.009	17.646	-0.027	-0.027	0.000	0.000	0.000	0.000
47	A	48	VAL	0	-0.051	-0.029	17.936	0.028	0.028	0.000	0.000	0.000	0.000
48	A	49	ALA	0	0.026	-0.005	17.612	0.029	0.029	0.000	0.000	0.000	0.000
49	A	50	ALA	0	0.011	0.012	14.945	-0.050	-0.050	0.000	0.000	0.000	0.000
50	A	51	ILE	0	-0.043	-0.021	14.244	0.058	0.058	0.000	0.000	0.000	0.000
51	A	52	ASN	0	0.057	0.009	13.902	-0.082	-0.082	0.000	0.000	0.000	0.000
52	A	53	MET	0	-0.050	-0.018	9.846	0.083	0.083	0.000	0.000	0.000	0.000
53	A	54	GLY	0	-0.001	-0.009	13.741	0.022	0.022	0.000	0.000	0.000	0.000
54	A	55	GLY	0	-0.031	-0.024	16.169	0.032	0.032	0.000	0.000	0.000	0.000
55	A	56	GLY	0	0.000	0.005	17.748	0.029	0.029	0.000	0.000	0.000	0.000
56	A	57	ILE	0	0.001	0.007	19.302	0.012	0.012	0.000	0.000	0.000	0.000
57	A	58	THR	0	-0.024	-0.011	18.676	-0.030	-0.030	0.000	0.000	0.000	0.000
58	A	59	TYR	0	-0.022	-0.035	17.840	0.007	0.007	0.000	0.000	0.000	0.000
59	A	60	TYR	0	0.013	0.005	20.186	-0.020	-0.020	0.000	0.000	0.000	0.000
60	A	61	ALA	0	0.062	0.039	22.287	0.011	0.011	0.000	0.000	0.000	0.000
61	A	62	ASP	-1	-0.862	-0.951	23.735	-0.168	-0.168	0.000	0.000	0.000	0.000
62	A	63	SER	0	-0.054	-0.039	25.228	0.009	0.009	0.000	0.000	0.000	0.000
63	A	64	VAL	0	0.012	0.001	22.620	0.008	0.008	0.000	0.000	0.000	0.000
64	A	65	LYS	1	0.830	0.924	26.093	0.183	0.183	0.000	0.000	0.000	0.000
65	A	66	GLY	0	-0.008	0.004	27.376	0.011	0.011	0.000	0.000	0.000	0.000
66	A	67	ARG	1	0.767	0.857	27.424	0.150	0.150	0.000	0.000	0.000	0.000
67	A	68	PHE	0	0.011	-0.012	21.618	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	69	THR	0	-0.025	-0.016	22.896	0.009	0.009	0.000	0.000	0.000	0.000
69	A	70	ILE	0	-0.016	0.003	15.045	0.000	0.000	0.000	0.000	0.000	0.000
70	A	71	SER	0	-0.010	-0.004	18.222	0.021	0.021	0.000	0.000	0.000	0.000
71	A	72	GLN	0	0.070	0.040	12.794	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	73	ASP	-1	-0.806	-0.891	15.346	-0.122	-0.122	0.000	0.000	0.000	0.000
73	A	74	ASN	0	0.020	0.007	16.014	0.006	0.006	0.000	0.000	0.000	0.000
74	A	75	ALA	0	0.003	-0.006	14.715	0.014	0.014	0.000	0.000	0.000	0.000
75	A	76	LYS	1	0.863	0.937	13.347	0.109	0.109	0.000	0.000	0.000	0.000
76	A	77	ASN	0	-0.041	-0.045	7.140	0.009	0.009	0.000	0.000	0.000	0.000
77	A	78	THR	0	-0.030	-0.004	9.372	-0.057	-0.057	0.000	0.000	0.000	0.000
78	A	79	VAL	0	0.011	0.000	11.833	0.039	0.039	0.000	0.000	0.000	0.000
79	A	80	TYR	0	-0.086	-0.066	14.227	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	81	LEU	0	-0.001	-0.002	17.136	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	82	LEU	0	-0.045	-0.018	18.875	0.018	0.018	0.000	0.000	0.000	0.000
82	A	83	MET	0	-0.032	-0.014	21.354	-0.005	-0.005	0.000	0.000	0.000	0.000
83	A	84	ASN	0	0.076	0.045	24.437	0.017	0.017	0.000	0.000	0.000	0.000
84	A	85	SER	0	0.020	0.002	28.222	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	86	LEU	0	-0.018	0.016	24.858	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	87	GLU	-1	-0.814	-0.913	28.966	-0.086	-0.086	0.000	0.000	0.000	0.000
87	A	88	PRO	0	0.015	0.004	29.200	-0.008	-0.008	0.000	0.000	0.000	0.000
88	A	89	GLU	-1	-0.918	-0.957	29.335	-0.112	-0.112	0.000	0.000	0.000	0.000
89	A	90	ASP	-1	-0.806	-0.852	25.281	-0.165	-0.165	0.000	0.000	0.000	0.000
90	A	91	THR	0	-0.035	-0.006	24.519	-0.012	-0.012	0.000	0.000	0.000	0.000
91	A	92	ALA	0	-0.056	-0.029	21.784	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	93	ILE	0	-0.010	0.009	16.965	0.002	0.002	0.000	0.000	0.000	0.000
93	A	94	TYR	0	-0.010	-0.029	16.704	-0.022	-0.022	0.000	0.000	0.000	0.000
94	A	95	TYR	0	0.013	-0.004	12.090	0.010	0.010	0.000	0.000	0.000	0.000
95	A	97	ALA	0	0.001	-0.007	7.880	-0.079	-0.079	0.000	0.000	0.000	0.000
96	A	98	ALA	0	0.020	-0.005	5.091	0.153	0.153	0.000	0.000	0.000	0.000
97	A	99	ASP	-1	-0.784	-0.856	6.747	-0.974	-0.974	0.000	0.000	0.000	0.000
98	A	100	SER	0	-0.033	-0.075	3.858	-0.742	-0.474	0.002	-0.094	-0.176	0.000
99	A	101	THR	0	-0.050	-0.006	6.127	0.170	0.170	0.000	0.000	0.000	0.000
100	A	102	ILE	0	-0.047	-0.027	8.443	0.032	0.032	0.000	0.000	0.000	0.000
101	A	103	TYR	0	-0.071	-0.061	11.541	0.119	0.119	0.000	0.000	0.000	0.000
102	A	104	ALA	0	-0.008	0.005	14.998	0.020	0.020	0.000	0.000	0.000	0.000
103	A	105	SER	0	-0.008	-0.003	18.045	0.023	0.023	0.000	0.000	0.000	0.000
104	A	106	TYR	0	-0.068	-0.064	18.845	-0.030	-0.030	0.000	0.000	0.000	0.000
105	A	107	TYR	0	0.030	0.017	13.460	0.038	0.038	0.000	0.000	0.000	0.000
106	A	108	GLU	-1	-0.798	-0.848	17.563	-0.275	-0.275	0.000	0.000	0.000	0.000
107	A	110	GLY	0	0.022	0.013	15.847	-0.025	-0.025	0.000	0.000	0.000	0.000
108	A	111	HIS	0	-0.032	-0.008	18.402	0.028	0.028	0.000	0.000	0.000	0.000
109	A	112	GLY	0	0.079	0.058	15.543	0.020	0.020	0.000	0.000	0.000	0.000
110	A	113	LEU	0	-0.074	-0.026	15.636	0.000	0.000	0.000	0.000	0.000	0.000
111	A	114	SER	0	-0.055	-0.030	16.772	0.018	0.018	0.000	0.000	0.000	0.000
112	A	115	THR	0	-0.027	-0.038	18.823	0.023	0.023	0.000	0.000	0.000	0.000
113	A	116	GLY	0	0.029	0.014	18.464	-0.006	-0.006	0.000	0.000	0.000	0.000
114	A	117	GLY	0	-0.020	-0.015	14.591	-0.020	-0.020	0.000	0.000	0.000	0.000
115	A	118	TYR	0	-0.012	0.001	13.116	-0.077	-0.077	0.000	0.000	0.000	0.000
116	A	119	GLY	0	0.041	0.014	11.834	0.018	0.018	0.000	0.000	0.000	0.000
117	A	120	TYR	0	-0.038	-0.037	8.904	-0.140	-0.140	0.000	0.000	0.000	0.000
118	A	121	ASP	-1	-0.780	-0.826	4.653	-2.418	-2.327	-0.001	-0.003	-0.087	0.000
119	A	122	SER	0	-0.014	-0.018	2.993	-1.772	-0.617	0.476	-0.604	-1.026	-0.006
120	A	123	TRP	0	-0.054	-0.057	4.967	0.256	0.331	-0.001	-0.002	-0.072	0.000
121	A	124	GLY	0	0.026	0.025	6.471	-0.129	-0.129	0.000	0.000	0.000	0.000
122	A	125	GLN	0	-0.046	-0.026	8.215	0.040	0.040	0.000	0.000	0.000	0.000
123	A	126	GLY	0	0.011	0.008	11.551	-0.011	-0.011	0.000	0.000	0.000	0.000
124	A	127	THR	0	-0.027	-0.015	14.354	0.034	0.034	0.000	0.000	0.000	0.000
125	A	128	GLN	0	-0.028	-0.030	16.930	-0.018	-0.018	0.000	0.000	0.000	0.000
126	A	129	VAL	0	0.001	0.014	20.149	0.009	0.009	0.000	0.000	0.000	0.000
127	A	130	THR	0	-0.030	-0.031	22.723	-0.005	-0.005	0.000	0.000	0.000	0.000
128	A	131	VAL	0	0.015	0.027	26.417	0.007	0.007	0.000	0.000	0.000	0.000
129	A	132	SER	0	0.010	0.013	29.166	0.003	0.003	0.000	0.000	0.000	0.000
130	A	133	SER	0	0.037	0.015	32.625	0.001	0.001	0.000	0.000	0.000	0.000

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