FMO DATABASE

FMODB ID: 6N53Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1061302.840726
FMO2-HF: Nuclear repulsion	1011322.610914
FMO2-HF: Total energy	-49980.229812
FMO2-MP2: Total energy	-50122.074486

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.
-11.864	-3.443	6.814	-5.235	-10	-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 : -0.028 / q_NPA : -0.014

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	0.026	0.011	3.852	-1.037	0.993	-0.015	-1.006	-1.009	0.001
4	A	5	GLN	0	-0.040	-0.020	6.242	0.285	0.285	0.000	0.000	0.000	0.000
5	A	6	ALA	0	0.032	0.016	9.391	0.051	0.051	0.000	0.000	0.000	0.000
6	A	7	SER	0	-0.045	-0.027	12.316	0.090	0.090	0.000	0.000	0.000	0.000
7	A	8	GLY	0	0.053	0.031	15.858	-0.016	-0.016	0.000	0.000	0.000	0.000
8	A	9	GLY	0	0.016	0.008	19.347	-0.007	-0.007	0.000	0.000	0.000	0.000
9	A	10	GLY	0	-0.005	-0.002	21.440	0.018	0.018	0.000	0.000	0.000	0.000
10	A	11	SER	0	-0.044	-0.021	24.527	-0.007	-0.007	0.000	0.000	0.000	0.000
11	A	12	VAL	0	-0.026	-0.014	27.902	0.006	0.006	0.000	0.000	0.000	0.000
12	A	13	GLN	0	-0.021	-0.006	29.992	0.003	0.003	0.000	0.000	0.000	0.000
13	A	14	ALA	0	0.032	0.009	32.357	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	15	GLY	0	0.029	0.020	33.401	0.007	0.007	0.000	0.000	0.000	0.000
15	A	16	GLY	0	-0.053	-0.015	31.811	0.002	0.002	0.000	0.000	0.000	0.000
16	A	17	SER	0	-0.020	-0.042	28.115	-0.005	-0.005	0.000	0.000	0.000	0.000
17	A	18	LEU	0	-0.037	-0.014	23.872	0.006	0.006	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.936	0.962	20.019	0.148	0.148	0.000	0.000	0.000	0.000
19	A	20	LEU	0	-0.007	0.022	17.098	0.012	0.012	0.000	0.000	0.000	0.000
20	A	21	SER	0	-0.035	-0.029	15.436	0.012	0.012	0.000	0.000	0.000	0.000
21	A	22	CYS	0	-0.027	-0.006	9.779	-0.086	-0.086	0.000	0.000	0.000	0.000
22	A	23	ALA	0	0.027	0.028	9.375	0.024	0.024	0.000	0.000	0.000	0.000
23	A	24	ALA	0	0.030	0.024	4.924	-0.130	-0.130	0.000	0.000	0.000	0.000
24	A	25	SER	0	-0.060	-0.039	3.951	0.243	0.470	-0.001	-0.043	-0.183	0.000
25	A	26	GLY	0	0.048	0.013	2.311	-2.345	-0.713	3.356	-2.452	-2.536	-0.019
26	A	27	TYR	0	-0.016	-0.019	2.706	-4.246	-0.998	3.102	-1.277	-5.074	-0.019
27	A	28	THR	0	-0.028	-0.010	3.546	0.204	0.148	0.020	0.122	-0.086	0.000
28	A	29	ILE	0	0.008	-0.009	6.319	0.014	0.014	0.000	0.000	0.000	0.000
29	A	30	GLY	0	0.006	0.034	6.296	-0.213	-0.213	0.000	0.000	0.000	0.000
30	A	31	PRO	0	0.016	0.003	5.516	0.064	0.064	0.000	0.000	0.000	0.000
31	A	32	TYR	0	-0.020	-0.004	7.119	0.244	0.244	0.000	0.000	0.000	0.000
32	A	33	CYS	0	-0.019	0.014	9.914	0.135	0.135	0.000	0.000	0.000	0.000
33	A	34	MET	0	0.016	-0.001	8.084	-0.195	-0.195	0.000	0.000	0.000	0.000
34	A	35	GLY	0	0.015	0.002	11.049	0.125	0.125	0.000	0.000	0.000	0.000
35	A	36	TRP	0	-0.020	-0.007	12.663	-0.078	-0.078	0.000	0.000	0.000	0.000
36	A	37	PHE	0	0.023	0.024	12.857	0.042	0.042	0.000	0.000	0.000	0.000
37	A	38	ARG	1	0.736	0.827	16.464	0.219	0.219	0.000	0.000	0.000	0.000
38	A	39	GLN	0	-0.032	-0.019	18.883	-0.018	-0.018	0.000	0.000	0.000	0.000
39	A	40	ALA	0	0.034	0.023	20.589	0.012	0.012	0.000	0.000	0.000	0.000
40	A	41	PRO	0	0.001	-0.003	24.222	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	42	GLY	0	-0.002	-0.009	26.686	0.004	0.004	0.000	0.000	0.000	0.000
42	A	43	LYS	1	0.898	0.962	25.416	0.167	0.167	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.855	-0.926	23.687	-0.202	-0.202	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.875	0.947	13.382	0.489	0.489	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.801	-0.852	19.709	-0.239	-0.239	0.000	0.000	0.000	0.000
46	A	47	GLY	0	0.063	0.017	18.179	-0.030	-0.030	0.000	0.000	0.000	0.000
47	A	48	VAL	0	-0.057	-0.020	18.741	0.021	0.021	0.000	0.000	0.000	0.000
48	A	49	ALA	0	0.024	-0.008	18.126	0.033	0.033	0.000	0.000	0.000	0.000
49	A	50	ALA	0	0.010	0.002	15.401	-0.053	-0.053	0.000	0.000	0.000	0.000
50	A	51	ILE	0	-0.023	-0.015	14.274	0.062	0.062	0.000	0.000	0.000	0.000
51	A	52	ASN	0	0.072	0.017	14.254	-0.086	-0.086	0.000	0.000	0.000	0.000
52	A	53	MET	0	-0.053	-0.008	9.622	0.074	0.074	0.000	0.000	0.000	0.000
53	A	54	GLY	0	-0.013	-0.008	13.572	0.024	0.024	0.000	0.000	0.000	0.000
54	A	55	GLY	0	-0.024	-0.019	16.057	0.036	0.036	0.000	0.000	0.000	0.000
55	A	56	GLY	0	-0.012	-0.002	17.800	0.026	0.026	0.000	0.000	0.000	0.000
56	A	57	ILE	0	0.002	0.004	19.636	0.011	0.011	0.000	0.000	0.000	0.000
57	A	58	THR	0	-0.027	-0.014	19.092	-0.031	-0.031	0.000	0.000	0.000	0.000
58	A	59	TYR	0	-0.038	-0.046	18.202	0.013	0.013	0.000	0.000	0.000	0.000
59	A	60	TYR	0	0.026	0.011	20.447	-0.022	-0.022	0.000	0.000	0.000	0.000
60	A	61	ALA	0	0.062	0.042	22.526	0.016	0.016	0.000	0.000	0.000	0.000
61	A	62	ASP	-1	-0.871	-0.953	24.214	-0.177	-0.177	0.000	0.000	0.000	0.000
62	A	63	SER	0	-0.030	-0.022	25.572	0.010	0.010	0.000	0.000	0.000	0.000
63	A	64	VAL	0	-0.001	-0.006	23.232	0.008	0.008	0.000	0.000	0.000	0.000
64	A	65	LYS	1	0.822	0.916	26.545	0.191	0.191	0.000	0.000	0.000	0.000
65	A	66	GLY	0	0.007	0.015	27.434	0.012	0.012	0.000	0.000	0.000	0.000
66	A	67	ARG	1	0.763	0.851	27.998	0.161	0.161	0.000	0.000	0.000	0.000
67	A	68	PHE	0	0.002	-0.016	22.493	0.000	0.000	0.000	0.000	0.000	0.000
68	A	69	THR	0	-0.039	-0.026	23.165	0.010	0.010	0.000	0.000	0.000	0.000
69	A	70	ILE	0	-0.025	0.001	15.497	0.000	0.000	0.000	0.000	0.000	0.000
70	A	71	SER	0	-0.012	-0.007	18.021	0.026	0.026	0.000	0.000	0.000	0.000
71	A	72	GLN	0	0.077	0.029	12.974	-0.025	-0.025	0.000	0.000	0.000	0.000
72	A	73	ASP	-1	-0.823	-0.880	15.578	-0.095	-0.095	0.000	0.000	0.000	0.000
73	A	74	ASN	0	-0.010	-0.025	15.871	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	75	ALA	0	0.030	0.014	15.078	0.023	0.023	0.000	0.000	0.000	0.000
75	A	76	LYS	1	0.879	0.955	13.353	0.076	0.076	0.000	0.000	0.000	0.000
76	A	77	ASN	0	-0.018	-0.029	7.143	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	78	THR	0	-0.035	-0.009	9.262	-0.093	-0.093	0.000	0.000	0.000	0.000
78	A	79	VAL	0	0.008	-0.001	11.563	0.044	0.044	0.000	0.000	0.000	0.000
79	A	80	TYR	0	-0.095	-0.076	14.016	0.002	0.002	0.000	0.000	0.000	0.000
80	A	81	LEU	0	0.008	0.005	17.024	-0.014	-0.014	0.000	0.000	0.000	0.000
81	A	82	LEU	0	-0.035	-0.006	19.248	0.016	0.016	0.000	0.000	0.000	0.000
82	A	83	MET	0	-0.023	-0.005	21.731	-0.010	-0.010	0.000	0.000	0.000	0.000
83	A	84	ASN	0	0.067	0.030	25.094	0.018	0.018	0.000	0.000	0.000	0.000
84	A	85	SER	0	0.018	0.015	28.933	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	86	LEU	0	-0.012	0.014	25.461	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	87	GLU	-1	-0.817	-0.927	29.595	-0.093	-0.093	0.000	0.000	0.000	0.000
87	A	88	PRO	0	0.019	0.005	29.900	-0.009	-0.009	0.000	0.000	0.000	0.000
88	A	89	GLU	-1	-0.911	-0.954	29.907	-0.124	-0.124	0.000	0.000	0.000	0.000
89	A	90	ASP	-1	-0.781	-0.849	25.822	-0.178	-0.178	0.000	0.000	0.000	0.000
90	A	91	THR	0	-0.047	-0.013	24.865	-0.015	-0.015	0.000	0.000	0.000	0.000
91	A	92	ALA	0	-0.041	-0.021	21.865	0.001	0.001	0.000	0.000	0.000	0.000
92	A	93	ILE	0	0.006	0.019	17.199	0.004	0.004	0.000	0.000	0.000	0.000
93	A	94	TYR	0	-0.002	-0.021	17.243	-0.021	-0.021	0.000	0.000	0.000	0.000
94	A	95	TYR	0	0.018	0.002	12.433	0.012	0.012	0.000	0.000	0.000	0.000
95	A	97	ALA	0	0.008	0.002	8.502	-0.084	-0.084	0.000	0.000	0.000	0.000
96	A	98	ALA	0	-0.006	-0.020	5.621	0.123	0.123	0.000	0.000	0.000	0.000
97	A	99	ASP	-1	-0.751	-0.831	7.254	-0.944	-0.944	0.000	0.000	0.000	0.000
98	A	100	SER	0	-0.016	-0.065	4.133	-0.520	-0.363	-0.001	-0.033	-0.123	0.000
99	A	101	THR	0	-0.054	-0.019	6.446	0.202	0.202	0.000	0.000	0.000	0.000
100	A	102	ILE	0	-0.036	-0.022	8.427	0.067	0.067	0.000	0.000	0.000	0.000
101	A	103	TYR	0	-0.076	-0.061	11.527	0.118	0.118	0.000	0.000	0.000	0.000
102	A	104	ALA	0	-0.003	-0.002	14.968	0.023	0.023	0.000	0.000	0.000	0.000
103	A	105	SER	0	-0.023	-0.002	17.856	0.031	0.031	0.000	0.000	0.000	0.000
104	A	106	TYR	0	-0.044	-0.054	18.358	-0.031	-0.031	0.000	0.000	0.000	0.000
105	A	107	TYR	0	0.015	0.007	13.705	0.038	0.038	0.000	0.000	0.000	0.000
106	A	108	GLU	-1	-0.775	-0.836	17.766	-0.276	-0.276	0.000	0.000	0.000	0.000
107	A	110	GLY	0	0.027	0.017	16.046	-0.032	-0.032	0.000	0.000	0.000	0.000
108	A	111	HIS	0	-0.028	0.000	18.727	0.027	0.027	0.000	0.000	0.000	0.000
109	A	112	GLY	0	0.077	0.059	15.345	0.017	0.017	0.000	0.000	0.000	0.000
110	A	113	LEU	0	-0.091	-0.030	15.979	0.001	0.001	0.000	0.000	0.000	0.000
111	A	114	SER	0	-0.035	-0.033	16.950	0.021	0.021	0.000	0.000	0.000	0.000
112	A	115	THR	0	-0.047	-0.047	18.960	0.022	0.022	0.000	0.000	0.000	0.000
113	A	116	GLY	0	0.026	0.013	18.581	-0.013	-0.013	0.000	0.000	0.000	0.000
114	A	117	GLY	0	0.007	-0.001	14.576	-0.019	-0.019	0.000	0.000	0.000	0.000
115	A	118	TYR	0	-0.015	0.000	13.284	-0.076	-0.076	0.000	0.000	0.000	0.000
116	A	119	GLY	0	0.031	0.016	12.136	0.012	0.012	0.000	0.000	0.000	0.000
117	A	120	TYR	0	-0.057	-0.044	9.216	-0.133	-0.133	0.000	0.000	0.000	0.000
118	A	121	ASP	-1	-0.757	-0.810	4.575	-2.554	-2.460	-0.001	-0.004	-0.088	0.000
119	A	122	SER	0	-0.020	-0.020	2.907	-1.721	-0.701	0.355	-0.540	-0.835	-0.006
120	A	123	TRP	0	-0.043	-0.055	5.136	0.367	0.436	-0.001	-0.002	-0.066	0.000
121	A	124	GLY	0	0.012	0.020	6.174	-0.242	-0.242	0.000	0.000	0.000	0.000
122	A	125	GLN	0	-0.044	-0.030	8.396	0.064	0.064	0.000	0.000	0.000	0.000
123	A	126	GLY	0	0.008	0.008	11.561	-0.007	-0.007	0.000	0.000	0.000	0.000
124	A	127	THR	0	-0.037	-0.024	14.655	0.035	0.035	0.000	0.000	0.000	0.000
125	A	128	GLN	0	-0.006	-0.017	17.360	-0.019	-0.019	0.000	0.000	0.000	0.000
126	A	129	VAL	0	0.002	0.009	20.936	0.009	0.009	0.000	0.000	0.000	0.000
127	A	130	THR	0	-0.011	-0.014	23.405	-0.006	-0.006	0.000	0.000	0.000	0.000
128	A	131	VAL	0	0.019	0.028	27.077	0.007	0.007	0.000	0.000	0.000	0.000
129	A	132	SER	0	-0.020	0.005	29.743	0.004	0.004	0.000	0.000	0.000	0.000
130	A	133	SER	0	0.052	0.013	33.062	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)