FMO DATABASE

FMODB ID: 7699K

Calculation Name: 3G3B-G-Xray372

Preferred Name: Lysozyme C

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3G3B

Chain ID: G

ChEMBL ID: CHEMBL1932892

UniProt ID: P00698

Base Structure: X-ray

Registration Date: 2023-09-24

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	77
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-506548.056281
FMO2-HF: Nuclear repulsion	475240.851078
FMO2-HF: Total energy	-31307.205203
FMO2-MP2: Total energy	-31400.156254

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(G:11:THR)

Summations of interaction energy for fragment #1(G:11:THR)

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.
2.135	3.972	-0.021	-0.896	-0.92	0.001

Interaction energy analysis for fragmet #1(G:11:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / 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	G	13	VAL	0	0.031	0.034	3.876	1.228	3.065	-0.021	-0.896	-0.920	0.001
4	G	21	ALA	0	0.017	-0.002	20.201	0.006	0.006	0.000	0.000	0.000	0.000
5	G	22	SER	0	-0.017	0.002	17.050	0.001	0.001	0.000	0.000	0.000	0.000
6	G	33	VAL	0	-0.042	-0.024	5.113	0.259	0.259	0.000	0.000	0.000	0.000
7	G	34	LEU	0	0.000	0.000	6.609	-0.077	-0.077	0.000	0.000	0.000	0.000
8	G	35	TYR	0	0.003	-0.003	8.959	0.042	0.042	0.000	0.000	0.000	0.000
9	G	36	LEU	0	-0.010	-0.007	12.207	0.114	0.114	0.000	0.000	0.000	0.000
10	G	37	TYR	0	-0.037	-0.001	14.803	0.094	0.094	0.000	0.000	0.000	0.000
11	G	56	THR	0	0.009	-0.012	6.138	-0.088	-0.088	0.000	0.000	0.000	0.000
12	G	57	ARG	1	0.804	0.860	8.577	1.028	1.028	0.000	0.000	0.000	0.000
13	G	58	LEU	0	0.004	0.016	10.180	-0.177	-0.177	0.000	0.000	0.000	0.000
14	G	59	ASP	-1	-0.768	-0.848	12.983	-0.565	-0.565	0.000	0.000	0.000	0.000
15	G	60	LEU	0	-0.015	-0.024	15.434	0.028	0.028	0.000	0.000	0.000	0.000
16	G	61	ASP	-1	-0.829	-0.859	18.721	-0.225	-0.225	0.000	0.000	0.000	0.000
17	G	76	LEU	0	0.019	0.002	12.001	0.026	0.026	0.000	0.000	0.000	0.000
18	G	77	THR	0	0.011	-0.001	14.510	-0.048	-0.048	0.000	0.000	0.000	0.000
19	G	78	GLN	0	0.053	0.032	8.691	0.160	0.160	0.000	0.000	0.000	0.000
20	G	79	LEU	0	-0.057	-0.014	10.658	-0.201	-0.201	0.000	0.000	0.000	0.000
21	G	80	THR	0	-0.018	-0.015	11.110	0.121	0.121	0.000	0.000	0.000	0.000
22	G	81	GLN	0	0.000	0.000	12.756	0.059	0.059	0.000	0.000	0.000	0.000
23	G	82	LEU	0	0.041	0.015	13.868	-0.089	-0.089	0.000	0.000	0.000	0.000
24	G	83	SER	0	-0.027	-0.041	16.560	0.032	0.032	0.000	0.000	0.000	0.000
25	G	84	LEU	0	-0.008	-0.009	18.960	-0.004	-0.004	0.000	0.000	0.000	0.000
26	G	85	ASN	0	0.009	0.008	22.013	0.004	0.004	0.000	0.000	0.000	0.000
27	G	97	PHE	0	0.035	0.001	21.068	-0.001	-0.001	0.000	0.000	0.000	0.000
28	G	98	ASP	-1	-0.815	-0.893	21.571	-0.254	-0.254	0.000	0.000	0.000	0.000
29	G	99	ASN	0	-0.006	-0.002	19.914	0.010	0.010	0.000	0.000	0.000	0.000
30	G	100	LEU	0	-0.013	0.015	16.274	-0.029	-0.029	0.000	0.000	0.000	0.000
31	G	101	ARG	1	0.927	0.946	17.010	0.363	0.363	0.000	0.000	0.000	0.000
32	G	102	SER	0	-0.051	-0.037	14.739	0.053	0.053	0.000	0.000	0.000	0.000
33	G	103	LEU	0	-0.039	0.001	15.833	-0.050	-0.050	0.000	0.000	0.000	0.000
34	G	104	THR	0	-0.031	-0.049	16.033	0.030	0.030	0.000	0.000	0.000	0.000
35	G	105	HIS	0	-0.010	0.017	16.638	-0.010	-0.010	0.000	0.000	0.000	0.000
36	G	106	ILE	0	-0.004	0.002	17.783	-0.047	-0.047	0.000	0.000	0.000	0.000
37	G	107	TRP	0	-0.024	0.000	16.548	0.016	0.016	0.000	0.000	0.000	0.000
38	G	108	LEU	0	0.023	-0.008	22.108	0.000	0.000	0.000	0.000	0.000	0.000
39	G	109	LEU	0	-0.007	0.016	24.834	0.015	0.015	0.000	0.000	0.000	0.000
40	G	110	ASN	0	0.012	-0.001	27.373	-0.010	-0.010	0.000	0.000	0.000	0.000
41	G	111	ASN	0	-0.031	0.010	26.704	0.020	0.020	0.000	0.000	0.000	0.000
42	G	121	LEU	0	0.039	0.016	35.150	-0.003	-0.003	0.000	0.000	0.000	0.000
43	G	122	TYR	0	-0.028	-0.048	26.612	-0.001	-0.001	0.000	0.000	0.000	0.000
44	G	123	LEU	0	0.069	0.035	27.703	-0.007	-0.007	0.000	0.000	0.000	0.000
45	G	124	SER	0	0.034	0.005	30.764	-0.007	-0.007	0.000	0.000	0.000	0.000
46	G	125	ARG	1	0.906	0.954	32.796	0.139	0.139	0.000	0.000	0.000	0.000
47	G	126	TRP	0	-0.006	-0.012	22.743	0.002	0.002	0.000	0.000	0.000	0.000
48	G	127	ILE	0	0.028	0.009	27.982	-0.010	-0.010	0.000	0.000	0.000	0.000
49	G	128	SER	0	-0.006	-0.015	29.407	0.000	0.000	0.000	0.000	0.000	0.000
50	G	129	GLN	0	-0.042	-0.008	30.629	0.003	0.003	0.000	0.000	0.000	0.000
51	G	130	HIS	1	0.831	0.924	25.401	0.220	0.220	0.000	0.000	0.000	0.000
52	G	131	PRO	0	0.043	0.029	26.455	-0.014	-0.014	0.000	0.000	0.000	0.000
53	G	132	TRP	0	0.030	0.008	23.223	0.012	0.012	0.000	0.000	0.000	0.000
54	G	133	LEU	0	0.004	0.010	20.642	-0.014	-0.014	0.000	0.000	0.000	0.000
55	G	134	VAL	0	-0.003	0.005	21.987	-0.024	-0.024	0.000	0.000	0.000	0.000
56	G	135	PHE	0	-0.008	-0.001	21.575	0.015	0.015	0.000	0.000	0.000	0.000
57	G	136	GLY	0	0.078	0.033	23.777	0.002	0.002	0.000	0.000	0.000	0.000
58	G	137	TYR	0	-0.061	-0.058	23.590	-0.018	-0.018	0.000	0.000	0.000	0.000
59	G	138	LEU	0	-0.018	0.004	24.467	0.009	0.009	0.000	0.000	0.000	0.000
60	G	139	ASN	0	0.018	-0.010	23.755	-0.021	-0.021	0.000	0.000	0.000	0.000
61	G	140	LEU	0	-0.025	0.009	24.449	-0.002	-0.002	0.000	0.000	0.000	0.000
62	G	141	ASP	-1	-0.776	-0.920	25.626	-0.122	-0.122	0.000	0.000	0.000	0.000
63	G	142	HIS	0	-0.010	0.011	28.264	-0.008	-0.008	0.000	0.000	0.000	0.000
64	G	143	ASP	-1	-0.829	-0.896	29.338	-0.109	-0.109	0.000	0.000	0.000	0.000
65	G	144	SER	0	-0.037	-0.027	27.801	0.005	0.005	0.000	0.000	0.000	0.000
66	G	145	ALA	0	-0.003	0.011	28.747	0.002	0.002	0.000	0.000	0.000	0.000
67	G	146	ARG	1	0.870	0.934	30.301	0.121	0.121	0.000	0.000	0.000	0.000
68	G	147	CYS	0	-0.013	0.018	33.603	-0.002	-0.002	0.000	0.000	0.000	0.000
69	G	148	SER	0	0.075	0.028	36.093	0.000	0.000	0.000	0.000	0.000	0.000
70	G	149	GLY	0	0.046	0.018	37.267	0.004	0.004	0.000	0.000	0.000	0.000
71	G	150	THR	0	-0.033	-0.008	35.332	0.003	0.003	0.000	0.000	0.000	0.000
72	G	151	ASN	0	-0.056	-0.054	36.909	-0.003	-0.003	0.000	0.000	0.000	0.000
73	G	152	THR	0	0.005	0.006	38.616	0.002	0.002	0.000	0.000	0.000	0.000
74	G	153	PRO	0	-0.016	0.000	34.950	-0.003	-0.003	0.000	0.000	0.000	0.000
75	G	154	VAL	0	0.007	-0.008	32.519	0.004	0.004	0.000	0.000	0.000	0.000
76	G	155	ARG	1	0.797	0.894	32.585	0.123	0.123	0.000	0.000	0.000	0.000
77	G	156	ALA	0	-0.003	0.018	34.645	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(G:11:THR)