FMO DATABASE

FMODB ID: 98332

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

Total energy (hartree)

FMO2-HF: Electronic energy	-503054.324521
FMO2-HF: Nuclear repulsion	471747.865088
FMO2-HF: Total energy	-31306.459433
FMO2-MP2: Total energy	-31399.407583

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.
0.08	1.618	-0.019	-0.575	-0.945	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 : -0.024 / q_NPA : -0.025

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	0.015	0.015	3.851	-0.423	0.986	-0.018	-0.559	-0.832	0.001
4	G	21	ALA	0	-0.005	-0.009	20.382	0.002	0.002	0.000	0.000	0.000	0.000
5	G	22	SER	0	0.005	0.009	17.214	-0.017	-0.017	0.000	0.000	0.000	0.000
6	G	33	VAL	0	-0.036	-0.031	4.636	-0.310	-0.181	-0.001	-0.016	-0.113	0.000
7	G	34	LEU	0	0.016	0.003	6.658	-0.019	-0.019	0.000	0.000	0.000	0.000
8	G	35	TYR	0	-0.011	0.005	9.350	-0.164	-0.164	0.000	0.000	0.000	0.000
9	G	36	LEU	0	-0.042	-0.031	12.577	0.021	0.021	0.000	0.000	0.000	0.000
10	G	37	TYR	0	0.019	0.035	14.966	-0.060	-0.060	0.000	0.000	0.000	0.000
11	G	56	THR	0	0.004	-0.013	6.199	0.053	0.053	0.000	0.000	0.000	0.000
12	G	57	ARG	1	0.837	0.900	8.656	-0.399	-0.399	0.000	0.000	0.000	0.000
13	G	58	LEU	0	0.014	0.023	10.531	0.025	0.025	0.000	0.000	0.000	0.000
14	G	59	ASP	-1	-0.785	-0.875	13.300	0.420	0.420	0.000	0.000	0.000	0.000
15	G	60	LEU	0	-0.035	-0.032	15.912	0.001	0.001	0.000	0.000	0.000	0.000
16	G	61	ASP	-1	-0.890	-0.932	19.173	0.240	0.240	0.000	0.000	0.000	0.000
17	G	76	LEU	0	0.007	-0.007	12.053	-0.003	-0.003	0.000	0.000	0.000	0.000
18	G	77	THR	0	-0.002	0.004	14.529	0.016	0.016	0.000	0.000	0.000	0.000
19	G	78	GLN	0	0.056	0.012	9.020	0.163	0.163	0.000	0.000	0.000	0.000
20	G	79	LEU	0	-0.045	-0.004	10.305	-0.047	-0.047	0.000	0.000	0.000	0.000
21	G	80	THR	0	-0.007	-0.001	10.945	0.065	0.065	0.000	0.000	0.000	0.000
22	G	81	GLN	0	0.007	0.007	12.515	0.114	0.114	0.000	0.000	0.000	0.000
23	G	82	LEU	0	0.047	0.009	13.929	-0.024	-0.024	0.000	0.000	0.000	0.000
24	G	83	SER	0	0.010	0.011	16.459	-0.010	-0.010	0.000	0.000	0.000	0.000
25	G	84	LEU	0	-0.021	-0.017	18.970	-0.015	-0.015	0.000	0.000	0.000	0.000
26	G	85	ASN	0	0.033	0.029	22.024	-0.007	-0.007	0.000	0.000	0.000	0.000
27	G	97	PHE	0	0.012	-0.013	21.644	-0.004	-0.004	0.000	0.000	0.000	0.000
28	G	98	ASP	-1	-0.805	-0.880	21.846	-0.132	-0.132	0.000	0.000	0.000	0.000
29	G	99	ASN	0	-0.023	-0.007	19.943	0.011	0.011	0.000	0.000	0.000	0.000
30	G	100	LEU	0	-0.029	0.004	16.452	-0.050	-0.050	0.000	0.000	0.000	0.000
31	G	101	ARG	1	0.939	0.956	16.897	0.400	0.400	0.000	0.000	0.000	0.000
32	G	102	SER	0	-0.045	-0.028	13.865	0.011	0.011	0.000	0.000	0.000	0.000
33	G	103	LEU	0	-0.037	0.001	15.718	0.010	0.010	0.000	0.000	0.000	0.000
34	G	104	THR	0	-0.041	-0.061	15.927	-0.006	-0.006	0.000	0.000	0.000	0.000
35	G	105	HIS	0	-0.012	0.018	16.577	0.005	0.005	0.000	0.000	0.000	0.000
36	G	106	ILE	0	-0.041	-0.013	17.940	-0.008	-0.008	0.000	0.000	0.000	0.000
37	G	107	TRP	0	0.000	0.001	16.673	0.007	0.007	0.000	0.000	0.000	0.000
38	G	108	LEU	0	-0.010	-0.032	22.130	-0.008	-0.008	0.000	0.000	0.000	0.000
39	G	109	LEU	0	-0.054	-0.008	25.438	-0.007	-0.007	0.000	0.000	0.000	0.000
40	G	110	ASN	0	-0.015	-0.022	27.669	0.014	0.014	0.000	0.000	0.000	0.000
41	G	111	ASN	0	0.066	0.057	27.557	0.009	0.009	0.000	0.000	0.000	0.000
42	G	121	LEU	0	0.048	0.014	35.060	0.000	0.000	0.000	0.000	0.000	0.000
43	G	122	TYR	0	-0.045	-0.070	26.723	0.003	0.003	0.000	0.000	0.000	0.000
44	G	123	LEU	0	0.035	0.027	27.678	-0.006	-0.006	0.000	0.000	0.000	0.000
45	G	124	SER	0	0.057	0.014	30.730	0.000	0.000	0.000	0.000	0.000	0.000
46	G	125	ARG	1	0.950	0.986	32.611	0.061	0.061	0.000	0.000	0.000	0.000
47	G	126	TRP	0	0.050	0.019	22.718	0.003	0.003	0.000	0.000	0.000	0.000
48	G	127	ILE	0	0.055	0.021	27.954	-0.005	-0.005	0.000	0.000	0.000	0.000
49	G	128	SER	0	-0.022	-0.010	29.309	0.002	0.002	0.000	0.000	0.000	0.000
50	G	129	GLN	0	-0.070	-0.026	30.033	-0.006	-0.006	0.000	0.000	0.000	0.000
51	G	130	HIS	1	0.828	0.914	24.734	0.072	0.072	0.000	0.000	0.000	0.000
52	G	131	PRO	0	0.055	0.038	26.579	0.006	0.006	0.000	0.000	0.000	0.000
53	G	132	TRP	0	0.019	0.001	22.763	0.014	0.014	0.000	0.000	0.000	0.000
54	G	133	LEU	0	-0.009	-0.005	20.537	0.002	0.002	0.000	0.000	0.000	0.000
55	G	134	VAL	0	-0.001	0.011	22.066	0.008	0.008	0.000	0.000	0.000	0.000
56	G	135	PHE	0	0.005	0.013	21.574	0.002	0.002	0.000	0.000	0.000	0.000
57	G	136	GLY	0	0.051	0.031	23.908	0.002	0.002	0.000	0.000	0.000	0.000
58	G	137	TYR	0	0.005	-0.025	23.907	0.007	0.007	0.000	0.000	0.000	0.000
59	G	138	LEU	0	-0.015	0.014	24.607	0.015	0.015	0.000	0.000	0.000	0.000
60	G	139	ASN	0	-0.006	-0.009	23.753	0.014	0.014	0.000	0.000	0.000	0.000
61	G	140	LEU	0	-0.036	-0.012	24.205	0.000	0.000	0.000	0.000	0.000	0.000
62	G	141	ASP	-1	-0.854	-0.952	25.920	0.051	0.051	0.000	0.000	0.000	0.000
63	G	142	HIS	0	0.018	0.003	28.345	-0.003	-0.003	0.000	0.000	0.000	0.000
64	G	143	ASP	-1	-0.880	-0.916	29.567	0.016	0.016	0.000	0.000	0.000	0.000
65	G	144	SER	0	-0.061	-0.029	27.774	0.005	0.005	0.000	0.000	0.000	0.000
66	G	145	ALA	0	0.012	0.012	28.853	0.006	0.006	0.000	0.000	0.000	0.000
67	G	146	ARG	1	0.982	0.991	30.407	-0.054	-0.054	0.000	0.000	0.000	0.000
68	G	147	CYS	0	-0.006	0.013	33.683	-0.001	-0.001	0.000	0.000	0.000	0.000
69	G	148	SER	0	0.072	0.031	36.195	0.004	0.004	0.000	0.000	0.000	0.000
70	G	149	GLY	0	0.047	0.018	37.237	0.004	0.004	0.000	0.000	0.000	0.000
71	G	150	THR	0	-0.040	-0.017	35.867	0.002	0.002	0.000	0.000	0.000	0.000
72	G	151	ASN	0	-0.061	-0.048	37.288	0.001	0.001	0.000	0.000	0.000	0.000
73	G	152	THR	0	0.016	0.003	38.859	-0.001	-0.001	0.000	0.000	0.000	0.000
74	G	153	PRO	0	-0.047	-0.010	35.129	0.002	0.002	0.000	0.000	0.000	0.000
75	G	154	VAL	0	0.018	0.005	32.555	-0.004	-0.004	0.000	0.000	0.000	0.000
76	G	155	ARG	1	0.778	0.872	32.668	-0.010	-0.010	0.000	0.000	0.000	0.000
77	G	156	ALA	0	-0.006	0.016	34.571	-0.006	-0.006	0.000	0.000	0.000	0.000

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