FMO DATABASE

FMODB ID: MN55Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-503440.8738
FMO2-HF: Nuclear repulsion	472133.98861
FMO2-HF: Total energy	-31306.885191
FMO2-MP2: Total energy	-31399.821858

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.
0.808	2.226	-0.019	-0.565	-0.834	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 : -0.016 / q_NPA : -0.022

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	0.018	0.019	3.851	0.068	1.486	-0.019	-0.565	-0.834	0.001
4	G	21	ALA	0	0.027	0.021	20.406	0.008	0.008	0.000	0.000	0.000	0.000
5	G	22	SER	0	-0.027	-0.021	17.282	-0.014	-0.014	0.000	0.000	0.000	0.000
6	G	33	VAL	0	-0.057	-0.037	5.106	-0.088	-0.088	0.000	0.000	0.000	0.000
7	G	34	LEU	0	0.020	0.005	6.556	-0.119	-0.119	0.000	0.000	0.000	0.000
8	G	35	TYR	0	-0.012	0.003	9.046	-0.169	-0.169	0.000	0.000	0.000	0.000
9	G	36	LEU	0	-0.033	-0.019	12.577	0.031	0.031	0.000	0.000	0.000	0.000
10	G	37	TYR	0	0.024	0.032	14.837	-0.040	-0.040	0.000	0.000	0.000	0.000
11	G	56	THR	0	-0.002	-0.014	6.568	0.038	0.038	0.000	0.000	0.000	0.000
12	G	57	ARG	1	0.798	0.847	9.010	-0.087	-0.087	0.000	0.000	0.000	0.000
13	G	58	LEU	0	0.006	0.019	10.517	-0.018	-0.018	0.000	0.000	0.000	0.000
14	G	59	ASP	-1	-0.762	-0.845	13.277	0.260	0.260	0.000	0.000	0.000	0.000
15	G	60	LEU	0	-0.020	-0.019	16.088	0.003	0.003	0.000	0.000	0.000	0.000
16	G	61	ASP	-1	-0.845	-0.890	19.128	0.148	0.148	0.000	0.000	0.000	0.000
17	G	76	LEU	0	0.002	-0.006	12.136	0.003	0.003	0.000	0.000	0.000	0.000
18	G	77	THR	0	0.015	0.009	14.370	0.001	0.001	0.000	0.000	0.000	0.000
19	G	78	GLN	0	0.048	0.022	8.840	0.181	0.181	0.000	0.000	0.000	0.000
20	G	79	LEU	0	-0.044	-0.004	10.622	-0.082	-0.082	0.000	0.000	0.000	0.000
21	G	80	THR	0	-0.004	0.001	11.260	0.085	0.085	0.000	0.000	0.000	0.000
22	G	81	GLN	0	0.027	0.017	12.828	0.136	0.136	0.000	0.000	0.000	0.000
23	G	82	LEU	0	0.037	0.007	14.262	-0.043	-0.043	0.000	0.000	0.000	0.000
24	G	83	SER	0	-0.012	-0.012	16.785	-0.003	-0.003	0.000	0.000	0.000	0.000
25	G	84	LEU	0	-0.009	-0.006	19.270	-0.018	-0.018	0.000	0.000	0.000	0.000
26	G	85	ASN	0	0.007	0.003	22.142	-0.012	-0.012	0.000	0.000	0.000	0.000
27	G	97	PHE	0	0.021	-0.007	21.444	-0.005	-0.005	0.000	0.000	0.000	0.000
28	G	98	ASP	-1	-0.834	-0.907	22.020	-0.183	-0.183	0.000	0.000	0.000	0.000
29	G	99	ASN	0	-0.031	-0.009	19.850	0.010	0.010	0.000	0.000	0.000	0.000
30	G	100	LEU	0	-0.023	0.001	16.688	-0.053	-0.053	0.000	0.000	0.000	0.000
31	G	101	ARG	1	0.940	0.959	17.020	0.462	0.462	0.000	0.000	0.000	0.000
32	G	102	SER	0	-0.050	-0.043	14.188	0.025	0.025	0.000	0.000	0.000	0.000
33	G	103	LEU	0	-0.039	0.002	15.990	0.003	0.003	0.000	0.000	0.000	0.000
34	G	104	THR	0	-0.037	-0.057	16.114	-0.001	-0.001	0.000	0.000	0.000	0.000
35	G	105	HIS	0	-0.027	0.006	16.774	0.008	0.008	0.000	0.000	0.000	0.000
36	G	106	ILE	0	-0.028	-0.010	18.228	-0.017	-0.017	0.000	0.000	0.000	0.000
37	G	107	TRP	0	-0.006	0.001	16.816	0.010	0.010	0.000	0.000	0.000	0.000
38	G	108	LEU	0	0.010	-0.017	22.406	-0.008	-0.008	0.000	0.000	0.000	0.000
39	G	109	LEU	0	-0.029	0.000	25.736	-0.003	-0.003	0.000	0.000	0.000	0.000
40	G	110	ASN	0	-0.009	-0.004	27.960	0.011	0.011	0.000	0.000	0.000	0.000
41	G	111	ASN	0	0.039	0.044	27.359	0.005	0.005	0.000	0.000	0.000	0.000
42	G	121	LEU	0	0.045	0.010	35.127	0.000	0.000	0.000	0.000	0.000	0.000
43	G	122	TYR	0	-0.025	-0.045	26.778	0.002	0.002	0.000	0.000	0.000	0.000
44	G	123	LEU	0	0.039	0.028	28.061	-0.008	-0.008	0.000	0.000	0.000	0.000
45	G	124	SER	0	0.060	0.020	30.989	-0.003	-0.003	0.000	0.000	0.000	0.000
46	G	125	ARG	1	0.931	0.984	32.722	0.093	0.093	0.000	0.000	0.000	0.000
47	G	126	TRP	0	0.051	0.015	22.816	0.005	0.005	0.000	0.000	0.000	0.000
48	G	127	ILE	0	0.031	0.006	28.161	-0.007	-0.007	0.000	0.000	0.000	0.000
49	G	128	SER	0	-0.026	-0.024	29.622	0.003	0.003	0.000	0.000	0.000	0.000
50	G	129	GLN	0	-0.041	-0.011	30.552	-0.004	-0.004	0.000	0.000	0.000	0.000
51	G	130	HIS	1	0.834	0.930	25.546	0.122	0.122	0.000	0.000	0.000	0.000
52	G	131	PRO	0	0.045	0.028	26.852	0.002	0.002	0.000	0.000	0.000	0.000
53	G	132	TRP	0	0.029	0.007	22.935	0.016	0.016	0.000	0.000	0.000	0.000
54	G	133	LEU	0	0.003	0.005	20.744	-0.001	-0.001	0.000	0.000	0.000	0.000
55	G	134	VAL	0	0.007	0.011	22.326	0.002	0.002	0.000	0.000	0.000	0.000
56	G	135	PHE	0	0.000	0.012	21.982	0.006	0.006	0.000	0.000	0.000	0.000
57	G	136	GLY	0	0.052	0.031	24.125	0.002	0.002	0.000	0.000	0.000	0.000
58	G	137	TYR	0	-0.023	-0.048	24.090	0.008	0.008	0.000	0.000	0.000	0.000
59	G	138	LEU	0	-0.012	0.012	24.770	0.015	0.015	0.000	0.000	0.000	0.000
60	G	139	ASN	0	-0.015	-0.014	23.879	0.002	0.002	0.000	0.000	0.000	0.000
61	G	140	LEU	0	-0.032	-0.006	24.719	0.000	0.000	0.000	0.000	0.000	0.000
62	G	141	ASP	-1	-0.830	-0.945	26.094	0.016	0.016	0.000	0.000	0.000	0.000
63	G	142	HIS	0	0.008	0.011	28.580	-0.005	-0.005	0.000	0.000	0.000	0.000
64	G	143	ASP	-1	-0.833	-0.913	29.815	-0.010	-0.010	0.000	0.000	0.000	0.000
65	G	144	SER	0	-0.024	-0.013	28.152	0.004	0.004	0.000	0.000	0.000	0.000
66	G	145	ALA	0	-0.010	0.005	29.095	0.006	0.006	0.000	0.000	0.000	0.000
67	G	146	ARG	1	0.913	0.950	30.694	-0.017	-0.017	0.000	0.000	0.000	0.000
68	G	147	CYS	0	-0.006	0.006	33.989	-0.002	-0.002	0.000	0.000	0.000	0.000
69	G	148	SER	0	0.068	0.026	36.517	0.004	0.004	0.000	0.000	0.000	0.000
70	G	149	GLY	0	0.054	0.021	37.798	0.004	0.004	0.000	0.000	0.000	0.000
71	G	150	THR	0	-0.048	-0.016	36.091	0.003	0.003	0.000	0.000	0.000	0.000
72	G	151	ASN	0	-0.052	-0.051	37.529	0.000	0.000	0.000	0.000	0.000	0.000
73	G	152	THR	0	0.012	0.010	39.228	0.000	0.000	0.000	0.000	0.000	0.000
74	G	153	PRO	0	-0.062	-0.017	35.392	0.001	0.001	0.000	0.000	0.000	0.000
75	G	154	VAL	0	-0.007	0.003	33.012	-0.002	-0.002	0.000	0.000	0.000	0.000
76	G	155	ARG	1	0.784	0.880	32.773	0.023	0.023	0.000	0.000	0.000	0.000
77	G	156	ALA	0	0.010	0.028	34.878	-0.005	-0.005	0.000	0.000	0.000	0.000

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