FMO DATABASE

FMODB ID: KGMN3

Calculation Name: 3ZVQ-B-Xray372

Preferred Name: Lysozyme C

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZVQ

Chain ID: B

ChEMBL ID: CHEMBL1932892

UniProt ID: P00698

Base Structure: X-ray

Registration Date: 2023-09-23

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	57
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-254890.583651
FMO2-HF: Nuclear repulsion	231466.162419
FMO2-HF: Total energy	-23424.421233
FMO2-MP2: Total energy	-23488.094551

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(B:72:SER)

Summations of interaction energy for fragment #1(B:72:SER)

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.
-1.165	0.404	-0.016	-0.645	-0.906	0.002

Interaction energy analysis for fragmet #1(B:72:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : 0.000

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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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	B	74	ASN	0	0.029	0.007	3.882	0.461	1.947	-0.015	-0.641	-0.829	0.002
4	B	75	LEU	0	0.039	0.014	5.729	-0.752	-0.669	-0.001	-0.004	-0.077	0.000
5	B	76	CYS	0	-0.095	-0.041	8.660	-0.126	-0.126	0.000	0.000	0.000	0.000
6	B	77	ASN	0	-0.006	0.012	9.309	-0.194	-0.194	0.000	0.000	0.000	0.000
7	B	78	ILE	0	0.041	0.030	9.177	-0.109	-0.109	0.000	0.000	0.000	0.000
8	B	79	PRO	0	0.044	0.040	8.553	-0.015	-0.015	0.000	0.000	0.000	0.000
9	B	80	CYS	0	0.025	-0.015	6.175	0.140	0.140	0.000	0.000	0.000	0.000
10	B	81	SER	0	0.045	0.025	9.290	0.081	0.081	0.000	0.000	0.000	0.000
11	B	82	ALA	0	0.018	0.008	12.571	0.042	0.042	0.000	0.000	0.000	0.000
12	B	83	LEU	0	-0.043	-0.026	10.096	0.057	0.057	0.000	0.000	0.000	0.000
13	B	84	LEU	0	-0.033	-0.017	13.736	0.030	0.030	0.000	0.000	0.000	0.000
14	B	85	SER	0	-0.006	0.017	16.340	-0.027	-0.027	0.000	0.000	0.000	0.000
15	B	86	SER	0	0.038	0.013	18.994	0.019	0.019	0.000	0.000	0.000	0.000
16	B	87	ASP	-1	-0.862	-0.895	21.624	0.079	0.079	0.000	0.000	0.000	0.000
17	B	88	ILE	0	0.037	0.003	19.687	0.009	0.009	0.000	0.000	0.000	0.000
18	B	89	THR	0	-0.032	-0.038	19.455	0.045	0.045	0.000	0.000	0.000	0.000
19	B	90	ALA	0	-0.001	0.001	15.276	0.031	0.031	0.000	0.000	0.000	0.000
20	B	91	SER	0	0.038	0.006	15.071	0.062	0.062	0.000	0.000	0.000	0.000
21	B	92	VAL	0	-0.007	0.004	16.138	0.070	0.070	0.000	0.000	0.000	0.000
22	B	93	ASN	0	0.031	0.008	17.607	0.039	0.039	0.000	0.000	0.000	0.000
23	B	95	ALA	0	0.019	-0.001	14.345	0.091	0.091	0.000	0.000	0.000	0.000
24	B	96	LYS	1	0.924	0.955	16.339	-0.205	-0.205	0.000	0.000	0.000	0.000
25	B	97	LYS	1	0.887	0.953	12.434	-0.606	-0.606	0.000	0.000	0.000	0.000
26	B	98	ILE	0	0.003	0.000	11.708	0.033	0.033	0.000	0.000	0.000	0.000
27	B	99	VAL	0	-0.045	-0.029	14.569	0.006	0.006	0.000	0.000	0.000	0.000
28	B	100	SER	0	-0.008	-0.027	17.588	-0.047	-0.047	0.000	0.000	0.000	0.000
29	B	101	ASP	-1	-0.939	-0.951	13.082	0.956	0.956	0.000	0.000	0.000	0.000
30	B	102	GLY	0	0.060	0.035	15.759	-0.005	-0.005	0.000	0.000	0.000	0.000
31	B	103	ASN	0	-0.070	-0.034	15.382	-0.109	-0.109	0.000	0.000	0.000	0.000
32	B	104	GLY	0	0.036	0.035	18.435	-0.054	-0.054	0.000	0.000	0.000	0.000
33	B	105	MET	0	-0.002	-0.024	18.361	0.044	0.044	0.000	0.000	0.000	0.000
34	B	106	ASN	0	-0.031	-0.015	19.733	-0.035	-0.035	0.000	0.000	0.000	0.000
35	B	107	ALA	0	0.057	0.040	14.328	0.001	0.001	0.000	0.000	0.000	0.000
36	B	108	TRP	0	-0.008	0.007	15.122	0.028	0.028	0.000	0.000	0.000	0.000
37	B	109	VAL	0	0.014	-0.004	16.249	-0.064	-0.064	0.000	0.000	0.000	0.000
38	B	110	ALA	0	0.017	0.008	18.992	-0.041	-0.041	0.000	0.000	0.000	0.000
39	B	111	TRP	0	0.096	0.029	21.186	-0.020	-0.020	0.000	0.000	0.000	0.000
40	B	112	ARG	1	0.880	0.936	18.416	-0.469	-0.469	0.000	0.000	0.000	0.000
41	B	113	ASN	0	0.007	0.003	22.849	0.006	0.006	0.000	0.000	0.000	0.000
42	B	114	ARG	1	0.935	0.971	24.881	-0.199	-0.199	0.000	0.000	0.000	0.000
43	B	115	CYS	0	-0.028	0.006	25.951	-0.012	-0.012	0.000	0.000	0.000	0.000
44	B	116	LYS	1	0.920	0.966	24.378	-0.324	-0.324	0.000	0.000	0.000	0.000
45	B	117	GLY	0	0.016	0.010	27.596	-0.005	-0.005	0.000	0.000	0.000	0.000
46	B	118	THR	0	-0.050	-0.025	30.511	-0.015	-0.015	0.000	0.000	0.000	0.000
47	B	119	ASP	-1	-0.783	-0.892	32.776	0.129	0.129	0.000	0.000	0.000	0.000
48	B	120	VAL	0	-0.025	-0.025	28.958	-0.004	-0.004	0.000	0.000	0.000	0.000
49	B	121	GLN	0	0.026	0.012	31.821	-0.008	-0.008	0.000	0.000	0.000	0.000
50	B	122	ALA	0	0.003	0.001	34.464	-0.008	-0.008	0.000	0.000	0.000	0.000
51	B	123	TRP	0	-0.056	-0.026	30.352	-0.008	-0.008	0.000	0.000	0.000	0.000
52	B	124	ILE	0	0.006	0.003	31.532	0.000	0.000	0.000	0.000	0.000	0.000
53	B	125	ARG	1	0.915	0.951	34.136	-0.102	-0.102	0.000	0.000	0.000	0.000
54	B	126	GLY	0	-0.008	-0.003	37.815	-0.003	-0.003	0.000	0.000	0.000	0.000
55	B	127	CYS	0	-0.042	-0.001	35.168	-0.005	-0.005	0.000	0.000	0.000	0.000
56	B	128	ARG	1	0.945	0.970	37.211	-0.050	-0.050	0.000	0.000	0.000	0.000
57	B	129	LEU	0	0.007	0.008	32.388	-0.003	-0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:72:SER)