FMO DATABASE

FMODB ID: YVJ32

Calculation Name: 3ZVQ-A-Xray372

Preferred Name: Lysozyme C

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZVQ

Chain ID: A

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	70
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-399854.379693
FMO2-HF: Nuclear repulsion	371300.006874
FMO2-HF: Total energy	-28554.372819
FMO2-MP2: Total energy	-28635.615796

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:1:LYS)

Summations of interaction energy for fragment #1(A:1:LYS)

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.
-91.275	-92.711	48.037	-20.382	-26.217	-0.229

Interaction energy analysis for fragmet #1(A:1:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.851 / q_NPA : 0.920

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	3	PHE	0	-0.015	-0.010	1.923	-46.667	-43.157	17.042	-7.503	-13.050	-0.077
4	A	4	GLY	0	0.053	0.028	3.220	15.387	15.527	0.030	0.250	-0.419	-0.001
5	A	5	ARG	1	0.992	0.987	5.267	24.957	24.988	-0.001	0.001	-0.030	0.000
6	A	6	CYS	0	-0.026	-0.029	8.506	1.869	1.869	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.758	-0.847	1.773	-131.763	-138.171	21.141	-8.244	-6.489	-0.106
8	A	8	LEU	0	0.033	0.009	5.784	1.464	1.464	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.012	0.010	6.746	3.520	3.520	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.026	0.009	8.885	2.422	2.422	0.000	0.000	0.000	0.000
11	A	11	ALA	0	0.008	0.004	6.460	2.419	2.419	0.000	0.000	0.000	0.000
12	A	12	MET	0	-0.026	-0.014	8.556	2.634	2.634	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.879	0.927	11.053	19.628	19.628	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.894	0.950	10.616	25.602	25.602	0.000	0.000	0.000	0.000
15	A	15	HIS	0	-0.034	-0.016	9.218	1.732	1.732	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.024	0.022	13.859	0.827	0.827	0.000	0.000	0.000	0.000
17	A	17	LEU	0	0.027	0.002	12.798	0.821	0.821	0.000	0.000	0.000	0.000
18	A	18	ASP	-1	-0.867	-0.924	16.384	-16.331	-16.331	0.000	0.000	0.000	0.000
19	A	19	ASN	0	0.013	0.000	17.776	0.957	0.957	0.000	0.000	0.000	0.000
20	A	20	TYR	0	0.009	0.024	19.382	0.995	0.995	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.921	0.941	21.189	11.557	11.557	0.000	0.000	0.000	0.000
22	A	22	GLY	0	0.036	0.027	23.865	0.433	0.433	0.000	0.000	0.000	0.000
23	A	23	TYR	0	-0.024	-0.002	19.972	0.004	0.004	0.000	0.000	0.000	0.000
24	A	24	SER	0	0.058	0.029	19.732	-0.758	-0.758	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.006	-0.018	12.559	-0.603	-0.603	0.000	0.000	0.000	0.000
26	A	26	GLY	0	-0.010	-0.002	14.999	-1.284	-1.284	0.000	0.000	0.000	0.000
27	A	27	ASN	0	0.002	0.009	16.619	-0.337	-0.337	0.000	0.000	0.000	0.000
28	A	28	TRP	0	0.039	0.023	13.774	-0.610	-0.610	0.000	0.000	0.000	0.000
29	A	29	VAL	0	0.005	-0.008	10.788	-1.391	-1.391	0.000	0.000	0.000	0.000
30	A	30	CYS	0	-0.025	-0.014	12.586	-0.844	-0.844	0.000	0.000	0.000	0.000
31	A	31	ALA	0	0.047	0.030	15.177	-0.011	-0.011	0.000	0.000	0.000	0.000
32	A	32	ALA	0	0.046	0.019	9.685	-0.365	-0.365	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.816	0.911	10.924	23.339	23.339	0.000	0.000	0.000	0.000
34	A	34	PHE	0	-0.051	-0.048	12.471	-0.119	-0.119	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.872	-0.918	13.385	-17.202	-17.202	0.000	0.000	0.000	0.000
36	A	36	SER	0	-0.017	-0.022	8.709	-1.170	-1.170	0.000	0.000	0.000	0.000
37	A	37	ASN	0	-0.023	0.002	9.349	-1.194	-1.194	0.000	0.000	0.000	0.000
38	A	38	PHE	0	-0.032	-0.022	6.281	-1.855	-1.855	0.000	0.000	0.000	0.000
39	A	39	ASN	0	0.048	0.023	3.922	-13.355	-13.225	0.000	-0.078	-0.052	0.000
40	A	40	THR	0	-0.030	-0.047	2.052	2.352	2.644	4.950	-2.227	-3.015	-0.017
41	A	41	GLN	0	0.001	-0.005	2.102	-4.794	-3.981	4.876	-2.577	-3.111	-0.028
42	A	42	ALA	0	-0.018	0.012	5.041	2.570	2.626	-0.001	-0.004	-0.051	0.000
43	A	43	THR	0	-0.039	-0.018	8.288	0.790	0.790	0.000	0.000	0.000	0.000
44	A	44	ASN	0	0.036	0.034	11.488	-0.527	-0.527	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.854	0.931	15.169	12.384	12.384	0.000	0.000	0.000	0.000
46	A	46	ASN	0	-0.025	-0.014	18.513	0.252	0.252	0.000	0.000	0.000	0.000
47	A	47	THR	0	0.026	-0.009	21.678	0.129	0.129	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.870	-0.899	23.693	-11.188	-11.188	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.002	0.008	23.735	0.263	0.263	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.075	-0.053	20.593	-0.440	-0.440	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.032	-0.031	14.918	0.155	0.155	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.793	-0.850	15.001	-14.895	-14.895	0.000	0.000	0.000	0.000
53	A	53	TYR	0	-0.029	-0.057	10.917	-0.737	-0.737	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.036	0.031	7.458	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	55	ILE	0	-0.042	-0.033	5.415	0.886	0.886	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.040	-0.020	8.457	0.140	0.140	0.000	0.000	0.000	0.000
57	A	57	GLN	0	0.001	-0.010	10.516	2.324	2.324	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.025	0.017	12.890	1.258	1.258	0.000	0.000	0.000	0.000
59	A	59	ASN	0	0.008	-0.016	14.890	0.439	0.439	0.000	0.000	0.000	0.000
60	A	60	SER	0	0.002	-0.050	17.474	0.270	0.270	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.864	0.954	18.728	10.809	10.809	0.000	0.000	0.000	0.000
62	A	62	TRP	0	-0.011	-0.016	21.354	0.859	0.859	0.000	0.000	0.000	0.000
63	A	63	TRP	0	-0.042	-0.002	18.169	0.190	0.190	0.000	0.000	0.000	0.000
64	A	64	CYS	0	-0.033	-0.004	15.826	-0.483	-0.483	0.000	0.000	0.000	0.000
65	A	65	ASN	0	0.054	0.029	17.853	0.158	0.158	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.717	-0.818	16.664	-13.815	-13.815	0.000	0.000	0.000	0.000
67	A	67	GLY	0	-0.021	-0.008	18.057	0.045	0.045	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.823	0.909	16.140	14.413	14.413	0.000	0.000	0.000	0.000
69	A	69	THR	0	0.055	0.023	20.429	-0.044	-0.044	0.000	0.000	0.000	0.000
70	A	70	PRO	0	-0.032	-0.011	23.145	0.259	0.259	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:LYS)