FMO DATABASE

FMODB ID: 5J8MZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-398725.866184
FMO2-HF: Nuclear repulsion	370171.548215
FMO2-HF: Total energy	-28554.317969
FMO2-MP2: Total energy	-28635.547749

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.
-75.342	-73.989	38.799	-18.451	-21.699	-0.173

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 : 0.892 / q_NPA : 0.939

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	-0.039	-0.025	2.452	-29.446	-22.065	7.248	-4.751	-9.877	-0.037
4	A	4	GLY	0	0.069	0.042	3.439	12.774	13.045	0.018	0.040	-0.329	0.000
5	A	5	ARG	1	0.998	0.984	5.587	24.321	24.321	0.000	0.000	0.000	0.000
6	A	6	CYS	0	-0.028	-0.036	8.774	0.909	0.909	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.774	-0.846	1.798	-134.771	-141.277	21.553	-8.973	-6.074	-0.106
8	A	8	LEU	0	0.036	0.015	5.729	0.601	0.601	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.014	0.010	6.502	3.514	3.514	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.014	0.009	8.542	2.541	2.541	0.000	0.000	0.000	0.000
11	A	11	ALA	0	0.010	0.001	6.228	2.432	2.432	0.000	0.000	0.000	0.000
12	A	12	MET	0	-0.024	-0.013	8.331	2.810	2.810	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.879	0.930	10.815	19.945	19.945	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.914	0.968	10.226	26.614	26.614	0.000	0.000	0.000	0.000
15	A	15	HIS	0	-0.067	-0.042	8.854	1.668	1.668	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.030	0.027	13.731	0.869	0.869	0.000	0.000	0.000	0.000
17	A	17	LEU	0	0.030	0.001	12.558	0.777	0.777	0.000	0.000	0.000	0.000
18	A	18	ASP	-1	-0.868	-0.931	16.104	-16.341	-16.341	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.001	0.001	17.653	0.862	0.862	0.000	0.000	0.000	0.000
20	A	20	TYR	0	0.014	0.030	19.065	1.018	1.018	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.930	0.946	20.881	11.698	11.698	0.000	0.000	0.000	0.000
22	A	22	GLY	0	0.026	0.016	23.770	0.340	0.340	0.000	0.000	0.000	0.000
23	A	23	TYR	0	-0.020	0.005	20.153	0.120	0.120	0.000	0.000	0.000	0.000
24	A	24	SER	0	0.032	0.015	19.757	-0.753	-0.753	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.034	-0.003	12.644	-0.497	-0.497	0.000	0.000	0.000	0.000
26	A	26	GLY	0	-0.017	-0.010	15.178	-1.200	-1.200	0.000	0.000	0.000	0.000
27	A	27	ASN	0	0.004	0.006	16.568	-0.328	-0.328	0.000	0.000	0.000	0.000
28	A	28	TRP	0	0.062	0.034	13.676	-0.628	-0.628	0.000	0.000	0.000	0.000
29	A	29	VAL	0	-0.011	-0.011	10.806	-1.413	-1.413	0.000	0.000	0.000	0.000
30	A	30	CYS	0	-0.025	-0.011	12.604	-0.884	-0.884	0.000	0.000	0.000	0.000
31	A	31	ALA	0	0.037	0.020	15.263	-0.021	-0.021	0.000	0.000	0.000	0.000
32	A	32	ALA	0	0.043	0.015	9.805	-0.356	-0.356	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.811	0.904	11.195	23.753	23.753	0.000	0.000	0.000	0.000
34	A	34	PHE	0	-0.025	-0.041	12.292	-0.282	-0.282	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.901	-0.908	13.228	-16.764	-16.764	0.000	0.000	0.000	0.000
36	A	36	SER	0	0.006	-0.009	8.454	-0.995	-0.995	0.000	0.000	0.000	0.000
37	A	37	ASN	0	-0.023	-0.008	8.881	-1.337	-1.337	0.000	0.000	0.000	0.000
38	A	38	PHE	0	-0.061	-0.035	6.223	-1.423	-1.423	0.000	0.000	0.000	0.000
39	A	39	ASN	0	0.051	0.033	3.409	-13.542	-13.132	0.015	-0.209	-0.215	-0.001
40	A	40	THR	0	-0.022	-0.032	1.902	2.464	0.269	9.123	-3.500	-3.428	-0.020
41	A	41	GLN	0	-0.019	-0.017	2.476	-0.324	1.610	0.843	-1.054	-1.723	-0.009
42	A	42	ALA	0	-0.020	0.016	4.979	2.568	2.626	-0.001	-0.004	-0.053	0.000
43	A	43	THR	0	-0.020	-0.008	7.985	0.857	0.857	0.000	0.000	0.000	0.000
44	A	44	ASN	0	0.033	0.022	11.278	-0.590	-0.590	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.859	0.938	14.794	12.331	12.331	0.000	0.000	0.000	0.000
46	A	46	ASN	0	-0.003	-0.006	18.139	0.174	0.174	0.000	0.000	0.000	0.000
47	A	47	THR	0	0.027	-0.013	21.202	0.138	0.138	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.897	-0.904	23.313	-11.214	-11.214	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.013	0.010	23.479	0.225	0.225	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.065	-0.039	20.444	-0.416	-0.416	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.028	-0.026	14.669	0.107	0.107	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.773	-0.846	14.748	-14.823	-14.823	0.000	0.000	0.000	0.000
53	A	53	TYR	0	-0.031	-0.068	10.828	-0.799	-0.799	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.025	0.027	7.309	-0.074	-0.074	0.000	0.000	0.000	0.000
55	A	55	ILE	0	-0.032	-0.025	5.556	0.717	0.717	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.020	-0.016	8.234	0.414	0.414	0.000	0.000	0.000	0.000
57	A	57	GLN	0	-0.017	-0.010	10.181	2.280	2.280	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.012	0.015	12.821	1.192	1.192	0.000	0.000	0.000	0.000
59	A	59	ASN	0	0.009	-0.018	14.873	0.387	0.387	0.000	0.000	0.000	0.000
60	A	60	SER	0	-0.022	-0.045	17.406	0.116	0.116	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.909	0.982	18.760	10.808	10.808	0.000	0.000	0.000	0.000
62	A	62	TRP	0	0.006	-0.021	21.579	0.760	0.760	0.000	0.000	0.000	0.000
63	A	63	TRP	0	-0.049	-0.002	18.094	0.110	0.110	0.000	0.000	0.000	0.000
64	A	64	CYS	0	-0.016	0.005	15.865	-0.386	-0.386	0.000	0.000	0.000	0.000
65	A	65	ASN	0	0.041	0.010	17.970	0.483	0.483	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.759	-0.855	16.716	-13.676	-13.676	0.000	0.000	0.000	0.000
67	A	67	GLY	0	-0.022	-0.009	18.080	0.085	0.085	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.842	0.922	16.587	13.963	13.963	0.000	0.000	0.000	0.000
69	A	69	THR	0	-0.002	0.001	20.481	0.069	0.069	0.000	0.000	0.000	0.000
70	A	70	PRO	0	-0.008	0.006	23.193	0.127	0.127	0.000	0.000	0.000	0.000

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