FMO DATABASE

FMODB ID: 4J87N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-398433.095477
FMO2-HF: Nuclear repulsion	369879.018493
FMO2-HF: Total energy	-28554.076983
FMO2-MP2: Total energy	-28635.325317

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.
-56.195	-44.351	15.926	-12.035	-15.735	-0.126

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 : 0.887 / q_NPA : 0.933

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	-0.055	-0.028	2.994	-21.514	-15.393	1.987	-2.450	-5.658	-0.020
4	A	4	GLY	0	0.065	0.040	3.826	10.460	10.698	0.009	-0.019	-0.229	0.000
5	A	5	ARG	1	0.991	0.981	6.367	22.959	22.959	0.000	0.000	0.000	0.000
6	A	6	CYS	0	-0.018	-0.033	9.199	0.824	0.824	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.787	-0.870	1.984	-119.266	-113.841	5.687	-6.167	-4.945	-0.087
8	A	8	LEU	0	0.032	0.010	5.816	0.113	0.113	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.022	0.014	6.639	2.969	2.969	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.009	0.006	8.770	2.312	2.312	0.000	0.000	0.000	0.000
11	A	11	ALA	0	0.005	0.000	6.253	2.108	2.108	0.000	0.000	0.000	0.000
12	A	12	MET	0	-0.005	0.001	8.393	2.675	2.675	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.976	0.993	10.955	19.974	19.974	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.936	0.976	8.864	28.400	28.400	0.000	0.000	0.000	0.000
15	A	15	HIS	0	-0.108	-0.070	8.825	1.209	1.209	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.026	0.025	13.650	0.880	0.880	0.000	0.000	0.000	0.000
17	A	17	LEU	0	0.021	-0.002	12.650	0.788	0.788	0.000	0.000	0.000	0.000
18	A	18	ASP	-1	-0.930	-0.973	16.254	-15.809	-15.809	0.000	0.000	0.000	0.000
19	A	19	ASN	0	0.012	0.009	17.796	0.805	0.805	0.000	0.000	0.000	0.000
20	A	20	TYR	0	0.000	0.021	19.170	0.950	0.950	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.916	0.940	21.037	11.759	11.759	0.000	0.000	0.000	0.000
22	A	22	GLY	0	0.028	0.019	23.926	0.346	0.346	0.000	0.000	0.000	0.000
23	A	23	TYR	0	-0.027	0.001	20.375	0.197	0.197	0.000	0.000	0.000	0.000
24	A	24	SER	0	0.042	0.024	19.919	-0.700	-0.700	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.015	-0.009	13.102	-0.457	-0.457	0.000	0.000	0.000	0.000
26	A	26	GLY	0	-0.015	-0.011	15.336	-1.110	-1.110	0.000	0.000	0.000	0.000
27	A	27	ASN	0	0.003	0.001	16.727	-0.222	-0.222	0.000	0.000	0.000	0.000
28	A	28	TRP	0	0.071	0.038	13.763	-0.583	-0.583	0.000	0.000	0.000	0.000
29	A	29	VAL	0	-0.010	-0.007	11.105	-1.323	-1.323	0.000	0.000	0.000	0.000
30	A	30	CYS	0	-0.055	-0.023	12.767	-0.822	-0.822	0.000	0.000	0.000	0.000
31	A	31	ALA	0	0.056	0.024	15.392	0.015	0.015	0.000	0.000	0.000	0.000
32	A	32	ALA	0	0.043	0.014	9.891	-0.312	-0.312	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.854	0.934	11.296	22.005	22.005	0.000	0.000	0.000	0.000
34	A	34	PHE	0	-0.027	-0.042	12.376	-0.183	-0.183	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.897	-0.907	13.003	-16.386	-16.386	0.000	0.000	0.000	0.000
36	A	36	SER	0	0.008	-0.011	8.312	-0.912	-0.912	0.000	0.000	0.000	0.000
37	A	37	ASN	0	-0.037	-0.022	8.821	-0.933	-0.933	0.000	0.000	0.000	0.000
38	A	38	PHE	0	-0.079	-0.045	6.293	-1.171	-1.171	0.000	0.000	0.000	0.000
39	A	39	ASN	0	0.046	0.031	3.873	-10.366	-10.105	0.005	-0.090	-0.175	0.000
40	A	40	THR	0	0.009	-0.011	1.951	-2.801	-4.546	7.598	-2.618	-3.235	-0.021
41	A	41	GLN	0	-0.043	-0.031	2.610	1.935	3.435	0.641	-0.688	-1.454	0.002
42	A	42	ALA	0	-0.016	0.019	4.879	2.176	2.220	-0.001	-0.003	-0.039	0.000
43	A	43	THR	0	-0.026	-0.010	7.960	0.461	0.461	0.000	0.000	0.000	0.000
44	A	44	ASN	0	0.036	0.017	11.215	-0.470	-0.470	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.874	0.953	14.777	12.055	12.055	0.000	0.000	0.000	0.000
46	A	46	ASN	0	-0.009	0.004	18.102	0.109	0.109	0.000	0.000	0.000	0.000
47	A	47	THR	0	0.029	-0.013	21.075	0.141	0.141	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.902	-0.916	23.273	-11.075	-11.075	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.002	0.002	23.395	0.203	0.203	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.040	-0.018	20.340	-0.415	-0.415	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.032	-0.030	14.407	0.152	0.152	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.788	-0.872	14.491	-14.727	-14.727	0.000	0.000	0.000	0.000
53	A	53	TYR	0	-0.050	-0.079	10.720	-0.770	-0.770	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.012	0.019	7.241	-0.181	-0.181	0.000	0.000	0.000	0.000
55	A	55	ILE	0	-0.029	-0.026	5.875	0.811	0.811	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.027	-0.021	8.122	0.560	0.560	0.000	0.000	0.000	0.000
57	A	57	GLN	0	-0.005	0.009	10.234	2.116	2.116	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.010	0.016	12.720	1.132	1.132	0.000	0.000	0.000	0.000
59	A	59	ASN	0	0.025	0.002	14.818	0.338	0.338	0.000	0.000	0.000	0.000
60	A	60	SER	0	0.000	-0.033	17.378	0.123	0.123	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.896	0.968	18.731	10.758	10.758	0.000	0.000	0.000	0.000
62	A	62	TRP	0	-0.006	-0.030	21.522	0.699	0.699	0.000	0.000	0.000	0.000
63	A	63	TRP	0	-0.043	0.002	18.120	0.044	0.044	0.000	0.000	0.000	0.000
64	A	64	CYS	0	-0.038	-0.005	14.528	-0.133	-0.133	0.000	0.000	0.000	0.000
65	A	65	ASN	0	0.057	0.014	17.998	0.661	0.661	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.771	-0.869	16.608	-13.681	-13.681	0.000	0.000	0.000	0.000
67	A	67	GLY	0	-0.036	-0.015	18.107	0.091	0.091	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.874	0.938	17.319	13.584	13.584	0.000	0.000	0.000	0.000
69	A	69	THR	0	0.004	0.011	20.474	0.117	0.117	0.000	0.000	0.000	0.000
70	A	70	PRO	0	-0.015	0.003	23.171	0.113	0.113	0.000	0.000	0.000	0.000

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