FMO DATABASE

FMODB ID: K3LQ3

Calculation Name: 4GI3-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GI3

Chain ID: C

ChEMBL ID:

UniProt ID: P85064

Base Structure: X-ray

Registration Date: 2023-06-19

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	53
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-299892.897754
FMO2-HF: Nuclear repulsion	275439.705569
FMO2-HF: Total energy	-24453.192185
FMO2-MP2: Total energy	-24516.961052

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(C:21:CYS)

Summations of interaction energy for fragment #1(C:21:CYS)

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.
-34.189	-26.97	8.264	-2.7	-12.781	-0.018

Interaction energy analysis for fragmet #1(C:21:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.109 / q_NPA : -0.064

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	C	23	SER	0	0.145	0.075	3.865	-1.650	-0.385	-0.011	-0.530	-0.724	0.002
4	C	24	ILE	0	-0.093	-0.036	6.110	0.588	0.588	0.000	0.000	0.000	0.000
5	C	25	CYS	0	-0.128	-0.047	8.190	-1.061	-1.061	0.000	0.000	0.000	0.000
6	C	26	PRO	0	0.003	0.006	10.910	0.274	0.274	0.000	0.000	0.000	0.000
7	C	27	LEU	0	0.019	0.000	14.470	-0.190	-0.190	0.000	0.000	0.000	0.000
8	C	28	ILE	0	-0.018	0.008	15.810	0.164	0.164	0.000	0.000	0.000	0.000
9	C	29	TYR	0	0.004	-0.001	16.438	-0.180	-0.180	0.000	0.000	0.000	0.000
10	C	30	ALA	0	0.001	-0.015	16.405	0.180	0.180	0.000	0.000	0.000	0.000
11	C	31	PRO	0	-0.056	-0.019	15.342	-0.161	-0.161	0.000	0.000	0.000	0.000
12	C	32	VAL	0	-0.008	0.003	11.412	0.187	0.187	0.000	0.000	0.000	0.000
13	C	33	CYS	0	-0.074	0.001	12.976	-0.326	-0.326	0.000	0.000	0.000	0.000
14	C	34	VAL	0	-0.007	-0.003	8.212	-0.003	-0.003	0.000	0.000	0.000	0.000
15	C	35	GLU	-1	-0.901	-0.956	11.335	-0.661	-0.661	0.000	0.000	0.000	0.000
16	C	36	ASP	-1	-0.845	-0.929	8.999	-1.514	-1.514	0.000	0.000	0.000	0.000
17	C	37	SER	0	0.015	-0.014	9.674	0.392	0.392	0.000	0.000	0.000	0.000
18	C	38	ASN	0	-0.136	-0.064	11.431	0.373	0.373	0.000	0.000	0.000	0.000
19	C	39	GLN	0	-0.026	-0.004	13.691	0.032	0.032	0.000	0.000	0.000	0.000
20	C	40	ASP	-1	-0.902	-0.926	13.479	-0.816	-0.816	0.000	0.000	0.000	0.000
21	C	41	PHE	0	-0.006	-0.026	13.035	-0.211	-0.211	0.000	0.000	0.000	0.000
22	C	42	TYR	0	-0.017	-0.010	10.681	-0.015	-0.015	0.000	0.000	0.000	0.000
23	C	43	LEU	0	0.007	0.001	12.259	-0.169	-0.169	0.000	0.000	0.000	0.000
24	C	44	PHE	0	0.046	0.022	7.352	-0.128	-0.128	0.000	0.000	0.000	0.000
25	C	45	VAL	0	0.011	-0.017	12.022	0.314	0.314	0.000	0.000	0.000	0.000
26	C	46	ASN	0	0.001	-0.008	11.456	-0.102	-0.102	0.000	0.000	0.000	0.000
27	C	47	GLU	-1	-0.863	-0.942	10.183	-2.541	-2.541	0.000	0.000	0.000	0.000
28	C	49	GLU	-1	-0.788	-0.911	6.804	-5.783	-5.783	0.000	0.000	0.000	0.000
29	C	50	VAL	0	-0.016	0.014	5.491	-1.488	-1.488	0.000	0.000	0.000	0.000
30	C	51	ARG	1	0.962	0.969	3.994	-1.488	-0.868	0.013	-0.256	-0.376	-0.001
31	C	52	LYS	1	0.831	0.928	2.067	-8.267	-6.821	4.648	-2.493	-3.601	-0.032
32	C	53	CYS	0	-0.014	-0.006	2.747	-4.549	-0.645	0.983	-2.316	-2.570	-0.014
35	C	57	ALA	0	-0.015	-0.009	3.847	0.620	2.766	0.006	-0.820	-1.333	0.001
36	C	58	GLY	0	-0.017	0.012	2.521	-4.490	-2.573	2.258	-1.969	-2.206	0.022
37	C	59	PHE	0	-0.029	-0.010	2.830	-1.803	-4.874	0.381	4.009	-1.319	0.007
38	C	60	VAL	0	0.012	-0.004	3.270	-1.156	-2.297	-0.016	1.661	-0.504	-0.003
39	C	61	TYR	0	-0.009	-0.004	3.765	-0.657	-0.524	0.002	0.014	-0.148	0.000
40	C	62	THR	0	0.019	0.006	7.609	0.395	0.395	0.000	0.000	0.000	0.000
41	C	63	PHE	0	-0.003	-0.004	9.871	-0.217	-0.217	0.000	0.000	0.000	0.000
42	C	64	VAL	0	0.006	0.010	12.547	0.277	0.277	0.000	0.000	0.000	0.000
43	C	65	PRO	0	0.010	-0.002	15.882	-0.098	-0.098	0.000	0.000	0.000	0.000
44	C	66	ARG	1	0.992	0.973	18.097	1.066	1.066	0.000	0.000	0.000	0.000
45	C	67	GLU	-1	-0.932	-0.972	19.110	-0.786	-0.786	0.000	0.000	0.000	0.000
46	C	68	MET	0	-0.023	0.006	17.669	0.073	0.073	0.000	0.000	0.000	0.000
47	C	70	LYS	1	0.978	0.993	18.274	1.034	1.034	0.000	0.000	0.000	0.000
48	C	71	ALA	0	0.013	-0.011	19.333	-0.082	-0.082	0.000	0.000	0.000	0.000
49	C	72	THR	0	-0.051	-0.022	20.009	-0.009	-0.009	0.000	0.000	0.000	0.000
50	C	73	THR	0	-0.008	-0.009	15.224	0.024	0.024	0.000	0.000	0.000	0.000
51	C	74	SER	0	-0.045	-0.016	13.092	0.237	0.237	0.000	0.000	0.000	0.000
52	C	75	LEU	0	-0.004	-0.003	11.776	-0.266	-0.266	0.000	0.000	0.000	0.000
53	C	77	PRO	0	0.009	0.028	7.772	0.448	0.448	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:21:CYS)