FMO DATABASE

FMODB ID: 89QKY

Calculation Name: 3C4S-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C4S

Chain ID: A

ChEMBL ID:

UniProt ID: P74795

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	-306534.530247
FMO2-HF: Nuclear repulsion	284144.986826
FMO2-HF: Total energy	-22389.54342
FMO2-MP2: Total energy	-22455.752871

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:MET)

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

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.
-1.624	0.908	0.405	-0.905	-2.032	0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.012

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	A	3	PHE	0	-0.014	-0.008	3.873	-1.027	0.530	-0.006	-0.637	-0.914	0.002
4	A	4	PRO	0	0.002	-0.021	6.231	0.306	0.306	0.000	0.000	0.000	0.000
5	A	5	GLY	0	0.024	0.018	10.076	-0.024	-0.024	0.000	0.000	0.000	0.000
6	A	6	ALA	0	-0.038	-0.003	6.483	0.106	0.106	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.028	0.005	8.586	0.131	0.131	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.030	-0.022	6.287	-0.111	-0.111	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.763	0.863	7.999	0.234	0.234	0.000	0.000	0.000	0.000
10	A	10	VAL	0	-0.017	0.006	9.097	-0.024	-0.024	0.000	0.000	0.000	0.000
11	A	11	THR	0	0.001	-0.010	8.427	0.021	0.021	0.000	0.000	0.000	0.000
12	A	12	ASN	0	-0.040	-0.039	11.500	0.023	0.023	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.031	-0.001	14.578	-0.012	-0.012	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.905	-0.942	17.752	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	15	ASH	0	-0.103	-0.067	15.944	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	16	THR	0	-0.010	-0.019	18.913	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	17	TYR	0	0.012	0.001	17.102	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	18	TYR	0	0.031	0.030	14.605	-0.013	-0.013	0.000	0.000	0.000	0.000
19	A	19	ARG	1	0.903	0.938	13.718	0.051	0.051	0.000	0.000	0.000	0.000
20	A	20	PHE	0	-0.008	0.017	14.777	0.001	0.001	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.822	-0.905	11.986	-0.150	-0.150	0.000	0.000	0.000	0.000
22	A	22	GLY	0	0.016	0.005	12.295	0.031	0.031	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.005	0.009	11.861	-0.065	-0.065	0.000	0.000	0.000	0.000
24	A	24	VAL	0	-0.005	0.006	7.856	0.085	0.085	0.000	0.000	0.000	0.000
25	A	25	GLN	0	0.001	-0.010	11.283	-0.030	-0.030	0.000	0.000	0.000	0.000
26	A	26	ARG	1	0.903	0.942	11.311	0.306	0.306	0.000	0.000	0.000	0.000
27	A	27	VAL	0	0.002	0.002	5.765	0.053	0.053	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.004	-0.014	9.157	-0.051	-0.051	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.811	-0.879	10.939	-0.100	-0.100	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.027	0.020	9.172	0.031	0.031	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.794	0.884	10.107	0.195	0.195	0.000	0.000	0.000	0.000
32	A	32	ALA	0	0.035	0.010	8.409	-0.073	-0.073	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.019	0.008	10.471	0.049	0.049	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.013	-0.017	11.275	-0.078	-0.078	0.000	0.000	0.000	0.000
35	A	35	LEU	0	0.017	0.019	14.007	0.038	0.038	0.000	0.000	0.000	0.000
36	A	36	PHE	0	-0.021	-0.010	13.886	-0.021	-0.021	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.878	-0.955	18.074	-0.171	-0.171	0.000	0.000	0.000	0.000
38	A	38	ASN	0	-0.043	-0.031	20.788	0.004	0.004	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.034	0.025	23.638	0.008	0.008	0.000	0.000	0.000	0.000
40	A	40	ASN	0	-0.028	-0.022	26.359	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	41	TRP	0	-0.045	-0.004	20.960	0.000	0.000	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.864	-0.944	22.137	-0.135	-0.135	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.886	0.937	20.890	0.116	0.116	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.023	0.036	17.552	-0.016	-0.016	0.000	0.000	0.000	0.000
45	A	45	VAL	0	-0.042	-0.019	17.105	0.025	0.025	0.000	0.000	0.000	0.000
46	A	46	THR	0	-0.048	-0.040	14.224	-0.033	-0.033	0.000	0.000	0.000	0.000
47	A	47	PHE	0	0.025	0.027	12.350	0.014	0.014	0.000	0.000	0.000	0.000
48	A	48	ARG	1	0.941	0.940	12.116	-0.024	-0.024	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.022	-0.002	5.448	-0.066	-0.066	0.000	0.000	0.000	0.000
50	A	50	SER	0	0.003	0.003	7.513	0.024	0.024	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.830	-0.857	9.337	-0.056	-0.056	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.008	0.002	7.587	-0.055	-0.055	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.850	-0.901	4.473	-0.369	-0.244	-0.001	-0.008	-0.116	0.000
54	A	54	ALA	0	-0.005	-0.008	2.634	-0.674	0.036	0.413	-0.252	-0.870	-0.001
55	A	55	VAL	0	-0.023	-0.006	4.228	0.115	0.255	-0.001	-0.008	-0.132	0.000
56	A	56	LYS	1	0.950	0.965	7.440	-0.200	-0.200	0.000	0.000	0.000	0.000
57	A	57	PRO	0	0.035	0.031	10.340	0.004	0.004	0.000	0.000	0.000	0.000

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