FMO DATABASE

FMODB ID: R5GY8

Calculation Name: 3T5V-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3T5V

Chain ID: C

ChEMBL ID:

UniProt ID: P46674

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	56
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-217678.882333
FMO2-HF: Nuclear repulsion	193755.846131
FMO2-HF: Total energy	-23923.036202
FMO2-MP2: Total energy	-23993.495083

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:23:GLU)

Summations of interaction energy for fragment #1(C:23:GLU)

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.
103.079	105.586	-0.031	-1.374	-1.102	0.004

Interaction energy analysis for fragmet #1(C:23:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.955 / q_NPA : -0.973

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	25	ASN	0	-0.021	-0.016	3.793	-3.855	-1.348	-0.031	-1.374	-1.102	0.004
4	C	26	LYS	1	0.926	0.970	6.533	-26.899	-26.899	0.000	0.000	0.000	0.000
5	C	27	LYS	1	0.970	0.977	9.450	-16.956	-16.956	0.000	0.000	0.000	0.000
6	C	28	SER	0	-0.002	-0.002	11.193	0.771	0.771	0.000	0.000	0.000	0.000
7	C	29	LEU	0	-0.056	-0.038	13.260	-0.716	-0.716	0.000	0.000	0.000	0.000
8	C	30	GLU	-1	-0.898	-0.929	16.235	16.643	16.643	0.000	0.000	0.000	0.000
9	C	31	GLU	-1	-1.012	-1.012	17.840	15.849	15.849	0.000	0.000	0.000	0.000
10	C	32	ASP	-1	-0.943	-0.974	20.337	12.111	12.111	0.000	0.000	0.000	0.000
11	C	33	ASP	-1	-0.882	-0.939	22.115	12.414	12.414	0.000	0.000	0.000	0.000
12	C	34	GLU	-1	-1.098	-1.025	24.058	10.545	10.545	0.000	0.000	0.000	0.000
13	C	35	PHE	0	-0.057	-0.037	26.466	-0.193	-0.193	0.000	0.000	0.000	0.000
14	C	36	GLU	-1	-0.902	-0.953	29.031	10.485	10.485	0.000	0.000	0.000	0.000
15	C	37	ASP	-1	-0.921	-0.966	31.005	8.756	8.756	0.000	0.000	0.000	0.000
16	C	38	PHE	0	-0.060	-0.032	34.281	-0.164	-0.164	0.000	0.000	0.000	0.000
17	C	39	PRO	0	-0.050	-0.038	37.275	-0.170	-0.170	0.000	0.000	0.000	0.000
18	C	40	ILE	0	-0.060	-0.015	40.287	-0.148	-0.148	0.000	0.000	0.000	0.000
19	C	41	ASP	-1	-0.973	-0.972	42.915	6.413	6.413	0.000	0.000	0.000	0.000
20	C	53	ALA	0	0.000	-0.014	49.519	-0.010	-0.010	0.000	0.000	0.000	0.000
21	C	54	VAL	0	0.000	0.003	48.658	-0.038	-0.038	0.000	0.000	0.000	0.000
22	C	55	THR	0	0.046	-0.002	44.643	0.102	0.102	0.000	0.000	0.000	0.000
23	C	56	GLN	0	-0.072	-0.008	45.689	0.055	0.055	0.000	0.000	0.000	0.000
24	C	57	THR	0	-0.001	-0.008	43.037	-0.107	-0.107	0.000	0.000	0.000	0.000
25	C	58	ASN	0	-0.086	-0.045	43.487	0.098	0.098	0.000	0.000	0.000	0.000
26	C	59	ILE	0	0.014	0.001	37.205	0.010	0.010	0.000	0.000	0.000	0.000
27	C	60	TRP	0	-0.033	-0.014	34.608	0.257	0.257	0.000	0.000	0.000	0.000
28	C	61	GLU	-1	-0.928	-0.963	38.782	7.392	7.392	0.000	0.000	0.000	0.000
29	C	62	GLU	-1	-0.925	-0.961	41.391	6.742	6.742	0.000	0.000	0.000	0.000
30	C	63	ASN	0	-0.030	-0.027	44.322	0.055	0.055	0.000	0.000	0.000	0.000
31	C	64	TRP	0	0.044	0.027	38.035	0.021	0.021	0.000	0.000	0.000	0.000
32	C	65	ASP	-1	-1.004	-1.010	41.553	7.106	7.106	0.000	0.000	0.000	0.000
33	C	66	ASP	-1	-0.971	-0.974	42.901	6.223	6.223	0.000	0.000	0.000	0.000
34	C	67	VAL	0	-0.032	-0.002	43.246	-0.084	-0.084	0.000	0.000	0.000	0.000
35	C	68	GLU	-1	-0.959	-0.966	43.792	6.571	6.571	0.000	0.000	0.000	0.000
36	C	69	VAL	0	-0.063	-0.049	40.731	-0.095	-0.095	0.000	0.000	0.000	0.000
37	C	70	ASP	-1	-0.995	-0.992	42.376	7.171	7.171	0.000	0.000	0.000	0.000
38	C	71	ASP	-1	-0.779	-0.914	36.978	8.480	8.480	0.000	0.000	0.000	0.000
39	C	72	ASP	-1	-0.917	-0.947	36.358	8.020	8.020	0.000	0.000	0.000	0.000
40	C	73	PHE	0	-0.006	-0.007	34.612	-0.098	-0.098	0.000	0.000	0.000	0.000
41	C	74	THR	0	0.024	0.006	36.910	-0.164	-0.164	0.000	0.000	0.000	0.000
42	C	75	ASN	0	-0.021	-0.012	40.057	-0.316	-0.316	0.000	0.000	0.000	0.000
43	C	76	GLU	-1	-0.955	-0.968	36.282	8.318	8.318	0.000	0.000	0.000	0.000
44	C	77	LEU	0	-0.030	-0.016	37.455	-0.148	-0.148	0.000	0.000	0.000	0.000
45	C	78	LYS	1	0.944	0.967	40.957	-6.957	-6.957	0.000	0.000	0.000	0.000
46	C	79	ALA	0	0.022	0.023	42.875	-0.161	-0.161	0.000	0.000	0.000	0.000
47	C	80	GLU	-1	-0.937	-0.974	41.105	7.205	7.205	0.000	0.000	0.000	0.000
48	C	81	LEU	0	-0.029	-0.017	43.549	-0.146	-0.146	0.000	0.000	0.000	0.000
49	C	82	ASP	-1	-0.941	-0.972	46.142	6.115	6.115	0.000	0.000	0.000	0.000
50	C	83	ARG	1	0.820	0.916	42.221	-7.390	-7.390	0.000	0.000	0.000	0.000
51	C	84	TYR	0	0.070	0.039	46.095	-0.174	-0.174	0.000	0.000	0.000	0.000
52	C	85	LYS	1	0.945	0.965	47.999	-5.887	-5.887	0.000	0.000	0.000	0.000
53	C	86	ARG	1	0.897	0.929	50.087	-6.236	-6.236	0.000	0.000	0.000	0.000
54	C	87	GLU	-1	-1.022	-0.991	47.721	6.441	6.441	0.000	0.000	0.000	0.000
55	C	88	ASN	0	-0.049	-0.004	49.628	-0.111	-0.111	0.000	0.000	0.000	0.000
56	C	89	GLN	0	-0.040	-0.020	53.614	-0.067	-0.067	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:23:GLU)