FMO DATABASE

FMODB ID: 94Z52

Calculation Name: 5MJ0-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5MJ0

Chain ID: B

ChEMBL ID:

UniProt ID: Q01151

Base Structure: X-ray

Registration Date: 2023-09-19

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	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	78
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-466785.800123
FMO2-HF: Nuclear repulsion	436265.385197
FMO2-HF: Total energy	-30520.414926
FMO2-MP2: Total energy	-30609.467916

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(B:19:GLY)

Summations of interaction energy for fragment #1(B:19:GLY)

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.
-1.147	-0.182	-0.007	-0.445	-0.513	0.001

Interaction energy analysis for fragmet #1(B:19:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / q_NPA : 0.010

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

Sort

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	B	21	PRO	0	0.017	0.024	3.861	-0.374	0.591	-0.007	-0.445	-0.513	0.001
4	B	22	GLU	-1	-0.827	-0.913	6.434	0.549	0.549	0.000	0.000	0.000	0.000
5	B	23	VAL	0	0.010	0.008	9.409	-0.092	-0.092	0.000	0.000	0.000	0.000
6	B	24	LYS	1	0.874	0.931	11.579	0.268	0.268	0.000	0.000	0.000	0.000
7	B	25	VAL	0	0.046	0.029	15.875	-0.021	-0.021	0.000	0.000	0.000	0.000
8	B	26	ALA	0	0.054	0.044	19.494	0.019	0.019	0.000	0.000	0.000	0.000
9	B	27	SER	0	0.002	-0.015	23.025	0.001	0.001	0.000	0.000	0.000	0.000
10	B	28	SER	0	-0.077	-0.050	25.044	-0.001	-0.001	0.000	0.000	0.000	0.000
11	B	29	GLU	-1	-0.888	-0.923	23.628	-0.100	-0.100	0.000	0.000	0.000	0.000
12	B	30	ASP	-1	-0.796	-0.886	24.399	-0.075	-0.075	0.000	0.000	0.000	0.000
13	B	31	VAL	0	-0.044	-0.035	17.832	-0.016	-0.016	0.000	0.000	0.000	0.000
14	B	32	ASP	-1	-0.804	-0.893	19.337	-0.142	-0.142	0.000	0.000	0.000	0.000
15	B	33	LEU	0	-0.029	-0.010	14.361	-0.047	-0.047	0.000	0.000	0.000	0.000
16	B	34	PRO	0	0.007	0.007	12.137	0.030	0.030	0.000	0.000	0.000	0.000
17	B	35	CYS	0	0.012	0.038	12.643	-0.058	-0.058	0.000	0.000	0.000	0.000
18	B	36	THR	0	-0.016	-0.041	8.066	0.047	0.047	0.000	0.000	0.000	0.000
19	B	37	ALA	0	0.006	0.007	8.997	-0.109	-0.109	0.000	0.000	0.000	0.000
20	B	38	PRO	0	-0.017	-0.010	9.335	-0.027	-0.027	0.000	0.000	0.000	0.000
21	B	39	TRP	0	-0.047	-0.029	11.672	0.047	0.047	0.000	0.000	0.000	0.000
22	B	40	ASP	-1	-0.851	-0.912	15.376	-0.162	-0.162	0.000	0.000	0.000	0.000
23	B	41	PRO	0	-0.038	-0.029	18.437	0.003	0.003	0.000	0.000	0.000	0.000
24	B	42	GLN	0	-0.019	-0.027	20.945	0.009	0.009	0.000	0.000	0.000	0.000
25	B	43	VAL	0	0.026	0.031	21.130	0.014	0.014	0.000	0.000	0.000	0.000
26	B	44	PRO	0	-0.029	-0.012	22.833	-0.011	-0.011	0.000	0.000	0.000	0.000
27	B	45	TYR	0	0.029	0.006	18.500	0.001	0.001	0.000	0.000	0.000	0.000
28	B	46	THR	0	-0.006	0.007	22.390	-0.004	-0.004	0.000	0.000	0.000	0.000
29	B	47	VAL	0	-0.015	-0.016	18.378	-0.002	-0.002	0.000	0.000	0.000	0.000
30	B	48	SER	0	-0.025	0.000	19.285	0.019	0.019	0.000	0.000	0.000	0.000
31	B	49	TRP	0	-0.001	-0.024	13.961	-0.012	-0.012	0.000	0.000	0.000	0.000
32	B	50	VAL	0	-0.003	0.008	16.188	0.017	0.017	0.000	0.000	0.000	0.000
33	B	51	LYS	1	0.863	0.930	16.344	-0.082	-0.082	0.000	0.000	0.000	0.000
34	B	52	LEU	0	-0.065	-0.037	12.188	0.026	0.026	0.000	0.000	0.000	0.000
35	B	53	LEU	0	0.020	0.014	16.232	0.012	0.012	0.000	0.000	0.000	0.000
36	B	87	GLU	-1	-0.827	-0.905	24.043	-0.140	-0.140	0.000	0.000	0.000	0.000
37	B	88	ARG	1	0.913	0.967	14.823	0.338	0.338	0.000	0.000	0.000	0.000
38	B	89	PRO	0	0.025	0.004	20.706	-0.001	-0.001	0.000	0.000	0.000	0.000
39	B	90	TYR	0	0.016	-0.002	17.830	-0.021	-0.021	0.000	0.000	0.000	0.000
40	B	91	SER	0	-0.023	-0.014	17.497	-0.024	-0.024	0.000	0.000	0.000	0.000
41	B	92	LEU	0	-0.033	0.003	17.684	0.029	0.029	0.000	0.000	0.000	0.000
42	B	93	LYS	1	0.823	0.885	19.462	0.129	0.129	0.000	0.000	0.000	0.000
43	B	94	ILE	0	-0.058	-0.028	19.239	0.021	0.021	0.000	0.000	0.000	0.000
44	B	95	ARG	1	0.896	0.927	22.941	0.073	0.073	0.000	0.000	0.000	0.000
45	B	96	ASN	0	-0.015	-0.005	25.981	0.008	0.008	0.000	0.000	0.000	0.000
46	B	97	THR	0	-0.050	-0.009	21.453	0.012	0.012	0.000	0.000	0.000	0.000
47	B	98	THR	0	0.065	0.021	23.907	0.008	0.008	0.000	0.000	0.000	0.000
48	B	99	SER	0	0.058	0.007	22.185	-0.004	-0.004	0.000	0.000	0.000	0.000
49	B	100	SER	0	-0.012	0.004	21.341	0.011	0.011	0.000	0.000	0.000	0.000
50	B	101	ASN	0	0.058	0.035	20.913	0.014	0.014	0.000	0.000	0.000	0.000
51	B	102	SER	0	0.040	0.046	17.217	-0.019	-0.019	0.000	0.000	0.000	0.000
52	B	103	GLY	0	0.003	0.007	15.381	0.024	0.024	0.000	0.000	0.000	0.000
53	B	104	THR	0	-0.022	-0.011	10.735	0.045	0.045	0.000	0.000	0.000	0.000
54	B	105	TYR	0	-0.011	-0.022	12.391	0.014	0.014	0.000	0.000	0.000	0.000
55	B	106	ARG	1	0.937	0.965	11.681	-0.251	-0.251	0.000	0.000	0.000	0.000
56	B	108	THR	0	0.002	-0.007	13.549	0.013	0.013	0.000	0.000	0.000	0.000
57	B	109	LEU	0	0.003	0.011	15.681	0.002	0.002	0.000	0.000	0.000	0.000
58	B	110	GLN	0	0.047	0.025	17.996	0.012	0.012	0.000	0.000	0.000	0.000
59	B	111	ASP	-1	-0.808	-0.905	20.959	-0.061	-0.061	0.000	0.000	0.000	0.000
60	B	112	PRO	0	0.006	-0.005	22.606	0.011	0.011	0.000	0.000	0.000	0.000
61	B	113	ASP	-1	-0.804	-0.883	24.866	-0.008	-0.008	0.000	0.000	0.000	0.000
62	B	114	GLY	0	-0.043	-0.021	25.470	0.006	0.006	0.000	0.000	0.000	0.000
63	B	115	GLN	0	-0.072	-0.036	24.694	0.012	0.012	0.000	0.000	0.000	0.000
64	B	116	ARG	1	0.786	0.876	19.187	0.038	0.038	0.000	0.000	0.000	0.000
65	B	117	ASN	0	-0.052	-0.032	17.325	0.002	0.002	0.000	0.000	0.000	0.000
66	B	118	LEU	0	0.032	0.041	13.669	0.009	0.009	0.000	0.000	0.000	0.000
67	B	119	SER	0	-0.062	-0.072	12.155	0.024	0.024	0.000	0.000	0.000	0.000
68	B	120	GLY	0	0.052	0.029	8.551	-0.039	-0.039	0.000	0.000	0.000	0.000
69	B	121	LYS	1	0.883	0.941	6.834	-0.879	-0.879	0.000	0.000	0.000	0.000
70	B	122	VAL	0	0.043	0.040	7.873	-0.398	-0.398	0.000	0.000	0.000	0.000
71	B	123	ILE	0	-0.055	-0.021	7.885	0.249	0.249	0.000	0.000	0.000	0.000
72	B	124	LEU	0	0.042	0.038	10.999	-0.101	-0.101	0.000	0.000	0.000	0.000
73	B	125	ARG	1	0.807	0.868	11.155	-0.020	-0.020	0.000	0.000	0.000	0.000
74	B	126	VAL	0	0.044	0.027	15.894	-0.029	-0.029	0.000	0.000	0.000	0.000
75	B	127	THR	0	-0.076	-0.043	18.679	0.016	0.016	0.000	0.000	0.000	0.000
76	B	128	GLY	0	0.052	0.010	21.485	-0.006	-0.006	0.000	0.000	0.000	0.000
77	B	129	SER	0	0.022	0.015	25.121	0.002	0.002	0.000	0.000	0.000	0.000
78	B	130	PRO	0	-0.016	0.009	28.041	0.005	0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:19:GLY)