FMO DATABASE

FMODB ID: 435ZN

Calculation Name: 3K5B-G-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K5B

Chain ID: G

ChEMBL ID:

UniProt ID: P74901

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	OptHSide
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	100
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-465686.852978
FMO2-HF: Nuclear repulsion	426599.239517
FMO2-HF: Total energy	-39087.613461
FMO2-MP2: Total energy	-39203.469725

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(G:21:GLY)

Summations of interaction energy for fragment #1(G:21: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.
0.501	1.564	-0.016	-0.497	-0.55	0

Interaction energy analysis for fragmet #1(G:21:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : 0.006

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].
3	G	23	ILE	0	0.050	0.033	3.815	0.648	1.711	-0.016	-0.497	-0.550
4	G	24	LYS	1	0.970	0.981	6.538	-0.123	-0.123	0.000	0.000	0.000
5	G	25	SER	0	0.001	0.007	6.680	0.064	0.064	0.000	0.000	0.000
6	G	26	LEU	0	0.049	0.012	8.823	-0.073	-0.073	0.000	0.000	0.000
7	G	27	ALA	0	0.029	0.025	10.351	-0.075	-0.075	0.000	0.000	0.000
8	G	28	GLU	-1	-0.847	-0.928	12.258	0.135	0.135	0.000	0.000	0.000
9	G	29	LYS	1	0.866	0.939	13.627	-0.069	-0.069	0.000	0.000	0.000
10	G	30	GLU	-1	-0.879	-0.941	14.919	0.318	0.318	0.000	0.000	0.000
11	G	31	LYS	1	0.858	0.900	14.748	-0.262	-0.262	0.000	0.000	0.000
12	G	32	GLN	0	0.034	0.044	17.589	-0.036	-0.036	0.000	0.000	0.000
13	G	33	LEU	0	-0.032	-0.020	18.020	-0.017	-0.017	0.000	0.000	0.000
14	G	34	LEU	0	0.019	0.013	20.812	-0.011	-0.011	0.000	0.000	0.000
15	G	35	GLU	-1	-0.890	-0.947	22.536	0.074	0.074	0.000	0.000	0.000
16	G	36	ARG	1	0.912	0.948	23.906	-0.034	-0.034	0.000	0.000	0.000
17	G	37	LEU	0	-0.016	-0.011	24.105	-0.008	-0.008	0.000	0.000	0.000
18	G	38	GLU	-1	-0.847	-0.913	27.031	0.073	0.073	0.000	0.000	0.000
19	G	39	ALA	0	-0.036	-0.017	28.750	-0.005	-0.005	0.000	0.000	0.000
20	G	40	ALA	0	-0.009	-0.003	30.001	-0.005	-0.005	0.000	0.000	0.000
21	G	41	LYS	1	0.942	0.969	30.945	-0.069	-0.069	0.000	0.000	0.000
22	G	42	LYS	1	0.921	0.956	30.270	-0.061	-0.061	0.000	0.000	0.000
23	G	43	GLU	-1	-0.864	-0.902	34.925	0.016	0.016	0.000	0.000	0.000
24	G	44	ALA	0	-0.017	-0.004	35.923	-0.003	-0.003	0.000	0.000	0.000
25	G	45	GLU	-1	-0.868	-0.949	37.493	0.036	0.036	0.000	0.000	0.000
26	G	46	GLU	-1	-0.871	-0.936	38.947	0.026	0.026	0.000	0.000	0.000
27	G	47	ARG	1	0.785	0.895	40.728	-0.021	-0.021	0.000	0.000	0.000
28	G	48	VAL	0	0.022	0.006	41.749	-0.002	-0.002	0.000	0.000	0.000
29	G	49	LYS	1	0.905	0.952	41.753	-0.032	-0.032	0.000	0.000	0.000
30	G	50	ARG	1	0.776	0.861	40.938	-0.020	-0.020	0.000	0.000	0.000
31	G	51	ALA	0	0.024	0.026	46.778	-0.001	-0.001	0.000	0.000	0.000
32	G	52	GLU	-1	-0.925	-0.961	47.294	0.028	0.028	0.000	0.000	0.000
33	G	53	ALA	0	-0.075	-0.044	49.422	-0.001	-0.001	0.000	0.000	0.000
34	G	54	GLU	-1	-0.841	-0.926	49.355	0.014	0.014	0.000	0.000	0.000
35	G	55	ALA	0	0.007	0.015	52.679	-0.001	-0.001	0.000	0.000	0.000
36	G	56	LYS	1	0.809	0.889	54.193	-0.017	-0.017	0.000	0.000	0.000
37	G	57	ALA	0	0.009	-0.003	55.561	-0.001	-0.001	0.000	0.000	0.000
38	G	58	LEU	0	-0.002	0.014	57.112	-0.001	-0.001	0.000	0.000	0.000
39	G	59	LEU	0	-0.007	-0.020	58.261	-0.001	-0.001	0.000	0.000	0.000
40	G	60	GLU	-1	-0.816	-0.884	59.023	0.015	0.015	0.000	0.000	0.000
41	G	61	GLU	-1	-0.911	-0.948	61.692	0.009	0.009	0.000	0.000	0.000
42	G	62	ALA	0	-0.061	-0.039	63.035	-0.001	-0.001	0.000	0.000	0.000
43	G	63	GLU	-1	-0.865	-0.931	64.853	0.012	0.012	0.000	0.000	0.000
44	G	64	ALA	0	-0.012	0.002	66.339	-0.001	-0.001	0.000	0.000	0.000
45	G	65	LYS	1	0.959	0.991	67.752	-0.008	-0.008	0.000	0.000	0.000
46	G	66	ALA	0	0.039	0.016	69.288	0.000	0.000	0.000	0.000	0.000
47	G	67	LYS	1	0.901	0.931	68.926	-0.012	-0.012	0.000	0.000	0.000
48	G	68	ALA	0	-0.003	0.003	72.108	0.000	0.000	0.000	0.000	0.000
49	G	69	LEU	0	-0.074	-0.036	72.748	-0.001	-0.001	0.000	0.000	0.000
50	G	70	GLU	-1	-0.790	-0.888	75.310	0.009	0.009	0.000	0.000	0.000
51	G	71	ALA	0	-0.056	-0.004	76.824	0.000	0.000	0.000	0.000	0.000
52	G	72	GLN	0	0.009	0.007	76.358	0.000	0.000	0.000	0.000	0.000
53	G	73	TYR	0	-0.004	-0.009	78.529	0.000	0.000	0.000	0.000	0.000
54	G	74	ARG	1	0.867	0.901	77.074	-0.009	-0.009	0.000	0.000	0.000
55	G	75	GLU	-1	-0.885	-0.945	83.004	0.005	0.005	0.000	0.000	0.000
56	G	76	ARG	1	0.854	0.942	80.331	-0.007	-0.007	0.000	0.000	0.000
57	G	77	GLU	-1	-0.869	-0.937	85.841	0.007	0.007	0.000	0.000	0.000
58	G	78	ARG	1	0.788	0.921	87.602	-0.005	-0.005	0.000	0.000	0.000
59	G	79	ALA	0	0.011	0.008	88.920	0.000	0.000	0.000	0.000	0.000
60	G	80	GLU	-1	-0.934	-0.964	88.627	0.006	0.006	0.000	0.000	0.000
61	G	81	THR	0	-0.129	-0.098	91.053	0.000	0.000	0.000	0.000	0.000
62	G	82	GLU	-1	-0.803	-0.885	93.459	0.005	0.005	0.000	0.000	0.000
63	G	83	ALA	0	0.026	0.007	94.871	0.000	0.000	0.000	0.000	0.000
64	G	84	LEU	0	-0.009	-0.009	95.019	0.000	0.000	0.000	0.000	0.000
65	G	85	LEU	0	0.002	-0.009	96.839	0.000	0.000	0.000	0.000	0.000
66	G	86	ALA	0	-0.011	-0.010	99.095	0.000	0.000	0.000	0.000	0.000
67	G	87	ARG	1	1.006	1.002	99.384	-0.004	-0.004	0.000	0.000	0.000
68	G	88	TYR	0	0.004	-0.002	99.343	0.000	0.000	0.000	0.000	0.000
69	G	89	ARG	1	0.905	0.960	101.520	-0.005	-0.005	0.000	0.000	0.000
70	G	90	GLU	-1	-0.876	-0.927	105.137	0.004	0.004	0.000	0.000	0.000
71	G	91	ARG	1	0.777	0.860	104.996	-0.005	-0.005	0.000	0.000	0.000
72	G	92	ALA	0	-0.008	-0.013	107.300	0.000	0.000	0.000	0.000	0.000
73	G	93	GLU	-1	-0.939	-0.974	109.041	0.004	0.004	0.000	0.000	0.000
74	G	94	ALA	0	0.019	0.015	111.085	0.000	0.000	0.000	0.000	0.000
75	G	95	GLU	-1	-0.827	-0.899	109.702	0.004	0.004	0.000	0.000	0.000
76	G	96	ALA	0	-0.036	-0.012	113.345	0.000	0.000	0.000	0.000	0.000
77	G	97	LYS	1	0.832	0.881	115.112	-0.003	-0.003	0.000	0.000	0.000
78	G	98	ALA	0	0.016	0.019	115.833	0.000	0.000	0.000	0.000	0.000
79	G	99	VAL	0	-0.015	-0.007	116.430	0.000	0.000	0.000	0.000	0.000
80	G	100	ARG	1	0.945	0.977	116.067	-0.004	-0.004	0.000	0.000	0.000
81	G	101	GLU	-1	-0.796	-0.888	120.850	0.003	0.003	0.000	0.000	0.000
82	G	102	LYS	1	0.867	0.929	118.200	-0.004	-0.004	0.000	0.000	0.000
83	G	103	ALA	0	0.002	0.006	123.578	0.000	0.000	0.000	0.000	0.000
84	G	104	MET	0	-0.037	-0.015	125.372	0.000	0.000	0.000	0.000	0.000
85	G	105	ALA	0	-0.007	0.007	127.490	0.000	0.000	0.000	0.000	0.000
86	G	106	ARG	1	0.791	0.891	128.590	-0.003	-0.003	0.000	0.000	0.000
87	G	107	LEU	0	0.045	0.031	128.223	0.000	0.000	0.000	0.000	0.000
88	G	108	ASP	-1	-0.863	-0.941	130.985	0.003	0.003	0.000	0.000	0.000
89	G	109	GLU	-1	-0.798	-0.894	132.867	0.003	0.003	0.000	0.000	0.000
90	G	110	ALA	0	-0.007	0.002	130.384	0.000	0.000	0.000	0.000	0.000
91	G	111	VAL	0	0.014	-0.002	132.426	0.000	0.000	0.000	0.000	0.000
92	G	112	ALA	0	-0.050	-0.027	134.700	0.000	0.000	0.000	0.000	0.000
93	G	113	LEU	0	-0.016	-0.011	132.184	0.000	0.000	0.000	0.000	0.000
94	G	114	VAL	0	0.026	0.017	132.423	0.000	0.000	0.000	0.000	0.000
95	G	115	LEU	0	0.017	0.011	135.511	0.000	0.000	0.000	0.000	0.000
96	G	116	LYS	1	0.898	0.931	138.935	-0.003	-0.003	0.000	0.000	0.000
97	G	117	GLU	-1	-0.899	-0.948	136.316	0.004	0.004	0.000	0.000	0.000
98	G	118	VAL	0	-0.101	-0.047	137.246	0.000	0.000	0.000	0.000	0.000
99	G	119	LEU	0	-0.065	-0.030	139.890	0.000	0.000	0.000	0.000	0.000
100	G	120	PRO	0	-0.038	0.012	141.759	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(G:21:GLY)