FMO DATABASE

FMODB ID: 7GKMK

Calculation Name: 3D33-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D33

Chain ID: A

ChEMBL ID:

UniProt ID: A6KX32

Base Structure: X-ray

Registration Date: 2023-03-14

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	94
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-666341.172578
FMO2-HF: Nuclear repulsion	629350.662046
FMO2-HF: Total energy	-36990.510532
FMO2-MP2: Total energy	-37097.958961

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:34:PRO)

Summations of interaction energy for fragment #1(A:34:PRO)

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.
-3.406	-1.742	0.02	-0.866	-0.819	0

Interaction energy analysis for fragmet #1(A:34:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / q_NPA : -0.028

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	A	36	LYS	1	0.881	0.948	3.447	-0.543	1.121	0.020	-0.866	-0.819
4	A	37	ASP	-1	-0.843	-0.938	5.803	-0.436	-0.436	0.000	0.000	0.000
5	A	38	VAL	0	-0.115	-0.062	7.719	-0.030	-0.030	0.000	0.000	0.000
6	A	39	GLU	-1	-0.885	-0.931	11.409	-0.521	-0.521	0.000	0.000	0.000
7	A	40	LEU	0	-0.062	-0.034	13.258	0.043	0.043	0.000	0.000	0.000
8	A	41	ASP	-1	-0.870	-0.915	16.864	-0.333	-0.333	0.000	0.000	0.000
9	A	42	GLY	0	-0.039	-0.033	20.163	0.008	0.008	0.000	0.000	0.000
10	A	43	ARG	1	0.740	0.827	23.412	0.145	0.145	0.000	0.000	0.000
11	A	44	TRP	0	0.026	-0.006	23.369	-0.008	-0.008	0.000	0.000	0.000
12	A	45	ASP	-1	-0.803	-0.854	25.338	-0.128	-0.128	0.000	0.000	0.000
13	A	46	ASP	-1	-0.923	-0.948	27.095	-0.094	-0.094	0.000	0.000	0.000
14	A	54	ASN	0	0.014	-0.003	15.574	-0.016	-0.016	0.000	0.000	0.000
15	A	55	CYS	0	-0.023	0.004	17.760	0.029	0.029	0.000	0.000	0.000
16	A	56	PRO	0	0.027	0.021	17.830	-0.012	-0.012	0.000	0.000	0.000
17	A	57	ILE	0	0.006	0.008	17.355	0.001	0.001	0.000	0.000	0.000
18	A	58	THR	0	-0.006	-0.007	12.208	-0.026	-0.026	0.000	0.000	0.000
19	A	59	VAL	0	0.025	-0.005	12.472	0.059	0.059	0.000	0.000	0.000
20	A	60	PHE	0	-0.013	0.005	7.569	-0.056	-0.056	0.000	0.000	0.000
21	A	61	THR	0	-0.011	-0.015	8.584	0.351	0.351	0.000	0.000	0.000
22	A	62	ASP	-1	-0.911	-0.957	6.511	-1.185	-1.185	0.000	0.000	0.000
23	A	63	GLY	0	0.015	0.003	7.672	0.369	0.369	0.000	0.000	0.000
24	A	64	TYR	0	-0.064	-0.041	9.616	-0.047	-0.047	0.000	0.000	0.000
25	A	65	LEU	0	-0.020	-0.011	11.782	0.102	0.102	0.000	0.000	0.000
26	A	66	LEU	0	0.030	0.026	11.480	-0.135	-0.135	0.000	0.000	0.000
27	A	67	THR	0	-0.032	-0.026	11.522	0.180	0.180	0.000	0.000	0.000
28	A	68	LEU	0	0.033	0.028	12.931	-0.092	-0.092	0.000	0.000	0.000
29	A	69	LYS	1	0.897	0.936	11.878	0.154	0.154	0.000	0.000	0.000
30	A	70	ASN	0	0.079	0.043	15.969	-0.034	-0.034	0.000	0.000	0.000
31	A	71	ALA	0	-0.036	-0.021	17.293	0.028	0.028	0.000	0.000	0.000
32	A	72	SER	0	-0.066	-0.052	19.086	0.022	0.022	0.000	0.000	0.000
33	A	73	PRO	0	-0.029	-0.015	22.161	-0.008	-0.008	0.000	0.000	0.000
34	A	74	ASP	-1	-0.803	-0.868	24.622	-0.115	-0.115	0.000	0.000	0.000
35	A	75	ARG	1	0.774	0.862	26.786	0.131	0.131	0.000	0.000	0.000
36	A	76	ASP	-1	-0.861	-0.919	27.414	-0.092	-0.092	0.000	0.000	0.000
37	A	77	MET	0	-0.052	-0.031	21.532	-0.009	-0.009	0.000	0.000	0.000
38	A	78	THR	0	-0.045	-0.026	26.214	0.010	0.010	0.000	0.000	0.000
39	A	79	ILE	0	-0.032	-0.002	19.836	-0.019	-0.019	0.000	0.000	0.000
40	A	80	ARG	1	0.860	0.903	22.879	0.194	0.194	0.000	0.000	0.000
41	A	81	ILE	0	-0.005	0.001	19.055	-0.030	-0.030	0.000	0.000	0.000
42	A	82	THR	0	-0.047	-0.029	22.512	0.035	0.035	0.000	0.000	0.000
43	A	83	ASP	-1	-0.755	-0.873	23.149	-0.252	-0.252	0.000	0.000	0.000
44	A	84	MET	0	0.010	-0.002	21.724	0.026	0.026	0.000	0.000	0.000
45	A	85	ALA	0	-0.024	0.006	24.849	0.012	0.012	0.000	0.000	0.000
46	A	86	LYS	1	0.797	0.880	27.664	0.183	0.183	0.000	0.000	0.000
47	A	87	GLY	0	0.019	0.029	28.138	0.013	0.013	0.000	0.000	0.000
48	A	88	GLY	0	-0.036	-0.017	28.626	0.011	0.011	0.000	0.000	0.000
49	A	89	VAL	0	-0.009	-0.014	26.703	-0.020	-0.020	0.000	0.000	0.000
50	A	90	VAL	0	-0.028	-0.007	22.799	0.016	0.016	0.000	0.000	0.000
51	A	91	TYR	0	-0.012	-0.017	22.961	0.004	0.004	0.000	0.000	0.000
52	A	92	GLU	-1	-0.858	-0.916	25.007	-0.168	-0.168	0.000	0.000	0.000
53	A	93	ASN	0	-0.032	-0.014	24.287	0.024	0.024	0.000	0.000	0.000
54	A	94	ASP	-1	-0.840	-0.888	26.303	-0.143	-0.143	0.000	0.000	0.000
55	A	95	ILE	0	-0.048	-0.033	23.063	0.007	0.007	0.000	0.000	0.000
56	A	96	PRO	0	0.019	0.006	27.135	-0.002	-0.002	0.000	0.000	0.000
57	A	97	GLU	-1	-0.869	-0.922	27.175	-0.074	-0.074	0.000	0.000	0.000
58	A	98	VAL	0	-0.041	-0.024	26.421	-0.003	-0.003	0.000	0.000	0.000
59	A	99	GLN	0	-0.061	-0.041	25.109	0.003	0.003	0.000	0.000	0.000
60	A	100	SER	0	-0.042	-0.037	23.182	-0.010	-0.010	0.000	0.000	0.000
61	A	101	ALA	0	0.017	0.017	20.838	-0.019	-0.019	0.000	0.000	0.000
62	A	102	TYR	0	-0.054	-0.040	14.440	-0.009	-0.009	0.000	0.000	0.000
63	A	103	ILE	0	0.017	0.028	17.504	0.021	0.021	0.000	0.000	0.000
64	A	104	THR	0	-0.022	-0.004	14.856	-0.031	-0.031	0.000	0.000	0.000
65	A	105	ILE	0	-0.008	-0.004	16.300	0.039	0.039	0.000	0.000	0.000
66	A	106	SER	0	-0.016	-0.009	16.391	-0.065	-0.065	0.000	0.000	0.000
67	A	107	ILE	0	0.042	0.023	13.543	0.026	0.026	0.000	0.000	0.000
68	A	108	ALA	0	0.001	0.004	17.112	0.000	0.000	0.000	0.000	0.000
69	A	109	ASN	0	-0.031	-0.029	17.930	0.005	0.005	0.000	0.000	0.000
70	A	110	PHE	0	0.023	0.024	19.318	0.020	0.020	0.000	0.000	0.000
71	A	111	PRO	0	0.006	-0.004	20.896	-0.007	-0.007	0.000	0.000	0.000
72	A	112	ALA	0	-0.005	0.013	19.480	-0.026	-0.026	0.000	0.000	0.000
73	A	113	GLU	-1	-0.868	-0.917	19.565	-0.274	-0.274	0.000	0.000	0.000
74	A	114	GLU	-1	-0.912	-0.961	17.843	-0.572	-0.572	0.000	0.000	0.000
75	A	115	TYR	0	-0.053	-0.047	18.694	0.075	0.075	0.000	0.000	0.000
76	A	116	LYS	1	0.905	0.953	18.634	0.202	0.202	0.000	0.000	0.000
77	A	117	LEU	0	-0.047	-0.022	16.110	0.018	0.018	0.000	0.000	0.000
78	A	118	GLU	-1	-0.826	-0.910	19.755	-0.233	-0.233	0.000	0.000	0.000
79	A	119	ILE	0	-0.010	-0.008	18.065	0.003	0.003	0.000	0.000	0.000
80	A	120	THR	0	0.015	0.000	22.359	0.000	0.000	0.000	0.000	0.000
81	A	121	GLY	0	0.004	0.002	25.858	0.002	0.002	0.000	0.000	0.000
82	A	122	THR	0	-0.035	0.013	27.926	0.002	0.002	0.000	0.000	0.000
83	A	123	PRO	0	-0.010	-0.024	31.668	0.005	0.005	0.000	0.000	0.000
84	A	124	SER	0	-0.034	-0.032	30.971	-0.002	-0.002	0.000	0.000	0.000
85	A	125	GLY	0	0.064	0.038	26.815	0.002	0.002	0.000	0.000	0.000
86	A	126	HIS	0	-0.087	-0.050	25.091	0.000	0.000	0.000	0.000	0.000
87	A	127	LEU	0	0.024	0.029	19.602	0.000	0.000	0.000	0.000	0.000
88	A	128	THR	0	-0.003	-0.014	20.737	0.010	0.010	0.000	0.000	0.000
89	A	129	GLY	0	0.064	0.043	16.582	-0.016	-0.016	0.000	0.000	0.000
90	A	130	TYR	0	-0.002	-0.009	15.726	0.060	0.060	0.000	0.000	0.000
91	A	131	PHE	0	-0.020	-0.026	13.453	-0.119	-0.119	0.000	0.000	0.000
92	A	132	THR	0	0.042	0.013	14.697	0.053	0.053	0.000	0.000	0.000
93	A	133	LYS	1	0.739	0.898	14.102	0.223	0.223	0.000	0.000	0.000
94	A	134	GLU	-1	-0.888	-0.945	13.516	-0.318	-0.318	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:34:PRO)