FMO DATABASE

FMODB ID: YQK42

Calculation Name: 2D1H-A-Xray310

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D1H

Chain ID: A

ChEMBL ID:

UniProt ID: F9VNN8

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	103
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-793297.691907
FMO2-HF: Nuclear repulsion	750955.394131
FMO2-HF: Total energy	-42342.297776
FMO2-MP2: Total energy	-42462.311171

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.
-30.148	-43.632	46.025	-14.567	-17.974	0.031

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 : 0.045 / q_NPA : 0.078

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	A	3	LYS	1	1.016	0.996	3.875	0.421	3.486	-0.012	-1.741	-1.313	0.004
4	A	4	GLU	-1	-0.914	-0.963	6.745	0.084	0.084	0.000	0.000	0.000	0.000
5	A	5	LYS	1	0.963	0.998	4.319	-0.881	-0.731	0.000	-0.012	-0.137	0.000
6	A	6	LEU	0	-0.012	0.009	3.020	0.836	1.386	0.080	-0.111	-0.520	-0.001
7	A	7	GLU	-1	-0.788	-0.888	6.046	0.903	0.903	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.095	-0.068	7.557	0.156	0.156	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.887	0.907	2.047	-19.663	-39.291	34.849	-9.921	-5.300	0.073
10	A	10	LYS	1	0.893	0.943	8.354	-0.908	-0.908	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.844	-0.921	10.413	0.946	0.946	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.868	-0.937	8.270	2.684	2.684	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.017	-0.013	5.759	-0.358	-0.358	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.916	0.964	8.674	-1.094	-1.094	0.000	0.000	0.000	0.000
15	A	15	CYS	0	-0.023	-0.013	12.359	-0.207	-0.207	0.000	0.000	0.000	0.000
16	A	100	CYS	0	-0.152	-0.070	9.680	-0.260	-0.260	0.000	0.000	0.000	0.000
17	A	17	TYR	0	-0.107	-0.091	7.159	-0.188	-0.188	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.897	0.962	12.347	-0.576	-0.576	0.000	0.000	0.000	0.000
19	A	19	ILE	0	-0.048	-0.008	11.679	-0.097	-0.097	0.000	0.000	0.000	0.000
20	A	20	THR	0	-0.005	-0.027	15.868	0.063	0.063	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.855	-0.948	16.248	0.515	0.515	0.000	0.000	0.000	0.000
22	A	22	THR	0	-0.012	-0.003	17.159	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.799	-0.901	15.302	0.112	0.112	0.000	0.000	0.000	0.000
24	A	24	VAL	0	0.003	-0.007	11.220	-0.064	-0.064	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.020	0.017	12.957	-0.038	-0.038	0.000	0.000	0.000	0.000
26	A	26	VAL	0	-0.001	0.003	15.344	-0.081	-0.081	0.000	0.000	0.000	0.000
27	A	27	LEU	0	0.013	0.003	8.385	-0.099	-0.099	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.017	-0.021	8.780	-0.152	-0.152	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.865	0.929	11.553	0.039	0.039	0.000	0.000	0.000	0.000
30	A	30	MET	0	-0.027	-0.032	13.795	-0.053	-0.053	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.029	-0.014	8.228	-0.145	-0.145	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.919	-0.950	11.335	-0.341	-0.341	0.000	0.000	0.000	0.000
33	A	33	ILE	0	-0.042	-0.003	13.438	-0.034	-0.034	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.961	-0.957	13.209	-1.082	-1.082	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.958	0.977	15.504	0.361	0.361	0.000	0.000	0.000	0.000
36	A	36	PRO	0	-0.050	-0.024	18.217	0.021	0.021	0.000	0.000	0.000	0.000
37	A	37	ILE	0	0.008	0.007	18.855	0.030	0.030	0.000	0.000	0.000	0.000
38	A	38	THR	0	-0.024	-0.023	21.428	0.004	0.004	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.014	-0.037	23.145	0.012	0.012	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.870	-0.939	24.160	-0.134	-0.134	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.830	-0.894	23.792	-0.237	-0.237	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.017	-0.004	18.620	0.018	0.018	0.000	0.000	0.000	0.000
43	A	43	ALA	0	-0.019	-0.008	22.593	0.029	0.029	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.903	-0.944	25.562	-0.048	-0.048	0.000	0.000	0.000	0.000
45	A	45	ILE	0	-0.046	-0.025	20.659	0.013	0.013	0.000	0.000	0.000	0.000
46	A	46	PHE	0	-0.055	-0.037	17.733	0.023	0.023	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.897	0.972	23.823	0.040	0.040	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.008	0.009	22.878	0.016	0.016	0.000	0.000	0.000	0.000
49	A	49	SER	0	0.027	0.005	26.944	-0.017	-0.017	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.994	0.966	26.782	0.099	0.099	0.000	0.000	0.000	0.000
51	A	51	THR	0	0.014	0.011	26.281	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	52	THR	0	-0.006	0.010	23.693	0.006	0.006	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.045	0.026	21.475	0.005	0.005	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.887	-0.958	21.447	-0.121	-0.121	0.000	0.000	0.000	0.000
55	A	55	ASN	0	-0.061	-0.027	22.260	-0.034	-0.034	0.000	0.000	0.000	0.000
56	A	56	SER	0	0.030	0.031	18.112	0.004	0.004	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.040	-0.029	17.682	-0.021	-0.021	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.923	0.960	17.956	0.035	0.035	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.908	0.964	15.754	-0.137	-0.137	0.000	0.000	0.000	0.000
60	A	60	LEU	0	0.042	0.002	12.209	-0.019	-0.019	0.000	0.000	0.000	0.000
61	A	61	ILE	0	-0.060	-0.017	13.758	-0.094	-0.094	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.890	-0.933	15.929	-0.037	-0.037	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.026	0.000	11.538	0.017	0.017	0.000	0.000	0.000	0.000
64	A	64	GLY	0	-0.023	-0.020	11.653	-0.087	-0.087	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.036	-0.003	7.814	-0.234	-0.234	0.000	0.000	0.000	0.000
66	A	66	VAL	0	0.000	0.001	10.982	-0.117	-0.117	0.000	0.000	0.000	0.000
67	A	67	VAL	0	0.029	0.016	14.282	0.055	0.055	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.904	0.968	17.373	0.226	0.226	0.000	0.000	0.000	0.000
69	A	69	THR	0	0.019	-0.005	20.934	-0.008	-0.008	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.919	0.964	23.620	0.225	0.225	0.000	0.000	0.000	0.000
71	A	71	THR	0	-0.015	-0.014	26.331	-0.014	-0.014	0.000	0.000	0.000	0.000
72	A	72	NME	0	0.050	0.063	29.002	0.019	0.019	0.000	0.000	0.000	0.000
73	A	78	ACE	0	0.076	-0.012	33.196	0.001	0.001	0.000	0.000	0.000	0.000
74	A	79	PRO	0	-0.001	0.005	31.845	-0.011	-0.011	0.000	0.000	0.000	0.000
75	A	80	LYS	1	0.884	0.964	28.249	0.223	0.223	0.000	0.000	0.000	0.000
76	A	81	TYR	0	0.029	-0.009	25.446	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	82	TYR	0	0.007	0.014	22.364	0.022	0.022	0.000	0.000	0.000	0.000
78	A	83	TYR	0	-0.007	-0.011	18.544	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	84	SER	0	0.019	0.003	16.576	-0.014	-0.014	0.000	0.000	0.000	0.000
80	A	85	ILE	0	0.043	0.028	9.841	0.041	0.041	0.000	0.000	0.000	0.000
81	A	86	SER	0	-0.024	-0.027	10.742	0.016	0.016	0.000	0.000	0.000	0.000
82	A	87	SER	0	0.042	0.005	10.759	-0.268	-0.268	0.000	0.000	0.000	0.000
83	A	88	ASN	0	-0.015	0.003	8.778	-0.273	-0.273	0.000	0.000	0.000	0.000
84	A	89	ILE	0	0.069	0.033	6.278	-0.317	-0.317	0.000	0.000	0.000	0.000
85	A	90	LEU	0	-0.012	-0.013	2.725	-1.257	0.101	0.361	-0.326	-1.393	-0.001
86	A	91	GLU	-1	-0.835	-0.928	2.300	-9.988	-9.169	2.806	-1.528	-2.097	-0.023
87	A	92	LYS	1	0.824	0.946	4.855	1.725	1.824	0.000	-0.005	-0.094	0.000
88	A	93	ILE	0	0.071	0.028	2.140	-0.014	0.215	1.448	-0.318	-1.359	-0.003
89	A	94	ARG	1	0.931	0.967	2.196	-3.032	-1.780	6.246	-2.581	-4.916	-0.014
90	A	95	ASN	0	0.001	-0.018	3.053	3.706	1.877	0.217	2.073	-0.461	-0.003
91	A	96	ASP	-1	-0.816	-0.867	6.105	0.113	0.113	0.000	0.000	0.000	0.000
92	A	97	LEU	0	-0.025	-0.019	3.817	0.031	0.482	0.030	-0.097	-0.384	-0.001
93	A	98	LEU	0	-0.002	0.012	6.458	-0.047	-0.047	0.000	0.000	0.000	0.000
94	A	99	ASN	0	0.022	0.007	8.676	-0.228	-0.228	0.000	0.000	0.000	0.000
95	A	101	ALA	0	0.042	0.010	10.303	-0.128	-0.128	0.000	0.000	0.000	0.000
96	A	102	LYS	1	0.831	0.913	12.108	-0.896	-0.896	0.000	0.000	0.000	0.000
97	A	103	ARG	1	0.921	0.952	12.415	-0.813	-0.813	0.000	0.000	0.000	0.000
98	A	104	MET	0	-0.007	0.000	14.469	-0.046	-0.046	0.000	0.000	0.000	0.000
99	A	105	GLU	-1	-0.837	-0.902	16.265	0.793	0.793	0.000	0.000	0.000	0.000
100	A	106	LEU	0	-0.025	-0.038	17.958	-0.080	-0.080	0.000	0.000	0.000	0.000
101	A	107	ALA	0	-0.060	-0.013	19.816	-0.063	-0.063	0.000	0.000	0.000	0.000
102	A	108	ALA	0	-0.070	-0.029	20.949	-0.027	-0.027	0.000	0.000	0.000	0.000
103	A	109	THR	-1	-0.966	-0.965	22.690	0.370	0.370	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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