FMO DATABASE

FMODB ID: 85K7Y

Calculation Name: 2D7T-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D7T

Chain ID: H

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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	115
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-950599.719523
FMO2-HF: Nuclear repulsion	904280.940649
FMO2-HF: Total energy	-46318.778875
FMO2-MP2: Total energy	-46450.499781

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(H:1:GLN)

Summations of interaction energy for fragment #1(H:1:GLN)

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.
-0.777	2.299	0.386	-1.247	-2.215	0.007

Interaction energy analysis for fragmet #1(H:1:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.012

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	H	3	GLN	0	-0.017	-0.012	3.785	-1.714	-0.408	0.012	-0.473	-0.845	0.002
4	H	4	LEU	0	-0.017	-0.018	5.955	0.236	0.236	0.000	0.000	0.000	0.000
5	H	5	VAL	0	0.015	0.010	9.325	-0.065	-0.065	0.000	0.000	0.000	0.000
6	H	6	GLN	0	0.002	-0.027	11.816	0.133	0.133	0.000	0.000	0.000	0.000
7	H	7	SER	0	0.032	0.030	15.527	-0.072	-0.072	0.000	0.000	0.000	0.000
8	H	8	GLY	0	0.018	0.013	18.621	0.024	0.024	0.000	0.000	0.000	0.000
9	H	9	ALA	0	-0.027	-0.011	21.112	0.028	0.028	0.000	0.000	0.000	0.000
10	H	10	GLU	-1	-0.911	-0.946	24.249	-0.034	-0.034	0.000	0.000	0.000	0.000
11	H	11	VAL	0	-0.005	-0.008	27.117	0.016	0.016	0.000	0.000	0.000	0.000
12	H	12	LYS	1	0.908	0.957	29.283	-0.019	-0.019	0.000	0.000	0.000	0.000
13	H	13	LYS	1	0.933	0.980	32.899	-0.006	-0.006	0.000	0.000	0.000	0.000
14	H	14	PRO	0	0.043	0.006	35.794	0.007	0.007	0.000	0.000	0.000	0.000
15	H	15	GLY	0	-0.046	-0.021	36.723	-0.006	-0.006	0.000	0.000	0.000	0.000
16	H	16	ALA	0	-0.038	-0.005	34.066	0.000	0.000	0.000	0.000	0.000	0.000
17	H	17	SER	0	-0.028	-0.021	30.862	0.009	0.009	0.000	0.000	0.000	0.000
18	H	18	VAL	0	-0.003	-0.006	25.858	-0.018	-0.018	0.000	0.000	0.000	0.000
19	H	19	LYS	1	0.967	0.990	23.400	-0.043	-0.043	0.000	0.000	0.000	0.000
20	H	20	VAL	0	0.014	0.025	19.656	-0.031	-0.031	0.000	0.000	0.000	0.000
21	H	21	SER	0	-0.008	-0.018	17.680	0.015	0.015	0.000	0.000	0.000	0.000
22	H	22	CYS	0	-0.031	-0.003	13.965	0.005	0.005	0.000	0.000	0.000	0.000
23	H	23	LYS	1	0.954	0.993	10.523	0.752	0.752	0.000	0.000	0.000	0.000
24	H	24	ALA	0	0.015	0.011	9.072	-0.086	-0.086	0.000	0.000	0.000	0.000
25	H	25	SER	0	-0.068	-0.041	5.395	-0.765	-0.765	0.000	0.000	0.000	0.000
26	H	26	GLY	0	0.081	0.027	3.229	-1.781	-0.836	0.252	-0.693	-0.504	0.005
27	H	27	TYR	0	0.020	0.014	3.343	4.154	4.979	0.122	-0.081	-0.866	0.000
28	H	28	THR	0	0.010	0.002	6.104	-1.232	-1.232	0.000	0.000	0.000	0.000
29	H	29	PHE	0	0.056	0.036	9.689	0.043	0.043	0.000	0.000	0.000	0.000
30	H	30	THR	0	-0.035	-0.038	11.576	0.050	0.050	0.000	0.000	0.000	0.000
31	H	31	GLY	0	-0.033	-0.015	12.854	-0.107	-0.107	0.000	0.000	0.000	0.000
32	H	32	ASN	0	0.044	0.040	9.514	-0.178	-0.178	0.000	0.000	0.000	0.000
33	H	33	TYR	0	-0.003	-0.007	13.627	-0.177	-0.177	0.000	0.000	0.000	0.000
34	H	34	MET	0	-0.034	0.011	12.421	0.207	0.207	0.000	0.000	0.000	0.000
35	H	35	HIS	0	0.055	0.057	15.682	-0.235	-0.235	0.000	0.000	0.000	0.000
36	H	36	TRP	0	0.040	0.001	16.977	-0.003	-0.003	0.000	0.000	0.000	0.000
37	H	37	VAL	0	-0.005	0.001	18.999	-0.009	-0.009	0.000	0.000	0.000	0.000
38	H	38	ARG	1	0.814	0.891	20.649	-0.246	-0.246	0.000	0.000	0.000	0.000
39	H	39	GLN	0	-0.017	-0.006	22.947	0.015	0.015	0.000	0.000	0.000	0.000
40	H	40	ALA	0	0.044	0.028	24.731	-0.022	-0.022	0.000	0.000	0.000	0.000
41	H	41	PRO	0	0.031	-0.001	28.102	0.010	0.010	0.000	0.000	0.000	0.000
42	H	42	GLY	0	0.006	0.009	30.024	-0.005	-0.005	0.000	0.000	0.000	0.000
43	H	43	GLN	0	-0.048	-0.015	29.609	0.010	0.010	0.000	0.000	0.000	0.000
44	H	44	GLY	0	0.025	0.020	27.787	0.008	0.008	0.000	0.000	0.000	0.000
45	H	45	LEU	0	0.006	-0.009	20.394	-0.009	-0.009	0.000	0.000	0.000	0.000
46	H	46	GLU	-1	-0.779	-0.879	24.408	0.258	0.258	0.000	0.000	0.000	0.000
47	H	47	TYR	0	-0.005	-0.038	19.946	-0.030	-0.030	0.000	0.000	0.000	0.000
48	H	48	MET	0	-0.054	-0.034	22.734	-0.042	-0.042	0.000	0.000	0.000	0.000
49	H	49	GLY	0	0.020	0.002	22.634	-0.039	-0.039	0.000	0.000	0.000	0.000
50	H	50	TRP	0	-0.013	0.012	20.197	0.056	0.056	0.000	0.000	0.000	0.000
51	H	51	ILE	0	0.004	-0.008	18.965	-0.074	-0.074	0.000	0.000	0.000	0.000
52	H	52	ASN	0	0.038	0.028	18.920	0.152	0.152	0.000	0.000	0.000	0.000
53	H	53	PRO	0	0.017	0.005	15.277	-0.116	-0.116	0.000	0.000	0.000	0.000
54	H	54	LYS	1	0.955	0.986	17.453	-0.737	-0.737	0.000	0.000	0.000	0.000
55	H	55	SER	0	-0.011	-0.011	19.381	-0.049	-0.049	0.000	0.000	0.000	0.000
56	H	56	GLY	0	-0.046	-0.019	21.874	-0.049	-0.049	0.000	0.000	0.000	0.000
57	H	57	ASP	-1	-0.883	-0.937	23.352	0.356	0.356	0.000	0.000	0.000	0.000
58	H	58	THR	0	-0.052	-0.034	23.456	0.035	0.035	0.000	0.000	0.000	0.000
59	H	59	ASN	0	0.038	0.022	24.952	-0.047	-0.047	0.000	0.000	0.000	0.000
60	H	60	TYR	0	0.012	0.009	25.137	0.030	0.030	0.000	0.000	0.000	0.000
61	H	61	ALA	0	0.037	0.016	26.846	-0.007	-0.007	0.000	0.000	0.000	0.000
62	H	62	GLN	0	0.058	0.009	28.427	-0.030	-0.030	0.000	0.000	0.000	0.000
63	H	63	LYS	1	0.824	0.913	30.414	-0.245	-0.245	0.000	0.000	0.000	0.000
64	H	64	PHE	0	-0.036	-0.022	27.466	-0.024	-0.024	0.000	0.000	0.000	0.000
65	H	65	GLN	0	0.068	0.036	30.702	-0.008	-0.008	0.000	0.000	0.000	0.000
66	H	66	GLY	0	0.020	0.020	32.217	-0.015	-0.015	0.000	0.000	0.000	0.000
67	H	67	ARG	1	0.656	0.794	31.744	-0.183	-0.183	0.000	0.000	0.000	0.000
68	H	68	VAL	0	0.020	0.011	26.057	-0.015	-0.015	0.000	0.000	0.000	0.000
69	H	69	THR	0	-0.023	-0.001	27.159	0.003	0.003	0.000	0.000	0.000	0.000
70	H	70	MET	0	-0.036	0.004	22.165	-0.002	-0.002	0.000	0.000	0.000	0.000
71	H	71	THR	0	0.010	0.003	22.509	-0.016	-0.016	0.000	0.000	0.000	0.000
72	H	72	ARG	1	0.865	0.928	18.030	-0.298	-0.298	0.000	0.000	0.000	0.000
73	H	73	ASP	-1	-0.798	-0.859	18.481	-0.011	-0.011	0.000	0.000	0.000	0.000
74	H	74	THR	0	0.007	-0.036	16.332	0.012	0.012	0.000	0.000	0.000	0.000
75	H	75	SER	0	-0.061	-0.036	16.047	-0.018	-0.018	0.000	0.000	0.000	0.000
76	H	76	ILE	0	0.009	0.008	14.875	-0.086	-0.086	0.000	0.000	0.000	0.000
77	H	77	SER	0	-0.041	-0.013	11.410	-0.011	-0.011	0.000	0.000	0.000	0.000
78	H	78	THR	0	-0.023	-0.009	12.668	0.004	0.004	0.000	0.000	0.000	0.000
79	H	79	VAL	0	0.027	0.007	15.327	0.020	0.020	0.000	0.000	0.000	0.000
80	H	80	TYR	0	-0.018	-0.027	17.470	-0.047	-0.047	0.000	0.000	0.000	0.000
81	H	81	MET	0	-0.005	0.006	20.588	0.048	0.048	0.000	0.000	0.000	0.000
82	H	82	GLU	-1	-0.942	-0.975	23.078	0.069	0.069	0.000	0.000	0.000	0.000
83	H	83	VAL	0	0.002	0.015	26.223	0.020	0.020	0.000	0.000	0.000	0.000
84	H	84	ARG	1	1.019	0.986	28.830	-0.137	-0.137	0.000	0.000	0.000	0.000
85	H	85	ARG	1	0.914	0.948	32.547	-0.121	-0.121	0.000	0.000	0.000	0.000
86	H	86	LEU	0	0.012	0.025	29.817	0.007	0.007	0.000	0.000	0.000	0.000
87	H	87	ARG	1	0.976	0.980	33.840	-0.138	-0.138	0.000	0.000	0.000	0.000
88	H	88	SER	0	0.090	0.031	33.827	0.002	0.002	0.000	0.000	0.000	0.000
89	H	89	ASP	-1	-0.925	-0.954	33.362	0.136	0.136	0.000	0.000	0.000	0.000
90	H	90	ASP	-1	-0.795	-0.851	29.954	0.168	0.168	0.000	0.000	0.000	0.000
91	H	91	THR	0	0.009	0.042	28.715	-0.002	-0.002	0.000	0.000	0.000	0.000
92	H	92	ALA	0	0.005	0.000	25.708	0.011	0.011	0.000	0.000	0.000	0.000
93	H	93	VAL	0	-0.014	0.009	20.124	-0.027	-0.027	0.000	0.000	0.000	0.000
94	H	94	TYR	0	-0.043	-0.055	21.094	0.046	0.046	0.000	0.000	0.000	0.000
95	H	95	TYR	0	0.042	0.024	15.679	-0.043	-0.043	0.000	0.000	0.000	0.000
96	H	97	ALA	0	0.071	0.019	12.423	0.013	0.013	0.000	0.000	0.000	0.000
97	H	98	THR	0	-0.040	-0.043	9.714	-0.028	-0.028	0.000	0.000	0.000	0.000
98	H	99	GLY	0	0.074	0.039	10.548	0.245	0.245	0.000	0.000	0.000	0.000
99	H	100	TRP	0	-0.035	-0.009	9.634	-0.215	-0.215	0.000	0.000	0.000	0.000
100	H	101	TRP	0	-0.019	-0.005	13.016	-0.241	-0.241	0.000	0.000	0.000	0.000
101	H	102	GLY	0	0.029	0.021	15.096	-0.152	-0.152	0.000	0.000	0.000	0.000
102	H	103	MET	0	-0.086	-0.050	13.999	0.056	0.056	0.000	0.000	0.000	0.000
103	H	104	ASP	-1	-0.861	-0.928	9.896	2.098	2.098	0.000	0.000	0.000	0.000
104	H	105	VAL	0	-0.051	-0.023	5.900	0.173	0.173	0.000	0.000	0.000	0.000
105	H	106	TRP	0	0.009	-0.003	8.981	-0.312	-0.312	0.000	0.000	0.000	0.000
106	H	107	GLY	0	0.006	0.001	10.113	-0.062	-0.062	0.000	0.000	0.000	0.000
107	H	108	GLN	0	0.022	0.008	12.125	0.080	0.080	0.000	0.000	0.000	0.000
108	H	109	GLY	0	-0.014	0.001	14.017	-0.009	-0.009	0.000	0.000	0.000	0.000
109	H	110	THR	0	-0.031	-0.031	17.408	-0.052	-0.052	0.000	0.000	0.000	0.000
110	H	111	LEU	0	-0.021	0.005	20.347	0.031	0.031	0.000	0.000	0.000	0.000
111	H	112	VAL	0	0.023	0.012	23.828	-0.023	-0.023	0.000	0.000	0.000	0.000
112	H	113	THR	0	0.017	-0.003	26.760	0.015	0.015	0.000	0.000	0.000	0.000
113	H	114	VAL	0	-0.040	-0.027	30.199	-0.012	-0.012	0.000	0.000	0.000	0.000
114	H	115	SER	0	0.005	0.003	33.257	0.000	0.000	0.000	0.000	0.000	0.000
115	H	116	SER	0	0.027	0.004	36.183	-0.007	-0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(H:1:GLN)