FMO DATABASE

FMODB ID: QV59Y

Calculation Name: 1D9C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1D9C

Chain ID: A

ChEMBL ID:

UniProt ID: P07353

Base Structure: X-ray

Registration Date: 2023-09-23

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	121
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-969619.040682
FMO2-HF: Nuclear repulsion	920123.374617
FMO2-HF: Total energy	-49495.666065
FMO2-MP2: Total energy	-49641.213879

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:GLN)

Summations of interaction energy for fragment #1(A: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.
-8.16	-4.037	1.985	-2.335	-3.774	0.01

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.009

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	A	3	GLN	0	0.020	0.025	3.435	-3.286	-0.774	0.037	-1.166	-1.383	0.006
4	A	4	PHE	0	0.049	0.007	2.586	-3.887	-2.610	1.949	-1.032	-2.194	0.004
5	A	5	PHE	0	0.021	0.017	4.009	-0.758	-0.424	-0.001	-0.137	-0.197	0.000
6	A	6	ARG	1	0.861	0.911	5.971	-0.981	-0.981	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.749	-0.828	7.951	0.773	0.773	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.002	0.002	6.873	-0.044	-0.044	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.784	-0.886	10.057	-1.071	-1.071	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.046	-0.020	12.015	0.012	0.012	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.025	-0.019	11.913	0.023	0.023	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.764	0.866	11.701	0.961	0.961	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.906	-0.946	16.016	-0.235	-0.235	0.000	0.000	0.000	0.000
14	A	14	TYR	0	-0.048	-0.044	17.798	0.025	0.025	0.000	0.000	0.000	0.000
15	A	15	PHE	0	-0.050	-0.042	17.230	0.021	0.021	0.000	0.000	0.000	0.000
16	A	16	ASN	0	-0.005	0.007	20.515	-0.010	-0.010	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.011	0.009	17.897	-0.020	-0.020	0.000	0.000	0.000	0.000
18	A	18	SER	0	-0.065	-0.050	17.407	-0.044	-0.044	0.000	0.000	0.000	0.000
19	A	19	SER	0	0.008	0.001	19.221	-0.036	-0.036	0.000	0.000	0.000	0.000
20	A	20	PRO	0	0.005	-0.028	22.996	0.000	0.000	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.921	-0.958	25.083	-0.237	-0.237	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.062	0.049	20.502	0.018	0.018	0.000	0.000	0.000	0.000
23	A	23	ALA	0	-0.018	-0.004	23.918	0.001	0.001	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.858	0.941	24.958	0.231	0.231	0.000	0.000	0.000	0.000
25	A	25	GLY	0	0.023	0.006	28.250	0.019	0.019	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.000	0.014	26.930	0.013	0.013	0.000	0.000	0.000	0.000
27	A	27	PRO	0	-0.043	-0.019	23.104	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.025	0.023	21.090	0.013	0.013	0.000	0.000	0.000	0.000
29	A	29	PHE	0	0.056	0.009	18.549	0.016	0.016	0.000	0.000	0.000	0.000
30	A	30	SER	0	0.015	0.006	18.851	0.009	0.009	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.753	-0.872	20.057	-0.392	-0.392	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.001	0.023	22.367	0.010	0.010	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.003	-0.019	16.216	0.008	0.008	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.795	0.888	20.147	0.397	0.397	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.041	-0.038	22.240	0.017	0.017	0.000	0.000	0.000	0.000
36	A	36	TRP	0	0.062	0.039	22.611	0.019	0.019	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.786	0.879	18.995	0.427	0.427	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.830	-0.904	20.475	-0.373	-0.373	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.862	-0.911	23.050	-0.139	-0.139	0.000	0.000	0.000	0.000
40	A	40	SER	0	-0.024	-0.020	24.078	0.002	0.002	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.851	-0.929	25.672	-0.079	-0.079	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.859	0.931	18.089	0.296	0.296	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.910	0.953	17.993	-0.055	-0.055	0.000	0.000	0.000	0.000
44	A	44	ILE	0	0.035	0.025	21.863	0.015	0.015	0.000	0.000	0.000	0.000
45	A	45	ILE	0	0.022	0.012	21.796	0.009	0.009	0.000	0.000	0.000	0.000
46	A	46	GLN	0	-0.010	-0.020	16.324	0.024	0.024	0.000	0.000	0.000	0.000
47	A	47	SER	0	0.044	0.023	19.227	0.021	0.021	0.000	0.000	0.000	0.000
48	A	48	GLN	0	-0.033	0.001	21.329	0.024	0.024	0.000	0.000	0.000	0.000
49	A	49	ILE	0	-0.003	0.016	17.164	0.009	0.009	0.000	0.000	0.000	0.000
50	A	50	VAL	0	0.005	-0.005	15.526	0.007	0.007	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.031	-0.020	17.894	0.035	0.035	0.000	0.000	0.000	0.000
52	A	52	PHE	0	0.024	0.011	19.392	0.018	0.018	0.000	0.000	0.000	0.000
53	A	53	TYR	0	0.020	0.004	16.076	0.006	0.006	0.000	0.000	0.000	0.000
54	A	54	PHE	0	-0.008	-0.009	15.380	0.040	0.040	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.885	0.937	19.238	-0.021	-0.021	0.000	0.000	0.000	0.000
56	A	56	LEU	0	0.002	0.018	18.916	0.007	0.007	0.000	0.000	0.000	0.000
57	A	57	PHE	0	0.051	-0.012	14.313	0.013	0.013	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.861	-0.920	19.735	0.249	0.249	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.087	-0.046	22.617	0.005	0.005	0.000	0.000	0.000	0.000
60	A	60	LEU	0	0.036	0.017	20.793	-0.015	-0.015	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.864	0.933	21.225	-0.179	-0.179	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.869	-0.929	22.059	0.172	0.172	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.020	0.014	21.590	-0.029	-0.029	0.000	0.000	0.000	0.000
64	A	64	GLN	0	-0.029	-0.037	20.319	0.006	0.006	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.009	-0.003	19.154	0.045	0.045	0.000	0.000	0.000	0.000
66	A	66	ILE	0	0.035	0.017	16.427	0.008	0.008	0.000	0.000	0.000	0.000
67	A	67	GLN	0	-0.018	0.007	16.212	0.020	0.020	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.952	0.954	12.116	-0.660	-0.660	0.000	0.000	0.000	0.000
69	A	69	SER	0	0.000	-0.028	11.882	0.124	0.124	0.000	0.000	0.000	0.000
70	A	70	MET	0	-0.028	0.012	11.898	0.028	0.028	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.875	-0.922	13.756	0.512	0.512	0.000	0.000	0.000	0.000
72	A	72	ILE	0	-0.053	-0.029	7.960	0.142	0.142	0.000	0.000	0.000	0.000
73	A	73	ILE	0	0.011	0.007	7.914	0.164	0.164	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.877	0.940	10.406	-0.362	-0.362	0.000	0.000	0.000	0.000
75	A	75	GLN	0	0.021	0.016	10.311	-0.049	-0.049	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.796	-0.883	6.986	0.612	0.612	0.000	0.000	0.000	0.000
77	A	77	MET	0	-0.029	-0.011	9.364	-0.143	-0.143	0.000	0.000	0.000	0.000
78	A	78	PHE	0	-0.022	-0.006	12.295	-0.057	-0.057	0.000	0.000	0.000	0.000
79	A	79	GLN	0	-0.018	-0.020	10.018	-0.090	-0.090	0.000	0.000	0.000	0.000
80	A	80	LYS	1	0.796	0.871	5.724	-0.217	-0.217	0.000	0.000	0.000	0.000
81	A	81	PHE	0	-0.054	-0.022	12.065	-0.091	-0.091	0.000	0.000	0.000	0.000
82	A	82	LEU	0	-0.040	-0.018	15.670	-0.033	-0.033	0.000	0.000	0.000	0.000
83	A	83	ASN	0	-0.018	-0.014	15.454	-0.008	-0.008	0.000	0.000	0.000	0.000
84	A	84	GLY	0	0.057	0.041	15.186	0.029	0.029	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.054	-0.034	15.711	0.023	0.023	0.000	0.000	0.000	0.000
86	A	86	SER	0	0.046	0.001	19.566	-0.015	-0.015	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.748	-0.831	20.793	0.204	0.204	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.864	0.913	20.718	-0.230	-0.230	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.035	-0.014	17.650	-0.025	-0.025	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.956	-0.973	20.828	0.204	0.204	0.000	0.000	0.000	0.000
91	A	91	ASP	-1	-0.778	-0.880	24.308	0.111	0.111	0.000	0.000	0.000	0.000
92	A	92	PHE	0	0.013	0.004	19.684	-0.019	-0.019	0.000	0.000	0.000	0.000
93	A	93	LYS	1	0.883	0.920	20.704	-0.254	-0.254	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.810	0.903	24.175	-0.135	-0.135	0.000	0.000	0.000	0.000
95	A	95	LEU	0	-0.002	-0.008	26.848	-0.014	-0.014	0.000	0.000	0.000	0.000
96	A	96	ILE	0	-0.034	-0.010	22.332	-0.015	-0.015	0.000	0.000	0.000	0.000
97	A	97	GLN	0	-0.016	-0.011	26.054	-0.024	-0.024	0.000	0.000	0.000	0.000
98	A	98	ILE	0	-0.037	0.004	28.529	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	99	PRO	0	-0.016	0.010	31.956	-0.008	-0.008	0.000	0.000	0.000	0.000
100	A	100	VAL	0	0.017	-0.011	34.101	0.000	0.000	0.000	0.000	0.000	0.000
101	A	101	ASP	-1	-0.897	-0.942	36.740	0.022	0.022	0.000	0.000	0.000	0.000
102	A	102	ASP	-1	-0.777	-0.880	38.864	0.048	0.048	0.000	0.000	0.000	0.000
103	A	103	LEU	0	0.026	0.011	40.609	0.000	0.000	0.000	0.000	0.000	0.000
104	A	104	GLN	0	-0.040	-0.024	41.898	0.003	0.003	0.000	0.000	0.000	0.000
105	A	105	ILE	0	0.024	-0.002	35.939	0.001	0.001	0.000	0.000	0.000	0.000
106	A	106	GLN	0	-0.029	-0.016	39.724	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.920	0.956	41.344	-0.036	-0.036	0.000	0.000	0.000	0.000
108	A	108	LYS	1	0.909	0.952	39.841	-0.068	-0.068	0.000	0.000	0.000	0.000
109	A	109	ALA	0	0.037	0.019	38.317	0.000	0.000	0.000	0.000	0.000	0.000
110	A	110	ILE	0	-0.012	-0.009	39.831	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	111	ASN	0	-0.063	-0.027	43.187	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	112	GLU	-1	-0.878	-0.932	39.644	0.064	0.064	0.000	0.000	0.000	0.000
113	A	113	LEU	0	0.021	0.026	39.748	0.001	0.001	0.000	0.000	0.000	0.000
114	A	114	ILE	0	0.016	0.000	40.849	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	115	LYS	1	0.843	0.904	39.039	-0.062	-0.062	0.000	0.000	0.000	0.000
116	A	116	VAL	0	0.026	0.015	35.309	0.000	0.000	0.000	0.000	0.000	0.000
117	A	117	MET	0	0.003	-0.003	37.279	-0.004	-0.004	0.000	0.000	0.000	0.000
118	A	118	ASN	0	-0.019	-0.006	39.699	-0.006	-0.006	0.000	0.000	0.000	0.000
119	A	119	ASP	-1	-0.984	-0.978	33.437	0.048	0.048	0.000	0.000	0.000	0.000
120	A	120	LEU	0	-0.036	-0.018	33.149	-0.003	-0.003	0.000	0.000	0.000	0.000
121	A	121	SER	0	-0.096	-0.038	36.049	-0.008	-0.008	0.000	0.000	0.000	0.000

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