FMO DATABASE

FMODB ID: 3Q8GL

Calculation Name: 1PDN-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1PDN

Chain ID: C

ChEMBL ID:

UniProt ID: P06601

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	123
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-816931.205208
FMO2-HF: Nuclear repulsion	768868.924308
FMO2-HF: Total energy	-48062.2809
FMO2-MP2: Total energy	-48201.3384

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(C:2:GLN)

Summations of interaction energy for fragment #1(C:2: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.
-6.118	-2.521	0.235	-1.602	-2.23	0.003

Interaction energy analysis for fragmet #1(C:2:GLN)

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 : 0.002

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	C	4	ARG	1	0.939	0.968	3.305	-1.066	1.502	0.024	-1.182	-1.410	0.000
4	C	5	VAL	0	0.053	0.023	5.485	0.613	0.613	0.000	0.000	0.000	0.000
5	C	6	ASN	0	-0.051	-0.016	9.116	-0.318	-0.318	0.000	0.000	0.000	0.000
6	C	7	GLN	0	0.070	0.011	12.151	0.075	0.075	0.000	0.000	0.000	0.000
7	C	8	LEU	0	-0.024	0.008	15.437	-0.006	-0.006	0.000	0.000	0.000	0.000
8	C	9	GLY	0	0.019	0.012	13.744	0.035	0.035	0.000	0.000	0.000	0.000
9	C	10	GLY	0	0.005	0.014	13.419	0.119	0.119	0.000	0.000	0.000	0.000
10	C	11	VAL	0	0.000	-0.007	7.882	-0.105	-0.105	0.000	0.000	0.000	0.000
11	C	12	PHE	0	-0.056	-0.031	8.241	-0.098	-0.098	0.000	0.000	0.000	0.000
12	C	13	ILE	0	0.061	0.031	2.758	-1.320	-0.450	0.212	-0.413	-0.669	0.003
13	C	14	ASN	0	-0.005	-0.009	4.621	-0.069	0.090	-0.001	-0.007	-0.151	0.000
14	C	15	GLY	0	0.052	0.032	5.282	-0.047	-0.047	0.000	0.000	0.000	0.000
15	C	16	ARG	1	0.906	0.957	5.914	-1.461	-1.461	0.000	0.000	0.000	0.000
16	C	17	PRO	0	-0.012	-0.009	8.389	-0.150	-0.150	0.000	0.000	0.000	0.000
17	C	18	LEU	0	0.013	0.012	10.539	0.264	0.264	0.000	0.000	0.000	0.000
18	C	19	PRO	0	0.051	0.017	10.890	-0.098	-0.098	0.000	0.000	0.000	0.000
19	C	20	ASN	0	0.050	0.004	13.322	-0.181	-0.181	0.000	0.000	0.000	0.000
20	C	21	ASN	0	0.061	0.027	15.705	0.000	0.000	0.000	0.000	0.000	0.000
21	C	22	ILE	0	0.026	0.019	13.752	-0.087	-0.087	0.000	0.000	0.000	0.000
22	C	23	ARG	1	0.818	0.903	15.474	-0.784	-0.784	0.000	0.000	0.000	0.000
23	C	24	LEU	0	0.016	0.005	18.859	-0.066	-0.066	0.000	0.000	0.000	0.000
24	C	25	LYS	1	0.915	0.944	20.864	-0.536	-0.536	0.000	0.000	0.000	0.000
25	C	26	ILE	0	-0.054	-0.027	18.408	-0.052	-0.052	0.000	0.000	0.000	0.000
26	C	27	VAL	0	0.010	-0.008	22.624	-0.043	-0.043	0.000	0.000	0.000	0.000
27	C	28	GLU	-1	-0.815	-0.885	25.042	0.464	0.464	0.000	0.000	0.000	0.000
28	C	29	MET	0	0.014	0.006	25.004	-0.011	-0.011	0.000	0.000	0.000	0.000
29	C	30	ALA	0	-0.031	-0.019	27.014	-0.027	-0.027	0.000	0.000	0.000	0.000
30	C	31	ALA	0	-0.031	-0.010	28.715	-0.024	-0.024	0.000	0.000	0.000	0.000
31	C	32	ASP	-1	-0.910	-0.941	30.631	0.291	0.291	0.000	0.000	0.000	0.000
32	C	33	GLY	0	-0.024	0.001	32.185	-0.015	-0.015	0.000	0.000	0.000	0.000
33	C	34	ILE	0	-0.057	-0.019	28.421	-0.014	-0.014	0.000	0.000	0.000	0.000
34	C	35	ARG	1	1.006	0.992	29.829	-0.132	-0.132	0.000	0.000	0.000	0.000
35	C	36	PRO	0	0.104	0.025	25.944	0.013	0.013	0.000	0.000	0.000	0.000
36	C	37	CYS	0	-0.057	-0.027	25.112	0.019	0.019	0.000	0.000	0.000	0.000
37	C	38	VAL	0	0.012	0.001	25.626	0.003	0.003	0.000	0.000	0.000	0.000
38	C	39	ILE	0	0.038	0.033	22.332	0.023	0.023	0.000	0.000	0.000	0.000
39	C	40	SER	0	-0.086	-0.044	20.601	0.026	0.026	0.000	0.000	0.000	0.000
40	C	41	ARG	1	0.975	0.970	20.735	-0.154	-0.154	0.000	0.000	0.000	0.000
41	C	42	GLN	0	0.005	0.023	21.869	-0.003	-0.003	0.000	0.000	0.000	0.000
42	C	43	LEU	0	-0.019	-0.024	19.120	0.041	0.041	0.000	0.000	0.000	0.000
43	C	44	ARG	1	0.900	0.963	16.796	-0.330	-0.330	0.000	0.000	0.000	0.000
44	C	45	VAL	0	0.023	0.023	15.571	0.043	0.043	0.000	0.000	0.000	0.000
45	C	46	SER	0	0.055	0.025	15.876	-0.039	-0.039	0.000	0.000	0.000	0.000
46	C	47	HIS	0	0.115	0.031	17.861	0.050	0.050	0.000	0.000	0.000	0.000
47	C	48	GLY	0	0.011	0.018	19.967	0.003	0.003	0.000	0.000	0.000	0.000
48	C	49	CYS	0	-0.061	-0.033	14.919	0.016	0.016	0.000	0.000	0.000	0.000
49	C	50	VAL	0	0.043	0.013	18.187	0.025	0.025	0.000	0.000	0.000	0.000
50	C	51	SER	0	0.003	0.011	20.963	0.004	0.004	0.000	0.000	0.000	0.000
51	C	52	LYS	1	0.973	0.992	16.569	-0.238	-0.238	0.000	0.000	0.000	0.000
52	C	53	ILE	0	-0.034	-0.030	16.864	0.009	0.009	0.000	0.000	0.000	0.000
53	C	54	LEU	0	0.036	0.019	21.239	0.004	0.004	0.000	0.000	0.000	0.000
54	C	55	ASN	0	-0.024	-0.014	24.752	-0.013	-0.013	0.000	0.000	0.000	0.000
55	C	56	ARG	1	0.858	0.922	21.201	-0.264	-0.264	0.000	0.000	0.000	0.000
56	C	57	TYR	0	0.003	0.012	24.731	-0.003	-0.003	0.000	0.000	0.000	0.000
57	C	58	GLN	0	-0.020	-0.001	26.163	-0.018	-0.018	0.000	0.000	0.000	0.000
58	C	59	GLU	-1	-0.847	-0.894	26.645	0.178	0.178	0.000	0.000	0.000	0.000
59	C	60	THR	0	-0.069	-0.061	25.227	0.007	0.007	0.000	0.000	0.000	0.000
60	C	61	GLY	0	0.068	0.050	28.018	0.003	0.003	0.000	0.000	0.000	0.000
61	C	62	SER	0	-0.041	-0.030	24.398	0.035	0.035	0.000	0.000	0.000	0.000
62	C	63	ILE	0	0.065	0.036	20.376	0.005	0.005	0.000	0.000	0.000	0.000
63	C	64	ARG	1	0.947	0.978	17.769	-0.505	-0.505	0.000	0.000	0.000	0.000
64	C	65	PRO	0	-0.040	-0.005	15.406	-0.048	-0.048	0.000	0.000	0.000	0.000
65	C	66	GLY	0	0.027	0.001	18.187	-0.020	-0.020	0.000	0.000	0.000	0.000
66	C	67	VAL	0	0.002	-0.008	17.764	0.073	0.073	0.000	0.000	0.000	0.000
67	C	68	ILE	0	-0.028	-0.020	12.871	-0.018	-0.018	0.000	0.000	0.000	0.000
68	C	69	GLY	0	0.006	0.008	16.520	0.030	0.030	0.000	0.000	0.000	0.000
69	C	70	GLY	0	0.043	0.027	17.199	0.020	0.020	0.000	0.000	0.000	0.000
70	C	71	SER	0	-0.022	-0.010	20.485	-0.026	-0.026	0.000	0.000	0.000	0.000
71	C	72	LYS	1	0.897	0.952	23.692	-0.005	-0.005	0.000	0.000	0.000	0.000
72	C	73	PRO	0	0.040	0.000	26.584	-0.013	-0.013	0.000	0.000	0.000	0.000
73	C	74	ARG	1	0.832	0.907	29.113	-0.001	-0.001	0.000	0.000	0.000	0.000
74	C	75	ILE	0	0.010	0.004	31.871	-0.001	-0.001	0.000	0.000	0.000	0.000
75	C	76	ALA	0	0.010	0.006	35.230	-0.003	-0.003	0.000	0.000	0.000	0.000
76	C	77	THR	0	-0.007	-0.029	32.821	-0.008	-0.008	0.000	0.000	0.000	0.000
77	C	78	PRO	0	0.009	0.007	33.783	-0.001	-0.001	0.000	0.000	0.000	0.000
78	C	79	GLU	-1	-0.925	-0.946	35.207	-0.047	-0.047	0.000	0.000	0.000	0.000
79	C	80	ILE	0	0.067	0.032	36.660	-0.002	-0.002	0.000	0.000	0.000	0.000
80	C	81	GLU	-1	-0.812	-0.882	33.146	-0.005	-0.005	0.000	0.000	0.000	0.000
81	C	82	ASN	0	-0.036	-0.033	34.257	-0.004	-0.004	0.000	0.000	0.000	0.000
82	C	83	ARG	0	0.028	0.001	37.424	0.001	0.001	0.000	0.000	0.000	0.000
83	C	84	ILE	0	-0.024	-0.014	40.244	0.002	0.002	0.000	0.000	0.000	0.000
84	C	85	GLU	-1	-0.893	-0.922	36.847	-0.045	-0.045	0.000	0.000	0.000	0.000
85	C	86	GLU	-1	-0.822	-0.901	40.167	-0.054	-0.054	0.000	0.000	0.000	0.000
86	C	87	TYR	0	-0.102	-0.046	42.176	0.001	0.001	0.000	0.000	0.000	0.000
87	C	88	LYS	1	0.788	0.866	39.285	0.051	0.051	0.000	0.000	0.000	0.000
88	C	89	ARG	0	-0.005	0.007	44.817	0.004	0.004	0.000	0.000	0.000	0.000
89	C	90	SER	0	-0.024	-0.035	48.196	0.000	0.000	0.000	0.000	0.000	0.000
90	C	91	SER	0	-0.059	-0.028	46.018	0.003	0.003	0.000	0.000	0.000	0.000
91	C	92	PRO	0	0.015	0.028	48.021	0.004	0.004	0.000	0.000	0.000	0.000
92	C	93	GLY	0	-0.004	-0.009	50.551	-0.001	-0.001	0.000	0.000	0.000	0.000
93	C	94	MET	0	-0.006	0.018	48.738	0.001	0.001	0.000	0.000	0.000	0.000
94	C	95	PHE	0	-0.018	-0.017	49.495	0.004	0.004	0.000	0.000	0.000	0.000
95	C	96	SER	0	-0.002	-0.016	46.719	-0.002	-0.002	0.000	0.000	0.000	0.000
96	C	97	TRP	0	-0.023	-0.044	48.573	-0.001	-0.001	0.000	0.000	0.000	0.000
97	C	98	GLU	-1	-0.845	-0.913	51.083	-0.003	-0.003	0.000	0.000	0.000	0.000
98	C	99	ILE	0	0.008	0.012	45.046	-0.002	-0.002	0.000	0.000	0.000	0.000
99	C	100	ARG	1	0.856	0.914	47.389	-0.017	-0.017	0.000	0.000	0.000	0.000
100	C	101	GLU	-1	-0.822	-0.895	48.472	-0.002	-0.002	0.000	0.000	0.000	0.000
101	C	102	LYN	0	-0.066	-0.039	47.902	0.000	0.000	0.000	0.000	0.000	0.000
102	C	103	LEU	0	0.018	0.014	43.240	-0.002	-0.002	0.000	0.000	0.000	0.000
103	C	104	ILE	0	-0.062	-0.018	47.433	-0.001	-0.001	0.000	0.000	0.000	0.000
104	C	105	ARG	1	0.809	0.892	49.825	0.008	0.008	0.000	0.000	0.000	0.000
105	C	106	GLU	-1	-0.777	-0.867	47.036	-0.031	-0.031	0.000	0.000	0.000	0.000
106	C	107	GLY	0	-0.043	-0.016	48.306	-0.004	-0.004	0.000	0.000	0.000	0.000
107	C	108	VAL	0	-0.055	-0.014	42.063	0.000	0.000	0.000	0.000	0.000	0.000
108	C	109	CYM	-1	-0.799	-0.896	43.653	0.000	0.000	0.000	0.000	0.000	0.000
109	C	110	ASP	-1	-0.815	-0.909	45.559	-0.003	-0.003	0.000	0.000	0.000	0.000
110	C	111	ARG	1	0.836	0.880	47.828	0.002	0.002	0.000	0.000	0.000	0.000
111	C	112	SER	0	-0.058	-0.034	47.576	0.004	0.004	0.000	0.000	0.000	0.000
112	C	113	THR	0	-0.092	-0.050	43.196	0.004	0.004	0.000	0.000	0.000	0.000
113	C	114	ALA	0	0.071	0.064	43.846	-0.001	-0.001	0.000	0.000	0.000	0.000
114	C	115	PRO	0	-0.013	-0.005	41.729	0.006	0.006	0.000	0.000	0.000	0.000
115	C	116	SER	0	0.005	0.002	43.910	-0.002	-0.002	0.000	0.000	0.000	0.000
116	C	117	VAL	0	0.137	0.053	45.020	0.000	0.000	0.000	0.000	0.000	0.000
117	C	118	SER	0	-0.030	0.018	45.129	0.001	0.001	0.000	0.000	0.000	0.000
118	C	119	ALA	0	-0.029	-0.025	40.899	0.002	0.002	0.000	0.000	0.000	0.000
119	C	120	ILE	0	0.066	0.033	41.073	0.001	0.001	0.000	0.000	0.000	0.000
120	C	121	SER	0	0.001	-0.011	42.584	-0.003	-0.003	0.000	0.000	0.000	0.000
121	C	122	ARG	1	0.871	0.949	37.686	-0.054	-0.054	0.000	0.000	0.000	0.000
122	C	123	LEU	0	-0.055	-0.028	35.777	0.003	0.003	0.000	0.000	0.000	0.000
123	C	124	VAL	0	-0.031	0.003	38.635	-0.004	-0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:2:GLN)