FMO DATABASE

FMODB ID: JLM99

Calculation Name: 1PDO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1PDO

Chain ID: A

ChEMBL ID:

UniProt ID: P69797

Base Structure: X-ray

Registration Date: 2023-06-21

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	129
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1068013.165907
FMO2-HF: Nuclear repulsion	1019075.424006
FMO2-HF: Total energy	-48937.7419
FMO2-MP2: Total energy	-49081.666943

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:2:THR)

Summations of interaction energy for fragment #1(A:2:THR)

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.
-21.739	-9.713	6.747	-7.924	-10.847	-0.008

Interaction energy analysis for fragmet #1(A:2:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : 0.021

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	4	ALA	0	0.014	0.019	3.521	1.125	3.872	0.027	-1.419	-1.355	0.006
4	A	5	ILE	0	0.007	0.005	5.716	-0.662	-0.551	-0.001	-0.009	-0.100	0.000
5	A	6	VAL	0	-0.004	0.000	8.007	-0.010	-0.010	0.000	0.000	0.000	0.000
6	A	7	ILE	0	0.003	0.004	11.376	-0.084	-0.084	0.000	0.000	0.000	0.000
7	A	8	GLY	0	0.036	0.008	14.124	-0.026	-0.026	0.000	0.000	0.000	0.000
8	A	9	THR	0	-0.052	-0.034	17.737	-0.003	-0.003	0.000	0.000	0.000	0.000
9	A	10	HIS	0	-0.044	-0.068	21.057	-0.014	-0.014	0.000	0.000	0.000	0.000
10	A	11	GLY	0	-0.032	-0.002	24.228	0.005	0.005	0.000	0.000	0.000	0.000
11	A	12	TRP	0	0.004	-0.025	22.640	0.002	0.002	0.000	0.000	0.000	0.000
12	A	13	ALA	0	0.015	0.009	21.720	0.005	0.005	0.000	0.000	0.000	0.000
13	A	14	ALA	0	0.018	0.021	16.629	0.009	0.009	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.796	-0.889	16.538	0.186	0.186	0.000	0.000	0.000	0.000
15	A	16	GLN	0	0.000	-0.019	17.195	0.011	0.011	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.008	0.018	16.689	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	18	LEU	0	0.039	0.027	10.598	0.001	0.001	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.866	0.928	14.293	-0.181	-0.181	0.000	0.000	0.000	0.000
19	A	20	THR	0	-0.063	-0.042	16.734	-0.026	-0.026	0.000	0.000	0.000	0.000
20	A	21	ALA	0	0.017	-0.001	12.735	-0.025	-0.025	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.824	-0.907	11.749	0.346	0.346	0.000	0.000	0.000	0.000
22	A	23	MET	0	-0.112	-0.038	13.894	-0.043	-0.043	0.000	0.000	0.000	0.000
23	A	24	LEU	0	-0.111	-0.065	15.363	-0.026	-0.026	0.000	0.000	0.000	0.000
24	A	25	LEU	0	-0.029	-0.016	9.794	-0.022	-0.022	0.000	0.000	0.000	0.000
25	A	26	GLY	0	-0.003	0.023	11.649	-0.034	-0.034	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-1.000	-1.016	11.532	0.193	0.193	0.000	0.000	0.000	0.000
27	A	28	GLN	0	-0.021	-0.017	6.950	0.146	0.146	0.000	0.000	0.000	0.000
28	A	29	GLU	-1	-0.915	-0.942	4.587	-0.478	-0.356	-0.001	-0.004	-0.116	0.000
29	A	30	ASN	0	-0.008	-0.017	2.818	-3.365	-0.538	0.298	-1.397	-1.727	0.012
30	A	31	VAL	0	0.038	0.014	5.176	0.742	0.743	-0.001	-0.006	0.006	0.000
31	A	32	GLY	0	-0.005	0.007	7.761	-0.320	-0.320	0.000	0.000	0.000	0.000
32	A	33	TRP	0	-0.027	-0.017	11.251	0.001	0.001	0.000	0.000	0.000	0.000
33	A	34	ILE	0	-0.007	0.003	14.598	-0.036	-0.036	0.000	0.000	0.000	0.000
34	A	35	ASP	-1	-0.841	-0.912	18.140	0.105	0.105	0.000	0.000	0.000	0.000
35	A	36	PHE	0	-0.034	-0.011	21.615	-0.011	-0.011	0.000	0.000	0.000	0.000
36	A	37	VAL	0	0.006	0.004	24.569	0.000	0.000	0.000	0.000	0.000	0.000
37	A	38	PRO	0	-0.001	-0.017	28.029	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	39	GLY	0	0.001	0.003	31.409	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	40	GLU	-1	-0.812	-0.885	26.011	0.060	0.060	0.000	0.000	0.000	0.000
40	A	41	ASN	0	0.018	0.005	28.760	0.002	0.002	0.000	0.000	0.000	0.000
41	A	42	ALA	0	0.053	0.004	25.681	0.004	0.004	0.000	0.000	0.000	0.000
42	A	43	GLU	-1	-0.823	-0.898	24.864	0.006	0.006	0.000	0.000	0.000	0.000
43	A	44	THR	0	0.007	0.003	25.364	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	45	LEU	0	-0.008	-0.010	21.914	0.003	0.003	0.000	0.000	0.000	0.000
45	A	46	ILE	0	-0.014	0.004	20.791	0.009	0.009	0.000	0.000	0.000	0.000
46	A	47	GLU	-1	-0.859	-0.924	20.330	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.747	0.858	19.764	-0.078	-0.078	0.000	0.000	0.000	0.000
48	A	49	TYR	0	-0.014	-0.040	15.956	0.024	0.024	0.000	0.000	0.000	0.000
49	A	50	ASN	0	-0.014	-0.004	15.650	0.001	0.001	0.000	0.000	0.000	0.000
50	A	51	ALA	0	-0.006	0.000	16.070	-0.015	-0.015	0.000	0.000	0.000	0.000
51	A	52	GLN	0	-0.032	-0.013	13.265	-0.019	-0.019	0.000	0.000	0.000	0.000
52	A	53	LEU	0	0.038	0.019	11.453	0.025	0.025	0.000	0.000	0.000	0.000
53	A	54	ALA	0	-0.051	-0.013	11.317	-0.064	-0.064	0.000	0.000	0.000	0.000
54	A	55	LYS	1	0.771	0.868	11.735	-0.127	-0.127	0.000	0.000	0.000	0.000
55	A	56	LEU	0	-0.047	-0.007	7.255	0.037	0.037	0.000	0.000	0.000	0.000
56	A	57	ASP	-1	-0.835	-0.879	3.235	-4.757	-3.787	0.039	-0.440	-0.570	-0.004
57	A	58	THR	0	0.001	-0.022	5.194	-0.149	-0.259	-0.001	-0.013	0.124	0.000
58	A	59	THR	0	-0.105	-0.078	5.082	0.186	0.186	0.000	0.000	0.000	0.000
59	A	60	LYS	1	0.817	0.894	2.550	-0.158	0.690	0.593	-0.398	-1.043	0.001
60	A	61	GLY	0	0.053	0.029	6.227	0.276	0.276	0.000	0.000	0.000	0.000
61	A	62	VAL	0	-0.091	-0.047	7.127	-0.097	-0.097	0.000	0.000	0.000	0.000
62	A	63	LEU	0	0.031	0.018	8.473	-0.048	-0.048	0.000	0.000	0.000	0.000
63	A	64	PHE	0	-0.026	-0.015	10.326	0.156	0.156	0.000	0.000	0.000	0.000
64	A	65	LEU	0	0.012	0.009	10.693	-0.049	-0.049	0.000	0.000	0.000	0.000
65	A	66	VAL	0	0.010	-0.014	14.383	0.005	0.005	0.000	0.000	0.000	0.000
66	A	67	ASP	-1	-0.745	-0.857	18.065	0.090	0.090	0.000	0.000	0.000	0.000
67	A	68	THR	0	-0.093	-0.042	21.111	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	69	TRP	0	0.056	0.009	21.584	0.002	0.002	0.000	0.000	0.000	0.000
69	A	70	GLY	0	-0.015	-0.002	24.348	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	71	GLY	0	0.038	0.037	25.320	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	72	SER	0	-0.027	-0.017	25.158	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	73	PRO	0	0.061	0.032	20.724	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	74	PHE	0	0.062	0.051	20.717	0.004	0.004	0.000	0.000	0.000	0.000
74	A	75	ASN	0	-0.028	-0.025	21.675	-0.009	-0.009	0.000	0.000	0.000	0.000
75	A	76	ALA	0	-0.008	-0.009	22.003	-0.009	-0.009	0.000	0.000	0.000	0.000
76	A	77	ALA	0	0.037	0.027	17.441	-0.010	-0.010	0.000	0.000	0.000	0.000
77	A	78	SER	0	-0.009	-0.026	18.965	-0.016	-0.016	0.000	0.000	0.000	0.000
78	A	79	ARG	1	0.776	0.866	21.129	-0.015	-0.015	0.000	0.000	0.000	0.000
79	A	80	ILE	0	-0.024	-0.001	16.752	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	81	VAL	0	0.016	-0.002	15.679	-0.020	-0.020	0.000	0.000	0.000	0.000
81	A	82	VAL	0	-0.082	-0.017	17.874	-0.016	-0.016	0.000	0.000	0.000	0.000
82	A	83	ASP	-1	-0.883	-0.929	20.779	-0.073	-0.073	0.000	0.000	0.000	0.000
83	A	84	LYS	1	0.793	0.906	15.377	0.073	0.073	0.000	0.000	0.000	0.000
84	A	85	GLU	-1	-0.904	-0.947	14.507	-0.210	-0.210	0.000	0.000	0.000	0.000
85	A	86	HIS	0	-0.021	-0.018	10.114	-0.051	-0.051	0.000	0.000	0.000	0.000
86	A	87	TYR	0	0.016	0.005	11.037	0.005	0.005	0.000	0.000	0.000	0.000
87	A	88	GLU	-1	-0.839	-0.911	12.953	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	89	VAL	0	-0.073	-0.044	13.885	0.045	0.045	0.000	0.000	0.000	0.000
89	A	90	ILE	0	0.017	0.020	13.160	-0.020	-0.020	0.000	0.000	0.000	0.000
90	A	91	ALA	0	-0.052	-0.034	16.608	0.025	0.025	0.000	0.000	0.000	0.000
91	A	92	GLY	0	-0.036	-0.017	19.208	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	93	VAL	0	-0.013	-0.001	15.030	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	94	ASN	0	-0.044	-0.032	17.075	-0.005	-0.005	0.000	0.000	0.000	0.000
94	A	95	ILE	0	0.055	0.010	16.444	0.022	0.022	0.000	0.000	0.000	0.000
95	A	96	PRO	0	-0.008	0.003	15.796	0.016	0.016	0.000	0.000	0.000	0.000
96	A	97	MET	0	0.037	0.042	13.381	0.010	0.010	0.000	0.000	0.000	0.000
97	A	98	LEU	0	-0.039	-0.006	10.724	0.023	0.023	0.000	0.000	0.000	0.000
98	A	99	VAL	0	0.027	-0.001	10.916	0.071	0.071	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.883	-0.951	11.093	0.044	0.044	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.054	-0.036	7.616	-0.059	-0.059	0.000	0.000	0.000	0.000
101	A	102	LEU	0	-0.045	-0.037	6.630	0.053	0.053	0.000	0.000	0.000	0.000
102	A	103	MET	0	-0.037	-0.007	6.114	-0.174	-0.174	0.000	0.000	0.000	0.000
103	A	104	ALA	0	0.029	0.015	7.377	-0.137	-0.137	0.000	0.000	0.000	0.000
104	A	105	ARG	1	0.800	0.905	2.080	-6.725	-6.187	5.164	-2.189	-3.513	-0.002
105	A	106	ASP	-1	-0.876	-0.941	2.863	-7.208	-3.728	0.629	-1.922	-2.187	-0.020
106	A	107	ASP	-1	-1.040	-0.998	3.998	0.063	0.102	0.000	0.026	-0.065	0.000
107	A	108	ASP	-1	-0.921	-0.953	3.867	-0.146	0.263	0.002	-0.144	-0.267	-0.001
108	A	109	PRO	0	-0.006	0.022	5.134	0.100	0.144	-0.001	-0.009	-0.034	0.000
109	A	110	SER	0	-0.047	-0.062	6.849	-0.101	-0.101	0.000	0.000	0.000	0.000
110	A	111	PHE	0	0.047	0.003	8.205	0.030	0.030	0.000	0.000	0.000	0.000
111	A	112	ASP	-1	-0.911	-0.966	9.572	-0.086	-0.086	0.000	0.000	0.000	0.000
112	A	113	GLU	-1	-0.873	-0.902	11.049	-0.142	-0.142	0.000	0.000	0.000	0.000
113	A	114	LEU	0	0.002	0.012	5.600	0.053	0.053	0.000	0.000	0.000	0.000
114	A	115	VAL	0	-0.019	-0.009	9.771	0.077	0.077	0.000	0.000	0.000	0.000
115	A	116	ALA	0	-0.021	-0.017	12.397	0.029	0.029	0.000	0.000	0.000	0.000
116	A	117	LEU	0	0.058	0.035	10.677	0.015	0.015	0.000	0.000	0.000	0.000
117	A	118	ALA	0	0.050	0.044	11.456	0.020	0.020	0.000	0.000	0.000	0.000
118	A	119	VAL	0	-0.044	-0.034	13.340	0.007	0.007	0.000	0.000	0.000	0.000
119	A	120	GLU	-1	-0.988	-0.989	16.807	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	121	THR	0	0.051	-0.004	14.653	0.012	0.012	0.000	0.000	0.000	0.000
121	A	122	GLY	0	0.008	0.014	16.892	0.006	0.006	0.000	0.000	0.000	0.000
122	A	123	ARG	1	0.878	0.935	18.208	-0.033	-0.033	0.000	0.000	0.000	0.000
123	A	124	GLU	-1	-0.929	-0.956	20.554	0.017	0.017	0.000	0.000	0.000	0.000
124	A	125	GLY	0	-0.026	-0.018	20.699	-0.004	-0.004	0.000	0.000	0.000	0.000
125	A	126	VAL	0	-0.084	-0.026	21.570	0.001	0.001	0.000	0.000	0.000	0.000
126	A	127	LYS	1	0.940	0.970	23.693	-0.041	-0.041	0.000	0.000	0.000	0.000
127	A	128	ALA	0	-0.028	-0.007	27.575	0.003	0.003	0.000	0.000	0.000	0.000
128	A	129	LEU	0	0.007	0.003	31.036	-0.002	-0.002	0.000	0.000	0.000	0.000
129	A	130	LYS	1	0.975	0.988	32.614	-0.025	-0.025	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:THR)