FMO DATABASE

FMODB ID: N93GQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1068748.275851
FMO2-HF: Nuclear repulsion	1019811.20206
FMO2-HF: Total energy	-48937.073791
FMO2-MP2: Total energy	-49080.9877

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.
-19.473	-7.976	5.808	-7.318	-9.98	0.005

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 : 0.047 / q_NPA : 0.018

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	0.026	0.027	3.473	2.445	5.039	0.056	-1.329	-1.321	0.005
4	A	5	ILE	0	0.010	0.008	5.517	-0.916	-0.812	-0.001	-0.008	-0.094	0.000
5	A	6	VAL	0	-0.006	0.002	7.873	0.016	0.016	0.000	0.000	0.000	0.000
6	A	7	ILE	0	0.000	0.003	11.234	-0.143	-0.143	0.000	0.000	0.000	0.000
7	A	8	GLY	0	0.033	0.004	14.020	-0.034	-0.034	0.000	0.000	0.000	0.000
8	A	9	THR	0	-0.057	-0.036	17.619	-0.008	-0.008	0.000	0.000	0.000	0.000
9	A	10	HIS	0	-0.060	-0.072	20.957	-0.025	-0.025	0.000	0.000	0.000	0.000
10	A	11	GLY	0	-0.037	-0.004	24.141	0.011	0.011	0.000	0.000	0.000	0.000
11	A	12	TRP	0	0.032	-0.013	22.590	0.003	0.003	0.000	0.000	0.000	0.000
12	A	13	ALA	0	0.012	0.008	21.672	0.013	0.013	0.000	0.000	0.000	0.000
13	A	14	ALA	0	0.014	0.016	16.486	0.020	0.020	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.840	-0.921	16.499	0.447	0.447	0.000	0.000	0.000	0.000
15	A	16	GLN	0	0.008	-0.018	17.185	0.037	0.037	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.017	0.000	16.724	-0.005	-0.005	0.000	0.000	0.000	0.000
17	A	18	LEU	0	0.058	0.036	10.854	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.914	0.962	14.338	-0.452	-0.452	0.000	0.000	0.000	0.000
19	A	20	THR	0	-0.049	-0.022	16.774	-0.041	-0.041	0.000	0.000	0.000	0.000
20	A	21	ALA	0	0.020	0.001	12.684	-0.043	-0.043	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.834	-0.911	11.801	0.917	0.917	0.000	0.000	0.000	0.000
22	A	23	MET	0	-0.112	-0.032	13.900	-0.081	-0.081	0.000	0.000	0.000	0.000
23	A	24	LEU	0	-0.118	-0.072	15.366	-0.055	-0.055	0.000	0.000	0.000	0.000
24	A	25	LEU	0	-0.038	-0.022	9.756	-0.054	-0.054	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.008	0.029	11.682	-0.016	-0.016	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.998	-1.006	11.539	0.666	0.666	0.000	0.000	0.000	0.000
27	A	28	GLN	0	-0.041	-0.035	7.101	0.355	0.355	0.000	0.000	0.000	0.000
28	A	29	GLU	-1	-0.907	-0.940	5.037	1.044	1.044	0.000	0.000	0.000	0.000
29	A	30	ASN	0	-0.020	-0.008	2.564	-5.699	-1.992	0.751	-1.969	-2.488	0.021
30	A	31	VAL	0	0.029	0.014	5.028	0.796	0.805	-0.001	-0.007	-0.001	0.000
31	A	32	GLY	0	0.009	0.011	7.675	-0.404	-0.404	0.000	0.000	0.000	0.000
32	A	33	TRP	0	-0.063	-0.026	11.130	-0.009	-0.009	0.000	0.000	0.000	0.000
33	A	34	ILE	0	-0.035	-0.014	14.487	-0.059	-0.059	0.000	0.000	0.000	0.000
34	A	35	ASP	-1	-0.863	-0.936	18.012	0.275	0.275	0.000	0.000	0.000	0.000
35	A	36	PHE	0	-0.045	-0.028	21.500	-0.021	-0.021	0.000	0.000	0.000	0.000
36	A	37	VAL	0	0.013	0.011	24.440	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	38	PRO	0	-0.008	-0.016	27.905	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	39	GLY	0	0.005	0.001	31.280	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	40	GLU	-1	-0.823	-0.892	26.000	0.163	0.163	0.000	0.000	0.000	0.000
40	A	41	ASN	0	0.018	-0.005	28.597	0.003	0.003	0.000	0.000	0.000	0.000
41	A	42	ALA	0	0.036	-0.005	25.502	0.009	0.009	0.000	0.000	0.000	0.000
42	A	43	GLU	-1	-0.892	-0.953	24.676	0.055	0.055	0.000	0.000	0.000	0.000
43	A	44	THR	0	0.019	0.022	25.049	0.001	0.001	0.000	0.000	0.000	0.000
44	A	45	LEU	0	-0.019	-0.021	21.740	0.011	0.011	0.000	0.000	0.000	0.000
45	A	46	ILE	0	0.005	0.015	20.607	0.023	0.023	0.000	0.000	0.000	0.000
46	A	47	GLU	-1	-0.924	-0.953	20.114	0.073	0.073	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.785	0.892	19.623	-0.199	-0.199	0.000	0.000	0.000	0.000
48	A	49	TYR	0	0.001	-0.017	15.683	0.050	0.050	0.000	0.000	0.000	0.000
49	A	50	ASN	0	0.030	0.012	15.454	0.024	0.024	0.000	0.000	0.000	0.000
50	A	51	ALA	0	-0.012	-0.002	15.835	-0.012	-0.012	0.000	0.000	0.000	0.000
51	A	52	GLN	0	-0.026	-0.011	13.077	0.101	0.101	0.000	0.000	0.000	0.000
52	A	53	LEU	0	0.059	0.026	11.056	0.054	0.054	0.000	0.000	0.000	0.000
53	A	54	ALA	0	-0.053	-0.010	11.056	-0.070	-0.070	0.000	0.000	0.000	0.000
54	A	55	LYS	1	0.787	0.880	11.703	-0.376	-0.376	0.000	0.000	0.000	0.000
55	A	56	LEU	0	-0.037	-0.003	7.225	0.106	0.106	0.000	0.000	0.000	0.000
56	A	57	ASP	-1	-0.829	-0.869	3.606	-4.705	-4.036	0.009	-0.243	-0.434	-0.002
57	A	58	THR	0	0.000	-0.022	4.727	-0.236	-0.329	-0.001	-0.013	0.107	0.000
58	A	59	THR	0	-0.099	-0.084	5.371	0.120	0.120	0.000	0.000	0.000	0.000
59	A	60	LYS	1	0.923	0.965	2.672	2.617	3.361	0.314	-0.297	-0.760	0.001
60	A	61	GLY	0	0.055	0.032	6.407	0.308	0.308	0.000	0.000	0.000	0.000
61	A	62	VAL	0	-0.086	-0.043	7.127	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	63	LEU	0	0.035	0.018	8.367	-0.118	-0.118	0.000	0.000	0.000	0.000
63	A	64	PHE	0	-0.030	-0.015	10.287	0.231	0.231	0.000	0.000	0.000	0.000
64	A	65	LEU	0	0.008	0.008	10.697	-0.085	-0.085	0.000	0.000	0.000	0.000
65	A	66	VAL	0	0.008	-0.013	14.352	0.012	0.012	0.000	0.000	0.000	0.000
66	A	67	ASP	-1	-0.751	-0.870	18.032	0.215	0.215	0.000	0.000	0.000	0.000
67	A	68	THR	0	-0.071	-0.029	21.083	-0.023	-0.023	0.000	0.000	0.000	0.000
68	A	69	TRP	0	0.054	0.009	21.551	0.005	0.005	0.000	0.000	0.000	0.000
69	A	70	GLY	0	-0.016	-0.002	24.318	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	71	GLY	0	0.030	0.032	25.285	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	72	SER	0	-0.034	-0.020	25.118	-0.006	-0.006	0.000	0.000	0.000	0.000
72	A	73	PRO	0	0.050	0.025	20.593	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	74	PHE	0	0.068	0.045	20.597	0.010	0.010	0.000	0.000	0.000	0.000
74	A	75	ASN	0	-0.017	-0.028	21.633	-0.015	-0.015	0.000	0.000	0.000	0.000
75	A	76	ALA	0	-0.015	-0.013	21.832	-0.017	-0.017	0.000	0.000	0.000	0.000
76	A	77	ALA	0	0.042	0.026	17.424	-0.016	-0.016	0.000	0.000	0.000	0.000
77	A	78	SER	0	-0.006	-0.009	18.919	-0.027	-0.027	0.000	0.000	0.000	0.000
78	A	79	ARG	1	0.867	0.928	21.085	-0.076	-0.076	0.000	0.000	0.000	0.000
79	A	80	ILE	0	-0.041	0.005	16.230	-0.023	-0.023	0.000	0.000	0.000	0.000
80	A	81	VAL	0	0.039	-0.004	15.667	-0.033	-0.033	0.000	0.000	0.000	0.000
81	A	82	VAL	0	-0.075	-0.010	17.874	-0.029	-0.029	0.000	0.000	0.000	0.000
82	A	83	ASP	-1	-0.913	-0.952	20.857	-0.076	-0.076	0.000	0.000	0.000	0.000
83	A	84	LYS	1	0.806	0.915	15.416	0.057	0.057	0.000	0.000	0.000	0.000
84	A	85	GLU	-1	-0.943	-0.966	14.663	-0.369	-0.369	0.000	0.000	0.000	0.000
85	A	86	HIS	0	0.008	-0.002	10.174	0.010	0.010	0.000	0.000	0.000	0.000
86	A	87	TYR	0	0.005	0.004	11.037	-0.011	-0.011	0.000	0.000	0.000	0.000
87	A	88	GLU	-1	-0.831	-0.905	12.907	0.033	0.033	0.000	0.000	0.000	0.000
88	A	89	VAL	0	-0.082	-0.048	13.847	0.084	0.084	0.000	0.000	0.000	0.000
89	A	90	ILE	0	0.020	0.019	13.322	-0.040	-0.040	0.000	0.000	0.000	0.000
90	A	91	ALA	0	-0.059	-0.037	16.581	0.044	0.044	0.000	0.000	0.000	0.000
91	A	92	GLY	0	-0.035	-0.018	19.188	-0.008	-0.008	0.000	0.000	0.000	0.000
92	A	93	VAL	0	-0.006	0.008	15.083	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	94	ASN	0	-0.033	-0.030	17.081	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	95	ILE	0	0.043	0.008	16.439	0.037	0.037	0.000	0.000	0.000	0.000
95	A	96	PRO	0	-0.016	-0.001	15.800	0.037	0.037	0.000	0.000	0.000	0.000
96	A	97	MET	0	0.034	0.042	13.309	0.027	0.027	0.000	0.000	0.000	0.000
97	A	98	LEU	0	-0.032	-0.015	10.946	0.043	0.043	0.000	0.000	0.000	0.000
98	A	99	VAL	0	0.025	-0.002	10.920	0.132	0.132	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.895	-0.955	11.144	0.242	0.242	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.040	-0.020	7.638	-0.077	-0.077	0.000	0.000	0.000	0.000
101	A	102	LEU	0	-0.046	-0.037	6.628	0.099	0.099	0.000	0.000	0.000	0.000
102	A	103	MET	0	-0.034	-0.007	6.170	-0.077	-0.077	0.000	0.000	0.000	0.000
103	A	104	ALA	0	0.040	0.020	7.458	-0.147	-0.147	0.000	0.000	0.000	0.000
104	A	105	ARG	1	0.781	0.875	1.891	-8.893	-8.332	4.350	-1.953	-2.957	-0.007
105	A	106	ASP	-1	-0.881	-0.939	3.043	-4.791	-2.002	0.333	-1.417	-1.705	-0.013
106	A	107	ASP	-1	-1.052	-1.004	4.087	-0.329	-0.273	-0.001	0.012	-0.067	0.000
107	A	108	ASP	-1	-1.024	-1.027	4.090	-2.355	-2.051	0.000	-0.086	-0.217	0.000
108	A	109	PRO	0	0.003	0.031	5.255	0.116	0.169	-0.001	-0.008	-0.043	0.000
109	A	110	SER	0	-0.010	-0.009	6.834	-0.183	-0.183	0.000	0.000	0.000	0.000
110	A	111	PHE	0	0.053	-0.001	8.179	0.093	0.093	0.000	0.000	0.000	0.000
111	A	112	ASP	-1	-0.909	-0.961	9.562	-0.115	-0.115	0.000	0.000	0.000	0.000
112	A	113	GLU	-1	-0.938	-0.969	10.980	-0.283	-0.283	0.000	0.000	0.000	0.000
113	A	114	LEU	0	0.006	0.013	5.596	0.095	0.095	0.000	0.000	0.000	0.000
114	A	115	VAL	0	-0.023	-0.012	9.774	0.125	0.125	0.000	0.000	0.000	0.000
115	A	116	ALA	0	-0.022	-0.017	12.387	0.045	0.045	0.000	0.000	0.000	0.000
116	A	117	LEU	0	0.056	0.034	10.743	0.023	0.023	0.000	0.000	0.000	0.000
117	A	118	ALA	0	0.042	0.033	11.476	0.035	0.035	0.000	0.000	0.000	0.000
118	A	119	VAL	0	-0.049	-0.035	13.339	0.008	0.008	0.000	0.000	0.000	0.000
119	A	120	GLU	-1	-0.996	-0.990	16.808	0.041	0.041	0.000	0.000	0.000	0.000
120	A	121	THR	0	0.070	0.014	14.627	0.023	0.023	0.000	0.000	0.000	0.000
121	A	122	GLY	0	-0.001	0.008	16.890	0.010	0.010	0.000	0.000	0.000	0.000
122	A	123	ARG	1	0.880	0.930	18.208	-0.099	-0.099	0.000	0.000	0.000	0.000
123	A	124	GLU	-1	-0.913	-0.952	20.367	0.075	0.075	0.000	0.000	0.000	0.000
124	A	125	GLY	0	-0.035	-0.016	20.691	-0.006	-0.006	0.000	0.000	0.000	0.000
125	A	126	VAL	0	-0.088	-0.031	21.579	0.003	0.003	0.000	0.000	0.000	0.000
126	A	127	LYS	1	0.960	0.979	23.628	-0.138	-0.138	0.000	0.000	0.000	0.000
127	A	128	ALA	0	-0.023	-0.010	27.583	0.006	0.006	0.000	0.000	0.000	0.000
128	A	129	LEU	0	0.003	0.004	31.045	-0.004	-0.004	0.000	0.000	0.000	0.000
129	A	130	LYS	1	0.972	0.985	32.628	-0.075	-0.075	0.000	0.000	0.000	0.000

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