FMO DATABASE

FMODB ID: 52MRZ

Calculation Name: 1PDK-B-Xray372

Preferred Name: Chaperone protein PapD

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1PDK

Chain ID: B

ChEMBL ID: CHEMBL3309037

UniProt ID: P15319

Base Structure: X-ray

Registration Date: 2023-09-20

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	148
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1261333.521217
FMO2-HF: Nuclear repulsion	1205947.467962
FMO2-HF: Total energy	-55386.053255
FMO2-MP2: Total energy	-55550.383263

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(B:9:LEU)

Summations of interaction energy for fragment #1(B:9:LEU)

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.
-4.61	-2.251	1.353	-0.648	-3.064	-0.008

Interaction energy analysis for fragmet #1(B:9:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / 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

Sort

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	B	11	ASP	-1	-0.849	-0.924	2.393	-4.851	-2.350	1.354	-0.638	-3.217	-0.008
4	B	12	ARG	1	0.869	0.956	3.876	1.311	1.330	0.000	0.018	-0.037	0.000
5	B	13	PRO	0	0.034	0.008	7.285	-0.159	-0.159	0.000	0.000	0.000	0.000
6	B	14	CYS	0	-0.094	-0.050	6.960	0.236	0.236	0.000	0.000	0.000	0.000
7	B	15	HIS	0	0.002	0.030	5.336	0.456	0.456	0.000	0.000	0.000	0.000
8	B	16	VAL	0	0.012	-0.010	10.246	0.025	0.025	0.000	0.000	0.000	0.000
9	B	17	SER	0	0.015	0.004	9.537	-0.115	-0.115	0.000	0.000	0.000	0.000
10	B	18	GLY	0	0.046	0.008	9.834	0.077	0.077	0.000	0.000	0.000	0.000
11	B	19	ASP	-1	-0.824	-0.880	11.702	-0.027	-0.027	0.000	0.000	0.000	0.000
12	B	20	SER	0	-0.121	-0.066	13.773	0.032	0.032	0.000	0.000	0.000	0.000
13	B	21	LEU	0	0.005	-0.006	12.679	-0.008	-0.008	0.000	0.000	0.000	0.000
14	B	22	ASN	0	-0.001	0.011	15.951	-0.006	-0.006	0.000	0.000	0.000	0.000
15	B	23	LYS	1	0.858	0.952	18.114	0.222	0.222	0.000	0.000	0.000	0.000
16	B	24	HIS	0	0.008	-0.001	21.569	0.003	0.003	0.000	0.000	0.000	0.000
17	B	25	VAL	0	0.004	0.017	25.365	0.010	0.010	0.000	0.000	0.000	0.000
18	B	26	VAL	0	0.063	0.034	28.053	-0.001	-0.001	0.000	0.000	0.000	0.000
19	B	27	PHE	0	0.021	0.007	31.344	0.008	0.008	0.000	0.000	0.000	0.000
20	B	28	LYS	1	0.840	0.922	31.604	0.055	0.055	0.000	0.000	0.000	0.000
21	B	29	THR	0	-0.020	0.000	37.177	0.000	0.000	0.000	0.000	0.000	0.000
22	B	30	ARG	1	0.857	0.910	40.225	0.033	0.033	0.000	0.000	0.000	0.000
23	B	31	ALA	0	0.044	0.023	44.000	0.000	0.000	0.000	0.000	0.000	0.000
24	B	32	SER	0	0.041	0.012	46.090	-0.001	-0.001	0.000	0.000	0.000	0.000
25	B	33	ARG	1	0.864	0.922	46.312	0.029	0.029	0.000	0.000	0.000	0.000
26	B	34	ASP	-1	-0.760	-0.855	42.041	-0.038	-0.038	0.000	0.000	0.000	0.000
27	B	35	PHE	0	-0.024	-0.020	39.795	-0.001	-0.001	0.000	0.000	0.000	0.000
28	B	36	TRP	0	-0.027	0.002	45.582	0.001	0.001	0.000	0.000	0.000	0.000
29	B	37	TYR	0	-0.005	-0.028	48.265	0.001	0.001	0.000	0.000	0.000	0.000
30	B	38	PRO	0	0.018	0.027	46.926	-0.001	-0.001	0.000	0.000	0.000	0.000
31	B	39	PRO	0	-0.008	-0.019	42.613	0.003	0.003	0.000	0.000	0.000	0.000
32	B	40	GLY	0	0.017	0.025	44.291	-0.003	-0.003	0.000	0.000	0.000	0.000
33	B	41	ARG	1	0.907	0.940	35.384	0.054	0.054	0.000	0.000	0.000	0.000
34	B	42	SER	0	0.016	0.040	35.937	0.003	0.003	0.000	0.000	0.000	0.000
35	B	43	PRO	0	0.006	-0.015	35.592	-0.002	-0.002	0.000	0.000	0.000	0.000
36	B	44	THR	0	-0.001	-0.012	30.441	-0.004	-0.004	0.000	0.000	0.000	0.000
37	B	45	GLU	-1	-0.828	-0.893	29.578	-0.051	-0.051	0.000	0.000	0.000	0.000
38	B	46	SER	0	-0.026	-0.016	25.337	-0.007	-0.007	0.000	0.000	0.000	0.000
39	B	47	PHE	0	-0.011	-0.005	22.119	0.002	0.002	0.000	0.000	0.000	0.000
40	B	48	VAL	0	0.006	0.000	17.953	-0.008	-0.008	0.000	0.000	0.000	0.000
41	B	49	ILE	0	-0.008	-0.008	16.142	-0.011	-0.011	0.000	0.000	0.000	0.000
42	B	50	ARG	1	0.845	0.901	11.400	0.161	0.161	0.000	0.000	0.000	0.000
43	B	51	LEU	0	-0.039	-0.015	11.725	-0.078	-0.078	0.000	0.000	0.000	0.000
44	B	52	GLU	-1	-0.807	-0.928	6.173	-0.385	-0.385	0.000	0.000	0.000	0.000
45	B	53	ASN	0	0.030	0.021	4.387	-1.397	-1.558	-0.001	-0.028	0.190	0.000
46	B	55	HIS	0	0.081	0.034	9.314	0.230	0.230	0.000	0.000	0.000	0.000
47	B	56	ALA	0	0.087	0.027	13.427	-0.029	-0.029	0.000	0.000	0.000	0.000
48	B	57	THR	0	-0.023	-0.029	17.187	-0.026	-0.026	0.000	0.000	0.000	0.000
49	B	58	ALA	0	-0.032	-0.009	14.872	0.005	0.005	0.000	0.000	0.000	0.000
50	B	59	VAL	0	0.179	0.082	16.071	-0.036	-0.036	0.000	0.000	0.000	0.000
51	B	60	GLY	0	-0.002	0.010	17.303	-0.030	-0.030	0.000	0.000	0.000	0.000
52	B	61	LYS	1	0.859	0.929	18.297	0.234	0.234	0.000	0.000	0.000	0.000
53	B	62	ILE	0	-0.020	-0.002	12.889	-0.008	-0.008	0.000	0.000	0.000	0.000
54	B	63	VAL	0	-0.015	-0.020	15.361	-0.030	-0.030	0.000	0.000	0.000	0.000
55	B	64	THR	0	-0.051	-0.005	17.618	0.057	0.057	0.000	0.000	0.000	0.000
56	B	65	LEU	0	-0.017	-0.001	17.140	-0.031	-0.031	0.000	0.000	0.000	0.000
57	B	66	THR	0	0.050	0.021	21.115	0.037	0.037	0.000	0.000	0.000	0.000
58	B	67	PHE	0	0.041	0.046	22.838	-0.022	-0.022	0.000	0.000	0.000	0.000
59	B	68	LYS	1	0.924	0.961	25.927	0.250	0.250	0.000	0.000	0.000	0.000
60	B	69	GLY	0	0.069	0.015	28.297	-0.004	-0.004	0.000	0.000	0.000	0.000
61	B	70	THR	0	-0.023	-0.009	31.083	0.000	0.000	0.000	0.000	0.000	0.000
62	B	71	GLU	-1	-0.789	-0.870	34.812	-0.115	-0.115	0.000	0.000	0.000	0.000
63	B	72	GLU	-1	-0.833	-0.917	36.603	-0.083	-0.083	0.000	0.000	0.000	0.000
64	B	73	ALA	0	0.010	-0.003	39.615	0.003	0.003	0.000	0.000	0.000	0.000
65	B	74	ALA	0	-0.003	0.006	42.465	0.003	0.003	0.000	0.000	0.000	0.000
66	B	75	LEU	0	-0.091	-0.043	39.905	0.004	0.004	0.000	0.000	0.000	0.000
67	B	76	PRO	0	0.047	0.016	39.091	-0.006	-0.006	0.000	0.000	0.000	0.000
68	B	77	GLY	0	-0.066	-0.051	35.319	0.003	0.003	0.000	0.000	0.000	0.000
69	B	78	HIS	0	-0.044	-0.021	34.358	-0.002	-0.002	0.000	0.000	0.000	0.000
70	B	79	LEU	0	-0.002	-0.007	29.934	-0.003	-0.003	0.000	0.000	0.000	0.000
71	B	80	LYS	1	0.862	0.925	34.594	0.103	0.103	0.000	0.000	0.000	0.000
72	B	81	VAL	0	-0.024	0.006	35.676	-0.006	-0.006	0.000	0.000	0.000	0.000
73	B	82	THR	0	-0.059	-0.042	36.774	0.003	0.003	0.000	0.000	0.000	0.000
74	B	83	GLY	0	0.080	0.028	39.103	0.003	0.003	0.000	0.000	0.000	0.000
75	B	84	VAL	0	0.035	-0.002	41.934	0.000	0.000	0.000	0.000	0.000	0.000
76	B	85	ASN	0	0.007	-0.007	42.605	0.004	0.004	0.000	0.000	0.000	0.000
77	B	86	ALA	0	0.038	0.029	41.853	-0.002	-0.002	0.000	0.000	0.000	0.000
78	B	87	GLY	0	0.010	0.013	42.287	0.003	0.003	0.000	0.000	0.000	0.000
79	B	88	ARG	1	0.842	0.926	43.851	0.059	0.059	0.000	0.000	0.000	0.000
80	B	89	LEU	0	-0.003	0.001	39.958	0.003	0.003	0.000	0.000	0.000	0.000
81	B	90	GLY	0	0.023	0.023	38.218	-0.004	-0.004	0.000	0.000	0.000	0.000
82	B	91	ILE	0	-0.035	-0.015	31.819	0.005	0.005	0.000	0.000	0.000	0.000
83	B	92	ALA	0	0.036	0.012	33.875	-0.007	-0.007	0.000	0.000	0.000	0.000
84	B	93	LEU	0	0.016	0.005	27.340	0.001	0.001	0.000	0.000	0.000	0.000
85	B	94	LEU	0	-0.030	-0.011	29.234	0.003	0.003	0.000	0.000	0.000	0.000
86	B	95	ASP	-1	-0.716	-0.844	25.183	-0.181	-0.181	0.000	0.000	0.000	0.000
87	B	96	THR	0	0.012	-0.025	21.647	0.005	0.005	0.000	0.000	0.000	0.000
88	B	97	ASP	-1	-0.902	-0.907	24.990	-0.082	-0.082	0.000	0.000	0.000	0.000
89	B	98	GLY	0	-0.006	-0.007	27.985	0.012	0.012	0.000	0.000	0.000	0.000
90	B	99	SER	0	-0.083	-0.052	29.596	0.010	0.010	0.000	0.000	0.000	0.000
91	B	100	SER	0	-0.043	-0.037	30.626	0.002	0.002	0.000	0.000	0.000	0.000
92	B	101	LEU	0	-0.041	-0.012	30.927	-0.006	-0.006	0.000	0.000	0.000	0.000
93	B	102	LEU	0	-0.041	-0.023	25.164	-0.004	-0.004	0.000	0.000	0.000	0.000
94	B	103	LYS	1	0.948	0.971	29.901	0.103	0.103	0.000	0.000	0.000	0.000
95	B	104	PRO	0	0.037	0.032	30.076	-0.013	-0.013	0.000	0.000	0.000	0.000
96	B	105	GLY	0	-0.052	-0.019	29.181	0.006	0.006	0.000	0.000	0.000	0.000
97	B	106	THR	0	-0.071	-0.039	29.626	-0.003	-0.003	0.000	0.000	0.000	0.000
98	B	107	SER	0	-0.029	-0.021	24.942	-0.003	-0.003	0.000	0.000	0.000	0.000
99	B	108	HIS	1	0.801	0.863	21.274	0.221	0.221	0.000	0.000	0.000	0.000
100	B	109	ASN	0	-0.021	-0.012	24.717	-0.015	-0.015	0.000	0.000	0.000	0.000
101	B	110	LYS	1	0.880	0.950	20.618	0.209	0.209	0.000	0.000	0.000	0.000
102	B	111	GLY	0	-0.013	-0.005	22.798	0.018	0.018	0.000	0.000	0.000	0.000
103	B	112	GLN	0	0.035	-0.005	23.461	0.004	0.004	0.000	0.000	0.000	0.000
104	B	113	GLY	0	0.068	0.044	24.489	-0.013	-0.013	0.000	0.000	0.000	0.000
105	B	114	GLU	-1	-0.873	-0.912	19.194	-0.204	-0.204	0.000	0.000	0.000	0.000
106	B	115	LYS	1	0.943	0.980	18.367	-0.032	-0.032	0.000	0.000	0.000	0.000
107	B	116	VAL	0	-0.005	-0.021	14.955	-0.032	-0.032	0.000	0.000	0.000	0.000
108	B	117	THR	0	0.002	0.006	14.524	0.062	0.062	0.000	0.000	0.000	0.000
109	B	118	GLY	0	0.046	0.034	11.500	-0.016	-0.016	0.000	0.000	0.000	0.000
110	B	119	ASN	0	0.008	-0.005	6.144	-0.434	-0.434	0.000	0.000	0.000	0.000
111	B	120	SER	0	-0.041	-0.010	9.168	-0.244	-0.244	0.000	0.000	0.000	0.000
112	B	121	LEU	0	-0.038	-0.021	10.379	0.096	0.096	0.000	0.000	0.000	0.000
113	B	122	GLU	-1	-0.882	-0.940	13.847	-0.120	-0.120	0.000	0.000	0.000	0.000
114	B	123	LEU	0	-0.022	-0.017	16.177	0.021	0.021	0.000	0.000	0.000	0.000
115	B	124	PRO	0	-0.011	-0.004	19.202	-0.009	-0.009	0.000	0.000	0.000	0.000
116	B	125	PHE	0	0.061	0.030	20.183	0.000	0.000	0.000	0.000	0.000	0.000
117	B	126	GLY	0	0.013	0.001	24.541	0.013	0.013	0.000	0.000	0.000	0.000
118	B	127	ALA	0	0.010	0.009	27.955	-0.010	-0.010	0.000	0.000	0.000	0.000
119	B	128	TYR	0	-0.027	-0.009	30.389	0.010	0.010	0.000	0.000	0.000	0.000
120	B	129	VAL	0	0.040	0.035	34.042	-0.006	-0.006	0.000	0.000	0.000	0.000
121	B	130	VAL	0	0.001	-0.017	36.931	0.006	0.006	0.000	0.000	0.000	0.000
122	B	131	ALA	0	0.027	0.022	40.009	-0.003	-0.003	0.000	0.000	0.000	0.000
123	B	132	THR	0	-0.016	-0.006	43.382	-0.001	-0.001	0.000	0.000	0.000	0.000
124	B	133	PRO	0	0.066	0.021	44.810	0.004	0.004	0.000	0.000	0.000	0.000
125	B	134	GLU	-1	-0.777	-0.882	47.702	-0.045	-0.045	0.000	0.000	0.000	0.000
126	B	135	ALA	0	-0.023	0.005	46.579	0.003	0.003	0.000	0.000	0.000	0.000
127	B	136	LEU	0	-0.006	0.010	46.868	0.002	0.002	0.000	0.000	0.000	0.000
128	B	137	ARG	1	0.823	0.895	49.088	0.046	0.046	0.000	0.000	0.000	0.000
129	B	138	THR	0	-0.076	-0.066	51.959	0.002	0.002	0.000	0.000	0.000	0.000
130	B	139	LYS	1	0.905	0.972	50.877	0.035	0.035	0.000	0.000	0.000	0.000
131	B	140	SER	0	-0.007	0.009	49.859	0.000	0.000	0.000	0.000	0.000	0.000
132	B	141	VAL	0	-0.015	-0.002	44.637	-0.001	-0.001	0.000	0.000	0.000	0.000
133	B	142	VAL	0	0.013	0.005	47.215	0.003	0.003	0.000	0.000	0.000	0.000
134	B	143	PRO	0	-0.067	-0.035	46.038	-0.002	-0.002	0.000	0.000	0.000	0.000
135	B	144	GLY	0	0.042	0.005	44.384	0.001	0.001	0.000	0.000	0.000	0.000
136	B	145	ASP	-1	-0.913	-0.941	39.124	-0.061	-0.061	0.000	0.000	0.000	0.000
137	B	146	TYR	0	-0.087	-0.066	36.039	-0.001	-0.001	0.000	0.000	0.000	0.000
138	B	147	GLU	-1	-0.860	-0.916	33.853	-0.098	-0.098	0.000	0.000	0.000	0.000
139	B	148	ALA	0	-0.001	-0.017	32.873	0.001	0.001	0.000	0.000	0.000	0.000
140	B	149	THR	0	-0.015	0.004	29.054	-0.006	-0.006	0.000	0.000	0.000	0.000
141	B	150	ALA	0	0.010	0.000	26.818	0.005	0.005	0.000	0.000	0.000	0.000
142	B	151	THR	0	-0.029	-0.008	23.232	-0.012	-0.012	0.000	0.000	0.000	0.000
143	B	152	PHE	0	0.020	0.015	17.255	0.008	0.008	0.000	0.000	0.000	0.000
144	B	153	GLU	-1	-0.912	-0.982	20.544	-0.343	-0.343	0.000	0.000	0.000	0.000
145	B	154	LEU	0	0.006	0.008	15.147	0.013	0.013	0.000	0.000	0.000	0.000
146	B	155	THR	0	0.006	0.000	18.524	-0.014	-0.014	0.000	0.000	0.000	0.000
147	B	156	TYR	0	-0.049	-0.037	12.019	0.008	0.008	0.000	0.000	0.000	0.000
148	B	157	ARG	1	0.921	0.979	17.278	0.338	0.338	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:9:LEU)