FMO DATABASE

FMODB ID: QV4NY

Calculation Name: 1PM3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1PM3

Chain ID: A

ChEMBL ID:

UniProt ID: O27887

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	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	69
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-378926.169621
FMO2-HF: Nuclear repulsion	352365.457761
FMO2-HF: Total energy	-26560.71186
FMO2-MP2: Total energy	-26637.203923

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:0:HIS)

Summations of interaction energy for fragment #1(A:0:HIS)

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.
1.266	3.348	-0.035	-1.077	-0.97	-0.001

Interaction energy analysis for fragmet #1(A:0:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : -0.027

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	2	ARG	1	0.904	0.959	3.823	-0.947	1.135	-0.035	-1.077	-0.970	-0.001
4	A	3	ILE	0	0.056	0.023	7.040	-0.146	-0.146	0.000	0.000	0.000	0.000
5	A	4	VAL	0	0.038	0.008	9.177	-0.162	-0.162	0.000	0.000	0.000	0.000
6	A	5	GLU	-1	-0.927	-0.972	10.885	0.334	0.334	0.000	0.000	0.000	0.000
7	A	6	GLU	-1	-0.850	-0.927	6.785	-1.001	-1.001	0.000	0.000	0.000	0.000
8	A	7	MET	0	-0.104	-0.039	7.603	-0.138	-0.138	0.000	0.000	0.000	0.000
9	A	8	VAL	0	0.085	0.023	10.354	0.110	0.110	0.000	0.000	0.000	0.000
10	A	9	GLY	0	-0.040	-0.004	13.759	-0.091	-0.091	0.000	0.000	0.000	0.000
11	A	10	LYS	1	0.847	0.930	9.524	-0.403	-0.403	0.000	0.000	0.000	0.000
12	A	11	GLU	-1	-0.931	-0.984	15.479	0.203	0.203	0.000	0.000	0.000	0.000
13	A	12	VAL	0	0.033	0.022	15.857	0.015	0.015	0.000	0.000	0.000	0.000
14	A	13	LEU	0	-0.029	-0.029	17.817	-0.041	-0.041	0.000	0.000	0.000	0.000
15	A	14	ASP	-1	-0.779	-0.884	19.272	0.222	0.222	0.000	0.000	0.000	0.000
16	A	15	SER	0	0.025	0.001	21.748	-0.014	-0.014	0.000	0.000	0.000	0.000
17	A	16	SER	0	-0.060	-0.028	22.822	-0.032	-0.032	0.000	0.000	0.000	0.000
18	A	17	ALA	0	-0.049	-0.015	22.936	-0.016	-0.016	0.000	0.000	0.000	0.000
19	A	18	LYS	1	0.949	0.987	24.007	-0.196	-0.196	0.000	0.000	0.000	0.000
20	A	19	VAL	0	-0.001	-0.004	21.497	0.021	0.021	0.000	0.000	0.000	0.000
21	A	20	ILE	0	-0.077	-0.040	20.864	-0.017	-0.017	0.000	0.000	0.000	0.000
22	A	21	GLY	0	0.034	0.016	21.653	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	22	LYS	1	0.894	0.953	18.765	-0.221	-0.221	0.000	0.000	0.000	0.000
24	A	23	VAL	0	-0.005	0.026	13.470	-0.017	-0.017	0.000	0.000	0.000	0.000
25	A	24	LYS	1	0.827	0.910	16.757	-0.426	-0.426	0.000	0.000	0.000	0.000
26	A	25	ASP	-1	-0.815	-0.923	15.483	0.795	0.795	0.000	0.000	0.000	0.000
27	A	26	VAL	0	-0.095	-0.087	11.177	0.031	0.031	0.000	0.000	0.000	0.000
28	A	27	GLU	-1	-0.930	-0.937	14.237	0.648	0.648	0.000	0.000	0.000	0.000
29	A	28	VAL	0	-0.028	-0.045	12.231	0.155	0.155	0.000	0.000	0.000	0.000
30	A	29	ASP	-1	-0.796	-0.890	14.793	0.571	0.571	0.000	0.000	0.000	0.000
31	A	30	ILE	0	-0.080	-0.060	15.960	0.086	0.086	0.000	0.000	0.000	0.000
32	A	31	GLU	-1	-0.902	-0.937	17.671	0.512	0.512	0.000	0.000	0.000	0.000
33	A	32	SER	0	-0.129	-0.067	15.433	0.069	0.069	0.000	0.000	0.000	0.000
34	A	33	GLN	0	-0.048	-0.028	10.316	0.188	0.188	0.000	0.000	0.000	0.000
35	A	34	ALA	0	-0.027	0.004	11.372	0.374	0.374	0.000	0.000	0.000	0.000
36	A	35	ILE	0	-0.028	-0.010	8.320	-0.090	-0.090	0.000	0.000	0.000	0.000
37	A	36	GLU	-1	-0.885	-0.935	12.228	0.642	0.642	0.000	0.000	0.000	0.000
38	A	37	SER	0	-0.004	-0.021	15.207	-0.105	-0.105	0.000	0.000	0.000	0.000
39	A	38	LEU	0	-0.036	-0.004	12.852	0.086	0.086	0.000	0.000	0.000	0.000
40	A	39	VAL	0	0.035	0.067	16.009	-0.098	-0.098	0.000	0.000	0.000	0.000
41	A	40	LEU	0	0.008	-0.031	17.504	0.000	0.000	0.000	0.000	0.000	0.000
42	A	41	GLY	0	-0.025	-0.020	20.230	-0.021	-0.021	0.000	0.000	0.000	0.000
43	A	42	LYS	1	0.959	0.993	22.993	-0.201	-0.201	0.000	0.000	0.000	0.000
44	A	43	GLY	0	0.014	-0.020	26.518	-0.012	-0.012	0.000	0.000	0.000	0.000
45	A	44	GLY	0	-0.042	-0.002	27.555	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	54	GLY	0	-0.023	-0.011	28.209	0.003	0.003	0.000	0.000	0.000	0.000
47	A	55	GLU	-1	-0.880	-0.965	22.872	0.414	0.414	0.000	0.000	0.000	0.000
48	A	56	THR	0	-0.031	-0.007	22.760	-0.033	-0.033	0.000	0.000	0.000	0.000
49	A	57	ILE	0	0.067	0.049	20.245	0.027	0.027	0.000	0.000	0.000	0.000
50	A	58	VAL	0	-0.050	-0.019	18.309	-0.050	-0.050	0.000	0.000	0.000	0.000
51	A	59	PRO	0	0.070	0.040	17.631	0.089	0.089	0.000	0.000	0.000	0.000
52	A	60	TYR	0	0.072	0.034	8.228	0.121	0.121	0.000	0.000	0.000	0.000
53	A	61	GLU	-1	-0.896	-0.955	14.203	0.778	0.778	0.000	0.000	0.000	0.000
54	A	62	MET	0	-0.045	-0.021	16.379	-0.105	-0.105	0.000	0.000	0.000	0.000
55	A	63	VAL	0	-0.009	-0.023	11.521	-0.110	-0.110	0.000	0.000	0.000	0.000
56	A	64	LYS	1	0.853	0.936	13.962	-0.148	-0.148	0.000	0.000	0.000	0.000
57	A	65	LYS	1	0.927	0.943	10.099	0.102	0.102	0.000	0.000	0.000	0.000
58	A	66	ILE	0	0.036	0.018	7.869	0.001	0.001	0.000	0.000	0.000	0.000
59	A	67	GLY	0	-0.010	0.008	8.525	-0.107	-0.107	0.000	0.000	0.000	0.000
60	A	68	ASP	-1	-0.888	-0.936	10.677	-0.103	-0.103	0.000	0.000	0.000	0.000
61	A	69	LYS	1	0.869	0.926	13.453	-0.061	-0.061	0.000	0.000	0.000	0.000
62	A	70	ILE	0	0.007	0.008	11.647	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	71	LEU	0	-0.045	-0.016	13.912	-0.055	-0.055	0.000	0.000	0.000	0.000
64	A	72	LEU	0	0.058	0.050	15.497	0.059	0.059	0.000	0.000	0.000	0.000
65	A	73	LYS	1	0.818	0.913	16.151	-0.495	-0.495	0.000	0.000	0.000	0.000
66	A	74	GLY	0	0.011	-0.001	19.516	0.009	0.009	0.000	0.000	0.000	0.000
67	A	75	PRO	0	-0.075	-0.033	23.132	0.021	0.021	0.000	0.000	0.000	0.000
68	A	76	GLU	-1	-0.873	-0.945	25.623	0.119	0.119	0.000	0.000	0.000	0.000
69	A	77	GLU	-1	-0.905	-0.946	20.675	0.139	0.139	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:HIS)