FMO DATABASE

FMODB ID: KGZ23

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

Total energy (hartree)

FMO2-HF: Electronic energy	-378323.491434
FMO2-HF: Nuclear repulsion	351762.061448
FMO2-HF: Total energy	-26561.429986
FMO2-MP2: Total energy	-26637.852175

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.
1.064	3.265	-0.036	-1.143	-1.022	-0.002

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 : -0.034 / q_NPA : -0.030

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	0.866	0.917	3.823	-1.147	1.054	-0.036	-1.143	-1.022	-0.002
4	A	3	ILE	0	0.027	0.015	6.754	-0.153	-0.153	0.000	0.000	0.000	0.000
5	A	4	VAL	0	0.033	0.005	9.170	-0.173	-0.173	0.000	0.000	0.000	0.000
6	A	5	GLU	-1	-0.860	-0.924	10.673	0.468	0.468	0.000	0.000	0.000	0.000
7	A	6	GLU	-1	-0.839	-0.921	6.767	-0.665	-0.665	0.000	0.000	0.000	0.000
8	A	7	MET	0	-0.100	-0.031	7.366	-0.164	-0.164	0.000	0.000	0.000	0.000
9	A	8	VAL	0	0.066	0.014	10.354	0.092	0.092	0.000	0.000	0.000	0.000
10	A	9	GLY	0	-0.022	0.007	13.747	-0.093	-0.093	0.000	0.000	0.000	0.000
11	A	10	LYS	1	0.833	0.917	9.752	-0.556	-0.556	0.000	0.000	0.000	0.000
12	A	11	GLU	-1	-0.851	-0.920	15.564	0.263	0.263	0.000	0.000	0.000	0.000
13	A	12	VAL	0	0.040	0.019	15.831	0.025	0.025	0.000	0.000	0.000	0.000
14	A	13	LEU	0	-0.024	-0.027	17.900	-0.051	-0.051	0.000	0.000	0.000	0.000
15	A	14	ASP	-1	-0.781	-0.893	19.346	0.285	0.285	0.000	0.000	0.000	0.000
16	A	15	SER	0	0.024	0.005	21.818	-0.013	-0.013	0.000	0.000	0.000	0.000
17	A	16	SER	0	-0.062	-0.029	22.886	-0.034	-0.034	0.000	0.000	0.000	0.000
18	A	17	ALA	0	-0.045	-0.015	22.993	-0.017	-0.017	0.000	0.000	0.000	0.000
19	A	18	LYS	1	0.933	0.985	24.077	-0.253	-0.253	0.000	0.000	0.000	0.000
20	A	19	VAL	0	-0.009	-0.006	21.451	0.025	0.025	0.000	0.000	0.000	0.000
21	A	20	ILE	0	-0.062	-0.038	20.746	-0.023	-0.023	0.000	0.000	0.000	0.000
22	A	21	GLY	0	0.036	0.021	21.725	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	22	LYS	1	0.819	0.910	18.852	-0.266	-0.266	0.000	0.000	0.000	0.000
24	A	23	VAL	0	0.011	0.027	13.454	-0.024	-0.024	0.000	0.000	0.000	0.000
25	A	24	LYS	1	0.819	0.901	16.737	-0.479	-0.479	0.000	0.000	0.000	0.000
26	A	25	ASP	-1	-0.846	-0.933	15.422	0.841	0.841	0.000	0.000	0.000	0.000
27	A	26	VAL	0	-0.089	-0.071	11.078	0.041	0.041	0.000	0.000	0.000	0.000
28	A	27	GLU	-1	-0.857	-0.894	14.215	0.679	0.679	0.000	0.000	0.000	0.000
29	A	28	VAL	0	-0.025	-0.039	11.975	0.157	0.157	0.000	0.000	0.000	0.000
30	A	29	ASP	-1	-0.731	-0.835	14.771	0.587	0.587	0.000	0.000	0.000	0.000
31	A	30	ILE	0	-0.086	-0.061	15.941	0.073	0.073	0.000	0.000	0.000	0.000
32	A	31	GLU	-1	-0.944	-0.962	17.657	0.471	0.471	0.000	0.000	0.000	0.000
33	A	32	SER	0	-0.139	-0.097	15.306	0.065	0.065	0.000	0.000	0.000	0.000
34	A	33	GLN	0	-0.058	-0.032	9.720	0.069	0.069	0.000	0.000	0.000	0.000
35	A	34	ALA	0	-0.012	0.012	11.348	0.379	0.379	0.000	0.000	0.000	0.000
36	A	35	ILE	0	-0.036	-0.017	8.013	-0.080	-0.080	0.000	0.000	0.000	0.000
37	A	36	GLU	-1	-0.899	-0.944	12.200	0.636	0.636	0.000	0.000	0.000	0.000
38	A	37	SER	0	-0.061	-0.051	15.162	-0.085	-0.085	0.000	0.000	0.000	0.000
39	A	38	LEU	0	0.004	0.009	12.300	0.091	0.091	0.000	0.000	0.000	0.000
40	A	39	VAL	0	0.052	0.048	15.981	-0.103	-0.103	0.000	0.000	0.000	0.000
41	A	40	LEU	0	-0.015	-0.032	17.385	0.005	0.005	0.000	0.000	0.000	0.000
42	A	41	GLY	0	-0.008	-0.011	20.206	-0.027	-0.027	0.000	0.000	0.000	0.000
43	A	42	LYS	1	0.962	0.992	22.973	-0.226	-0.226	0.000	0.000	0.000	0.000
44	A	43	GLY	0	0.006	-0.022	26.497	-0.011	-0.011	0.000	0.000	0.000	0.000
45	A	44	GLY	0	-0.039	-0.002	27.538	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	54	GLY	0	-0.024	-0.013	28.188	0.003	0.003	0.000	0.000	0.000	0.000
47	A	55	GLU	-1	-0.858	-0.941	22.525	0.461	0.461	0.000	0.000	0.000	0.000
48	A	56	THR	0	-0.045	-0.016	22.985	-0.035	-0.035	0.000	0.000	0.000	0.000
49	A	57	ILE	0	0.055	0.043	20.328	0.030	0.030	0.000	0.000	0.000	0.000
50	A	58	VAL	0	-0.049	-0.019	18.248	-0.054	-0.054	0.000	0.000	0.000	0.000
51	A	59	PRO	0	0.075	0.043	17.631	0.094	0.094	0.000	0.000	0.000	0.000
52	A	60	TYR	0	0.065	0.030	8.364	0.173	0.173	0.000	0.000	0.000	0.000
53	A	61	GLU	-1	-0.878	-0.943	14.203	0.790	0.790	0.000	0.000	0.000	0.000
54	A	62	MET	0	-0.016	0.004	16.379	-0.109	-0.109	0.000	0.000	0.000	0.000
55	A	63	VAL	0	0.001	-0.003	11.683	-0.104	-0.104	0.000	0.000	0.000	0.000
56	A	64	LYS	1	0.779	0.880	14.017	-0.209	-0.209	0.000	0.000	0.000	0.000
57	A	65	LYS	1	0.919	0.940	10.135	-0.104	-0.104	0.000	0.000	0.000	0.000
58	A	66	ILE	0	0.041	0.022	7.867	-0.043	-0.043	0.000	0.000	0.000	0.000
59	A	67	GLY	0	0.006	0.015	8.589	-0.059	-0.059	0.000	0.000	0.000	0.000
60	A	68	ASP	-1	-0.899	-0.937	10.740	0.039	0.039	0.000	0.000	0.000	0.000
61	A	69	LYS	1	0.859	0.911	13.520	-0.146	-0.146	0.000	0.000	0.000	0.000
62	A	70	ILE	0	0.001	0.006	11.694	0.015	0.015	0.000	0.000	0.000	0.000
63	A	71	LEU	0	-0.033	-0.010	13.990	-0.070	-0.070	0.000	0.000	0.000	0.000
64	A	72	LEU	0	0.046	0.036	15.562	0.069	0.069	0.000	0.000	0.000	0.000
65	A	73	LYS	1	0.734	0.849	15.315	-0.653	-0.653	0.000	0.000	0.000	0.000
66	A	74	GLY	0	0.021	0.001	19.573	0.005	0.005	0.000	0.000	0.000	0.000
67	A	75	PRO	0	-0.057	-0.027	23.185	0.020	0.020	0.000	0.000	0.000	0.000
68	A	76	GLU	-1	-0.891	-0.954	25.613	0.161	0.161	0.000	0.000	0.000	0.000
69	A	77	GLU	-1	-0.817	-0.876	20.795	0.200	0.200	0.000	0.000	0.000	0.000

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