FMO DATABASE

FMODB ID: 4G12N

Calculation Name: 1PM4-A-Xray549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1PM4

Chain ID: A

ChEMBL ID:

UniProt ID: Q57221

Base Structure: X-ray

Registration Date: 2025-10-11

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	116
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-939175.121002
FMO2-HF: Nuclear repulsion	893717.08531
FMO2-HF: Total energy	-45458.035692
FMO2-MP2: Total energy	-45590.777835

3D Structure Molmil

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:15:ILE)

Summations of interaction energy for fragment #1(A:15:ILE)

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.
-48.597	-47.395	-0.01	-0.427	-0.765	0.001

Interaction energy analysis for fragmet #1(A:15:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.853 / q_NPA : 0.909

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	A	17	ASN	0	0.045	0.032	3.916	-1.140	0.062	-0.010	-0.427	-0.765	0.001
4	A	18	ILE	0	-0.029	-0.020	6.520	2.816	2.816	0.000	0.000	0.000	0.000
5	A	19	ALA	0	0.048	0.034	9.230	0.442	0.442	0.000	0.000	0.000	0.000
6	A	20	THR	0	-0.004	-0.012	12.533	0.146	0.146	0.000	0.000	0.000	0.000
7	A	21	TYR	0	-0.049	-0.047	15.737	0.727	0.727	0.000	0.000	0.000	0.000
8	A	22	THR	0	-0.049	-0.054	19.039	-0.052	-0.052	0.000	0.000	0.000	0.000
9	A	23	GLY	0	0.030	0.030	22.264	0.148	0.148	0.000	0.000	0.000	0.000
10	A	24	THR	0	-0.028	-0.017	26.005	0.112	0.112	0.000	0.000	0.000	0.000
11	A	25	ILE	0	-0.016	0.007	27.881	0.065	0.065	0.000	0.000	0.000	0.000
12	A	26	GLN	0	0.057	0.012	30.240	0.188	0.188	0.000	0.000	0.000	0.000
13	A	27	GLY	0	0.037	0.039	33.552	-0.204	-0.204	0.000	0.000	0.000	0.000
14	A	28	LYS	1	0.824	0.896	35.061	8.742	8.742	0.000	0.000	0.000	0.000
15	A	29	GLY	0	0.021	0.026	33.295	0.020	0.020	0.000	0.000	0.000	0.000
16	A	30	GLU	-1	-0.856	-0.947	29.893	-10.334	-10.334	0.000	0.000	0.000	0.000
17	A	31	VAL	0	0.025	0.016	25.303	0.199	0.199	0.000	0.000	0.000	0.000
18	A	32	CYS	0	-0.037	0.010	24.682	-0.727	-0.727	0.000	0.000	0.000	0.000
19	A	33	ILE	0	0.018	0.014	19.348	0.180	0.180	0.000	0.000	0.000	0.000
20	A	34	ILE	0	-0.040	-0.018	19.803	-0.393	-0.393	0.000	0.000	0.000	0.000
21	A	35	GLY	0	0.041	0.021	15.762	-0.493	-0.493	0.000	0.000	0.000	0.000
22	A	36	ASN	0	-0.042	-0.046	13.817	0.530	0.530	0.000	0.000	0.000	0.000
23	A	37	LYS	1	0.847	0.912	15.556	16.487	16.487	0.000	0.000	0.000	0.000
24	A	38	GLU	-1	-0.832	-0.914	16.569	-16.905	-16.905	0.000	0.000	0.000	0.000
25	A	39	GLY	0	-0.028	-0.001	17.687	0.482	0.482	0.000	0.000	0.000	0.000
26	A	40	LYS	1	0.839	0.926	12.560	20.462	20.462	0.000	0.000	0.000	0.000
27	A	41	THR	0	-0.022	-0.031	13.563	-0.332	-0.332	0.000	0.000	0.000	0.000
28	A	42	ARG	1	0.790	0.894	7.207	30.691	30.691	0.000	0.000	0.000	0.000
29	A	43	GLY	0	0.041	0.035	9.561	1.685	1.685	0.000	0.000	0.000	0.000
30	A	44	GLY	0	0.022	0.010	7.839	-3.484	-3.484	0.000	0.000	0.000	0.000
31	A	45	GLU	-1	-0.824	-0.916	8.448	-27.506	-27.506	0.000	0.000	0.000	0.000
32	A	46	LEU	0	-0.035	0.004	8.988	-2.610	-2.610	0.000	0.000	0.000	0.000
33	A	47	TYR	0	0.002	-0.012	10.395	1.281	1.281	0.000	0.000	0.000	0.000
34	A	48	ALA	0	0.026	0.008	12.325	-0.236	-0.236	0.000	0.000	0.000	0.000
35	A	49	VAL	0	-0.035	-0.009	14.780	0.467	0.467	0.000	0.000	0.000	0.000
36	A	50	LEU	0	0.019	0.020	17.017	-0.169	-0.169	0.000	0.000	0.000	0.000
37	A	51	HIS	1	0.849	0.910	16.650	16.743	16.743	0.000	0.000	0.000	0.000
38	A	52	SER	0	0.038	-0.014	21.946	0.314	0.314	0.000	0.000	0.000	0.000
39	A	53	THR	0	-0.025	-0.012	25.165	-0.042	-0.042	0.000	0.000	0.000	0.000
40	A	54	ASN	0	-0.067	-0.041	26.972	0.405	0.405	0.000	0.000	0.000	0.000
41	A	55	VAL	0	0.027	0.000	28.973	-0.233	-0.233	0.000	0.000	0.000	0.000
42	A	56	ASN	0	-0.013	-0.004	30.091	-0.073	-0.073	0.000	0.000	0.000	0.000
43	A	57	ALA	0	-0.041	-0.006	28.229	0.166	0.166	0.000	0.000	0.000	0.000
44	A	58	ASP	-1	-0.845	-0.907	29.259	-10.166	-10.166	0.000	0.000	0.000	0.000
45	A	59	MET	0	-0.036	-0.034	26.618	-0.020	-0.020	0.000	0.000	0.000	0.000
46	A	60	THR	0	-0.036	-0.009	26.448	-0.161	-0.161	0.000	0.000	0.000	0.000
47	A	61	LEU	0	-0.015	0.000	18.845	0.017	0.017	0.000	0.000	0.000	0.000
48	A	62	ILE	0	-0.009	-0.017	23.553	0.101	0.101	0.000	0.000	0.000	0.000
49	A	63	LEU	0	-0.016	0.015	17.095	-0.286	-0.286	0.000	0.000	0.000	0.000
50	A	64	LEU	0	0.010	0.003	21.017	0.530	0.530	0.000	0.000	0.000	0.000
51	A	65	ARG	1	0.857	0.891	15.313	16.364	16.364	0.000	0.000	0.000	0.000
52	A	66	ASN	0	0.010	0.009	21.732	0.873	0.873	0.000	0.000	0.000	0.000
53	A	67	VAL	0	-0.003	-0.013	22.942	-0.390	-0.390	0.000	0.000	0.000	0.000
54	A	68	GLY	0	0.008	0.005	25.227	-0.108	-0.108	0.000	0.000	0.000	0.000
55	A	69	GLY	0	-0.021	-0.001	26.195	0.326	0.326	0.000	0.000	0.000	0.000
56	A	70	ASN	0	-0.033	-0.026	28.203	0.366	0.366	0.000	0.000	0.000	0.000
57	A	71	GLY	0	0.048	0.037	28.701	0.340	0.340	0.000	0.000	0.000	0.000
58	A	72	TRP	0	-0.020	-0.012	21.920	-0.494	-0.494	0.000	0.000	0.000	0.000
59	A	73	GLY	0	0.027	0.015	25.605	0.484	0.484	0.000	0.000	0.000	0.000
60	A	74	GLU	-1	-0.816	-0.876	24.578	-12.242	-12.242	0.000	0.000	0.000	0.000
61	A	75	ILE	0	-0.042	-0.011	18.789	0.186	0.186	0.000	0.000	0.000	0.000
62	A	76	LYS	1	0.873	0.919	18.364	16.399	16.399	0.000	0.000	0.000	0.000
63	A	77	ARG	1	0.845	0.887	23.002	10.909	10.909	0.000	0.000	0.000	0.000
64	A	78	ASN	0	-0.031	-0.020	20.734	-0.362	-0.362	0.000	0.000	0.000	0.000
65	A	79	ASP	-1	-0.803	-0.888	23.354	-11.706	-11.706	0.000	0.000	0.000	0.000
66	A	80	ILE	0	0.015	0.001	22.911	-0.776	-0.776	0.000	0.000	0.000	0.000
67	A	81	ASP	-1	-0.849	-0.914	20.713	-13.621	-13.621	0.000	0.000	0.000	0.000
68	A	82	LYS	1	0.785	0.893	20.255	12.113	12.113	0.000	0.000	0.000	0.000
69	A	83	PRO	0	-0.043	-0.031	14.927	-0.103	-0.103	0.000	0.000	0.000	0.000
70	A	84	LEU	0	-0.016	0.021	16.923	0.375	0.375	0.000	0.000	0.000	0.000
71	A	85	LYS	1	0.843	0.903	10.577	25.698	25.698	0.000	0.000	0.000	0.000
72	A	86	TYR	0	-0.054	-0.057	14.175	1.962	1.962	0.000	0.000	0.000	0.000
73	A	87	GLU	-1	-0.868	-0.896	11.457	-24.674	-24.674	0.000	0.000	0.000	0.000
74	A	88	ASP	-1	-0.776	-0.860	12.598	-16.256	-16.256	0.000	0.000	0.000	0.000
75	A	89	TYR	0	-0.036	-0.062	9.661	-2.451	-2.451	0.000	0.000	0.000	0.000
76	A	90	TYR	0	-0.021	0.012	14.020	0.892	0.892	0.000	0.000	0.000	0.000
77	A	91	THR	0	0.037	0.010	15.790	-0.583	-0.583	0.000	0.000	0.000	0.000
78	A	92	SER	0	-0.005	0.012	17.401	0.056	0.056	0.000	0.000	0.000	0.000
79	A	93	GLY	0	0.022	0.016	16.207	-0.449	-0.449	0.000	0.000	0.000	0.000
80	A	94	LEU	0	-0.005	-0.005	16.596	0.977	0.977	0.000	0.000	0.000	0.000
81	A	95	SER	0	0.042	0.050	16.735	-1.044	-1.044	0.000	0.000	0.000	0.000
82	A	96	TRP	0	-0.074	-0.046	11.950	0.305	0.305	0.000	0.000	0.000	0.000
83	A	97	ILE	0	-0.010	-0.007	18.935	-0.086	-0.086	0.000	0.000	0.000	0.000
84	A	98	TRP	0	0.059	0.032	14.242	0.457	0.457	0.000	0.000	0.000	0.000
85	A	99	LYS	1	0.873	0.918	20.814	11.052	11.052	0.000	0.000	0.000	0.000
86	A	100	ILE	0	0.012	0.007	22.228	-0.151	-0.151	0.000	0.000	0.000	0.000
87	A	101	LYS	1	0.859	0.924	25.532	10.040	10.040	0.000	0.000	0.000	0.000
88	A	102	ASN	0	-0.007	-0.022	28.867	-0.246	-0.246	0.000	0.000	0.000	0.000
89	A	103	ASN	0	-0.013	-0.012	30.101	0.277	0.277	0.000	0.000	0.000	0.000
90	A	104	SER	0	0.111	0.068	32.853	0.558	0.558	0.000	0.000	0.000	0.000
91	A	105	SER	0	-0.051	-0.036	34.845	-0.052	-0.052	0.000	0.000	0.000	0.000
92	A	106	GLU	-1	-0.869	-0.916	34.769	-8.935	-8.935	0.000	0.000	0.000	0.000
93	A	107	THR	0	-0.020	-0.008	33.914	-0.338	-0.338	0.000	0.000	0.000	0.000
94	A	108	SER	0	0.030	0.022	30.065	0.123	0.123	0.000	0.000	0.000	0.000
95	A	109	ASN	0	0.019	0.016	25.073	-0.329	-0.329	0.000	0.000	0.000	0.000
96	A	110	TYR	0	0.018	0.028	22.776	0.250	0.250	0.000	0.000	0.000	0.000
97	A	111	SER	0	0.010	-0.005	19.870	0.068	0.068	0.000	0.000	0.000	0.000
98	A	112	LEU	0	0.009	0.004	17.474	0.304	0.304	0.000	0.000	0.000	0.000
99	A	113	ASP	-1	-0.814	-0.880	13.253	-20.230	-20.230	0.000	0.000	0.000	0.000
100	A	114	ALA	0	0.011	-0.016	13.546	0.398	0.398	0.000	0.000	0.000	0.000
101	A	115	THR	0	-0.037	-0.015	8.549	-1.005	-1.005	0.000	0.000	0.000	0.000
102	A	116	VAL	0	-0.002	0.012	10.050	2.562	2.562	0.000	0.000	0.000	0.000
103	A	117	HIS	0	-0.015	-0.031	9.192	-2.745	-2.745	0.000	0.000	0.000	0.000
104	A	118	ASP	-1	-0.847	-0.918	9.926	-22.110	-22.110	0.000	0.000	0.000	0.000
105	A	119	ASP	-1	-0.918	-0.968	11.460	-24.646	-24.646	0.000	0.000	0.000	0.000
106	A	120	LYS	1	0.834	0.910	13.471	17.585	17.585	0.000	0.000	0.000	0.000
107	A	121	GLU	-1	-0.843	-0.918	15.959	-14.808	-14.808	0.000	0.000	0.000	0.000
108	A	122	ASP	-1	-0.906	-0.961	19.521	-13.272	-13.272	0.000	0.000	0.000	0.000
109	A	123	SER	0	-0.086	-0.046	21.897	0.308	0.308	0.000	0.000	0.000	0.000
110	A	124	ASP	-1	-0.723	-0.823	17.918	-17.310	-17.310	0.000	0.000	0.000	0.000
111	A	125	VAL	0	-0.056	-0.024	21.026	0.019	0.019	0.000	0.000	0.000	0.000
112	A	126	LEU	0	-0.005	0.003	24.063	0.474	0.474	0.000	0.000	0.000	0.000
113	A	127	THR	0	-0.018	-0.017	26.429	0.117	0.117	0.000	0.000	0.000	0.000
114	A	128	LYS	1	0.884	0.946	29.506	9.986	9.986	0.000	0.000	0.000	0.000
115	A	130	PRO	0	-0.007	-0.018	26.898	0.370	0.370	0.000	0.000	0.000	0.000
116	A	131	VAL	-1	-0.922	-0.944	29.965	-9.228	-9.228	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:15:ILE)