FMO DATABASE

FMODB ID: Y1272

Calculation Name: 1CXY-A-Xray547

Preferred Name:

Target Type:

Ligand Name: protoporphyrin ix containing fe

Ligand 3-letter code: HEM

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1CXY

Chain ID: A

ChEMBL ID:

UniProt ID: P82291

Base Structure: X-ray

Registration Date: 2025-10-05

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	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	80
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-531752.64557
FMO2-HF: Nuclear repulsion	499241.417496
FMO2-HF: Total energy	-32511.228073
FMO2-MP2: Total energy	-32603.81718

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:6:THR)

Summations of interaction energy for fragment #1(A:6: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.
-80.833	-77.443	0.584	-1.911	-2.063	-0.017

Interaction energy analysis for fragmet #1(A:6:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.821 / q_NPA : 0.899

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	8	PRO	0	0.020	0.017	2.672	-8.330	-5.036	0.585	-1.905	-1.974	-0.017
4	A	9	VAL	0	-0.004	0.015	4.776	1.184	1.280	-0.001	-0.006	-0.089	0.000
5	A	10	PHE	0	-0.012	-0.004	7.161	0.397	0.397	0.000	0.000	0.000	0.000
6	A	11	THR	0	0.027	-0.005	10.777	0.023	0.023	0.000	0.000	0.000	0.000
7	A	12	LEU	0	0.057	0.013	14.113	-0.033	-0.033	0.000	0.000	0.000	0.000
8	A	13	GLU	-1	-0.848	-0.916	17.244	-15.435	-15.435	0.000	0.000	0.000	0.000
9	A	14	GLN	0	-0.023	-0.010	12.269	-0.657	-0.657	0.000	0.000	0.000	0.000
10	A	15	VAL	0	-0.025	-0.011	14.702	-0.143	-0.143	0.000	0.000	0.000	0.000
11	A	16	ALA	0	0.005	0.009	16.947	0.491	0.491	0.000	0.000	0.000	0.000
12	A	17	GLU	-1	-0.948	-0.977	19.179	-12.768	-12.768	0.000	0.000	0.000	0.000
13	A	18	HIS	1	0.744	0.874	16.375	17.427	17.427	0.000	0.000	0.000	0.000
14	A	19	HIS	1	0.931	0.961	20.753	12.046	12.046	0.000	0.000	0.000	0.000
15	A	20	SER	0	-0.013	-0.006	24.000	0.707	0.707	0.000	0.000	0.000	0.000
16	A	21	PRO	0	-0.013	-0.031	25.135	-0.375	-0.375	0.000	0.000	0.000	0.000
17	A	22	ASP	-1	-0.925	-0.964	26.279	-11.771	-11.771	0.000	0.000	0.000	0.000
18	A	23	ASP	-1	-0.841	-0.894	20.390	-15.755	-15.755	0.000	0.000	0.000	0.000
19	A	24	CYS	0	-0.087	-0.008	21.630	-0.404	-0.404	0.000	0.000	0.000	0.000
20	A	25	TRP	0	-0.031	-0.026	13.276	-1.138	-1.138	0.000	0.000	0.000	0.000
21	A	26	MET	0	-0.032	-0.009	17.317	0.937	0.937	0.000	0.000	0.000	0.000
22	A	27	ALA	0	0.021	0.017	15.913	-1.416	-1.416	0.000	0.000	0.000	0.000
23	A	28	ILE	0	0.033	0.009	16.117	1.103	1.103	0.000	0.000	0.000	0.000
24	A	29	HIS	0	-0.065	-0.052	15.628	-1.655	-1.655	0.000	0.000	0.000	0.000
25	A	30	GLY	0	0.014	0.013	13.489	-0.880	-0.880	0.000	0.000	0.000	0.000
26	A	31	LYS	1	0.826	0.917	10.403	18.909	18.909	0.000	0.000	0.000	0.000
27	A	32	VAL	0	0.038	0.022	11.193	1.918	1.918	0.000	0.000	0.000	0.000
28	A	33	TYR	0	0.015	-0.008	12.206	-2.136	-2.136	0.000	0.000	0.000	0.000
29	A	34	ASP	-1	-0.792	-0.873	14.914	-16.904	-16.904	0.000	0.000	0.000	0.000
30	A	35	LEU	0	0.013	-0.018	16.746	0.075	0.075	0.000	0.000	0.000	0.000
31	A	36	THR	0	0.043	0.031	20.042	1.050	1.050	0.000	0.000	0.000	0.000
32	A	37	PRO	0	-0.036	-0.024	19.239	0.726	0.726	0.000	0.000	0.000	0.000
33	A	38	TYR	0	-0.071	-0.048	21.788	0.460	0.460	0.000	0.000	0.000	0.000
34	A	39	VAL	0	0.048	0.030	23.553	0.569	0.569	0.000	0.000	0.000	0.000
35	A	40	PRO	0	-0.050	-0.029	25.849	0.446	0.446	0.000	0.000	0.000	0.000
36	A	41	ASN	0	-0.082	-0.043	25.377	0.721	0.721	0.000	0.000	0.000	0.000
37	A	42	HIS	0	0.022	0.021	26.810	-0.297	-0.297	0.000	0.000	0.000	0.000
38	A	43	PRO	0	-0.033	-0.019	28.270	0.402	0.402	0.000	0.000	0.000	0.000
39	A	44	GLY	0	0.014	0.019	31.279	-0.102	-0.102	0.000	0.000	0.000	0.000
40	A	45	PRO	0	-0.010	-0.018	34.064	0.109	0.109	0.000	0.000	0.000	0.000
41	A	46	ALA	0	0.049	0.018	33.896	-0.272	-0.272	0.000	0.000	0.000	0.000
42	A	47	GLY	0	0.002	-0.005	32.082	0.144	0.144	0.000	0.000	0.000	0.000
43	A	48	MET	0	0.004	0.007	31.287	-0.134	-0.134	0.000	0.000	0.000	0.000
44	A	49	MET	0	-0.009	0.001	22.814	-0.095	-0.095	0.000	0.000	0.000	0.000
45	A	50	LEU	0	0.018	-0.005	26.430	-0.358	-0.358	0.000	0.000	0.000	0.000
46	A	51	VAL	0	-0.029	-0.012	27.389	-0.180	-0.180	0.000	0.000	0.000	0.000
47	A	52	TRP	0	0.032	0.017	24.104	-0.067	-0.067	0.000	0.000	0.000	0.000
48	A	54	GLY	0	0.017	0.011	20.384	0.511	0.511	0.000	0.000	0.000	0.000
49	A	55	GLN	0	-0.027	-0.016	20.885	-0.171	-0.171	0.000	0.000	0.000	0.000
50	A	56	GLU	-1	-0.815	-0.869	18.929	-15.599	-15.599	0.000	0.000	0.000	0.000
51	A	57	SER	0	0.021	-0.004	20.681	0.884	0.884	0.000	0.000	0.000	0.000
52	A	58	THR	0	-0.058	-0.068	19.807	0.066	0.066	0.000	0.000	0.000	0.000
53	A	59	GLU	-1	-0.927	-0.961	22.136	-10.319	-10.319	0.000	0.000	0.000	0.000
54	A	60	ALA	0	0.036	0.038	25.839	0.308	0.308	0.000	0.000	0.000	0.000
55	A	61	TRP	0	-0.047	-0.025	21.369	0.021	0.021	0.000	0.000	0.000	0.000
56	A	62	GLU	-1	-0.845	-0.923	22.813	-12.838	-12.838	0.000	0.000	0.000	0.000
57	A	63	THR	0	-0.013	-0.019	25.877	0.452	0.452	0.000	0.000	0.000	0.000
58	A	64	LYS	0	0.009	0.030	28.350	0.501	0.501	0.000	0.000	0.000	0.000
59	A	65	SER	0	-0.047	-0.031	29.984	0.159	0.159	0.000	0.000	0.000	0.000
60	A	66	TYR	-1	-0.997	-1.001	31.744	-8.739	-8.739	0.000	0.000	0.000	0.000
61	A	67	GLY	0	-0.028	-0.007	33.080	0.251	0.251	0.000	0.000	0.000	0.000
62	A	68	GLU	0	-0.067	-0.048	31.554	0.024	0.024	0.000	0.000	0.000	0.000
63	A	69	PRO	0	0.044	0.031	27.587	-0.218	-0.218	0.000	0.000	0.000	0.000
64	A	70	HIS	0	-0.008	-0.011	24.497	0.178	0.178	0.000	0.000	0.000	0.000
65	A	71	SER	0	0.026	0.015	25.810	-0.287	-0.287	0.000	0.000	0.000	0.000
66	A	72	SER	0	0.060	-0.002	23.493	-0.432	-0.432	0.000	0.000	0.000	0.000
67	A	73	LEU	0	-0.072	-0.026	22.830	-0.553	-0.553	0.000	0.000	0.000	0.000
68	A	74	ALA	0	0.073	0.032	22.887	-0.523	-0.523	0.000	0.000	0.000	0.000
69	A	75	ALA	0	0.052	0.025	19.902	-0.574	-0.574	0.000	0.000	0.000	0.000
70	A	76	ARG	1	0.904	0.950	18.425	12.445	12.445	0.000	0.000	0.000	0.000
71	A	77	LEU	0	-0.062	-0.027	18.522	-0.686	-0.686	0.000	0.000	0.000	0.000
72	A	78	LEU	0	0.050	0.035	17.020	-0.590	-0.590	0.000	0.000	0.000	0.000
73	A	79	GLN	0	-0.025	-0.018	13.073	-1.278	-1.278	0.000	0.000	0.000	0.000
74	A	80	ARG	1	0.874	0.941	13.561	14.240	14.240	0.000	0.000	0.000	0.000
75	A	81	TYR	0	0.017	0.017	14.742	-0.110	-0.110	0.000	0.000	0.000	0.000
76	A	82	LEU	0	-0.048	-0.007	8.976	0.040	0.040	0.000	0.000	0.000	0.000
77	A	83	ILE	0	-0.015	-0.008	10.115	-1.613	-1.613	0.000	0.000	0.000	0.000
78	A	84	GLY	0	-0.040	-0.030	7.268	-4.093	-4.093	0.000	0.000	0.000	0.000
79	A	85	THR	0	-0.092	-0.045	6.481	2.248	2.248	0.000	0.000	0.000	0.000
80	A	86	LEU	-1	-0.878	-0.931	8.905	-23.077	-23.077	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:THR)