FMO DATABASE

FMODB ID: 9QY92

Calculation Name: 1X9F-B-Xray547

Preferred Name:

Target Type:

Ligand Name: protoporphyrin ix containing fe | phosphate ion | carbon monoxide

Ligand 3-letter code: HEM | PO4 | CMO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1X9F

Chain ID: B

ChEMBL ID:

UniProt ID: P02218

Base Structure: X-ray

Registration Date: 2025-10-06

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	144
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1358888.483817
FMO2-HF: Nuclear repulsion	1302296.673996
FMO2-HF: Total energy	-56591.809821
FMO2-MP2: Total energy	-56758.896392

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(B:1:LYS)

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

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.
-401.467	-395.093	2.863	-4.19	-5.045	-0.039

Interaction energy analysis for fragmet #1(B:1:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.792 / q_NPA : 1.887

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	3	GLN	0	0.042	0.008	3.179	-13.001	-10.514	0.050	-1.381	-1.156	-0.007
128	B	128	GLU	-1	-0.922	-0.973	2.421	-125.769	-122.264	2.816	-2.752	-3.568	-0.032
129	B	129	ALA	0	-0.005	-0.003	4.781	-4.043	-4.047	-0.001	-0.003	0.008	0.000
131	B	131	ASP	-1	-0.927	-0.952	4.402	-97.790	-97.491	-0.001	-0.043	-0.255	0.000
132	B	132	ALA	0	0.017	0.008	4.244	2.365	2.452	-0.001	-0.011	-0.074	0.000
4	B	4	CYS	0	-0.043	-0.014	5.782	9.141	9.141	0.000	0.000	0.000	0.000
5	B	5	GLY	0	0.051	0.035	9.068	3.867	3.867	0.000	0.000	0.000	0.000
6	B	6	VAL	0	0.040	0.003	11.547	0.760	0.760	0.000	0.000	0.000	0.000
7	B	7	LEU	0	-0.009	-0.002	13.326	1.517	1.517	0.000	0.000	0.000	0.000
8	B	8	GLU	-1	-0.891	-0.953	8.545	-52.808	-52.808	0.000	0.000	0.000	0.000
9	B	9	GLY	0	0.082	0.042	11.611	0.654	0.654	0.000	0.000	0.000	0.000
10	B	10	LEU	0	-0.026	-0.020	13.892	1.846	1.846	0.000	0.000	0.000	0.000
11	B	11	LYS	1	0.833	0.926	11.146	46.884	46.884	0.000	0.000	0.000	0.000
12	B	12	VAL	0	0.034	0.015	11.289	1.495	1.495	0.000	0.000	0.000	0.000
13	B	13	LYS	1	0.846	0.925	14.323	30.088	30.088	0.000	0.000	0.000	0.000
14	B	14	SER	0	-0.064	-0.034	17.708	2.178	2.178	0.000	0.000	0.000	0.000
15	B	15	GLU	-1	-0.895	-0.964	13.516	-39.784	-39.784	0.000	0.000	0.000	0.000
16	B	16	TRP	0	0.001	-0.022	17.295	-0.155	-0.155	0.000	0.000	0.000	0.000
17	B	17	GLY	0	-0.013	0.005	18.646	1.234	1.234	0.000	0.000	0.000	0.000
18	B	18	ARG	1	0.865	0.933	18.375	30.819	30.819	0.000	0.000	0.000	0.000
19	B	19	ALA	0	0.000	0.001	18.801	0.729	0.729	0.000	0.000	0.000	0.000
20	B	20	TYR	0	0.021	0.017	20.865	0.761	0.761	0.000	0.000	0.000	0.000
21	B	21	GLY	0	0.057	0.034	23.004	0.852	0.852	0.000	0.000	0.000	0.000
22	B	22	SER	0	-0.051	-0.038	26.394	0.398	0.398	0.000	0.000	0.000	0.000
23	B	23	GLY	0	0.057	0.024	29.773	0.073	0.073	0.000	0.000	0.000	0.000
24	B	24	HIS	0	-0.012	-0.029	30.699	-0.112	-0.112	0.000	0.000	0.000	0.000
25	B	25	ASP	-1	-0.915	-0.943	27.461	-20.900	-20.900	0.000	0.000	0.000	0.000
26	B	26	ARG	1	0.834	0.937	26.116	21.547	21.547	0.000	0.000	0.000	0.000
27	B	27	GLU	-1	-0.818	-0.904	26.431	-19.291	-19.291	0.000	0.000	0.000	0.000
28	B	28	ALA	0	0.004	0.002	27.178	-0.474	-0.474	0.000	0.000	0.000	0.000
29	B	29	PHE	0	-0.006	0.001	18.859	-0.844	-0.844	0.000	0.000	0.000	0.000
30	B	30	SER	0	0.013	-0.041	22.518	-1.462	-1.462	0.000	0.000	0.000	0.000
31	B	31	GLN	0	-0.063	-0.054	24.017	-0.452	-0.452	0.000	0.000	0.000	0.000
32	B	32	ALA	0	-0.044	-0.012	21.848	-0.287	-0.287	0.000	0.000	0.000	0.000
33	B	33	ILE	0	0.038	0.028	18.072	-0.749	-0.749	0.000	0.000	0.000	0.000
34	B	34	TRP	0	0.057	0.032	20.006	-0.820	-0.820	0.000	0.000	0.000	0.000
35	B	35	ARG	1	0.853	0.922	22.593	21.899	21.899	0.000	0.000	0.000	0.000
36	B	36	ALA	0	0.001	0.002	17.732	0.139	0.139	0.000	0.000	0.000	0.000
37	B	37	THR	0	0.019	-0.003	18.237	-1.091	-1.091	0.000	0.000	0.000	0.000
38	B	38	PHE	0	-0.046	-0.042	19.285	0.182	0.182	0.000	0.000	0.000	0.000
39	B	39	ALA	0	-0.032	-0.007	19.987	0.799	0.799	0.000	0.000	0.000	0.000
40	B	40	GLN	0	0.011	0.017	12.652	0.092	0.092	0.000	0.000	0.000	0.000
41	B	41	VAL	0	-0.015	-0.009	17.492	0.108	0.108	0.000	0.000	0.000	0.000
42	B	42	PRO	0	0.017	0.025	20.182	0.833	0.833	0.000	0.000	0.000	0.000
43	B	43	GLU	-1	-0.912	-0.959	23.344	-22.529	-22.529	0.000	0.000	0.000	0.000
44	B	44	SER	0	-0.017	-0.014	21.949	0.927	0.927	0.000	0.000	0.000	0.000
45	B	45	ARG	1	0.829	0.898	24.085	22.309	22.309	0.000	0.000	0.000	0.000
46	B	46	SER	0	-0.057	-0.036	26.751	0.844	0.844	0.000	0.000	0.000	0.000
47	B	47	LEU	0	0.007	0.006	24.741	0.820	0.820	0.000	0.000	0.000	0.000
48	B	48	PHE	0	0.017	0.011	24.046	0.667	0.667	0.000	0.000	0.000	0.000
49	B	49	LYS	1	0.894	0.952	29.709	18.440	18.440	0.000	0.000	0.000	0.000
50	B	50	ARG	1	0.918	0.956	33.086	18.582	18.582	0.000	0.000	0.000	0.000
51	B	51	VAL	0	-0.052	-0.032	30.432	0.392	0.392	0.000	0.000	0.000	0.000
52	B	52	HIS	0	0.031	0.014	32.870	-0.025	-0.025	0.000	0.000	0.000	0.000
53	B	53	GLY	0	0.056	0.033	29.878	-0.156	-0.156	0.000	0.000	0.000	0.000
54	B	54	ASP	-1	-0.886	-0.928	29.605	-18.555	-18.555	0.000	0.000	0.000	0.000
55	B	55	ASP	-1	-0.812	-0.907	31.836	-18.448	-18.448	0.000	0.000	0.000	0.000
56	B	56	THR	0	-0.008	0.003	27.135	-0.037	-0.037	0.000	0.000	0.000	0.000
57	B	57	SER	0	-0.008	-0.013	30.131	-0.574	-0.574	0.000	0.000	0.000	0.000
58	B	58	HIS	0	0.053	0.049	32.935	0.168	0.168	0.000	0.000	0.000	0.000
59	B	59	PRO	0	0.037	0.015	33.824	-0.513	-0.513	0.000	0.000	0.000	0.000
60	B	60	ALA	0	-0.029	-0.019	34.689	-0.240	-0.240	0.000	0.000	0.000	0.000
61	B	61	PHE	0	0.013	0.006	26.285	-0.512	-0.512	0.000	0.000	0.000	0.000
62	B	62	ILE	0	0.009	0.008	29.823	-0.812	-0.812	0.000	0.000	0.000	0.000
63	B	63	ALA	0	0.014	0.002	29.994	-0.546	-0.546	0.000	0.000	0.000	0.000
64	B	64	HIS	0	-0.044	-0.029	26.239	0.520	0.520	0.000	0.000	0.000	0.000
65	B	65	ALA	0	-0.018	0.003	25.782	-0.695	-0.695	0.000	0.000	0.000	0.000
66	B	66	ASP	-1	-0.782	-0.886	25.419	-22.586	-22.586	0.000	0.000	0.000	0.000
67	B	67	ARG	1	0.850	0.950	26.642	19.993	19.993	0.000	0.000	0.000	0.000
68	B	68	VAL	0	-0.030	-0.016	21.746	-0.287	-0.287	0.000	0.000	0.000	0.000
69	B	69	LEU	0	-0.008	-0.004	20.716	-1.101	-1.101	0.000	0.000	0.000	0.000
70	B	70	GLY	0	0.001	0.010	22.674	-0.481	-0.481	0.000	0.000	0.000	0.000
71	B	71	GLY	0	0.050	0.029	23.056	-0.038	-0.038	0.000	0.000	0.000	0.000
72	B	72	LEU	0	-0.007	-0.003	15.941	-0.940	-0.940	0.000	0.000	0.000	0.000
73	B	73	ASP	-1	-0.860	-0.913	19.159	-26.443	-26.443	0.000	0.000	0.000	0.000
74	B	74	ILE	0	0.000	0.026	21.435	-0.308	-0.308	0.000	0.000	0.000	0.000
75	B	75	ALA	0	0.029	0.033	17.551	-0.339	-0.339	0.000	0.000	0.000	0.000
76	B	76	ILE	0	0.008	-0.008	15.388	-1.376	-1.376	0.000	0.000	0.000	0.000
77	B	77	SER	0	-0.080	-0.065	17.535	-0.297	-0.297	0.000	0.000	0.000	0.000
78	B	78	THR	0	-0.019	-0.032	19.862	0.500	0.500	0.000	0.000	0.000	0.000
79	B	79	LEU	0	0.016	0.008	13.386	-0.538	-0.538	0.000	0.000	0.000	0.000
80	B	80	ASP	-1	-0.873	-0.919	16.293	-28.927	-28.927	0.000	0.000	0.000	0.000
81	B	81	GLN	0	-0.105	-0.060	18.742	2.080	2.080	0.000	0.000	0.000	0.000
82	B	82	PRO	0	0.037	0.008	17.877	0.457	0.457	0.000	0.000	0.000	0.000
83	B	83	ALA	0	-0.006	0.002	19.550	-0.041	-0.041	0.000	0.000	0.000	0.000
84	B	84	THR	0	0.037	0.002	23.008	0.299	0.299	0.000	0.000	0.000	0.000
85	B	85	LEU	0	-0.010	0.016	15.602	0.122	0.122	0.000	0.000	0.000	0.000
86	B	86	LYS	1	0.806	0.881	19.673	26.522	26.522	0.000	0.000	0.000	0.000
87	B	87	GLU	-1	-0.898	-0.951	20.986	-22.126	-22.126	0.000	0.000	0.000	0.000
88	B	88	GLU	-1	-0.884	-0.947	21.783	-23.876	-23.876	0.000	0.000	0.000	0.000
89	B	89	LEU	0	-0.060	-0.026	16.313	-0.043	-0.043	0.000	0.000	0.000	0.000
90	B	90	ASP	-1	-0.736	-0.841	20.480	-25.830	-25.830	0.000	0.000	0.000	0.000
91	B	91	HIS	0	-0.036	-0.015	23.204	0.921	0.921	0.000	0.000	0.000	0.000
92	B	92	LEU	0	-0.027	-0.019	20.805	0.468	0.468	0.000	0.000	0.000	0.000
93	B	93	GLN	0	0.021	0.030	21.417	-0.533	-0.533	0.000	0.000	0.000	0.000
94	B	94	VAL	0	0.003	0.005	22.906	0.596	0.596	0.000	0.000	0.000	0.000
95	B	95	GLN	0	-0.074	-0.022	25.906	0.326	0.326	0.000	0.000	0.000	0.000
96	B	96	HIS	0	-0.091	-0.071	22.954	0.236	0.236	0.000	0.000	0.000	0.000
97	B	97	GLU	-1	-0.856	-0.914	24.940	-22.433	-22.433	0.000	0.000	0.000	0.000
98	B	98	GLY	0	-0.027	-0.015	26.001	0.835	0.835	0.000	0.000	0.000	0.000
99	B	99	ARG	1	0.764	0.873	25.685	22.374	22.374	0.000	0.000	0.000	0.000
100	B	100	LYS	1	0.927	0.955	25.699	20.023	20.023	0.000	0.000	0.000	0.000
101	B	101	ILE	0	0.010	0.009	20.268	0.406	0.406	0.000	0.000	0.000	0.000
102	B	102	PRO	0	0.008	0.017	19.658	-0.528	-0.528	0.000	0.000	0.000	0.000
103	B	103	ASP	-1	-0.786	-0.910	14.730	-36.156	-36.156	0.000	0.000	0.000	0.000
104	B	104	ASN	0	-0.037	-0.024	15.164	-2.779	-2.779	0.000	0.000	0.000	0.000
105	B	105	TYR	0	-0.029	-0.035	16.027	0.415	0.415	0.000	0.000	0.000	0.000
106	B	106	PHE	0	0.024	0.029	14.627	0.675	0.675	0.000	0.000	0.000	0.000
107	B	107	ASP	-1	-0.884	-0.935	10.013	-54.333	-54.333	0.000	0.000	0.000	0.000
108	B	108	ALA	0	-0.002	-0.001	12.155	-1.835	-1.835	0.000	0.000	0.000	0.000
109	B	109	PHE	0	-0.021	0.001	14.677	0.875	0.875	0.000	0.000	0.000	0.000
110	B	110	LYS	1	0.866	0.912	7.009	70.457	70.457	0.000	0.000	0.000	0.000
111	B	111	THR	0	-0.072	-0.042	10.798	-2.407	-2.407	0.000	0.000	0.000	0.000
112	B	112	ALA	0	-0.035	-0.017	12.067	0.565	0.565	0.000	0.000	0.000	0.000
113	B	113	ILE	0	0.035	0.017	13.886	1.290	1.290	0.000	0.000	0.000	0.000
114	B	114	LEU	0	-0.043	-0.030	7.703	0.313	0.313	0.000	0.000	0.000	0.000
115	B	115	HIS	0	-0.027	0.008	11.820	-1.326	-1.326	0.000	0.000	0.000	0.000
116	B	116	VAL	0	-0.006	-0.011	14.002	1.534	1.534	0.000	0.000	0.000	0.000
117	B	117	VAL	0	0.018	0.006	14.207	1.779	1.779	0.000	0.000	0.000	0.000
118	B	118	ALA	0	-0.016	0.000	12.892	0.922	0.922	0.000	0.000	0.000	0.000
119	B	119	ALA	0	-0.055	-0.030	14.872	1.501	1.501	0.000	0.000	0.000	0.000
120	B	120	GLN	0	-0.013	-0.001	18.448	1.627	1.627	0.000	0.000	0.000	0.000
121	B	121	LEU	0	-0.027	-0.002	16.068	1.092	1.092	0.000	0.000	0.000	0.000
122	B	122	GLY	0	0.010	0.014	18.089	0.526	0.526	0.000	0.000	0.000	0.000
123	B	123	ARG	1	0.898	0.931	15.608	28.675	28.675	0.000	0.000	0.000	0.000
124	B	124	CYS	0	-0.087	-0.030	15.195	-1.436	-1.436	0.000	0.000	0.000	0.000
125	B	125	TYR	0	0.020	-0.007	10.388	-0.996	-0.996	0.000	0.000	0.000	0.000
126	B	126	ASP	-1	-0.815	-0.890	7.665	-63.414	-63.414	0.000	0.000	0.000	0.000
127	B	127	ARG	1	1.010	1.002	4.952	68.401	68.401	0.000	0.000	0.000	0.000
130	B	130	TRP	0	0.001	-0.026	7.674	1.510	1.510	0.000	0.000	0.000	0.000
133	B	134	ILE	0	0.009	0.018	9.285	4.435	4.435	0.000	0.000	0.000	0.000
134	B	135	ASP	-1	-0.803	-0.882	6.475	-67.802	-67.802	0.000	0.000	0.000	0.000
135	B	136	HIS	0	-0.020	-0.004	9.086	2.599	2.599	0.000	0.000	0.000	0.000
136	B	137	ILE	0	-0.024	-0.010	10.883	3.576	3.576	0.000	0.000	0.000	0.000
137	B	138	GLU	-1	-0.825	-0.953	12.570	-39.547	-39.547	0.000	0.000	0.000	0.000
138	B	139	ASP	-1	-0.863	-0.935	10.653	-46.704	-46.704	0.000	0.000	0.000	0.000
139	B	140	GLY	0	-0.010	-0.010	14.017	2.280	2.280	0.000	0.000	0.000	0.000
140	B	141	ILE	0	-0.031	-0.015	16.694	1.957	1.957	0.000	0.000	0.000	0.000
141	B	142	LYS	1	0.771	0.886	12.499	44.303	44.303	0.000	0.000	0.000	0.000
142	B	143	GLY	0	0.000	0.016	18.191	1.484	1.484	0.000	0.000	0.000	0.000
143	B	144	HIS	0	-0.126	-0.061	16.599	0.964	0.964	0.000	0.000	0.000	0.000
144	B	145	HIS	-1	-0.869	-0.931	12.003	-45.029	-45.029	0.000	0.000	0.000	0.000

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