FMO DATABASE

FMODB ID: N61VQ

Calculation Name: 1X9F-D-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: D

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	139
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1321674.325031
FMO2-HF: Nuclear repulsion	1266080.000237
FMO2-HF: Total energy	-55594.324794
FMO2-MP2: Total energy	-55758.059277

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(D:1:GLU)

Summations of interaction energy for fragment #1(D:1:GLU)

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.
-97.7	-94.523	11.761	-8.544	-6.392	-0.095

Interaction energy analysis for fragmet #1(D:1:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.204 / q_NPA : -0.112

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	D	3	LEU	0	0.030	0.025	3.816	7.885	9.582	-0.021	-0.603	-1.073	0.000
4	D	4	VAL	0	0.017	-0.005	5.034	-2.406	-2.354	-0.001	-0.002	-0.049	0.000
6	D	6	GLU	-1	-0.832	-0.902	5.192	-11.935	-11.976	-0.001	-0.010	0.053	0.000
130	D	130	ASP	-1	-0.820	-0.912	1.858	-71.209	-69.942	11.787	-7.921	-5.133	-0.095
131	D	132	VAL	0	-0.011	-0.010	5.399	2.715	2.795	-0.001	-0.001	-0.078	0.000
132	D	133	ASP	-1	-0.806	-0.902	4.595	-14.520	-14.449	-0.001	-0.001	-0.068	0.000
133	D	134	GLN	0	-0.045	-0.012	4.510	0.943	0.994	-0.001	-0.006	-0.044	0.000
5	D	5	THR	0	-0.005	-0.013	8.841	-0.775	-0.775	0.000	0.000	0.000	0.000
7	D	7	SER	0	0.075	0.009	8.274	0.092	0.092	0.000	0.000	0.000	0.000
8	D	8	LEU	0	-0.038	-0.010	9.831	0.327	0.327	0.000	0.000	0.000	0.000
9	D	9	LYS	1	0.846	0.895	11.762	3.190	3.190	0.000	0.000	0.000	0.000
10	D	10	VAL	0	0.023	0.016	8.960	0.417	0.417	0.000	0.000	0.000	0.000
11	D	11	LYS	1	0.825	0.908	12.304	3.112	3.112	0.000	0.000	0.000	0.000
12	D	12	LEU	0	-0.041	-0.023	15.073	0.325	0.325	0.000	0.000	0.000	0.000
13	D	13	GLN	0	0.004	-0.007	14.945	-0.228	-0.228	0.000	0.000	0.000	0.000
14	D	14	TRP	0	-0.015	-0.021	15.039	-0.046	-0.046	0.000	0.000	0.000	0.000
15	D	15	ALA	0	-0.035	-0.017	16.955	0.240	0.240	0.000	0.000	0.000	0.000
16	D	16	SER	0	-0.089	-0.039	19.778	0.297	0.297	0.000	0.000	0.000	0.000
17	D	17	ALA	0	-0.015	-0.011	18.573	0.144	0.144	0.000	0.000	0.000	0.000
18	D	18	PHE	0	-0.009	0.004	19.683	0.095	0.095	0.000	0.000	0.000	0.000
19	D	19	GLY	0	0.066	0.039	21.518	0.146	0.146	0.000	0.000	0.000	0.000
20	D	20	HIS	0	-0.028	-0.028	24.749	-0.018	-0.018	0.000	0.000	0.000	0.000
21	D	21	ALA	0	0.007	-0.006	27.555	-0.031	-0.031	0.000	0.000	0.000	0.000
22	D	22	HIS	0	0.012	-0.009	29.179	-0.072	-0.072	0.000	0.000	0.000	0.000
23	D	23	GLU	-1	-0.864	-0.920	26.557	-1.371	-1.371	0.000	0.000	0.000	0.000
24	D	24	ARG	1	0.892	0.962	24.072	1.628	1.628	0.000	0.000	0.000	0.000
25	D	25	VAL	0	-0.033	-0.005	25.273	-0.097	-0.097	0.000	0.000	0.000	0.000
26	D	26	ALA	0	-0.029	-0.017	27.624	-0.038	-0.038	0.000	0.000	0.000	0.000
27	D	27	PHE	0	0.041	0.019	18.127	-0.019	-0.019	0.000	0.000	0.000	0.000
28	D	28	GLY	0	0.038	0.008	22.849	-0.151	-0.151	0.000	0.000	0.000	0.000
29	D	29	LEU	0	-0.049	-0.029	23.884	-0.025	-0.025	0.000	0.000	0.000	0.000
30	D	30	GLU	-1	-0.828	-0.875	24.679	-1.931	-1.931	0.000	0.000	0.000	0.000
31	D	31	LEU	0	0.032	0.031	18.368	-0.004	-0.004	0.000	0.000	0.000	0.000
32	D	32	TRP	0	0.012	-0.028	20.641	-0.079	-0.079	0.000	0.000	0.000	0.000
33	D	33	ARG	1	0.920	0.966	24.152	1.656	1.656	0.000	0.000	0.000	0.000
34	D	34	ASP	-1	-0.858	-0.918	23.004	-2.056	-2.056	0.000	0.000	0.000	0.000
35	D	35	ILE	0	-0.032	-0.019	19.282	-0.015	-0.015	0.000	0.000	0.000	0.000
36	D	36	ILE	0	-0.089	-0.045	22.851	0.077	0.077	0.000	0.000	0.000	0.000
37	D	37	ASP	-1	-0.933	-0.976	26.416	-1.428	-1.428	0.000	0.000	0.000	0.000
38	D	38	ASP	-1	-0.849	-0.901	22.163	-2.455	-2.455	0.000	0.000	0.000	0.000
39	D	39	HIS	1	0.821	0.904	22.585	2.287	2.287	0.000	0.000	0.000	0.000
40	D	40	PRO	0	0.045	0.035	25.457	-0.008	-0.008	0.000	0.000	0.000	0.000
41	D	41	GLU	-1	-0.876	-0.962	25.783	-1.773	-1.773	0.000	0.000	0.000	0.000
42	D	42	ILE	0	0.001	0.006	21.789	0.075	0.075	0.000	0.000	0.000	0.000
43	D	43	LYS	1	0.940	0.976	25.953	1.328	1.328	0.000	0.000	0.000	0.000
44	D	44	ALA	0	-0.023	-0.001	29.207	0.070	0.070	0.000	0.000	0.000	0.000
45	D	45	PRO	0	-0.022	-0.011	25.485	0.097	0.097	0.000	0.000	0.000	0.000
46	D	46	PHE	0	0.020	0.009	22.881	0.049	0.049	0.000	0.000	0.000	0.000
47	D	47	SER	0	0.022	0.025	28.999	0.077	0.077	0.000	0.000	0.000	0.000
48	D	48	ARG	1	0.926	0.956	30.915	1.171	1.171	0.000	0.000	0.000	0.000
49	D	49	VAL	0	-0.072	-0.045	28.267	0.050	0.050	0.000	0.000	0.000	0.000
50	D	50	ARG	1	0.867	0.916	31.577	0.969	0.969	0.000	0.000	0.000	0.000
51	D	51	GLY	0	0.055	0.025	30.282	-0.017	-0.017	0.000	0.000	0.000	0.000
52	D	52	ASP	-1	-0.900	-0.920	30.947	-1.085	-1.085	0.000	0.000	0.000	0.000
53	D	53	ASN	0	-0.006	-0.015	33.737	-0.016	-0.016	0.000	0.000	0.000	0.000
54	D	54	ILE	0	0.059	0.039	28.472	0.040	0.040	0.000	0.000	0.000	0.000
55	D	55	TYR	0	0.023	0.010	31.104	-0.041	-0.041	0.000	0.000	0.000	0.000
56	D	56	SER	0	-0.062	-0.020	33.726	0.065	0.065	0.000	0.000	0.000	0.000
57	D	57	PRO	0	0.030	0.013	33.370	-0.066	-0.066	0.000	0.000	0.000	0.000
58	D	58	GLU	-1	-0.884	-0.957	33.211	-1.014	-1.014	0.000	0.000	0.000	0.000
59	D	59	PHE	0	0.016	0.024	25.959	-0.067	-0.067	0.000	0.000	0.000	0.000
60	D	60	GLY	0	0.035	0.022	28.739	-0.111	-0.111	0.000	0.000	0.000	0.000
61	D	61	ALA	0	-0.011	-0.026	28.707	-0.081	-0.081	0.000	0.000	0.000	0.000
62	D	62	HIS	0	-0.059	-0.036	24.579	0.057	0.057	0.000	0.000	0.000	0.000
63	D	63	SER	0	0.054	0.032	24.510	-0.178	-0.178	0.000	0.000	0.000	0.000
64	D	64	GLN	0	0.017	-0.012	23.798	-0.204	-0.204	0.000	0.000	0.000	0.000
65	D	65	ARG	1	0.884	0.959	24.323	1.399	1.399	0.000	0.000	0.000	0.000
66	D	66	VAL	0	-0.010	0.006	19.565	-0.082	-0.082	0.000	0.000	0.000	0.000
67	D	67	LEU	0	0.022	0.017	19.089	-0.236	-0.236	0.000	0.000	0.000	0.000
68	D	68	SER	0	-0.027	0.000	19.633	-0.119	-0.119	0.000	0.000	0.000	0.000
69	D	69	GLY	0	0.013	0.001	19.311	-0.012	-0.012	0.000	0.000	0.000	0.000
70	D	70	LEU	0	0.020	0.010	13.406	-0.162	-0.162	0.000	0.000	0.000	0.000
71	D	71	ASP	-1	-0.850	-0.901	15.353	-2.609	-2.609	0.000	0.000	0.000	0.000
72	D	72	ILE	0	-0.006	0.010	17.181	0.013	0.013	0.000	0.000	0.000	0.000
73	D	73	THR	0	-0.034	-0.031	12.638	-0.135	-0.135	0.000	0.000	0.000	0.000
74	D	74	ILE	0	0.047	0.022	11.899	-0.390	-0.390	0.000	0.000	0.000	0.000
75	D	75	SER	0	-0.056	-0.041	13.424	0.224	0.224	0.000	0.000	0.000	0.000
76	D	76	MET	0	-0.018	-0.011	14.365	0.264	0.264	0.000	0.000	0.000	0.000
77	D	77	LEU	0	-0.028	-0.007	8.297	0.338	0.338	0.000	0.000	0.000	0.000
78	D	78	ASP	-1	-0.876	-0.921	9.218	-1.827	-1.827	0.000	0.000	0.000	0.000
79	D	79	THR	0	-0.028	-0.009	11.623	0.861	0.861	0.000	0.000	0.000	0.000
80	D	80	PRO	0	0.029	0.007	9.994	-0.419	-0.419	0.000	0.000	0.000	0.000
81	D	81	ASP	-1	-0.875	-0.942	11.876	-0.467	-0.467	0.000	0.000	0.000	0.000
82	D	82	MET	0	-0.042	-0.026	15.382	-0.175	-0.175	0.000	0.000	0.000	0.000
83	D	83	LEU	0	0.023	0.017	9.217	-0.140	-0.140	0.000	0.000	0.000	0.000
84	D	84	ALA	0	0.009	0.004	12.901	-0.329	-0.329	0.000	0.000	0.000	0.000
85	D	85	ALA	0	-0.020	-0.009	13.864	-0.078	-0.078	0.000	0.000	0.000	0.000
86	D	86	GLN	0	0.008	0.000	15.774	0.163	0.163	0.000	0.000	0.000	0.000
87	D	87	LEU	0	-0.004	0.005	10.580	-0.005	-0.005	0.000	0.000	0.000	0.000
88	D	88	ALA	0	0.038	0.024	15.137	0.056	0.056	0.000	0.000	0.000	0.000
89	D	89	HIS	0	-0.042	-0.019	17.679	0.173	0.173	0.000	0.000	0.000	0.000
90	D	90	LEU	0	-0.008	-0.011	16.458	0.122	0.122	0.000	0.000	0.000	0.000
91	D	91	LYS	1	0.929	0.971	16.436	2.764	2.764	0.000	0.000	0.000	0.000
92	D	92	VAL	0	-0.019	-0.006	19.086	0.143	0.143	0.000	0.000	0.000	0.000
93	D	93	GLN	0	-0.056	-0.023	22.247	-0.005	-0.005	0.000	0.000	0.000	0.000
94	D	94	HIS	0	-0.058	-0.053	20.151	0.027	0.027	0.000	0.000	0.000	0.000
95	D	95	VAL	0	0.012	0.014	21.650	0.019	0.019	0.000	0.000	0.000	0.000
96	D	96	GLU	-1	-0.914	-0.936	22.924	-1.098	-1.098	0.000	0.000	0.000	0.000
97	D	97	ARG	1	0.803	0.888	24.474	1.650	1.650	0.000	0.000	0.000	0.000
98	D	98	ASN	0	-0.018	-0.003	25.024	-0.102	-0.102	0.000	0.000	0.000	0.000
99	D	99	LEU	0	-0.012	-0.009	21.104	0.041	0.041	0.000	0.000	0.000	0.000
100	D	100	LYS	1	0.886	0.956	21.380	1.804	1.804	0.000	0.000	0.000	0.000
101	D	101	PRO	0	0.062	0.034	16.264	-0.122	-0.122	0.000	0.000	0.000	0.000
102	D	102	GLU	-1	-0.782	-0.913	16.066	-3.020	-3.020	0.000	0.000	0.000	0.000
103	D	103	PHE	0	-0.054	-0.047	17.376	-0.033	-0.033	0.000	0.000	0.000	0.000
104	D	104	PHE	0	0.012	0.006	14.036	0.080	0.080	0.000	0.000	0.000	0.000
105	D	105	ASP	-1	-0.786	-0.882	12.453	-6.382	-6.382	0.000	0.000	0.000	0.000
106	D	106	ILE	0	-0.076	-0.039	14.045	-0.065	-0.065	0.000	0.000	0.000	0.000
107	D	107	PHE	0	-0.009	-0.008	14.474	0.140	0.140	0.000	0.000	0.000	0.000
108	D	108	LEU	0	0.040	0.025	8.911	0.405	0.405	0.000	0.000	0.000	0.000
109	D	109	LYS	1	0.843	0.921	13.283	3.118	3.118	0.000	0.000	0.000	0.000
110	D	110	HIS	0	-0.017	-0.026	15.285	0.186	0.186	0.000	0.000	0.000	0.000
111	D	111	LEU	0	0.003	0.001	12.936	0.254	0.254	0.000	0.000	0.000	0.000
112	D	112	LEU	0	-0.012	-0.018	10.312	0.265	0.265	0.000	0.000	0.000	0.000
113	D	113	HIS	0	-0.059	-0.014	14.584	0.318	0.318	0.000	0.000	0.000	0.000
114	D	114	VAL	0	0.043	0.017	18.270	0.151	0.151	0.000	0.000	0.000	0.000
115	D	115	LEU	0	-0.041	-0.019	14.005	0.259	0.259	0.000	0.000	0.000	0.000
116	D	116	GLY	0	0.028	0.017	17.535	0.181	0.181	0.000	0.000	0.000	0.000
117	D	117	ASP	-1	-0.894	-0.949	18.535	-2.075	-2.075	0.000	0.000	0.000	0.000
118	D	118	ARG	1	0.706	0.819	20.483	2.283	2.283	0.000	0.000	0.000	0.000
119	D	119	LEU	0	-0.045	-0.014	16.640	0.178	0.178	0.000	0.000	0.000	0.000
120	D	120	GLY	0	0.011	0.013	20.496	0.179	0.179	0.000	0.000	0.000	0.000
121	D	121	THR	0	-0.028	-0.043	19.583	-0.190	-0.190	0.000	0.000	0.000	0.000
122	D	122	HIS	0	-0.028	-0.003	18.773	-0.039	-0.039	0.000	0.000	0.000	0.000
123	D	123	PHE	0	0.001	0.025	13.441	-0.205	-0.205	0.000	0.000	0.000	0.000
124	D	124	ASP	-1	-0.817	-0.890	10.629	-5.077	-5.077	0.000	0.000	0.000	0.000
125	D	125	PHE	0	0.020	0.000	10.428	-1.077	-1.077	0.000	0.000	0.000	0.000
126	D	126	GLY	0	0.020	0.021	7.704	-1.141	-1.141	0.000	0.000	0.000	0.000
127	D	127	ALA	0	0.055	0.026	6.439	-3.527	-3.527	0.000	0.000	0.000	0.000
128	D	128	TRP	0	-0.026	-0.039	6.840	-2.373	-2.373	0.000	0.000	0.000	0.000
129	D	129	HIS	0	-0.031	-0.010	5.872	1.606	1.606	0.000	0.000	0.000	0.000
134	D	135	ILE	0	-0.037	-0.022	6.194	3.154	3.154	0.000	0.000	0.000	0.000
135	D	136	ILE	0	-0.014	-0.011	9.192	1.780	1.780	0.000	0.000	0.000	0.000
136	D	137	ASP	-1	-0.834	-0.922	7.773	-8.734	-8.734	0.000	0.000	0.000	0.000
137	D	138	GLY	0	-0.054	-0.017	10.444	1.040	1.040	0.000	0.000	0.000	0.000
138	D	139	ILE	0	-0.113	-0.069	12.292	0.911	0.911	0.000	0.000	0.000	0.000
139	D	140	LYS	0	-0.087	-0.013	10.844	4.147	4.147	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:1:GLU)