FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 3KRVL

Calculation Name: 1V5X-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1V5X

Chain ID: A

ChEMBL ID:

UniProt ID: P83825

Base Structure: X-ray

Registration Date: 2025-10-03

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 200
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2192108.934434
FMO2-HF: Nuclear repulsion 2117683.21096
FMO2-HF: Total energy -74425.723473
FMO2-MP2: Total energy -74647.387087


3D Structure Molmil
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


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


Summations of interaction energy for fragment #1(A:1:MET)
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.
-92.824-82.47311.07-5.795-15.627-0.061
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.848 / q_NPA : 0.943
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   
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].
3A3VAL00.0220.0132.537-4.972-1.4911.003-1.836-2.649-0.016
4A4LYS10.7520.8194.94523.32323.385-0.001-0.007-0.0540.000
164A164LEU0-0.030-0.0092.471-6.412-5.3532.297-0.737-2.619-0.006
165A165ALA00.0110.0083.841-1.562-1.3830.0000.001-0.1800.000
167A167ARG10.8860.9592.38032.87133.1691.093-0.514-0.877-0.001
168A168PRO00.0350.0322.2671.3751.8721.975-0.151-2.321-0.004
169A169TYR0-0.009-0.0082.553-10.346-7.8321.142-1.622-2.035-0.023
170A170ALA0-0.018-0.0233.188-4.010-3.2061.047-0.677-1.173-0.002
171A171LEU00.0130.0142.3591.2631.8781.9080.111-2.634-0.005
172A172ASP-1-0.799-0.8984.666-23.372-23.357-0.001-0.007-0.0070.000
196A196LEU0-0.028-0.0252.398-3.737-2.9100.607-0.356-1.078-0.004
5A5ILE00.0050.0048.358-0.543-0.5430.0000.0000.0000.000
6A6CYS-1-0.799-0.79511.037-16.861-16.8610.0000.0000.0000.000
7A7GLY00.009-0.03113.8760.2860.2860.0000.0000.0000.000
8A8ILE0-0.039-0.02514.8340.3150.3150.0000.0000.0000.000
9A9THR0-0.030-0.02618.3860.6540.6540.0000.0000.0000.000
10A10ARG10.8030.86121.22014.03014.0300.0000.0000.0000.000
11A11LEU00.0520.02120.878-0.666-0.6660.0000.0000.0000.000
12A12GLU-1-0.859-0.91521.097-13.565-13.5650.0000.0000.0000.000
13A13ASP-1-0.765-0.87117.574-15.555-15.5550.0000.0000.0000.000
14A14ALA0-0.013-0.00216.588-1.228-1.2280.0000.0000.0000.000
15A15LEU00.0560.02716.479-1.111-1.1110.0000.0000.0000.000
16A16LEU0-0.057-0.01115.412-0.739-0.7390.0000.0000.0000.000
17A17ALA00.018-0.00412.479-1.285-1.2850.0000.0000.0000.000
18A18GLU-1-0.847-0.92812.221-20.024-20.0240.0000.0000.0000.000
19A19ALA0-0.025-0.01612.954-1.370-1.3700.0000.0000.0000.000
20A20LEU0-0.081-0.03610.7160.1310.1310.0000.0000.0000.000
21A21GLY00.0040.0178.496-2.967-2.9670.0000.0000.0000.000
22A22ALA0-0.045-0.0247.672-5.181-5.1810.0000.0000.0000.000
23A23PHE0-0.002-0.0145.2120.9170.9170.0000.0000.0000.000
24A24ALA0-0.033-0.0179.4182.5802.5800.0000.0000.0000.000
25A25LEU00.0240.01311.058-0.984-0.9840.0000.0000.0000.000
26A26GLY00.0260.00213.8650.7570.7570.0000.0000.0000.000
27A27PHE00.0140.00615.4670.3660.3660.0000.0000.0000.000
28A28VAL0-0.016-0.01518.7440.2590.2590.0000.0000.0000.000
29A29LEU00.0340.01720.9620.4560.4560.0000.0000.0000.000
30A30ALA00.0120.02023.3690.4880.4880.0000.0000.0000.000
31A31PRO0-0.029-0.02525.047-0.039-0.0390.0000.0000.0000.000
32A32GLY00.0250.01628.0340.0240.0240.0000.0000.0000.000
33A33SER0-0.025-0.00421.729-0.107-0.1070.0000.0000.0000.000
34A34ARG10.8960.92721.15212.73712.7370.0000.0000.0000.000
35A35ARG10.7570.85018.19515.08915.0890.0000.0000.0000.000
36A36ARG10.9250.98421.72610.01410.0140.0000.0000.0000.000
37A37ILE0-0.0080.01122.2110.1490.1490.0000.0000.0000.000
38A38ALA0-0.0090.00124.9290.1520.1520.0000.0000.0000.000
39A39PRO00.0560.02626.237-0.434-0.4340.0000.0000.0000.000
40A40GLU-1-0.820-0.93726.854-10.087-10.0870.0000.0000.0000.000
41A41ALA0-0.027-0.00626.924-0.077-0.0770.0000.0000.0000.000
42A42ALA0-0.012-0.01322.606-0.362-0.3620.0000.0000.0000.000
43A43ARG10.9290.98923.2939.8819.8810.0000.0000.0000.000
44A44ALA00.0140.01425.535-0.236-0.2360.0000.0000.0000.000
45A45ILE0-0.064-0.03920.691-0.216-0.2160.0000.0000.0000.000
46A46GLY00.009-0.00121.558-0.472-0.4720.0000.0000.0000.000
47A47GLU-1-0.957-0.98522.601-10.981-10.9810.0000.0000.0000.000
48A48ALA0-0.038-0.01424.2830.1860.1860.0000.0000.0000.000
49A49LEU0-0.0360.00317.765-0.428-0.4280.0000.0000.0000.000
50A50GLY00.0370.02119.0190.6300.6300.0000.0000.0000.000
51A51PRO0-0.032-0.02819.175-0.154-0.1540.0000.0000.0000.000
52A52PHE0-0.066-0.04514.508-0.010-0.0100.0000.0000.0000.000
53A53VAL00.0380.03712.828-1.863-1.8630.0000.0000.0000.000
54A54VAL0-0.041-0.02312.9371.3921.3920.0000.0000.0000.000
55A55ARG10.8510.92214.51014.93214.9320.0000.0000.0000.000
56A56VAL00.0120.00113.2890.4320.4320.0000.0000.0000.000
57A57GLY00.0600.03316.6350.2290.2290.0000.0000.0000.000
58A58VAL0-0.060-0.03316.765-0.216-0.2160.0000.0000.0000.000
59A59PHE00.0440.00519.5560.5430.5430.0000.0000.0000.000
60A60ARG10.8570.89822.00411.62211.6220.0000.0000.0000.000
61A61ASP-1-0.872-0.93224.641-10.461-10.4610.0000.0000.0000.000
62A62GLN0-0.041-0.03426.492-0.027-0.0270.0000.0000.0000.000
63A63PRO00.0420.02828.119-0.265-0.2650.0000.0000.0000.000
64A64PRO00.031-0.00228.628-0.161-0.1610.0000.0000.0000.000
65A65GLU-1-0.939-0.96329.694-8.791-8.7910.0000.0000.0000.000
66A66GLU-1-0.860-0.92029.315-9.573-9.5730.0000.0000.0000.000
67A67VAL0-0.025-0.01424.414-0.196-0.1960.0000.0000.0000.000
68A68LEU0-0.017-0.00826.519-0.343-0.3430.0000.0000.0000.000
69A69ARG10.9720.99928.1468.6978.6970.0000.0000.0000.000
70A70LEU00.0290.00626.757-0.123-0.1230.0000.0000.0000.000
71A71MET0-0.054-0.00620.758-0.393-0.3930.0000.0000.0000.000
72A72GLU-1-0.954-0.95825.268-9.939-9.9390.0000.0000.0000.000
73A73GLU-1-0.968-0.97928.032-9.745-9.7450.0000.0000.0000.000
74A74ALA00.005-0.01424.6160.0770.0770.0000.0000.0000.000
75A75ARG10.8120.90024.66510.14310.1430.0000.0000.0000.000
76A76LEU0-0.0180.00120.263-0.625-0.6250.0000.0000.0000.000
77A77GLN00.022-0.00218.261-0.279-0.2790.0000.0000.0000.000
78A78VAL0-0.020-0.01415.069-0.075-0.0750.0000.0000.0000.000
79A79ALA00.0660.03918.2490.0680.0680.0000.0000.0000.000
80A80GLN0-0.011-0.01914.128-1.369-1.3690.0000.0000.0000.000
81A81LEU00.0080.01217.7980.4910.4910.0000.0000.0000.000
82A82HIS00.0490.01215.470-0.644-0.6440.0000.0000.0000.000
83A83GLY0-0.047-0.01120.2910.1260.1260.0000.0000.0000.000
84A84GLU-1-0.945-0.96322.989-12.427-12.4270.0000.0000.0000.000
85A85GLU-1-0.731-0.87123.284-11.856-11.8560.0000.0000.0000.000
86A86PRO00.0320.04025.223-0.328-0.3280.0000.0000.0000.000
87A87PRO00.0380.01425.049-0.284-0.2840.0000.0000.0000.000
88A88GLU-1-0.844-0.93726.086-10.021-10.0210.0000.0000.0000.000
89A89TRP0-0.023-0.02527.2950.0610.0610.0000.0000.0000.000
90A90ALA00.0200.01822.285-0.150-0.1500.0000.0000.0000.000
91A91GLU-1-0.852-0.92624.047-11.425-11.4250.0000.0000.0000.000
92A92ALA0-0.036-0.01626.0680.0170.0170.0000.0000.0000.000
93A93VAL00.010-0.01323.1560.0510.0510.0000.0000.0000.000
94A94GLY00.0350.00722.806-0.242-0.2420.0000.0000.0000.000
95A95ARG10.7750.88623.68610.35410.3540.0000.0000.0000.000
96A96PHE0-0.074-0.02525.4770.2900.2900.0000.0000.0000.000
97A97TYR00.0180.01321.305-0.248-0.2480.0000.0000.0000.000
98A98PRO0-0.041-0.01617.1160.0380.0380.0000.0000.0000.000
99A99VAL00.0400.03218.283-0.083-0.0830.0000.0000.0000.000
100A100ILE0-0.049-0.02812.363-0.789-0.7890.0000.0000.0000.000
101A101LYS10.8510.93915.82913.65613.6560.0000.0000.0000.000
102A102ALA0-0.028-0.00515.881-0.924-0.9240.0000.0000.0000.000
103A103PHE00.0290.00216.4520.7930.7930.0000.0000.0000.000
104A104PRO00.0010.01316.869-0.798-0.7980.0000.0000.0000.000
105A105LEU0-0.025-0.01913.9940.3850.3850.0000.0000.0000.000
106A106GLU-1-0.898-0.95318.277-11.216-11.2160.0000.0000.0000.000
107A107GLY00.012-0.00119.8370.5590.5590.0000.0000.0000.000
108A108PRO0-0.052-0.02217.935-0.697-0.6970.0000.0000.0000.000
109A109ALA00.0330.00915.5970.4540.4540.0000.0000.0000.000
110A110ARG10.9410.97417.66911.78711.7870.0000.0000.0000.000
111A111PRO0-0.002-0.00717.934-0.297-0.2970.0000.0000.0000.000
112A112GLU-1-0.882-0.92818.933-11.195-11.1950.0000.0000.0000.000
113A113TRP00.0160.00317.142-0.185-0.1850.0000.0000.0000.000
114A114ALA0-0.047-0.03116.578-0.464-0.4640.0000.0000.0000.000
115A115ASP-1-0.857-0.92117.678-12.470-12.4700.0000.0000.0000.000
116A116TYR0-0.030-0.03319.6720.2470.2470.0000.0000.0000.000
117A117PRO00.0070.01119.681-0.742-0.7420.0000.0000.0000.000
118A118ALA0-0.007-0.00517.1040.0380.0380.0000.0000.0000.000
119A119GLN0-0.023-0.01115.078-1.087-1.0870.0000.0000.0000.000
120A120ALA0-0.067-0.04010.956-1.173-1.1730.0000.0000.0000.000
121A121LEU00.0310.02612.0660.9500.9500.0000.0000.0000.000
122A122LEU0-0.018-0.00811.291-1.402-1.4020.0000.0000.0000.000
123A123LEU00.0190.00911.1311.2531.2530.0000.0000.0000.000
124A124ASP-1-0.754-0.90112.361-18.220-18.2200.0000.0000.0000.000
125A125GLY00.0410.01014.9080.5370.5370.0000.0000.0000.000
126A126LYS10.8450.93117.09711.52311.5230.0000.0000.0000.000
127A127ARG10.9300.95320.67512.67912.6790.0000.0000.0000.000
128A128PRO00.0610.06118.826-0.476-0.4760.0000.0000.0000.000
129A129GLY00.0340.02517.1930.4190.4190.0000.0000.0000.000
130A130SER0-0.051-0.05418.2330.4250.4250.0000.0000.0000.000
131A131GLY0-0.035-0.01516.9730.3940.3940.0000.0000.0000.000
132A132GLU-1-0.933-0.95217.129-13.618-13.6180.0000.0000.0000.000
133A133ALA00.0260.01814.768-0.712-0.7120.0000.0000.0000.000
134A134TYR0-0.029-0.01911.3500.7990.7990.0000.0000.0000.000
135A135PRO0-0.0010.01714.422-0.935-0.9350.0000.0000.0000.000
136A136ARG10.9250.9329.50622.28922.2890.0000.0000.0000.000
137A137ALA0-0.019-0.01111.753-0.690-0.6900.0000.0000.0000.000
138A138TRP00.0190.00214.3400.0020.0020.0000.0000.0000.000
139A139ALA00.0980.05010.4370.4670.4670.0000.0000.0000.000
140A140LYS10.9200.96811.65118.28918.2890.0000.0000.0000.000
141A141PRO0-0.0080.00113.271-0.154-0.1540.0000.0000.0000.000
142A142LEU00.0540.04013.1130.3640.3640.0000.0000.0000.000
143A143LEU0-0.0070.0007.256-0.167-0.1670.0000.0000.0000.000
144A144ALA0-0.027-0.01410.899-0.341-0.3410.0000.0000.0000.000
145A145THR0-0.031-0.03213.7680.4690.4690.0000.0000.0000.000
146A146GLY0-0.0040.00611.6180.4480.4480.0000.0000.0000.000
147A147ARG10.7970.90211.90015.13615.1360.0000.0000.0000.000
148A148ARG10.9210.9599.00720.04620.0460.0000.0000.0000.000
149A149VAL00.0310.0308.1130.8070.8070.0000.0000.0000.000
150A150ILE0-0.017-0.0197.006-3.071-3.0710.0000.0000.0000.000
151A151LEU0-0.0170.0005.7772.1152.1150.0000.0000.0000.000
152A152ALA00.0680.0208.040-1.785-1.7850.0000.0000.0000.000
153A153GLY00.0060.00110.750-0.143-0.1430.0000.0000.0000.000
154A154GLY0-0.022-0.01112.671-0.492-0.4920.0000.0000.0000.000
155A155ILE0-0.051-0.0066.801-0.154-0.1540.0000.0000.0000.000
156A156ALA00.0220.00210.2460.6620.6620.0000.0000.0000.000
157A157PRO00.0200.0069.692-1.652-1.6520.0000.0000.0000.000
158A158GLU-1-0.855-0.92310.679-21.159-21.1590.0000.0000.0000.000
159A159ASN00.0210.01210.695-1.931-1.9310.0000.0000.0000.000
160A160LEU00.0220.0165.486-1.163-1.1630.0000.0000.0000.000
161A161GLU-1-0.821-0.9076.482-26.768-26.7680.0000.0000.0000.000
162A162GLU-1-0.882-0.9257.926-21.443-21.4430.0000.0000.0000.000
163A163VAL0-0.005-0.0184.9580.2350.2350.0000.0000.0000.000
166A166LEU0-0.073-0.0405.7281.9741.9740.0000.0000.0000.000
173A173LEU0-0.003-0.0066.1660.6660.6660.0000.0000.0000.000
174A174ALA00.0540.01710.0250.7880.7880.0000.0000.0000.000
175A175SER00.030-0.01013.802-0.132-0.1320.0000.0000.0000.000
176A176GLY00.0020.01812.7680.5990.5990.0000.0000.0000.000
177A177VAL0-0.004-0.01410.949-0.071-0.0710.0000.0000.0000.000
178A178GLU-1-0.750-0.82413.984-15.308-15.3080.0000.0000.0000.000
179A179GLU-1-0.930-0.95517.497-13.315-13.3150.0000.0000.0000.000
180A180ALA00.0160.00821.0340.6290.6290.0000.0000.0000.000
181A181PRO0-0.089-0.04320.324-0.558-0.5580.0000.0000.0000.000
182A182GLY00.0300.00619.6850.5570.5570.0000.0000.0000.000
183A183VAL0-0.0050.02320.684-0.049-0.0490.0000.0000.0000.000
184A184LYS10.7800.86115.11816.75816.7580.0000.0000.0000.000
185A185SER00.0480.03717.4860.3820.3820.0000.0000.0000.000
186A186ALA00.042-0.00416.613-1.125-1.1250.0000.0000.0000.000
187A187GLU-1-0.957-0.96516.592-18.258-18.2580.0000.0000.0000.000
188A188LYS10.9350.96214.49815.84515.8450.0000.0000.0000.000
189A189LEU00.0010.00011.690-1.950-1.9500.0000.0000.0000.000
190A190ARG10.9790.98911.47716.65016.6500.0000.0000.0000.000
191A191ALA00.0300.01812.117-1.713-1.7130.0000.0000.0000.000
192A192LEU0-0.021-0.0086.775-1.466-1.4660.0000.0000.0000.000
193A193PHE00.025-0.0026.504-3.831-3.8310.0000.0000.0000.000
194A194ALA0-0.0060.0057.845-2.349-2.3490.0000.0000.0000.000
195A195ARG10.7520.8568.67725.09925.0990.0000.0000.0000.000
197A197ALA00.0010.0065.348-4.093-4.0930.0000.0000.0000.000
198A198SER0-0.038-0.0126.9302.6502.6500.0000.0000.0000.000
199A199LEU0-0.107-0.0536.5012.5112.5110.0000.0000.0000.000
200A200ARG00.0200.0245.288-19.679-19.6790.0000.0000.0000.000